From c77f4f828b4f6193f1acdb57f8ae6379635ae601 Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Tue, 13 Oct 2020 11:25:09 -0700 Subject: [PATCH 01/15] Minor clarification --- README.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index a47f675a..596d96fb 100644 --- a/README.md +++ b/README.md @@ -25,11 +25,10 @@ See [dev branch](https://github.com/Exabyte-io/rewotes/tree/dev) also. ## Notes -Examples listed here are only meant as guidelines and do not necessarily reflect on the type of work to be performed at the company. +Examples listed here are only meant as guidelines and do not necessarily reflect on the type of work to be performed at the company. Modifications to the individual assignments with an advance notice are encouraged. -Modifications to the individual assignments with an advance notice are encouraged. Candidates are free to share the results. +We will screen for the ability to (1) pick up new concepts quickly, (2) implement a working proof-of-concept solution, and (3) outline how the PoC can become more mature. We value attention to details and modularity. -We will screen for the ability to pick up new concepts quickly and implement a working solution. We value attention to details and modularity. ## Hiring process From e727baac7010847ddcb4d0b53a16df93000752df Mon Sep 17 00:00:00 2001 From: vitalypro <64281595+vitalypro@users.noreply.github.com> Date: Mon, 25 Oct 2021 20:37:25 -0600 Subject: [PATCH 02/15] Create README.md project overview --- vitalypro/README.md | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 vitalypro/README.md diff --git a/vitalypro/README.md b/vitalypro/README.md new file mode 100644 index 00000000..7517c72f --- /dev/null +++ b/vitalypro/README.md @@ -0,0 +1,26 @@ +**Prediction of Electronic Band-structure in SiGe Superlattices** + +**Overview** +The idea of this task is to train an ML model to predict electronic band-structure of a SiGe superlattice with any kind of interfacial disorder, external strain, and composition*. +*please see the list of assumptions that will be used in this work +Superlattices are periodic structures that contain layers of different materials. The interfaces significantly impact the electronic and phonon transport and make superlattices ideal candidates as thermoelectric materials. The efficiency or figure of merit of thermoelectric material is calculated as: +zT=S2ρkT, +where zT is the dimensionless figure of merit, S, , k are the Seebeck coefficient, electrical resistivity, and thermal conductivity. In order to improve the efficiency of thermoelectric material, we need to increase the Seebeck coefficient and electrical conductivity and at the same time decrease the thermal conductivity. The former two parameters can be easily and quickly computed from the energy bands using Boltzmann equations (see https://arxiv.org/pdf/cond-mat/0602203.pdf eq. 12-16). The most time-consuming part in the computation of S is the bandstructure calculation that we will speed up with ML modeling. + +**Workflow** +Compute bandstructures for n SiGe SLs to build a training set for a supervised ML model. +Train the ML model +Test the model on 1-2 new SiGe structures + +**Assumptions** +This task is very interesting, but it’s also complicated, and it would take a significant amount of time to complete. For this reason, I will make some assumptions that would simplify this problem: +I will only study superlattices that have a constant number of atoms to avoid band structure unfolding. As example, the electronic band structure unfolding can be done with GPAW (https://wiki.fysik.dtu.dk/gpaw/tutorialsexercises/electronic/unfold/unfold.html) +I will use a smaller number of atoms in the cell to speed up calculations +For the transport we only care about the bands that are close to the Fermi level. Therefore, I will only be predicting those bands. +In this work, I will only consider superlattices with the ideal interfaces. It would be interesting to investigate disordered interfaces and introduce some defects far away from the interface as well in the future work. This would require studying larger cells and introduce Voronoi tessellations to correctly describe the neighboring atoms. In this work, however, I will study the effect of external strain that comes from growing a superlattice on different substrates. +I will predict bandstructure along a short path (e.g. Gamma -Z) +I will use the PBE exchange-correlation functional for the DFT calculations. The band gap will be underestimated but the bands shape should not be affected significantly. + +**Timeline** +I will be traveling 10/21 – 10/25. I can start working on this problem Monday /Tuesday next week. + From 0cc0f24071338b78c55b3d0ce8f3eb3ddaeb5f77 Mon Sep 17 00:00:00 2001 From: vitalypro <64281595+vitalypro@users.noreply.github.com> Date: Mon, 25 Oct 2021 20:37:42 -0600 Subject: [PATCH 03/15] Update README.md --- vitalypro/README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/vitalypro/README.md b/vitalypro/README.md index 7517c72f..eac17cb6 100644 --- a/vitalypro/README.md +++ b/vitalypro/README.md @@ -1,6 +1,7 @@ **Prediction of Electronic Band-structure in SiGe Superlattices** **Overview** + The idea of this task is to train an ML model to predict electronic band-structure of a SiGe superlattice with any kind of interfacial disorder, external strain, and composition*. *please see the list of assumptions that will be used in this work Superlattices are periodic structures that contain layers of different materials. The interfaces significantly impact the electronic and phonon transport and make superlattices ideal candidates as thermoelectric materials. The efficiency or figure of merit of thermoelectric material is calculated as: @@ -8,11 +9,13 @@ zT=S2ρkT, where zT is the dimensionless figure of merit, S, , k are the Seebeck coefficient, electrical resistivity, and thermal conductivity. In order to improve the efficiency of thermoelectric material, we need to increase the Seebeck coefficient and electrical conductivity and at the same time decrease the thermal conductivity. The former two parameters can be easily and quickly computed from the energy bands using Boltzmann equations (see https://arxiv.org/pdf/cond-mat/0602203.pdf eq. 12-16). The most time-consuming part in the computation of S is the bandstructure calculation that we will speed up with ML modeling. **Workflow** + Compute bandstructures for n SiGe SLs to build a training set for a supervised ML model. Train the ML model Test the model on 1-2 new SiGe structures **Assumptions** + This task is very interesting, but it’s also complicated, and it would take a significant amount of time to complete. For this reason, I will make some assumptions that would simplify this problem: I will only study superlattices that have a constant number of atoms to avoid band structure unfolding. As example, the electronic band structure unfolding can be done with GPAW (https://wiki.fysik.dtu.dk/gpaw/tutorialsexercises/electronic/unfold/unfold.html) I will use a smaller number of atoms in the cell to speed up calculations @@ -22,5 +25,6 @@ I will predict bandstructure along a short path (e.g. Gamma -Z) I will use the PBE exchange-correlation functional for the DFT calculations. The band gap will be underestimated but the bands shape should not be affected significantly. **Timeline** + I will be traveling 10/21 – 10/25. I can start working on this problem Monday /Tuesday next week. From f7c1faddcb3936792bd08cc8f09613d6a0942cd6 Mon Sep 17 00:00:00 2001 From: vitalypro <64281595+vitalypro@users.noreply.github.com> Date: Tue, 26 Oct 2021 08:55:13 -0600 Subject: [PATCH 04/15] Update README.md --- vitalypro/README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/vitalypro/README.md b/vitalypro/README.md index eac17cb6..377e0583 100644 --- a/vitalypro/README.md +++ b/vitalypro/README.md @@ -3,7 +3,8 @@ **Overview** The idea of this task is to train an ML model to predict electronic band-structure of a SiGe superlattice with any kind of interfacial disorder, external strain, and composition*. -*please see the list of assumptions that will be used in this work +(**please see the list of assumptions that will be used in this work*) + Superlattices are periodic structures that contain layers of different materials. The interfaces significantly impact the electronic and phonon transport and make superlattices ideal candidates as thermoelectric materials. The efficiency or figure of merit of thermoelectric material is calculated as: zT=S2ρkT, where zT is the dimensionless figure of merit, S, , k are the Seebeck coefficient, electrical resistivity, and thermal conductivity. In order to improve the efficiency of thermoelectric material, we need to increase the Seebeck coefficient and electrical conductivity and at the same time decrease the thermal conductivity. The former two parameters can be easily and quickly computed from the energy bands using Boltzmann equations (see https://arxiv.org/pdf/cond-mat/0602203.pdf eq. 12-16). The most time-consuming part in the computation of S is the bandstructure calculation that we will speed up with ML modeling. From 7e34ff4f02bd547749842990225bee9beb12da71 Mon Sep 17 00:00:00 2001 From: vitalypro <64281595+vitalypro@users.noreply.github.com> Date: Tue, 26 Oct 2021 09:16:09 -0600 Subject: [PATCH 05/15] Update README.md --- vitalypro/README.md | 36 +++++++++++++++++++++--------------- 1 file changed, 21 insertions(+), 15 deletions(-) diff --git a/vitalypro/README.md b/vitalypro/README.md index 377e0583..f6204a7f 100644 --- a/vitalypro/README.md +++ b/vitalypro/README.md @@ -6,26 +6,32 @@ The idea of this task is to train an ML model to predict electronic band-structu (**please see the list of assumptions that will be used in this work*) Superlattices are periodic structures that contain layers of different materials. The interfaces significantly impact the electronic and phonon transport and make superlattices ideal candidates as thermoelectric materials. The efficiency or figure of merit of thermoelectric material is calculated as: -zT=S2ρkT, -where zT is the dimensionless figure of merit, S, , k are the Seebeck coefficient, electrical resistivity, and thermal conductivity. In order to improve the efficiency of thermoelectric material, we need to increase the Seebeck coefficient and electrical conductivity and at the same time decrease the thermal conductivity. The former two parameters can be easily and quickly computed from the energy bands using Boltzmann equations (see https://arxiv.org/pdf/cond-mat/0602203.pdf eq. 12-16). The most time-consuming part in the computation of S is the bandstructure calculation that we will speed up with ML modeling. - -**Workflow** -Compute bandstructures for n SiGe SLs to build a training set for a supervised ML model. -Train the ML model -Test the model on 1-2 new SiGe structures +*zT=(S^2/ρk)T*, + +where *zT* is the dimensionless figure of merit, S, ρ, k are the Seebeck coefficient, electrical resistivity, and thermal conductivity. In order to improve the efficiency of thermoelectric material, we need to increase the Seebeck coefficient and electrical conductivity and at the same time decrease the thermal conductivity. The former two parameters can be easily and quickly computed from the energy bands using Boltzmann equations (see https://arxiv.org/pdf/cond-mat/0602203.pdf eq. 12-16). The most time-consuming part in the computation of S is the bandstructure calculation that we will speed up with ML modeling. + **Assumptions** This task is very interesting, but it’s also complicated, and it would take a significant amount of time to complete. For this reason, I will make some assumptions that would simplify this problem: -I will only study superlattices that have a constant number of atoms to avoid band structure unfolding. As example, the electronic band structure unfolding can be done with GPAW (https://wiki.fysik.dtu.dk/gpaw/tutorialsexercises/electronic/unfold/unfold.html) -I will use a smaller number of atoms in the cell to speed up calculations -For the transport we only care about the bands that are close to the Fermi level. Therefore, I will only be predicting those bands. -In this work, I will only consider superlattices with the ideal interfaces. It would be interesting to investigate disordered interfaces and introduce some defects far away from the interface as well in the future work. This would require studying larger cells and introduce Voronoi tessellations to correctly describe the neighboring atoms. In this work, however, I will study the effect of external strain that comes from growing a superlattice on different substrates. -I will predict bandstructure along a short path (e.g. Gamma -Z) -I will use the PBE exchange-correlation functional for the DFT calculations. The band gap will be underestimated but the bands shape should not be affected significantly. +1. I will only study superlattices that have a constant number of atoms to avoid band structure folding. As example, the electronic band structure unfolding can be done with GPAW (https://wiki.fysik.dtu.dk/gpaw/tutorialsexercises/electronic/unfold/unfold.html) +2. I will use a smaller number of atoms in the cell to speed up calculations +3. For the transport we only care about the bands that are close to the Fermi level. Therefore, I will only predict those bands. +4. In this work, I will only consider superlattices with the ideal interfaces. It would be interesting to investigate disordered interfaces and introduce some defects far away from the interface as well in the future work. This would require studying larger cells and introduce Voronoi tessellations to correctly describe the neighboring atoms. In this work, however, I will study the effect of external strain that comes from growing a superlattice on different substrates. +5. I will predict bandstructure along a short path (e.g. Gamma -Z) +6. I will use the PBE exchange-correlation functional for the DFT calculations. The band gap will be underestimated but the bands shape should not be affected significantly. -**Timeline** +**Project details** -I will be traveling 10/21 – 10/25. I can start working on this problem Monday /Tuesday next week. +1. **Step 1: DFT calculations** +.... +Compute bandstructures for n SiGe SLs to build a training set for a supervised ML model. +.... + +2. **Step 2: Develop a module for ML modeling** + ... + +3. **Step 3: Predict a SL bandstructure with the ML model** +... From bc4fa533885078365d382c7e696b285ea530cc5f Mon Sep 17 00:00:00 2001 From: vitalypro <64281595+vitalypro@users.noreply.github.com> Date: Wed, 27 Oct 2021 10:37:22 -0600 Subject: [PATCH 06/15] Update README.md --- vitalypro/README.md | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/vitalypro/README.md b/vitalypro/README.md index f6204a7f..8b71b8b7 100644 --- a/vitalypro/README.md +++ b/vitalypro/README.md @@ -1,4 +1,4 @@ -**Prediction of Electronic Band-structure in SiGe Superlattices** +**Prediction of Electronic Band-structure in Ultra-thin SiGe Superlattices with Tree-Based Machine Learning Models** **Overview** @@ -16,18 +16,16 @@ where *zT* is the dimensionless figure of merit, S, ρ, k are the Seebeck coeff This task is very interesting, but it’s also complicated, and it would take a significant amount of time to complete. For this reason, I will make some assumptions that would simplify this problem: 1. I will only study superlattices that have a constant number of atoms to avoid band structure folding. As example, the electronic band structure unfolding can be done with GPAW (https://wiki.fysik.dtu.dk/gpaw/tutorialsexercises/electronic/unfold/unfold.html) -2. I will use a smaller number of atoms in the cell to speed up calculations -3. For the transport we only care about the bands that are close to the Fermi level. Therefore, I will only predict those bands. -4. In this work, I will only consider superlattices with the ideal interfaces. It would be interesting to investigate disordered interfaces and introduce some defects far away from the interface as well in the future work. This would require studying larger cells and introduce Voronoi tessellations to correctly describe the neighboring atoms. In this work, however, I will study the effect of external strain that comes from growing a superlattice on different substrates. +2. I will use a smaller number of atoms in the cell to speed up calculations (8 atom cells) +3. For the transport we only care about the bands that are close to the Fermi level. Therefore, I will only predict 2 valence and 2 conduction bands. +4. In this work, I will only consider superlattices with the ideal interfaces. It would be interesting to investigate disordered interfaces and introduce some defects far away from the interface as well in the future work. This would require studying larger cells and introduce Voronoi tessellations to correctly describe the neighboring atoms. In this work, however, I will study the effect of composition and external strain. 5. I will predict bandstructure along a short path (e.g. Gamma -Z) 6. I will use the PBE exchange-correlation functional for the DFT calculations. The band gap will be underestimated but the bands shape should not be affected significantly. **Project details** 1. **Step 1: DFT calculations** -.... -Compute bandstructures for n SiGe SLs to build a training set for a supervised ML model. -.... +In the first step I perform DFT calculation of ultra-thin SixGe1-x superlattices at different external strain (x is the number of monolayers). 2. **Step 2: Develop a module for ML modeling** ... From 44dce5909c36af1a79c4a1a16a2bbb5938a1225f Mon Sep 17 00:00:00 2001 From: vitaly Date: Wed, 27 Oct 2021 11:11:19 -0600 Subject: [PATCH 07/15] ML module: Random Forest model with automatic HPO search --- vitalypro/ml_modeling_module.py | 144 ++++++++++++++++++++++++++++++++ 1 file changed, 144 insertions(+) create mode 100644 vitalypro/ml_modeling_module.py diff --git a/vitalypro/ml_modeling_module.py b/vitalypro/ml_modeling_module.py new file mode 100644 index 00000000..bdd63db1 --- /dev/null +++ b/vitalypro/ml_modeling_module.py @@ -0,0 +1,144 @@ +# -*- coding: utf-8 -*- +""" +@author: Vitaly Proshchenko +""" + +from datetime import datetime +from hyperopt import hp, fmin, tpe, STATUS_OK, Trials, space_eval +from hyperopt.fmin import generate_trials_to_calculate +from sklearn.model_selection import cross_val_score +from functools import partial +import numpy as np + + + +""" +1. Add class for data (energy bands, cell geometry etc) extraction from QE output files +2. Add class for data preparation for ML modeling +3. Add class for ML modeling with RF, XGB (more ML algorithms -?) +4. If time permitted, add class to solve reverse problems (e.g. for known bandstructure, find SL structure) +""" + +class modeling: + def __init__(self, X_train, Y_train, X_test, Y_test, scaler= 'None'): + """ + since we use tree based ML algorithms, + there is no need to scale data (scaler='None'). + In the future work scaler='minmax', 'standard' etc can be added for other ML algorithms + + """ + self.scaler = scaler + if scaler== 'None': + self.X_train = X_train + self.Y_train = Y_train + self.X_test = X_test + self.Y_test = Y_test + + """ if scaler != 'None' -- perform data scaling""" + + + def verbose_output(self, model, y_fit, y_predict): + """ print train/test model scores if verbose output is chosen""" + + from sklearn.metrics import mean_squared_error + from sklearn.metrics import r2_score + + text=("\nTrain:\nR^2:"+str(round(model.score(self.X_train, self.Y_train),2))+ + ' RMSE:'+str(round(np.sqrt(mean_squared_error(self.Y_train, y_fit, multioutput='uniform_average')),2))+ + '\nTest:\nR^2:'+str(round(r2_score(self.Y_test, y_predict, multioutput='uniform_average'),2)) + + ' RMSE: '+str( round(np.sqrt(mean_squared_error(self.Y_test, y_predict)),2)) + ) + return text + + def RandomForest(self, max_evals=40, timeout=600, loss_threshold=0.5, init_vals='None' , n_jobs=10, cv=5, verbose=1): + """ + Random Forest Regressor with Sequential Model-based Optimization with Tree-Parzen estimators (Bayesian optimization) + The idea is to build a probability model of the objective function and use it to select the most promising hyperparameters to evaluate in the true objective function + + :max_evals - number of max evaluation in hyperparameter search algorithm. the search will stop when number of max itteration is reached. Can be any integer number. Default value is 40, + :timeout - search time. the search will stop when the time is out. Can be any integer number. Default value is 600 sec + :loss_threshold - the search will stop when the loss threshold is achieved. (in our case loss function is MSE). Can be any float number. + :init_vals - initial guess for the hyperparameter optimization search. Default - 'None'. Can be list of parameters such as n_estimators, max_depth etc. + :n_jobs - number of CPUs for parallelization = 10, + :cv - cross-validation. default = 5 + :verbose - verbose output. Can be either 0 or 1. + + """ + from sklearn.ensemble import RandomForestRegressor + startTime = datetime.now() + + def objective(space): + """Define our function""" + clf = RandomForestRegressor(n_estimators =int(space['n_estimators']), + random_state = int(space['random_state']), + max_depth = int(space['max_depth']), + min_samples_split = int(space['min_samples_split']) + ) + + """To reduce overfitting, we perform n-fold cross validation. + The goal is to minimize our loss function (MSE)""" + mse_scr = cross_val_score(clf, self.X_train, self.Y_train, scoring='neg_root_mean_squared_error', cv=cv,verbose=0,n_jobs=n_jobs).mean() + + return {'loss': -mse_scr, 'status': STATUS_OK } + + """Here we define the space for Random Forest model + More hyperparameters to build the sapce can also be used """ + + space ={'max_depth': hp.quniform('max_depth', 1, 18, 1), + 'random_state' : hp.quniform('random_state', 1, 18, 1), + 'n_estimators' : hp.quniform('n_estimators', 10, 800, 1), + 'min_samples_split' : hp.quniform('min_samples_split', 1, 8, 1) + } + + """ in case if we do not provide the initial guess for Random forest model, + we will first randomly pick 8 sets of hyperparameters (HPs) and build a probabalistic space. + The next HPs will be chosen based on probabalistic model + Otherwise, we will start with initial guess, then randomly pick 4 sets of HPs and initialize a probobalistic search + """ + if init_vals=='None': + trials = Trials() + random=8 + else: + trials = generate_trials_to_calculate(init_vals) + random=4 + """Details for minimization """ + best = fmin(fn=objective, + space=space, + algo=partial(tpe.suggest,n_startup_jobs=random), + max_evals=max_evals, + timeout=timeout, + loss_threshold=loss_threshold, + trials=trials, + show_progressbar=False) + + + best_space=space_eval(space, best) + + + + RF = RandomForestRegressor(**{'max_depth': int(best['max_depth']), + 'n_estimators': int(best['n_estimators']), + 'random_state': int(best['random_state']), + 'min_samples_split': int(best['min_samples_split'])} ).fit(self.X_train, self.Y_train) + + + y_fit = RF.predict(self.X_train) + y_predict = RF.predict(self.X_test) + + text=str("Time taken for RF: " + str(datetime.now() - startTime) ) + if verbose==1: + text=str("Time taken for RF: " + str(datetime.now() - startTime) ) + str(modeling.verbose_output(self, RF, y_fit, y_predict)) + + return y_fit, y_predict, trials.trials, best_space, RF, text + + + + + + ####### later def XGB(self,...): + + + + + + From e7828c2201e61303b6b7b6361a1089f910c3e248 Mon Sep 17 00:00:00 2001 From: vitaly Date: Wed, 27 Oct 2021 19:18:08 -0600 Subject: [PATCH 08/15] ML module: read bands from QE, data preparation, XGB model. folder with DFT calculated bands. Test to predict bandstructure in jupyter --- ...de_implementation_example-checkpoint.ipynb | 3475 +++++++++++++++++ .../ml_modeling_module.cpython-36.pyc | Bin 0 -> 10234 bytes vitalypro/bands/bands_0.dat | 34 + vitalypro/bands/bands_1.dat | 34 + vitalypro/bands/bands_2.dat | 34 + vitalypro/bands/bands_3.dat | 34 + vitalypro/bands/bands_4.dat | 34 + vitalypro/bands/bands_5.dat | 34 + vitalypro/bands/bands_relax.dat | 34 + vitalypro/code_implementation_example.ipynb | 3475 +++++++++++++++++ vitalypro/ml_modeling_module.py | 182 +- 11 files changed, 7366 insertions(+), 4 deletions(-) create mode 100644 vitalypro/.ipynb_checkpoints/code_implementation_example-checkpoint.ipynb create mode 100644 vitalypro/__pycache__/ml_modeling_module.cpython-36.pyc create mode 100644 vitalypro/bands/bands_0.dat create mode 100644 vitalypro/bands/bands_1.dat create mode 100644 vitalypro/bands/bands_2.dat create mode 100644 vitalypro/bands/bands_3.dat create mode 100644 vitalypro/bands/bands_4.dat create mode 100644 vitalypro/bands/bands_5.dat create mode 100644 vitalypro/bands/bands_relax.dat create mode 100644 vitalypro/code_implementation_example.ipynb diff --git a/vitalypro/.ipynb_checkpoints/code_implementation_example-checkpoint.ipynb b/vitalypro/.ipynb_checkpoints/code_implementation_example-checkpoint.ipynb new file mode 100644 index 00000000..a1258ac9 --- /dev/null +++ b/vitalypro/.ipynb_checkpoints/code_implementation_example-checkpoint.ipynb @@ -0,0 +1,3475 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-27T18:59:04.286973Z", + "start_time": "2021-10-27T18:59:01.347246Z" + } + }, + "outputs": [ + { + "data": { + "text/html": [ + " \n", + " " + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "application/vnd.plotly.v1+json": { + "config": { + "plotlyServerURL": "https://plot.ly" + }, + "data": [ + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -2.8999998569488525, + -2.8899998664855957, + -2.860999822616577, + -2.811999797821045, + -2.744999885559082, + -2.6589999198913574, + -2.553999900817871, + -2.5189998149871826, + -2.4079997539520264, + -2.311999797821045, + -2.2689998149871826 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -0.4329996109008789, + -0.5479998588562012, + -0.8379998207092285, + -1.2189998626708984, + -1.6419997215270996, + -2.0839996337890625, + -2.5349998474121094, + -2.430999755859375, + -2.2909998893737793, + -2.138000011444092, + -2.0190000534057617 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -0.0429997444152832, + -0.09200000762939453, + -0.2259998321533203, + -0.4159998893737793, + -0.6349997520446777, + -0.866999626159668, + -1.0999999046325684, + -1.3269996643066406, + -1.5439996719360352, + -1.7430000305175781, + -1.8779997825622559 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -0.013000011444091797, + -0.06199979782104492, + -0.19499969482421875, + -0.38299989700317383, + -0.5980000495910645, + -0.8229999542236328, + -1.0460000038146973, + -1.2569999694824219, + -1.4439997673034668, + -1.5869998931884766, + -1.6449999809265137 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.14300012588500977, + 0.20300006866455078, + 0.37400007247924805, + 0.5989999771118164, + 0.6040000915527344, + 0.6280002593994141, + 0.6680002212524414, + 0.7220001220703125, + 0.7820000648498535, + 0.8340001106262207, + 0.8570003509521484 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.14400005340576172, + 0.20399999618530273, + 0.375, + 0.6400003433227539, + 0.9809999465942383, + 1.3819999694824219, + 1.569000244140625, + 1.5789999961853027, + 1.5120000839233398, + 1.439000129699707, + 1.4079999923706055 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.6579999923706055, + 0.6380000114440918, + 0.6110000610351562, + 0.6410002708435059, + 0.9820003509521484, + 1.383000373840332, + 1.830000400543213, + 2.2480006217956543, + 2.4390006065368652, + 2.6790003776550293, + 2.8680005073547363 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.8220000267028809, + 0.8700003623962402, + 1.010000228881836, + 1.1620001792907715, + 1.308000087738037, + 1.4580001831054688, + 1.8309998512268066, + 2.316000461578369, + 2.8340001106262207, + 3.2170004844665527, + 3.0450005531311035 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -2.809000015258789, + -2.8459999561309814, + -2.9469997882843018, + -3.0889999866485596, + -3.0239999294281006, + -2.934000015258789, + -2.8259999752044678, + -2.7779998779296875, + -2.6610000133514404, + -2.557999849319458, + -2.5119998455047607 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -0.3249998092651367, + -0.36999988555908203, + -0.6719999313354492, + -1.0869998931884766, + -1.5180001258850098, + -1.9529998302459717, + -2.384999990463257, + -2.6989998817443848, + -2.553999900817871, + -2.3969998359680176, + -2.2769999504089355 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -0.29199981689453125, + -0.3359999656677246, + -0.4930000305175781, + -0.6719999313354492, + -0.8829998970031738, + -1.1100001335144043, + -1.3420000076293945, + -1.5699996948242188, + -1.7879998683929443, + -1.9909999370574951, + -2.126999855041504 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -0.15000009536743164, + -0.315000057220459, + -0.4590001106262207, + -0.6359996795654297, + -0.8439998626708984, + -1.065999984741211, + -1.2880001068115234, + -1.5, + -1.691999912261963, + -1.8399999141693115, + -1.9019999504089355 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.2670001983642578, + 0.22700023651123047, + 0.17500019073486328, + 0.14400005340576172, + 0.1360001564025879, + 0.1510000228881836, + 0.18800020217895508, + 0.24300003051757812, + 0.30900001525878906, + 0.3710002899169922, + 0.3990001678466797 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.3959999084472656, + 0.46199989318847656, + 0.6500000953674316, + 0.8340001106262207, + 1.0120000839233398, + 1.1800003051757812, + 1.25, + 1.1760001182556152, + 1.0560002326965332, + 0.9530000686645508, + 0.9100003242492676 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.3970003128051758, + 0.4630002975463867, + 0.6519999504089355, + 0.940000057220459, + 1.308000087738037, + 1.7360000610351562, + 1.8020000457763672, + 1.9770002365112305, + 2.2280001640319824, + 2.492000102996826, + 2.672999858856201 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.5180001258850098, + 0.560999870300293, + 0.6770000457763672, + 0.9419999122619629, + 1.309999942779541, + 1.7379999160766602, + 2.2100000381469727, + 2.7219996452331543, + 3.073000431060791, + 2.9830002784729004, + 2.858999729156494 + ], + "yaxis": "y2" + }, + { + "line": { + "color": "RoyalBlue", + "dash": "dot", + "width": 3 + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 11 + ], + "xaxis": "x", + "y": [ + 0, + 0 + ], + "yaxis": "y" + }, + { + "line": { + "color": "RoyalBlue", + "dash": "dot", + "width": 3 + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 11 + ], + "xaxis": "x2", + "y": [ + 0, + 0 + ], + "yaxis": "y2" + } + ], + "layout": { + "annotations": [ + { + "font": { + "size": 16 + }, + "showarrow": false, + "text": "strain 0%", + "x": 0.225, + "xanchor": "center", + "xref": "paper", + "y": 1, + "yanchor": "bottom", + "yref": "paper" + }, + { + "font": { + "size": 16 + }, + "showarrow": false, + "text": "strain 5%", + "x": 0.775, + "xanchor": "center", + "xref": "paper", + "y": 1, + "yanchor": "bottom", + "yref": "paper" + } + ], + "height": 650, + "plot_bgcolor": "white", + "template": { + "data": { + "bar": [ + { + "error_x": { + "color": "#2a3f5f" + }, + "error_y": { + "color": "#2a3f5f" + }, + "marker": { + "line": { + "color": "#E5ECF6", + "width": 0.5 + } + }, + "type": "bar" + } + ], + "barpolar": [ + { + "marker": { + "line": { + "color": "#E5ECF6", + "width": 0.5 + } + }, + "type": "barpolar" + } + ], + "carpet": [ + { + "aaxis": { + "endlinecolor": "#2a3f5f", + "gridcolor": "white", + "linecolor": "white", + "minorgridcolor": "white", + "startlinecolor": "#2a3f5f" + }, + "baxis": { + "endlinecolor": "#2a3f5f", + "gridcolor": "white", + "linecolor": "white", + "minorgridcolor": "white", + "startlinecolor": "#2a3f5f" + }, + "type": "carpet" + } + ], + "choropleth": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "type": "choropleth" + } + ], + "contour": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "contour" + } + ], + "contourcarpet": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "type": "contourcarpet" + } + ], + "heatmap": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "heatmap" + } + ], + "heatmapgl": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "heatmapgl" + } + ], + "histogram": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "histogram" + } + ], + "histogram2d": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "histogram2d" + } + ], + "histogram2dcontour": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "histogram2dcontour" + } + ], + "mesh3d": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "type": "mesh3d" + } + ], + "parcoords": [ + { + "line": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "parcoords" + } + ], + "pie": [ + { + "automargin": true, + "type": "pie" + } + ], + "scatter": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatter" + } + ], + "scatter3d": [ + { + "line": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatter3d" + } + ], + "scattercarpet": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scattercarpet" + } + ], + "scattergeo": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scattergeo" + } + ], + "scattergl": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scattergl" + } + ], + "scattermapbox": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scattermapbox" + } + ], + "scatterpolar": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatterpolar" + } + ], + "scatterpolargl": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatterpolargl" + } + ], + "scatterternary": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatterternary" + } + ], + "surface": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "surface" + } + ], + "table": [ + { + "cells": { + "fill": { + "color": "#EBF0F8" + }, + "line": { + "color": "white" + } + }, + "header": { + "fill": { + "color": "#C8D4E3" + }, + "line": { + "color": "white" + } + }, + "type": "table" + } + ] + }, + "layout": { + "annotationdefaults": { + "arrowcolor": "#2a3f5f", + "arrowhead": 0, + "arrowwidth": 1 + }, + "coloraxis": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "colorscale": { + "diverging": [ + [ + 0, + "#8e0152" + ], + [ + 0.1, + "#c51b7d" + ], + [ + 0.2, + "#de77ae" + ], + [ + 0.3, + "#f1b6da" + ], + [ + 0.4, + "#fde0ef" + ], + [ + 0.5, + "#f7f7f7" + ], + [ + 0.6, + "#e6f5d0" + ], + [ + 0.7, + "#b8e186" + ], + [ + 0.8, + "#7fbc41" + ], + [ + 0.9, + "#4d9221" + ], + [ + 1, + "#276419" + ] + ], + "sequential": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "sequentialminus": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ] + }, + "colorway": [ + "#636efa", + "#EF553B", + "#00cc96", + "#ab63fa", + "#FFA15A", + "#19d3f3", + "#FF6692", + "#B6E880", + "#FF97FF", + "#FECB52" + ], + "font": { + "color": "#2a3f5f" + }, + "geo": { + "bgcolor": "white", + "lakecolor": "white", + "landcolor": "#E5ECF6", + "showlakes": true, + "showland": true, + "subunitcolor": "white" + }, + "hoverlabel": { + "align": "left" + }, + "hovermode": "closest", + "mapbox": { + "style": "light" + }, + "paper_bgcolor": "white", + "plot_bgcolor": "#E5ECF6", + "polar": { + "angularaxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + }, + "bgcolor": "#E5ECF6", + "radialaxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + } + }, + "scene": { + "xaxis": { + "backgroundcolor": "#E5ECF6", + "gridcolor": "white", + "gridwidth": 2, + "linecolor": "white", + "showbackground": true, + "ticks": "", + "zerolinecolor": "white" + }, + "yaxis": { + "backgroundcolor": "#E5ECF6", + "gridcolor": "white", + "gridwidth": 2, + "linecolor": "white", + "showbackground": true, + "ticks": "", + "zerolinecolor": "white" + }, + "zaxis": { + "backgroundcolor": "#E5ECF6", + "gridcolor": "white", + "gridwidth": 2, + "linecolor": "white", + "showbackground": true, + "ticks": "", + "zerolinecolor": "white" + } + }, + "shapedefaults": { + "line": { + "color": "#2a3f5f" + } + }, + "ternary": { + "aaxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + }, + "baxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + }, + "bgcolor": "#E5ECF6", + "caxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + } + }, + "title": { + "x": 0.05 + }, + "xaxis": { + "automargin": true, + "gridcolor": "white", + "linecolor": "white", + "ticks": "", + "title": { + "standoff": 15 + }, + "zerolinecolor": "white", + "zerolinewidth": 2 + }, + "yaxis": { + "automargin": true, + "gridcolor": "white", + "linecolor": "white", + "ticks": "", + "title": { + "standoff": 15 + }, + "zerolinecolor": "white", + "zerolinewidth": 2 + } + } + }, + "width": 900, + "xaxis": { + "anchor": "y", + "domain": [ + 0, + 0.45 + ], + "gridcolor": "lightgrey", + "gridwidth": 0.5, + "linecolor": "black", + "linewidth": 1, + "mirror": true, + "range": [ + 1, + 11 + ], + "showgrid": true, + "ticks": "inside", + "ticktext": [ + "G", + "Z" + ], + "tickvals": [ + 1, + 11 + ] + }, + "xaxis2": { + "anchor": "y2", + "domain": [ + 0.55, + 1 + ], + "gridcolor": "lightgrey", + "gridwidth": 0.5, + "linecolor": "black", + "linewidth": 1, + "mirror": true, + "range": [ + 1, + 11 + ], + "showgrid": true, + "ticks": "inside", + "ticktext": [ + "G", + "Z" + ], + "tickvals": [ + 1, + 11 + ] + }, + "yaxis": { + "anchor": "x", + "domain": [ + 0, + 1 + ], + "gridcolor": "lightgrey", + "gridwidth": 0.5, + "linecolor": "black", + "linewidth": 1, + "mirror": true, + "showgrid": true, + "ticks": "inside", + "title": { + "text": "Energy, eV" + } + }, + "yaxis2": { + "anchor": "x2", + "domain": [ + 0, + 1 + ], + "gridcolor": "lightgrey", + "gridwidth": 0.5, + "linecolor": "black", + "linewidth": 1, + "mirror": true, + "showgrid": true, + "ticks": "inside", + "title": { + "text": "Energy, eV" + } + } + } + }, + "text/html": [ + "
\n", + " \n", + " \n", + "
\n", + " \n", + "
" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "#load ml_modeling_module \n", + "from ml_modeling_module import *\n", + "\n", + "#first let's plot sige bandstructure\n", + "#read QE output file with bands for 0% strain\n", + "data=read_data('bands/bands_0.dat')\n", + "bands0=data.read_bands_ml(fermi=6.18, bands_num=4)\n", + "\n", + "#read QE output file with bands for 5% strain\n", + "data=read_data('bands/bands_5.dat')\n", + "bands5=data.read_bands_ml(fermi=5.60, bands_num=4)\n", + "# reshape data: 8 bands 11 k-points\n", + "bands0=bands0.reshape(8,11)\n", + "bands5=bands5.reshape(8,11)\n", + "\n", + "import plotly.graph_objects as go\n", + "from plotly.subplots import make_subplots\n", + "fig = make_subplots(rows=1, cols=2,subplot_titles=(\"strain 0%\", \"strain 5%\"))\n", + "\n", + "for i in range(bands0.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands0[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), col=1, row=1) \n", + "for i in range(bands5.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands5[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), col=2, row=1) \n", + "fig.add_trace(go.Scatter(x=[1,11], y=[0,0],\n", + " mode='lines', line=dict(color= \"RoyalBlue\",width=3, dash='dot'), showlegend=False, \n", + " name='markers'), col=1, row=1) \n", + "fig.add_trace(go.Scatter(x=[1,11], y=[0,0],\n", + " mode='lines', line=dict(color= \"RoyalBlue\",width=3, dash='dot'), showlegend=False, \n", + " name='markers'), col=2, row=1) \n", + "fig.update_xaxes(showgrid=True, \n", + " gridwidth=0.5, \n", + " gridcolor='lightgrey', \n", + " ticks='inside' , \n", + " linecolor= 'black', \n", + " linewidth= 1,\n", + " mirror= True,\n", + " ticktext=['G', 'Z'],\n", + " tickvals=[1,11],\n", + " range=[1,11],\n", + " )\n", + "fig.update_yaxes(title='Energy, eV', \n", + " showgrid=True, \n", + " gridwidth=0.5, \n", + " gridcolor='lightgrey', \n", + " ticks='inside' , \n", + " linecolor= 'black',\n", + " linewidth= 1,\n", + " mirror= True,\n", + " )\n", + "\n", + "fig.update_layout(width=900, height=650, plot_bgcolor='white')\n", + "fig.show()\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-27T18:59:06.968840Z", + "start_time": "2021-10-27T18:59:06.951835Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "(7, 44)" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# reading bands from all QE output file\n", + "from os import walk\n", + "mypath='bands/'\n", + "filenames = next(walk(mypath), (None, None, []))[2]\n", + "fermi=[6.18,6.02,5.83,5.71,5.66,5.60,5.75]\n", + "y=[]\n", + "for i in range(len(filenames)):\n", + " data=read_data(mypath+filenames[i])\n", + " bands_ml=data.read_bands_ml(fermi=fermi[i], bands_num=2)\n", + " y= np.append(y, bands_ml)\n", + "y=y.reshape(len(filenames),44)\n", + "y.shape" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-27T18:59:08.734621Z", + "start_time": "2021-10-27T18:59:08.718617Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "(7, 2)" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# reading cell parameters from QE output file : NEED TO add a fucntion \n", + "#(lattice constants are in bohr)\n", + "X=np.array([[10.34568, 10.79211],\n", + " [10.45682, 10.71265],\n", + " [10.56082, 10.64615], \n", + " [10.66056, 10.57623],\n", + " [10.76056, 10.50342],\n", + " [10.87056, 10.42435],\n", + " [10.60789, 10.610219]\n", + " ])\n", + "X.shape" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# prepare data for modeling: split for training and testig sets" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-27T19:11:11.691912Z", + "start_time": "2021-10-27T19:11:06.561755Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Time taken for RF: 0:00:05.113152\n", + "Train:\n", + "R^2:0.97 RMSE:0.02\n", + "Test:\n", + "R^2:nan RMSE: 0.03\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\exx\\Anaconda3\\envs\\tensorflow\\lib\\site-packages\\sklearn\\base.py:434: FutureWarning:\n", + "\n", + "The default value of multioutput (not exposed in score method) will change from 'variance_weighted' to 'uniform_average' in 0.23 to keep consistent with 'metrics.r2_score'. To specify the default value manually and avoid the warning, please either call 'metrics.r2_score' directly or make a custom scorer with 'metrics.make_scorer' (the built-in scorer 'r2' uses multioutput='uniform_average').\n", + "\n", + "C:\\Users\\exx\\Anaconda3\\envs\\tensorflow\\lib\\site-packages\\sklearn\\metrics\\_regression.py:582: UndefinedMetricWarning:\n", + "\n", + "R^2 score is not well-defined with less than two samples.\n", + "\n" + ] + } + ], + "source": [ + "my_data=data_preparation(X,y)\n", + "(X_train, X_test, Y_train, Y_test)=my_data.select_train_test(test_row_number=[6])\n", + "#random split could also be used\n", + "#(X_train, X_test, Y_train, Y_test)=my_data.random_split(train_split=0.8, seed=42)\n", + "\n", + "my_model=modeling(X_train, Y_train, X_test, Y_test, scaler='None')\n", + "\n", + "#train Random forest model with No initial guess\n", + "(y_fit_RF, y_predict_RF, trials_RF, best_space_RF, regressorRF, text_RF)=my_model.RandomForest( max_evals=10, timeout=150*60,loss_threshold=0.01, cv=5, verbose=1)\n", + "\n", + "print(text_RF)\n", + "\n", + "\n", + "#" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-27T19:18:56.522361Z", + "start_time": "2021-10-27T19:11:21.055477Z" + } + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\exx\\Anaconda3\\envs\\tensorflow\\lib\\site-packages\\xgboost\\core.py:614: UserWarning:\n", + "\n", + "Use subset (sliced data) of np.ndarray is not recommended because it will generate extra copies and increase memory consumption\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Time taken for XGB: 0:07:34.327627\n", + "Train:\n", + "R^2:-0.0 RMSE:0.11\n", + "Test:\n", + "R^2:nan RMSE: 0.08\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\exx\\Anaconda3\\envs\\tensorflow\\lib\\site-packages\\sklearn\\metrics\\_regression.py:582: UndefinedMetricWarning:\n", + "\n", + "R^2 score is not well-defined with less than two samples.\n", + "\n" + ] + } + ], + "source": [ + "## DOES NOT WORK YET \n", + "\n", + "# train XGboost model with initial guess\n", + "# best_space = {'alpha': 0.0, 'max_depth': 3.0, 'min_split_loss': 5.6, 'n_estimators': 100, 'x_reg_lambda': 1.00, 'x_subsample': 1.0}\n", + "# (y_fit_XG, y_predict_XG, trials_XG, best_space_XG, regressorXGB, text_XG)=my_model.XGB( max_evals=4, timeout=150*60,loss_threshold=0.01,init_vals=[best_space],cv=5, verbose=1) \n", + "# print(text_XG)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# let's plot predicted bands vs calculated bands" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-28T00:13:37.642491Z", + "start_time": "2021-10-28T00:13:37.587466Z" + } + }, + "outputs": [ + { + "data": { + "application/vnd.plotly.v1+json": { + "config": { + "plotlyServerURL": "https://plot.ly" + }, + "data": [ + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + -2.8399999141693115, + -2.874000072479248, + -2.8910000324249268, + -2.8420000076293945, + -2.7730000019073486, + -2.684999942779541, + -2.578000068664551, + -2.5290000438690186, + -2.4159998893737793, + -2.316999912261963, + -2.2730000019073486 + ] + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + -0.1490001678466797, + -0.2839999198913574, + -0.6040000915527344, + -1.001999855041504, + -1.428999900817871, + -1.86899995803833, + -2.309999942779541, + -2.453000068664551, + -2.311000108718872, + -2.1559998989105225, + -2.0369999408721924 + ] + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + -0.06799983978271484, + -0.11499977111816406, + -0.24399995803833008, + -0.4289999008178711, + -0.6449999809265137, + -0.875999927520752, + -1.1079998016357422, + -1.3359999656677246, + -1.553999900817871, + -1.755000114440918, + -1.8900001049041748 + ] + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + -0.034999847412109375, + -0.0819997787475586, + -0.2090001106262207, + -0.39099979400634766, + -0.6030001640319824, + -0.8260002136230469, + -1.0479998588562012, + -1.2589998245239258, + -1.4479999542236328, + -1.5929999351501465, + -1.6529998779296875 + ] + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + 0.39099979400634766, + 0.4530000686645508, + 0.5139999389648438, + 0.49200010299682617, + 0.4910001754760742, + 0.5110001564025879, + 0.5500001907348633, + 0.6040000915527344, + 0.6680002212524414, + 0.7249999046325684, + 0.75 + ] + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + 0.40399980545043945, + 0.46700000762939453, + 0.6329998970031738, + 0.9099998474121094, + 1.2649998664855957, + 1.433000087738037, + 1.5300002098083496, + 1.500999927520752, + 1.4060001373291016, + 1.3179998397827148, + 1.2810001373291016 + ] + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + 0.5850000381469727, + 0.5539999008178711, + 0.6469998359680176, + 0.9239997863769531, + 1.2729997634887695, + 1.6779999732971191, + 2.0929999351501465, + 2.2170000076293945, + 2.439999580383301, + 2.694000244140625, + 2.878999710083008 + ] + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + 0.809999942779541, + 0.8610000610351562, + 0.9699997901916504, + 1.1110000610351562, + 1.2789998054504395, + 1.6929998397827148, + 2.1399998664855957, + 2.6389999389648438, + 3.168999671936035, + 3.2170000076293945, + 3.067999839782715 + ] + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + -0.09595230647495814, + -0.14447627748761857, + -0.273000058673677, + -0.4575714837937128, + -0.6735715411958241, + -0.9026190439860026, + -1.1351429167247953, + -1.3621905417669387, + -1.579666705358596, + -1.7811428365253268, + -1.9161428156353177 + ] + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + -0.06428573245093935, + -0.11333329336983818, + -0.24095240093412854, + -0.423904850369408, + -0.635476203191848, + -0.8590000243414015, + -1.0815715335664295, + -1.293047655196417, + -1.4815711975097656, + -1.6275237060728527, + -1.6875238872709728 + ] + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + 0.36623800368536086, + 0.4240001042683919, + 0.4799047424679711, + 0.4622381755283901, + 0.4617620195661272, + 0.4812858445303781, + 0.5202856745038714, + 0.5748095512390137, + 0.6377619334629604, + 0.6956665402367002, + 0.7201904569353376 + ] + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + 0.3667620023091634, + 0.4297143164135161, + 0.6082857222784133, + 0.8856191862197149, + 1.2063332739330472, + 1.4045239630199613, + 1.5010477020626976, + 1.471857229868571, + 1.376666750226702, + 1.287809621720087, + 1.2509046963282995 + ] + }, + { + "line": { + "color": "RoyalBlue", + "dash": "dot", + "width": 3 + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 11 + ], + "y": [ + 0, + 0 + ] + } + ], + "layout": { + "height": 650, + "plot_bgcolor": "white", + "template": { + "data": { + "bar": [ + { + "error_x": { + "color": "#2a3f5f" + }, + "error_y": { + "color": "#2a3f5f" + }, + "marker": { + "line": { + "color": "#E5ECF6", + "width": 0.5 + } + }, + "type": "bar" + } + ], + "barpolar": [ + { + "marker": { + "line": { + "color": "#E5ECF6", + "width": 0.5 + } + }, + "type": "barpolar" + } + ], + "carpet": [ + { + "aaxis": { + "endlinecolor": "#2a3f5f", + "gridcolor": "white", + "linecolor": "white", + "minorgridcolor": "white", + "startlinecolor": "#2a3f5f" + }, + "baxis": { + "endlinecolor": "#2a3f5f", + "gridcolor": "white", + "linecolor": "white", + "minorgridcolor": "white", + "startlinecolor": "#2a3f5f" + }, + "type": "carpet" + } + ], + "choropleth": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "type": "choropleth" + } + ], + "contour": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "contour" + } + ], + "contourcarpet": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "type": "contourcarpet" + } + ], + "heatmap": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "heatmap" + } + ], + "heatmapgl": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "heatmapgl" + } + ], + "histogram": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "histogram" + } + ], + "histogram2d": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "histogram2d" + } + ], + "histogram2dcontour": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "histogram2dcontour" + } + ], + "mesh3d": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "type": "mesh3d" + } + ], + "parcoords": [ + { + "line": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "parcoords" + } + ], + "pie": [ + { + "automargin": true, + "type": "pie" + } + ], + "scatter": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatter" + } + ], + "scatter3d": [ + { + "line": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatter3d" + } + ], + "scattercarpet": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scattercarpet" + } + ], + "scattergeo": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scattergeo" + } + ], + "scattergl": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scattergl" + } + ], + "scattermapbox": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scattermapbox" + } + ], + "scatterpolar": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatterpolar" + } + ], + "scatterpolargl": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatterpolargl" + } + ], + "scatterternary": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatterternary" + } + ], + "surface": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "surface" + } + ], + "table": [ + { + "cells": { + "fill": { + "color": "#EBF0F8" + }, + "line": { + "color": "white" + } + }, + "header": { + "fill": { + "color": "#C8D4E3" + }, + "line": { + "color": "white" + } + }, + "type": "table" + } + ] + }, + "layout": { + "annotationdefaults": { + "arrowcolor": "#2a3f5f", + "arrowhead": 0, + "arrowwidth": 1 + }, + "coloraxis": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "colorscale": { + "diverging": [ + [ + 0, + "#8e0152" + ], + [ + 0.1, + "#c51b7d" + ], + [ + 0.2, + "#de77ae" + ], + [ + 0.3, + "#f1b6da" + ], + [ + 0.4, + "#fde0ef" + ], + [ + 0.5, + "#f7f7f7" + ], + [ + 0.6, + "#e6f5d0" + ], + [ + 0.7, + "#b8e186" + ], + [ + 0.8, + "#7fbc41" + ], + [ + 0.9, + "#4d9221" + ], + [ + 1, + "#276419" + ] + ], + "sequential": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "sequentialminus": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ] + }, + "colorway": [ + "#636efa", + "#EF553B", + "#00cc96", + "#ab63fa", + "#FFA15A", + "#19d3f3", + "#FF6692", + "#B6E880", + "#FF97FF", + "#FECB52" + ], + "font": { + "color": "#2a3f5f" + }, + "geo": { + "bgcolor": "white", + "lakecolor": "white", + "landcolor": "#E5ECF6", + "showlakes": true, + "showland": true, + "subunitcolor": "white" + }, + "hoverlabel": { + "align": "left" + }, + "hovermode": "closest", + "mapbox": { + "style": "light" + }, + "paper_bgcolor": "white", + "plot_bgcolor": "#E5ECF6", + "polar": { + "angularaxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + }, + "bgcolor": "#E5ECF6", + "radialaxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + } + }, + "scene": { + "xaxis": { + "backgroundcolor": "#E5ECF6", + "gridcolor": "white", + "gridwidth": 2, + "linecolor": "white", + "showbackground": true, + "ticks": "", + "zerolinecolor": "white" + }, + "yaxis": { + "backgroundcolor": "#E5ECF6", + "gridcolor": "white", + "gridwidth": 2, + "linecolor": "white", + "showbackground": true, + "ticks": "", + "zerolinecolor": "white" + }, + "zaxis": { + "backgroundcolor": "#E5ECF6", + "gridcolor": "white", + "gridwidth": 2, + "linecolor": "white", + "showbackground": true, + "ticks": "", + "zerolinecolor": "white" + } + }, + "shapedefaults": { + "line": { + "color": "#2a3f5f" + } + }, + "ternary": { + "aaxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + }, + "baxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + }, + "bgcolor": "#E5ECF6", + "caxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + } + }, + "title": { + "x": 0.05 + }, + "xaxis": { + "automargin": true, + "gridcolor": "white", + "linecolor": "white", + "ticks": "", + "title": { + "standoff": 15 + }, + "zerolinecolor": "white", + "zerolinewidth": 2 + }, + "yaxis": { + "automargin": true, + "gridcolor": "white", + "linecolor": "white", + "ticks": "", + "title": { + "standoff": 15 + }, + "zerolinecolor": "white", + "zerolinewidth": 2 + } + } + }, + "title": { + "text": "Si2Ge2 relaxed" + }, + "width": 450, + "xaxis": { + "gridcolor": "lightgrey", + "gridwidth": 0.5, + "linecolor": "black", + "linewidth": 1, + "mirror": true, + "range": [ + 1, + 11 + ], + "showgrid": true, + "ticks": "inside", + "ticktext": [ + "G", + "Z" + ], + "tickvals": [ + 1, + 11 + ] + }, + "yaxis": { + "gridcolor": "lightgrey", + "gridwidth": 0.5, + "linecolor": "black", + "linewidth": 1, + "mirror": true, + "showgrid": true, + "ticks": "inside", + "title": { + "text": "Energy, eV" + } + } + } + }, + "text/html": [ + "
\n", + " \n", + " \n", + "
\n", + " \n", + "
" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "# let's plot predicted bands vs calculated bands\n", + "#reading calculated bands:\n", + "data=read_data('bands/bands_relax.dat')\n", + "bands=data.read_bands_ml(fermi=5.75, bands_num=4)\n", + "bands=bands.reshape(8,11)\n", + "#predicted bands\n", + "bands_RF=y_predict_RF.reshape(4,11)\n", + "#bands_XG=y_predict_XG.reshape(4,11)\n", + "\n", + "import plotly.graph_objects as go\n", + "fig = go.Figure()\n", + "\n", + "for i in range(bands.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'))\n", + " \n", + "for i in range(bands_RF.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_RF[i],\n", + " mode='markers', marker=dict(color='red'), showlegend=False, \n", + " name='markers'))\n", + "fig.add_trace(go.Scatter(x=[1,11], y=[0,0],\n", + " mode='lines', line=dict(color= \"RoyalBlue\",width=3, dash='dot'), showlegend=False, \n", + " name='markers')) \n", + "\n", + "fig.update_xaxes(showgrid=True, \n", + " gridwidth=0.5, \n", + " gridcolor='lightgrey', \n", + " ticks='inside' , \n", + " linecolor= 'black', \n", + " linewidth= 1,\n", + " mirror= True,\n", + " ticktext=['G', 'Z'],\n", + " tickvals=[1,11],\n", + " range=[1,11]\n", + " )\n", + "fig.update_yaxes(title='Energy, eV', \n", + " showgrid=True, \n", + " gridwidth=0.5, \n", + " gridcolor='lightgrey', \n", + " ticks='inside' , \n", + " linecolor= 'black',\n", + " linewidth= 1,\n", + " mirror= True,\n", + " )\n", + "fig.update_layout(title='Si2Ge2 relaxed', width=450, height=650, plot_bgcolor='white')\n", + "fig.show()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# example of solving reverse problem " + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-28T00:13:54.951932Z", + "start_time": "2021-10-28T00:13:42.105295Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Lattice parameters:[10.58181053 10.62970763]\n", + "MSE: 0.0006365325686575999\n" + ] + } + ], + "source": [ + "# in this example we predict lattice constants for a given bandstructure (lattice constants are in bohr)\n", + "\n", + "import GPyOpt\n", + "from GPyOpt.methods import BayesianOptimization\n", + "from sklearn.metrics import mean_squared_error\n", + "\n", + "data=read_data('bands/bands_relax.dat')\n", + "bands=data.read_bands_ml(fermi=5.75, bands_num=2)\n", + "\n", + "\n", + "def objfunc(x):\n", + "\n", + " x1 = float(x[0,0])\n", + " x2 = float(x[0,1])\n", + "\n", + " return mean_squared_error(regressorRF.predict([[x1,x2]]).reshape(1,44), bands.reshape(1,44))\n", + "\n", + "maxiter = 40\n", + "domain = [\n", + " {'name': 'a_paral', 'type': 'continuous', 'domain': (10.3, 10.8)},\n", + " {'name': 'a_perp', 'type': 'continuous', 'domain': (10.3, 10.8)}\n", + " ]\n", + "\n", + "\n", + "\n", + "Bopt = GPyOpt.methods.BayesianOptimization(objfunc, domain=domain)\n", + "Bopt.run_optimization(max_iter = maxiter)\n", + "\n", + "print(\"Lattice parameters:\"+str(Bopt.x_opt)) \n", + "print(\"MSE: \"+str(Bopt.fx_opt)) " + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.10" + }, + "varInspector": { + "cols": { + "lenName": 16, + "lenType": 16, + "lenVar": 40 + }, + "kernels_config": { + "python": { + "delete_cmd_postfix": "", + "delete_cmd_prefix": "del ", + "library": "var_list.py", + "varRefreshCmd": "print(var_dic_list())" + }, + "r": { + "delete_cmd_postfix": ") ", + "delete_cmd_prefix": "rm(", + "library": "var_list.r", + "varRefreshCmd": "cat(var_dic_list()) " + } + }, + "types_to_exclude": [ + "module", + "function", + "builtin_function_or_method", + "instance", + "_Feature" + ], + "window_display": false + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/vitalypro/__pycache__/ml_modeling_module.cpython-36.pyc b/vitalypro/__pycache__/ml_modeling_module.cpython-36.pyc new file mode 100644 index 0000000000000000000000000000000000000000..c031464c0c5b7c6c62a9b9cf1a97763d8cc0592c GIT binary patch literal 10234 zcmb7K-ILqab;lRKKrZ)F+LavJXr@z(t+Xr4ZO5~g!FR}0j>+Ei7_>w(tS zn|j}98vR1E&@VQN{Zg~kFE`6vZv>UT*)%y{2&(;Bv&Q*iu+XnJ>zpqIi_N8X6u0bF zK2hAtq1If+lj&CRRK?Q@o@(v_o)+-5>XvRRjr!9Dh(WwpsSm08h?7_ zLi{F5Jf*2ZkeaJDbysusPn4#C#g^RiCu+0cRqt9a_n* zA6xy%9R{AY=ULRsqE=Q%M1AYKZ(GqY84MH430+Bv_EqZO%-K4L9z<6yB9m*E*=DvLU%H-`h5yN&e6rP3EJAE(lM9eejc%tuH zf%ni0VViH$Qle&98<%!s|9BNou&pA@l(pWnXn z=Jvf0V=U>Ox4)0uX&ofqJ>l&|i5K5{$f}2F-s=bURJfGE4s8w&va)Uap`Y0HvotbK zM;)!?ySq897T9Iwi0Y4MdTj#Q&Q~L)euE|IBlyCk^e_+~S6k z>TAmQOnN4%Q5%eRHeE?;>FPNpJ(HgORC@()eNTZT77i6vL5;ehjBA+FI_{1APEt>6 zy+x7_&uV9U4y&xD>u7lneQ=6-80QpMOXcjf@jAEJIMGHyd#wryY``M%I<@h}m+FJ- z7=OLDWdb;sc*~X;bb=03v&yziK{s)`ON=rw5ht7Ft7`78X3R(AK zYwnPu?)Z5p?X^xG)Xn`(c?_t>Z^Hr%alF}rv|$A-oEs!bGKjagwz__@J8W&XqyE;x z!NKs#<;z>&eVgpTAc&H!RuHwe`c90Ky*1dgsobUtXm~#580GiLw>OLvGDXx~JZ(B>GfuoP5Pq0gQ3y-l@kN|ip#{_Hg>8=wL5NX8 z7%G;S>@xHm!Q;<$I+Mt@EWKpS*Iw}MH1ct`xf?qi_Ay_iEm)eUGaYs7^zr6~;zTR@-z!&GpSgMlYj@HEmab7cI$`sk02s(3v5 zUtEoqOcP#aL<28mvn8PeCflbVukyHVS= z#WLOze?|$x)m%br5;Y`eaK{89<&vS64K8crF~3OFuHlZaAUTzvEWo6fn4f^8b+wMl z^h|9Q-5MFMY>8NdJrEu-06KxApGy`078w~Z67gz5ovw%tb_i)FI*lJN7ojWOu9OQrV_kTy%(bc0r z#2fj1%6P~z{uMk(jPI*s9Z04V&g0e-!_^7Z4%Jk1jmO44V{D8I<07!$NDFB(Ep-gc zz2H0#`!O>x7LKnQ^=&Dysr)R5B+6D-*2AiT`e0XPLd1K=#3*-*>^ZG)4qL2k7W`z0 zOIEzgU85l@1KCV&fDzC=wn?JG-fjfcqB5VDEwW^%Hmx@$`(xd>OpQTP-|{-nFo-R{ z;^obkbL(ks#~#!OrOsrXR-AyHvkpNUnY#KdAN?N88C{Fd9IWe-oH!|qoV_>;`8Tv? zMHcxZFRM)jNF6r{*?N3G0I-CctfRJ+8dP4qjaO%i0((gIwNYjTYF6h&L@d*DxqVi; z3-1D2n-!74G_un7rv=EM;Do}>rbEK|7(?>WR*E&4o6)mR>E3km)cUA^=0~JzIWeXO z(%d(3$JdZR({LWnDPz((m2-Nc^+*d*?y846xTkzZEk75ae;PDUXZ_Pg|1ncODIB>V zUQK?0=M=E-gs^L*fCI1Xcd$`XTfVmbZS!V{Xpf+pKpOf$`ZR-V)KQU>SbKgDkZ&=J z$^5|5(7P}h($E0hpp9rcH6$cY*0x;br0N*6jTVFySrL8}JfB8UZujDeDT#N{NZg?0 zJCwXf$#GMXEk7l#9$K-xq7+Ra%@Y1b-+XF|pL*?PLld;2g5axB5@b`vtCYM($yG`i zHf~bx7A3Q(aE?veHB@{LcT5JVY!G&srl8U`?))ktcMbP(^jK!!mV8{pEwGQf!cIK- zxT|j6T?CpG-6a^TwX8g~_L*@r3cWTdC0+EJ8)`C{P%?OJX@MPvKVY*BV~8@1%%rVD z5f$5THT0^F{ypEa*e8+*6vC!sYdsH?leQoJuoHA60q)z6FXqjmIsh$bK^R#fnHQL# z7>@r0y)JNGy!ryo^@WB67vgm6pTqRbIknTK2s-qg{TD7;FTgy7t|QzREH7zW6Gzu^ z-HA3zclOxC@_Ee}FtGz^+=MYI$`R(2Dp$0LDxOv)KE&&Dd!8fN9?D|^Jf&0wjVa1M zZL~byp&ZL{50$pRf}1VK6J&DqGB~=U2TC74D)L4G3`^A>HnCU4T{_gAI^WBpLg+rZ1@9_W4ept3%%HBa<_7S#8&p1fnIMRl}2q2zqTx9FHk zvVko|300!?V|;yIk6#!BCFLOTW<6P{~(LPP>sQWjTa9B5QCcgTKh zo40;=Wm{7BqIK)W?YFm^i^I@|)#=*~264KG88xf@VF1d+ftyj)+`)|Go1>C^$!b)a zi#h0c;PmZS+<~M8oz6@LMu4P~cL$PAiJ!n}a=MQ&K3fMx2lp-fL>sN=igLW=(FHU;x{K5N8)R_(=T&CA z;(g>9blYTQ=pqtq;?{A;yWlcYh58(hJwXq`8|BZG&(zPf&j2|tEX*fmgf=+LK|B?1 zx4}>4V^0<0ta)7xbzrrJhFgDPjLp<=7ZKdpPm1Wh>Mo3HVJ!i%LcpTxE{$tRIjy8- zQb|k%4QlT4V-41atWMQkaaSLg#|sEdm?;93U?)jgA}N(rQ8B7*C<5g@^e?`vPG;?C(U z@XlKA%p*NrOqbH-L#zqmlNHLR)!x~(j`Ecb9gee(11>N_?_10qt?P6y66==N#V@=u zU}&;y-S!>~;dUX|Y2Bcp;w5QQ-ya~_>W|n7kPUZWa4&t}h>;gs=*RCnNrV95g*Ti7 zFZRLpqPbTZv(a~e;BW&S#^Y!b&U7fs(Q+n?j+Kq+CE7-<9_Xw8kSy>da6$}%Y`)L5 zQ{p5ugMNesp{KqNZ0K6Mv7JJw7OSup`>LGeFvulvtKBYl)L+VC^BkJx6S)TR%ZuMhcu{1^*I3a5v}CPI!Rf z60ZwlBpK0^PA3$~z_RetA78#Wll(RX%qdO_Dlf;Ug5NbEVq4UPy26Y9zp?-H@@0(E zo`bh-1Ri2L*@eErM{qF@8elS)6SANhYK|t;=9mOT;3Mt~DO`Z4qoDxQLJ_!Ot{!Ly zque+)TPE#OIn6eegSe0uZ7StS?Yl!92gxBZhZEa5uhf&7&%}PolH?&DIq;#6aFgbA zFdmXNfP~nyLvs;PwSC+51~`A951aEM3+-OiI<9kXe(<53A9V|tJD8r!SFIP1?RWbj zmc?H)E@6#67$$Ud({kDAN~~9{KbcdGDLP&{fs^@SJeUXQ+GPu-;>8&~%7rO(c($1n!9p;c|{c%$(ENs!}ZixCHu-jj@Ulxe7a~;nv;a zBh@WE(m*K?7>A8VkhiKN_}=n_*rGXFg@=iV6syWqL9*Js@Wpk^A*|^! z-GdW4j6v-z>YZS62KJdj-3wyP4V|KX_?DIF?VyvD`mqOYA}~LfULn6i1e9=aBd7dX zB{!n~h}xKYJtF56SZ)ke4k{gaVu=Vnk~>Bp9B-Z1-peqtzXl2vkpCHI+k{65#P9BE-9rsgChi)8Z$_p z&;LAwBoCDsWT8i&uHbgKB``>OBFY)n0sr6QHuTJ>q8a+?= zC*{vD|2*qHpPWrtekb^6iTUS~s<1;OpWqgL(b3lEh3y(8z(G4~@@w*4G zsXopxdH9olj(=v$=faeizMp&emjisQ3jF(?g$d3@L4jjbGVvx6Z2(b`5eMQfi030T zN&iiN5AA?;8I6!3D0x)K!r;j9`@9lF1!!5+lsON+%}|g`MjtKf21((4b{li>oWV4i zt2xJVx;zq7zNkFIAVi3(B6*}h7Zv&xEm7IkIL~M-u^1`5Af)){ zj1-@n>EApam!VH;0v`&xrQ@dmfT+4PVDtj;xsc;?5#AZ$^Wsg$1v1LG{`D$b>#VwO z$HSIH;H=;TgIy=9?b`xq8#w)z>tuC?Xo`K>1O=ld)NM~3cj>p6x#Q*nhjf9zHf<4i z->l@Fi@(OGO>@?<_yPseev%xd7fZwiCef#Y+}^VJMLe!gr6IK_Wi_ZtzGZCoPawI7 zsCAKA>(W3!paMY!hWIJvbM(&i{ccOfayX1bM*X+A<259Twgii6P6IirsRP8H&#fpa z@bAKIk)R9lGbCO4>Ed6mc7L??t9Slu^oy%3lgWml{w2PCeN{ZBS6Dnl$}yrk$Vtp6 z)d729u%&*vm$`SiIR&@GLu#oCibw(N#XglWRvl38INULQi67G&lfJp1(*_{%Jgo+! zwG&7W$pGrlH%kyM8KLIt6!Yf}mD~w}eevg%5blVdQ1VrXFaCmR8SVduauy}uqU0|r z`3@!TQF2JhyOexw%om?fbJmNQ_I*lawB{Mki@&1B&nS6>q*;SnOUE9I{tB2su5#i_ zdYNHf$2&)OifQUfjlP2d-&Z8QGsf#V#_LaG{0d{djBRhw7t|@z*XDH;mWjzAqF1Cz zqD4uY64n&bsaYK9>oz(O6z6#O$JEp3l>D3$=EbvwkJoKfkZQ`HxN0t!7ZB~E(#D#M ztdl-8%j^!q36x5~ysv-?KGae@NDG<^({`Kmk7<%5zC-OyBw2+$kthmcCXHDE{`=s7 sKREDLTyc$>(%`4fH7maYDdHcIUZde-;^78lZ1Hz$@G!IfM*aE!1EbfCz5oCK literal 0 HcmV?d00001 diff --git a/vitalypro/bands/bands_0.dat b/vitalypro/bands/bands_0.dat new file mode 100644 index 00000000..f022ce12 --- /dev/null +++ b/vitalypro/bands/bands_0.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.311 -2.568 -2.568 -2.484 -2.408 -1.871 -1.871 2.913 2.914 3.051 + 3.052 3.234 3.280 5.747 6.137 6.167 6.323 6.324 6.838 7.002 + 0.000001 0.000001 0.047932 + -6.301 -2.804 -2.566 -2.566 -2.074 -1.868 -1.868 2.891 2.892 3.020 + 3.020 3.244 3.290 5.632 6.088 6.118 6.383 6.384 6.818 7.050 + 0.000003 0.000003 0.095863 + -6.271 -3.145 -2.559 -2.559 -1.861 -1.860 -1.692 2.830 2.831 2.934 + 2.934 3.271 3.319 5.342 5.954 5.985 6.554 6.555 6.791 7.190 + 0.000004 0.000004 0.143795 + -6.222 -3.470 -2.548 -2.548 -1.849 -1.849 -1.297 2.739 2.740 2.811 + 2.811 3.317 3.368 4.961 5.764 5.797 6.779 6.820 6.821 7.342 + 0.000005 0.000005 0.191727 + -6.154 -3.780 -2.535 -2.534 -1.834 -1.834 -0.892 2.632 2.632 2.670 + 2.671 3.380 3.435 4.538 5.545 5.582 6.784 7.161 7.162 7.488 + 0.000007 0.000007 0.239658 + -6.067 -4.072 -2.519 -2.519 -1.817 -1.816 -0.477 2.520 2.520 2.529 + 2.530 3.460 3.521 4.096 5.313 5.357 6.808 7.562 7.563 7.638 + 0.000008 0.000008 0.287590 + -5.961 -4.346 -2.503 -2.503 -1.799 -1.799 -0.056 2.400 2.400 2.414 + 2.415 3.555 3.626 3.645 5.080 5.134 6.848 7.749 8.010 8.011 + 0.000009 0.000009 0.335522 + -5.839 -4.599 -2.489 -2.489 -1.783 -1.783 0.370 2.291 2.291 2.323 + 2.324 3.195 3.661 3.749 4.853 4.923 6.902 7.759 8.428 8.496 + 0.000010 0.000010 0.383453 + -5.704 -4.828 -2.477 -2.477 -1.770 -1.770 0.792 2.209 2.209 2.254 + 2.254 2.754 3.772 3.889 4.636 4.736 6.962 7.692 8.619 9.014 + 0.000012 0.000012 0.431385 + -5.569 -5.019 -2.470 -2.470 -1.762 -1.762 1.186 2.158 2.158 2.211 + 2.211 2.349 3.868 4.042 4.437 4.593 7.014 7.619 8.859 9.397 + 0.000013 0.000013 0.479317 + -5.496 -5.111 -2.467 -2.467 -1.759 -1.759 1.407 2.125 2.141 2.141 + 2.196 2.196 3.911 4.161 4.302 4.535 7.037 7.588 9.048 9.225 diff --git a/vitalypro/bands/bands_1.dat b/vitalypro/bands/bands_1.dat new file mode 100644 index 00000000..7f9bcb77 --- /dev/null +++ b/vitalypro/bands/bands_1.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.359 -2.700 -2.699 -2.519 -2.442 -2.007 -2.007 2.846 2.847 2.988 + 2.989 3.036 3.081 5.689 5.940 5.971 6.248 6.249 6.619 6.851 + 0.000001 0.000001 0.048806 + -6.349 -2.838 -2.698 -2.697 -2.109 -2.005 -2.004 2.824 2.824 2.955 + 2.957 3.046 3.091 5.567 5.891 5.923 6.309 6.310 6.596 6.898 + 0.000003 0.000003 0.097612 + -6.319 -3.179 -2.691 -2.690 -1.997 -1.996 -1.728 2.760 2.761 2.867 + 2.868 3.074 3.120 5.265 5.760 5.792 6.484 6.485 6.563 7.001 + 0.000004 0.000004 0.146418 + -6.270 -3.505 -2.680 -2.679 -1.985 -1.984 -1.335 2.666 2.667 2.740 + 2.741 3.120 3.169 4.878 5.572 5.607 6.547 6.755 6.756 7.133 + 0.000005 0.000005 0.195224 + -6.201 -3.815 -2.666 -2.665 -1.970 -1.969 -0.932 2.555 2.555 2.595 + 2.596 3.183 3.237 4.453 5.354 5.393 6.550 7.101 7.103 7.286 + 0.000006 0.000006 0.244030 + -6.113 -4.109 -2.650 -2.649 -1.952 -1.951 -0.521 2.439 2.440 2.450 + 2.451 3.264 3.324 4.011 5.123 5.168 6.572 7.440 7.508 7.509 + 0.000008 0.000008 0.292836 + -6.006 -4.383 -2.634 -2.633 -1.934 -1.933 -0.103 2.317 2.318 2.330 + 2.331 3.360 3.430 3.565 4.890 4.945 6.612 7.547 7.962 7.963 + 0.000009 0.000009 0.341642 + -5.883 -4.638 -2.619 -2.618 -1.917 -1.917 0.318 2.206 2.206 2.237 + 2.237 3.119 3.467 3.554 4.663 4.734 6.666 7.541 8.225 8.455 + 0.000010 0.000010 0.390448 + -5.747 -4.869 -2.607 -2.606 -1.904 -1.903 0.735 2.122 2.122 2.165 + 2.166 2.685 3.579 3.694 4.446 4.546 6.727 7.461 8.431 8.979 + 0.000012 0.000012 0.439254 + -5.610 -5.062 -2.599 -2.598 -1.895 -1.895 1.121 2.070 2.070 2.121 + 2.121 2.288 3.677 3.848 4.245 4.402 6.782 7.381 8.678 9.212 + 0.000013 0.000013 0.488060 + -5.535 -5.155 -2.596 -2.596 -1.892 -1.892 1.334 2.052 2.052 2.071 + 2.105 2.106 3.720 3.967 4.111 4.343 6.805 7.348 8.866 9.049 diff --git a/vitalypro/bands/bands_2.dat b/vitalypro/bands/bands_2.dat new file mode 100644 index 00000000..e776d146 --- /dev/null +++ b/vitalypro/bands/bands_2.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.404 -2.823 -2.821 -2.557 -2.481 -2.133 -2.131 2.782 2.782 2.857 + 2.901 2.926 2.928 5.624 5.758 5.790 6.174 6.175 6.418 6.650 + 0.000001 0.000001 0.049599 + -6.394 -2.876 -2.820 -2.818 -2.149 -2.131 -2.129 2.759 2.759 2.867 + 2.893 2.894 2.911 5.493 5.711 5.743 6.236 6.237 6.390 6.699 + 0.000003 0.000003 0.099199 + -6.364 -3.217 -2.813 -2.811 -2.123 -2.121 -1.770 2.693 2.693 2.801 + 2.803 2.895 2.941 5.179 5.581 5.614 6.354 6.414 6.415 6.805 + 0.000004 0.000004 0.148798 + -6.314 -3.542 -2.802 -2.800 -2.111 -2.108 -1.380 2.596 2.596 2.671 + 2.672 2.941 2.990 4.784 5.396 5.430 6.334 6.689 6.690 6.943 + 0.000005 0.000005 0.198397 + -6.245 -3.853 -2.787 -2.786 -2.095 -2.092 -0.980 2.481 2.482 2.523 + 2.524 3.006 3.058 4.357 5.179 5.218 6.335 7.040 7.042 7.102 + 0.000006 0.000006 0.247996 + -6.157 -4.146 -2.771 -2.769 -2.077 -2.074 -0.572 2.362 2.363 2.375 + 2.376 3.087 3.146 3.917 4.950 4.994 6.355 7.260 7.451 7.453 + 0.000008 0.000008 0.297596 + -6.049 -4.422 -2.755 -2.753 -2.058 -2.056 -0.158 2.239 2.240 2.251 + 2.252 3.183 3.252 3.474 4.717 4.771 6.394 7.360 7.910 7.912 + 0.000009 0.000009 0.347195 + -5.925 -4.677 -2.739 -2.738 -2.041 -2.039 0.258 2.125 2.126 2.155 + 2.156 3.033 3.292 3.377 4.490 4.560 6.449 7.339 8.042 8.407 + 0.000010 0.000010 0.396794 + -5.788 -4.909 -2.727 -2.725 -2.028 -2.025 0.668 2.040 2.040 2.082 + 2.083 2.605 3.405 3.518 4.273 4.372 6.511 7.249 8.260 8.936 + 0.000012 0.000012 0.446393 + -5.651 -5.103 -2.719 -2.717 -2.019 -2.017 1.047 1.987 1.987 2.036 + 2.037 2.216 3.503 3.673 4.072 4.227 6.568 7.163 8.511 9.036 + 0.000013 0.000013 0.495993 + -5.575 -5.197 -2.716 -2.715 -2.016 -2.014 1.252 1.969 1.969 2.007 + 2.020 2.021 3.547 3.791 3.937 4.167 6.592 7.127 8.697 8.883 diff --git a/vitalypro/bands/bands_3.dat b/vitalypro/bands/bands_3.dat new file mode 100644 index 00000000..bcfa4ce6 --- /dev/null +++ b/vitalypro/bands/bands_3.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.444 -2.933 -2.930 -2.587 -2.512 -2.245 -2.243 2.695 2.730 2.730 + 2.738 2.877 2.877 5.569 5.596 5.626 6.113 6.113 6.233 6.469 + 0.000001 0.000001 0.050399 + -6.434 -2.930 -2.928 -2.906 -2.242 -2.240 -2.181 2.704 2.706 2.706 + 2.748 2.842 2.843 5.428 5.549 5.579 6.176 6.177 6.202 6.518 + 0.000003 0.000003 0.100797 + -6.403 -3.246 -2.923 -2.920 -2.234 -2.232 -1.803 2.638 2.638 2.733 + 2.748 2.749 2.778 5.101 5.422 5.453 6.161 6.357 6.358 6.628 + 0.000004 0.000004 0.151196 + -6.353 -3.571 -2.911 -2.909 -2.221 -2.220 -1.415 2.538 2.538 2.614 + 2.615 2.779 2.827 4.699 5.238 5.271 6.138 6.637 6.638 6.771 + 0.000005 0.000005 0.201595 + -6.284 -3.882 -2.896 -2.894 -2.205 -2.203 -1.018 2.420 2.420 2.462 + 2.463 2.844 2.896 4.270 5.023 5.060 6.136 6.936 6.994 6.994 + 0.000006 0.000006 0.251993 + -6.195 -4.176 -2.880 -2.877 -2.186 -2.185 -0.614 2.297 2.298 2.310 + 2.311 2.926 2.984 3.832 4.794 4.837 6.155 7.098 7.410 7.411 + 0.000008 0.000008 0.302392 + -6.087 -4.452 -2.863 -2.860 -2.168 -2.166 -0.205 2.172 2.172 2.182 + 2.183 3.024 3.091 3.392 4.562 4.615 6.194 7.191 7.746 7.874 + 0.000009 0.000009 0.352791 + -5.962 -4.708 -2.847 -2.845 -2.150 -2.148 0.206 2.055 2.056 2.084 + 2.085 2.956 3.133 3.216 4.335 4.403 6.248 7.153 7.880 8.376 + 0.000010 0.000010 0.403190 + -5.823 -4.941 -2.835 -2.832 -2.136 -2.134 0.611 1.968 1.968 2.009 + 2.010 2.534 3.247 3.359 4.117 4.214 6.312 7.052 8.109 8.909 + 0.000011 0.000011 0.453588 + -5.685 -5.136 -2.826 -2.824 -2.127 -2.125 0.982 1.913 1.914 1.962 + 1.963 2.152 3.348 3.514 3.915 4.067 6.371 6.960 8.366 8.882 + 0.000013 0.000013 0.503987 + -5.608 -5.232 -2.824 -2.821 -2.124 -2.122 1.181 1.895 1.896 1.946 + 1.947 1.950 3.392 3.634 3.780 4.007 6.396 6.922 8.551 8.737 diff --git a/vitalypro/bands/bands_4.dat b/vitalypro/bands/bands_4.dat new file mode 100644 index 00000000..4e77074a --- /dev/null +++ b/vitalypro/bands/bands_4.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.480 -3.036 -3.033 -2.615 -2.538 -2.351 -2.350 2.539 2.581 2.683 + 2.684 2.834 2.835 5.440 5.471 5.515 6.056 6.056 6.057 6.297 + 0.000001 0.000001 0.051224 + -6.470 -3.034 -3.031 -2.932 -2.348 -2.347 -2.209 2.549 2.591 2.658 + 2.659 2.798 2.799 5.363 5.394 5.426 6.021 6.121 6.122 6.345 + 0.000003 0.000003 0.102448 + -6.440 -3.271 -3.026 -3.023 -2.340 -2.339 -1.834 2.577 2.588 2.589 + 2.621 2.701 2.702 5.022 5.269 5.301 5.975 6.306 6.307 6.457 + 0.000004 0.000004 0.153672 + -6.389 -3.597 -3.014 -3.011 -2.327 -2.326 -1.448 2.485 2.486 2.563 + 2.564 2.625 2.671 4.614 5.087 5.122 5.948 6.590 6.591 6.607 + 0.000005 0.000005 0.204896 + -6.319 -3.908 -2.999 -2.996 -2.310 -2.309 -1.054 2.363 2.364 2.407 + 2.408 2.690 2.740 4.183 4.874 4.912 5.943 6.778 6.952 6.954 + 0.000006 0.000006 0.256120 + -6.229 -4.202 -2.982 -2.979 -2.291 -2.290 -0.654 2.237 2.238 2.251 + 2.252 2.773 2.829 3.746 4.646 4.690 5.960 6.943 7.374 7.376 + 0.000008 0.000008 0.307345 + -6.121 -4.479 -2.964 -2.961 -2.272 -2.271 -0.249 2.109 2.110 2.119 + 2.120 2.871 2.937 3.310 4.414 4.467 5.998 7.026 7.577 7.843 + 0.000009 0.000009 0.358569 + -5.995 -4.737 -2.948 -2.945 -2.254 -2.253 0.156 1.990 1.990 2.017 + 2.018 2.880 2.982 3.063 4.186 4.255 6.053 6.971 7.731 8.349 + 0.000010 0.000010 0.409793 + -5.855 -4.970 -2.935 -2.932 -2.239 -2.238 0.554 1.900 1.901 1.940 + 1.941 2.463 3.097 3.206 3.968 4.065 6.118 6.861 7.971 8.845 + 0.000011 0.000011 0.461017 + -5.715 -5.167 -2.927 -2.924 -2.230 -2.229 0.918 1.845 1.845 1.892 + 1.893 2.089 3.199 3.363 3.766 3.917 6.178 6.763 8.231 8.737 + 0.000013 0.000013 0.512241 + -5.638 -5.264 -2.924 -2.921 -2.226 -2.226 1.110 1.826 1.826 1.876 + 1.877 1.894 3.244 3.483 3.630 3.856 6.205 6.723 8.415 8.601 diff --git a/vitalypro/bands/bands_5.dat b/vitalypro/bands/bands_5.dat new file mode 100644 index 00000000..e1c156d3 --- /dev/null +++ b/vitalypro/bands/bands_5.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.519 -3.145 -3.143 -2.645 -2.568 -2.465 -2.462 2.375 2.415 2.636 + 2.637 2.791 2.791 5.275 5.308 5.450 5.867 5.996 5.997 6.118 + 0.000001 0.000001 0.052140 + -6.509 -3.142 -3.140 -2.961 -2.462 -2.459 -2.241 2.385 2.425 2.610 + 2.611 2.754 2.754 5.230 5.264 5.285 5.827 6.062 6.063 6.161 + 0.000003 0.000003 0.104281 + -6.478 -3.299 -3.134 -3.132 -2.453 -2.451 -1.868 2.414 2.456 2.537 + 2.538 2.653 2.653 4.928 5.107 5.141 5.775 6.250 6.252 6.277 + 0.000004 0.000004 0.156421 + -6.427 -3.625 -3.122 -3.120 -2.440 -2.437 -1.486 2.430 2.431 2.461 + 2.506 2.510 2.511 4.513 4.928 4.964 5.744 6.434 6.540 6.542 + 0.000005 0.000005 0.208561 + -6.356 -3.936 -3.106 -3.104 -2.422 -2.420 -1.096 2.304 2.305 2.350 + 2.350 2.528 2.576 4.082 4.717 4.756 5.736 6.612 6.908 6.910 + 0.000006 0.000006 0.260701 + -6.266 -4.230 -3.088 -3.086 -2.403 -2.400 -0.701 2.174 2.175 2.189 + 2.190 2.611 2.666 3.647 4.490 4.534 5.751 6.780 7.336 7.338 + 0.000008 0.000008 0.312842 + -6.156 -4.508 -3.070 -3.068 -2.382 -2.380 -0.302 2.043 2.044 2.052 + 2.053 2.711 2.774 3.215 4.258 4.312 5.788 6.850 7.402 7.810 + 0.000009 0.000009 0.364982 + -6.029 -4.766 -3.054 -3.052 -2.364 -2.362 0.097 1.921 1.922 1.948 + 1.948 2.790 2.822 2.901 4.030 4.100 5.843 6.776 7.577 8.322 + 0.000010 0.000010 0.417122 + -5.889 -5.001 -3.040 -3.038 -2.349 -2.347 0.488 1.829 1.830 1.868 + 1.869 2.381 2.939 3.046 3.812 3.908 5.909 6.656 7.828 8.673 + 0.000011 0.000011 0.469262 + -5.747 -5.199 -3.031 -3.029 -2.339 -2.337 0.843 1.772 1.773 1.819 + 1.819 2.016 3.042 3.203 3.609 3.760 5.971 6.553 8.092 8.583 + 0.000013 0.000013 0.521403 + -5.668 -5.297 -3.028 -3.026 -2.336 -2.334 1.027 1.753 1.754 1.802 + 1.802 1.827 3.088 3.323 3.473 3.698 5.999 6.510 8.273 8.459 diff --git a/vitalypro/bands/bands_relax.dat b/vitalypro/bands/bands_relax.dat new file mode 100644 index 00000000..b137e447 --- /dev/null +++ b/vitalypro/bands/bands_relax.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.422 -2.873 -2.871 -2.564 -2.498 -2.186 -2.183 2.755 2.764 2.785 + 2.819 2.901 2.910 5.601 5.682 5.715 6.141 6.154 6.335 6.560 + -0.000016 -0.000016 0.049989 + -6.412 -2.887 -2.871 -2.869 -2.184 -2.181 -2.161 2.731 2.741 2.794 + 2.829 2.867 2.876 5.466 5.635 5.668 6.203 6.217 6.304 6.611 + -0.000031 -0.000031 0.099978 + -6.382 -3.228 -2.863 -2.861 -2.176 -2.173 -1.783 2.665 2.674 2.775 + 2.783 2.822 2.859 5.146 5.506 5.541 6.264 6.383 6.397 6.720 + -0.000047 -0.000047 0.149967 + -6.332 -3.554 -2.852 -2.850 -2.163 -2.160 -1.393 2.566 2.575 2.643 + 2.651 2.869 2.908 4.748 5.321 5.359 6.242 6.660 6.674 6.861 + -0.000063 -0.000063 0.199956 + -6.262 -3.864 -2.837 -2.835 -2.147 -2.144 -0.995 2.450 2.458 2.493 + 2.500 2.933 2.977 4.321 5.105 5.147 6.241 7.015 7.023 7.029 + -0.000079 -0.000079 0.249945 + -6.174 -4.158 -2.821 -2.819 -2.129 -2.126 -0.588 2.330 2.337 2.343 + 2.350 3.015 3.065 3.881 4.874 4.924 6.261 7.183 7.428 7.443 + -0.000094 -0.000094 0.299934 + -6.066 -4.434 -2.804 -2.802 -2.110 -2.107 -0.176 2.206 2.212 2.217 + 2.224 3.112 3.172 3.440 4.642 4.702 6.300 7.280 7.843 7.890 + -0.000110 -0.000110 0.349924 + -5.942 -4.690 -2.789 -2.786 -2.093 -2.090 0.237 2.091 2.096 2.121 + 2.126 3.002 3.221 3.297 4.414 4.491 6.354 7.251 7.967 8.389 + -0.000126 -0.000126 0.399913 + -5.803 -4.923 -2.777 -2.774 -2.079 -2.077 0.645 2.005 2.009 2.047 + 2.051 2.576 3.334 3.439 4.196 4.302 6.418 7.156 8.190 8.919 + -0.000142 -0.000142 0.449902 + -5.665 -5.117 -2.769 -2.765 -2.070 -2.068 1.020 1.951 1.956 2.001 + 2.005 2.190 3.433 3.594 3.995 4.157 6.475 7.068 8.444 8.967 + -0.000157 -0.000157 0.499891 + -5.589 -5.213 -2.766 -2.763 -2.066 -2.065 1.222 1.933 1.937 1.983 + 1.987 1.989 3.477 3.713 3.860 4.097 6.500 7.031 8.629 8.818 diff --git a/vitalypro/code_implementation_example.ipynb b/vitalypro/code_implementation_example.ipynb new file mode 100644 index 00000000..a1258ac9 --- /dev/null +++ b/vitalypro/code_implementation_example.ipynb @@ -0,0 +1,3475 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-27T18:59:04.286973Z", + "start_time": "2021-10-27T18:59:01.347246Z" + } + }, + "outputs": [ + { + "data": { + "text/html": [ + " \n", + " " + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "application/vnd.plotly.v1+json": { + "config": { + "plotlyServerURL": "https://plot.ly" + }, + "data": [ + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -2.8999998569488525, + -2.8899998664855957, + -2.860999822616577, + -2.811999797821045, + -2.744999885559082, + -2.6589999198913574, + -2.553999900817871, + -2.5189998149871826, + -2.4079997539520264, + -2.311999797821045, + -2.2689998149871826 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -0.4329996109008789, + -0.5479998588562012, + -0.8379998207092285, + -1.2189998626708984, + -1.6419997215270996, + -2.0839996337890625, + -2.5349998474121094, + -2.430999755859375, + -2.2909998893737793, + -2.138000011444092, + -2.0190000534057617 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -0.0429997444152832, + -0.09200000762939453, + -0.2259998321533203, + -0.4159998893737793, + -0.6349997520446777, + -0.866999626159668, + -1.0999999046325684, + -1.3269996643066406, + -1.5439996719360352, + -1.7430000305175781, + -1.8779997825622559 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -0.013000011444091797, + -0.06199979782104492, + -0.19499969482421875, + -0.38299989700317383, + -0.5980000495910645, + -0.8229999542236328, + -1.0460000038146973, + -1.2569999694824219, + -1.4439997673034668, + -1.5869998931884766, + -1.6449999809265137 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.14300012588500977, + 0.20300006866455078, + 0.37400007247924805, + 0.5989999771118164, + 0.6040000915527344, + 0.6280002593994141, + 0.6680002212524414, + 0.7220001220703125, + 0.7820000648498535, + 0.8340001106262207, + 0.8570003509521484 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.14400005340576172, + 0.20399999618530273, + 0.375, + 0.6400003433227539, + 0.9809999465942383, + 1.3819999694824219, + 1.569000244140625, + 1.5789999961853027, + 1.5120000839233398, + 1.439000129699707, + 1.4079999923706055 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.6579999923706055, + 0.6380000114440918, + 0.6110000610351562, + 0.6410002708435059, + 0.9820003509521484, + 1.383000373840332, + 1.830000400543213, + 2.2480006217956543, + 2.4390006065368652, + 2.6790003776550293, + 2.8680005073547363 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.8220000267028809, + 0.8700003623962402, + 1.010000228881836, + 1.1620001792907715, + 1.308000087738037, + 1.4580001831054688, + 1.8309998512268066, + 2.316000461578369, + 2.8340001106262207, + 3.2170004844665527, + 3.0450005531311035 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -2.809000015258789, + -2.8459999561309814, + -2.9469997882843018, + -3.0889999866485596, + -3.0239999294281006, + -2.934000015258789, + -2.8259999752044678, + -2.7779998779296875, + -2.6610000133514404, + -2.557999849319458, + -2.5119998455047607 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -0.3249998092651367, + -0.36999988555908203, + -0.6719999313354492, + -1.0869998931884766, + -1.5180001258850098, + -1.9529998302459717, + -2.384999990463257, + -2.6989998817443848, + -2.553999900817871, + -2.3969998359680176, + -2.2769999504089355 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -0.29199981689453125, + -0.3359999656677246, + -0.4930000305175781, + -0.6719999313354492, + -0.8829998970031738, + -1.1100001335144043, + -1.3420000076293945, + -1.5699996948242188, + -1.7879998683929443, + -1.9909999370574951, + -2.126999855041504 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -0.15000009536743164, + -0.315000057220459, + -0.4590001106262207, + -0.6359996795654297, + -0.8439998626708984, + -1.065999984741211, + -1.2880001068115234, + -1.5, + -1.691999912261963, + -1.8399999141693115, + -1.9019999504089355 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.2670001983642578, + 0.22700023651123047, + 0.17500019073486328, + 0.14400005340576172, + 0.1360001564025879, + 0.1510000228881836, + 0.18800020217895508, + 0.24300003051757812, + 0.30900001525878906, + 0.3710002899169922, + 0.3990001678466797 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.3959999084472656, + 0.46199989318847656, + 0.6500000953674316, + 0.8340001106262207, + 1.0120000839233398, + 1.1800003051757812, + 1.25, + 1.1760001182556152, + 1.0560002326965332, + 0.9530000686645508, + 0.9100003242492676 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.3970003128051758, + 0.4630002975463867, + 0.6519999504089355, + 0.940000057220459, + 1.308000087738037, + 1.7360000610351562, + 1.8020000457763672, + 1.9770002365112305, + 2.2280001640319824, + 2.492000102996826, + 2.672999858856201 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.5180001258850098, + 0.560999870300293, + 0.6770000457763672, + 0.9419999122619629, + 1.309999942779541, + 1.7379999160766602, + 2.2100000381469727, + 2.7219996452331543, + 3.073000431060791, + 2.9830002784729004, + 2.858999729156494 + ], + "yaxis": "y2" + }, + { + "line": { + "color": "RoyalBlue", + "dash": "dot", + "width": 3 + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 11 + ], + "xaxis": "x", + "y": [ + 0, + 0 + ], + "yaxis": "y" + }, + { + "line": { + "color": "RoyalBlue", + "dash": "dot", + "width": 3 + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 11 + ], + "xaxis": "x2", + "y": [ + 0, + 0 + ], + "yaxis": "y2" + } + ], + "layout": { + "annotations": [ + { + "font": { + "size": 16 + }, + "showarrow": false, + "text": "strain 0%", + "x": 0.225, + "xanchor": "center", + "xref": "paper", + "y": 1, + "yanchor": "bottom", + "yref": "paper" + }, + { + "font": { + "size": 16 + }, + "showarrow": false, + "text": "strain 5%", + "x": 0.775, + "xanchor": "center", + "xref": "paper", + "y": 1, + "yanchor": "bottom", + "yref": "paper" + } + ], + "height": 650, + "plot_bgcolor": "white", + "template": { + "data": { + "bar": [ + { + "error_x": { + "color": "#2a3f5f" + }, + "error_y": { + "color": "#2a3f5f" + }, + "marker": { + "line": { + "color": "#E5ECF6", + "width": 0.5 + } + }, + "type": "bar" + } + ], + "barpolar": [ + { + "marker": { + "line": { + "color": "#E5ECF6", + "width": 0.5 + } + }, + "type": "barpolar" + } + ], + "carpet": [ + { + "aaxis": { + "endlinecolor": "#2a3f5f", + "gridcolor": "white", + "linecolor": "white", + "minorgridcolor": "white", + "startlinecolor": "#2a3f5f" + }, + "baxis": { + "endlinecolor": "#2a3f5f", + "gridcolor": "white", + "linecolor": "white", + "minorgridcolor": "white", + "startlinecolor": "#2a3f5f" + }, + "type": "carpet" + } + ], + "choropleth": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "type": "choropleth" + } + ], + "contour": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "contour" + } + ], + "contourcarpet": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "type": "contourcarpet" + } + ], + "heatmap": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "heatmap" + } + ], + "heatmapgl": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "heatmapgl" + } + ], + "histogram": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "histogram" + } + ], + "histogram2d": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "histogram2d" + } + ], + "histogram2dcontour": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "histogram2dcontour" + } + ], + "mesh3d": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "type": "mesh3d" + } + ], + "parcoords": [ + { + "line": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "parcoords" + } + ], + "pie": [ + { + "automargin": true, + "type": "pie" + } + ], + "scatter": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatter" + } + ], + "scatter3d": [ + { + "line": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatter3d" + } + ], + "scattercarpet": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scattercarpet" + } + ], + "scattergeo": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scattergeo" + } + ], + "scattergl": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scattergl" + } + ], + "scattermapbox": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scattermapbox" + } + ], + "scatterpolar": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatterpolar" + } + ], + "scatterpolargl": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatterpolargl" + } + ], + "scatterternary": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatterternary" + } + ], + "surface": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "surface" + } + ], + "table": [ + { + "cells": { + "fill": { + "color": "#EBF0F8" + }, + "line": { + "color": "white" + } + }, + "header": { + "fill": { + "color": "#C8D4E3" + }, + "line": { + "color": "white" + } + }, + "type": "table" + } + ] + }, + "layout": { + "annotationdefaults": { + "arrowcolor": "#2a3f5f", + "arrowhead": 0, + "arrowwidth": 1 + }, + "coloraxis": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "colorscale": { + "diverging": [ + [ + 0, + "#8e0152" + ], + [ + 0.1, + "#c51b7d" + ], + [ + 0.2, + "#de77ae" + ], + [ + 0.3, + "#f1b6da" + ], + [ + 0.4, + "#fde0ef" + ], + [ + 0.5, + "#f7f7f7" + ], + [ + 0.6, + "#e6f5d0" + ], + [ + 0.7, + "#b8e186" + ], + [ + 0.8, + "#7fbc41" + ], + [ + 0.9, + "#4d9221" + ], + [ + 1, + "#276419" + ] + ], + "sequential": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "sequentialminus": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ] + }, + "colorway": [ + "#636efa", + "#EF553B", + "#00cc96", + "#ab63fa", + "#FFA15A", + "#19d3f3", + "#FF6692", + "#B6E880", + "#FF97FF", + "#FECB52" + ], + "font": { + "color": "#2a3f5f" + }, + "geo": { + "bgcolor": "white", + "lakecolor": "white", + "landcolor": "#E5ECF6", + "showlakes": true, + "showland": true, + "subunitcolor": "white" + }, + "hoverlabel": { + "align": "left" + }, + "hovermode": "closest", + "mapbox": { + "style": "light" + }, + "paper_bgcolor": "white", + "plot_bgcolor": "#E5ECF6", + "polar": { + "angularaxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + }, + "bgcolor": "#E5ECF6", + "radialaxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + } + }, + "scene": { + "xaxis": { + "backgroundcolor": "#E5ECF6", + "gridcolor": "white", + "gridwidth": 2, + "linecolor": "white", + "showbackground": true, + "ticks": "", + "zerolinecolor": "white" + }, + "yaxis": { + "backgroundcolor": "#E5ECF6", + "gridcolor": "white", + "gridwidth": 2, + "linecolor": "white", + "showbackground": true, + "ticks": "", + "zerolinecolor": "white" + }, + "zaxis": { + "backgroundcolor": "#E5ECF6", + "gridcolor": "white", + "gridwidth": 2, + "linecolor": "white", + "showbackground": true, + "ticks": "", + "zerolinecolor": "white" + } + }, + "shapedefaults": { + "line": { + "color": "#2a3f5f" + } + }, + "ternary": { + "aaxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + }, + "baxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + }, + "bgcolor": "#E5ECF6", + "caxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + } + }, + "title": { + "x": 0.05 + }, + "xaxis": { + "automargin": true, + "gridcolor": "white", + "linecolor": "white", + "ticks": "", + "title": { + "standoff": 15 + }, + "zerolinecolor": "white", + "zerolinewidth": 2 + }, + "yaxis": { + "automargin": true, + "gridcolor": "white", + "linecolor": "white", + "ticks": "", + "title": { + "standoff": 15 + }, + "zerolinecolor": "white", + "zerolinewidth": 2 + } + } + }, + "width": 900, + "xaxis": { + "anchor": "y", + "domain": [ + 0, + 0.45 + ], + "gridcolor": "lightgrey", + "gridwidth": 0.5, + "linecolor": "black", + "linewidth": 1, + "mirror": true, + "range": [ + 1, + 11 + ], + "showgrid": true, + "ticks": "inside", + "ticktext": [ + "G", + "Z" + ], + "tickvals": [ + 1, + 11 + ] + }, + "xaxis2": { + "anchor": "y2", + "domain": [ + 0.55, + 1 + ], + "gridcolor": "lightgrey", + "gridwidth": 0.5, + "linecolor": "black", + "linewidth": 1, + "mirror": true, + "range": [ + 1, + 11 + ], + "showgrid": true, + "ticks": "inside", + "ticktext": [ + "G", + "Z" + ], + "tickvals": [ + 1, + 11 + ] + }, + "yaxis": { + "anchor": "x", + "domain": [ + 0, + 1 + ], + "gridcolor": "lightgrey", + "gridwidth": 0.5, + "linecolor": "black", + "linewidth": 1, + "mirror": true, + "showgrid": true, + "ticks": "inside", + "title": { + "text": "Energy, eV" + } + }, + "yaxis2": { + "anchor": "x2", + "domain": [ + 0, + 1 + ], + "gridcolor": "lightgrey", + "gridwidth": 0.5, + "linecolor": "black", + "linewidth": 1, + "mirror": true, + "showgrid": true, + "ticks": "inside", + "title": { + "text": "Energy, eV" + } + } + } + }, + "text/html": [ + "
\n", + " \n", + " \n", + "
\n", + " \n", + "
" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "#load ml_modeling_module \n", + "from ml_modeling_module import *\n", + "\n", + "#first let's plot sige bandstructure\n", + "#read QE output file with bands for 0% strain\n", + "data=read_data('bands/bands_0.dat')\n", + "bands0=data.read_bands_ml(fermi=6.18, bands_num=4)\n", + "\n", + "#read QE output file with bands for 5% strain\n", + "data=read_data('bands/bands_5.dat')\n", + "bands5=data.read_bands_ml(fermi=5.60, bands_num=4)\n", + "# reshape data: 8 bands 11 k-points\n", + "bands0=bands0.reshape(8,11)\n", + "bands5=bands5.reshape(8,11)\n", + "\n", + "import plotly.graph_objects as go\n", + "from plotly.subplots import make_subplots\n", + "fig = make_subplots(rows=1, cols=2,subplot_titles=(\"strain 0%\", \"strain 5%\"))\n", + "\n", + "for i in range(bands0.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands0[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), col=1, row=1) \n", + "for i in range(bands5.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands5[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), col=2, row=1) \n", + "fig.add_trace(go.Scatter(x=[1,11], y=[0,0],\n", + " mode='lines', line=dict(color= \"RoyalBlue\",width=3, dash='dot'), showlegend=False, \n", + " name='markers'), col=1, row=1) \n", + "fig.add_trace(go.Scatter(x=[1,11], y=[0,0],\n", + " mode='lines', line=dict(color= \"RoyalBlue\",width=3, dash='dot'), showlegend=False, \n", + " name='markers'), col=2, row=1) \n", + "fig.update_xaxes(showgrid=True, \n", + " gridwidth=0.5, \n", + " gridcolor='lightgrey', \n", + " ticks='inside' , \n", + " linecolor= 'black', \n", + " linewidth= 1,\n", + " mirror= True,\n", + " ticktext=['G', 'Z'],\n", + " tickvals=[1,11],\n", + " range=[1,11],\n", + " )\n", + "fig.update_yaxes(title='Energy, eV', \n", + " showgrid=True, \n", + " gridwidth=0.5, \n", + " gridcolor='lightgrey', \n", + " ticks='inside' , \n", + " linecolor= 'black',\n", + " linewidth= 1,\n", + " mirror= True,\n", + " )\n", + "\n", + "fig.update_layout(width=900, height=650, plot_bgcolor='white')\n", + "fig.show()\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-27T18:59:06.968840Z", + "start_time": "2021-10-27T18:59:06.951835Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "(7, 44)" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# reading bands from all QE output file\n", + "from os import walk\n", + "mypath='bands/'\n", + "filenames = next(walk(mypath), (None, None, []))[2]\n", + "fermi=[6.18,6.02,5.83,5.71,5.66,5.60,5.75]\n", + "y=[]\n", + "for i in range(len(filenames)):\n", + " data=read_data(mypath+filenames[i])\n", + " bands_ml=data.read_bands_ml(fermi=fermi[i], bands_num=2)\n", + " y= np.append(y, bands_ml)\n", + "y=y.reshape(len(filenames),44)\n", + "y.shape" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-27T18:59:08.734621Z", + "start_time": "2021-10-27T18:59:08.718617Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "(7, 2)" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# reading cell parameters from QE output file : NEED TO add a fucntion \n", + "#(lattice constants are in bohr)\n", + "X=np.array([[10.34568, 10.79211],\n", + " [10.45682, 10.71265],\n", + " [10.56082, 10.64615], \n", + " [10.66056, 10.57623],\n", + " [10.76056, 10.50342],\n", + " [10.87056, 10.42435],\n", + " [10.60789, 10.610219]\n", + " ])\n", + "X.shape" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# prepare data for modeling: split for training and testig sets" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-27T19:11:11.691912Z", + "start_time": "2021-10-27T19:11:06.561755Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Time taken for RF: 0:00:05.113152\n", + "Train:\n", + "R^2:0.97 RMSE:0.02\n", + "Test:\n", + "R^2:nan RMSE: 0.03\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\exx\\Anaconda3\\envs\\tensorflow\\lib\\site-packages\\sklearn\\base.py:434: FutureWarning:\n", + "\n", + "The default value of multioutput (not exposed in score method) will change from 'variance_weighted' to 'uniform_average' in 0.23 to keep consistent with 'metrics.r2_score'. To specify the default value manually and avoid the warning, please either call 'metrics.r2_score' directly or make a custom scorer with 'metrics.make_scorer' (the built-in scorer 'r2' uses multioutput='uniform_average').\n", + "\n", + "C:\\Users\\exx\\Anaconda3\\envs\\tensorflow\\lib\\site-packages\\sklearn\\metrics\\_regression.py:582: UndefinedMetricWarning:\n", + "\n", + "R^2 score is not well-defined with less than two samples.\n", + "\n" + ] + } + ], + "source": [ + "my_data=data_preparation(X,y)\n", + "(X_train, X_test, Y_train, Y_test)=my_data.select_train_test(test_row_number=[6])\n", + "#random split could also be used\n", + "#(X_train, X_test, Y_train, Y_test)=my_data.random_split(train_split=0.8, seed=42)\n", + "\n", + "my_model=modeling(X_train, Y_train, X_test, Y_test, scaler='None')\n", + "\n", + "#train Random forest model with No initial guess\n", + "(y_fit_RF, y_predict_RF, trials_RF, best_space_RF, regressorRF, text_RF)=my_model.RandomForest( max_evals=10, timeout=150*60,loss_threshold=0.01, cv=5, verbose=1)\n", + "\n", + "print(text_RF)\n", + "\n", + "\n", + "#" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-27T19:18:56.522361Z", + "start_time": "2021-10-27T19:11:21.055477Z" + } + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\exx\\Anaconda3\\envs\\tensorflow\\lib\\site-packages\\xgboost\\core.py:614: UserWarning:\n", + "\n", + "Use subset (sliced data) of np.ndarray is not recommended because it will generate extra copies and increase memory consumption\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Time taken for XGB: 0:07:34.327627\n", + "Train:\n", + "R^2:-0.0 RMSE:0.11\n", + "Test:\n", + "R^2:nan RMSE: 0.08\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\exx\\Anaconda3\\envs\\tensorflow\\lib\\site-packages\\sklearn\\metrics\\_regression.py:582: UndefinedMetricWarning:\n", + "\n", + "R^2 score is not well-defined with less than two samples.\n", + "\n" + ] + } + ], + "source": [ + "## DOES NOT WORK YET \n", + "\n", + "# train XGboost model with initial guess\n", + "# best_space = {'alpha': 0.0, 'max_depth': 3.0, 'min_split_loss': 5.6, 'n_estimators': 100, 'x_reg_lambda': 1.00, 'x_subsample': 1.0}\n", + "# (y_fit_XG, y_predict_XG, trials_XG, best_space_XG, regressorXGB, text_XG)=my_model.XGB( max_evals=4, timeout=150*60,loss_threshold=0.01,init_vals=[best_space],cv=5, verbose=1) \n", + "# print(text_XG)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# let's plot predicted bands vs calculated bands" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-28T00:13:37.642491Z", + "start_time": "2021-10-28T00:13:37.587466Z" + } + }, + "outputs": [ + { + "data": { + "application/vnd.plotly.v1+json": { + "config": { + "plotlyServerURL": "https://plot.ly" + }, + "data": [ + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + -2.8399999141693115, + -2.874000072479248, + -2.8910000324249268, + -2.8420000076293945, + -2.7730000019073486, + -2.684999942779541, + -2.578000068664551, + -2.5290000438690186, + -2.4159998893737793, + -2.316999912261963, + -2.2730000019073486 + ] + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + -0.1490001678466797, + -0.2839999198913574, + -0.6040000915527344, + -1.001999855041504, + -1.428999900817871, + -1.86899995803833, + -2.309999942779541, + -2.453000068664551, + -2.311000108718872, + -2.1559998989105225, + -2.0369999408721924 + ] + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + -0.06799983978271484, + -0.11499977111816406, + -0.24399995803833008, + -0.4289999008178711, + -0.6449999809265137, + -0.875999927520752, + -1.1079998016357422, + -1.3359999656677246, + -1.553999900817871, + -1.755000114440918, + -1.8900001049041748 + ] + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + -0.034999847412109375, + -0.0819997787475586, + -0.2090001106262207, + -0.39099979400634766, + -0.6030001640319824, + -0.8260002136230469, + -1.0479998588562012, + -1.2589998245239258, + -1.4479999542236328, + -1.5929999351501465, + -1.6529998779296875 + ] + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + 0.39099979400634766, + 0.4530000686645508, + 0.5139999389648438, + 0.49200010299682617, + 0.4910001754760742, + 0.5110001564025879, + 0.5500001907348633, + 0.6040000915527344, + 0.6680002212524414, + 0.7249999046325684, + 0.75 + ] + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + 0.40399980545043945, + 0.46700000762939453, + 0.6329998970031738, + 0.9099998474121094, + 1.2649998664855957, + 1.433000087738037, + 1.5300002098083496, + 1.500999927520752, + 1.4060001373291016, + 1.3179998397827148, + 1.2810001373291016 + ] + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + 0.5850000381469727, + 0.5539999008178711, + 0.6469998359680176, + 0.9239997863769531, + 1.2729997634887695, + 1.6779999732971191, + 2.0929999351501465, + 2.2170000076293945, + 2.439999580383301, + 2.694000244140625, + 2.878999710083008 + ] + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + 0.809999942779541, + 0.8610000610351562, + 0.9699997901916504, + 1.1110000610351562, + 1.2789998054504395, + 1.6929998397827148, + 2.1399998664855957, + 2.6389999389648438, + 3.168999671936035, + 3.2170000076293945, + 3.067999839782715 + ] + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + -0.09595230647495814, + -0.14447627748761857, + -0.273000058673677, + -0.4575714837937128, + -0.6735715411958241, + -0.9026190439860026, + -1.1351429167247953, + -1.3621905417669387, + -1.579666705358596, + -1.7811428365253268, + -1.9161428156353177 + ] + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + -0.06428573245093935, + -0.11333329336983818, + -0.24095240093412854, + -0.423904850369408, + -0.635476203191848, + -0.8590000243414015, + -1.0815715335664295, + -1.293047655196417, + -1.4815711975097656, + -1.6275237060728527, + -1.6875238872709728 + ] + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + 0.36623800368536086, + 0.4240001042683919, + 0.4799047424679711, + 0.4622381755283901, + 0.4617620195661272, + 0.4812858445303781, + 0.5202856745038714, + 0.5748095512390137, + 0.6377619334629604, + 0.6956665402367002, + 0.7201904569353376 + ] + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "y": [ + 0.3667620023091634, + 0.4297143164135161, + 0.6082857222784133, + 0.8856191862197149, + 1.2063332739330472, + 1.4045239630199613, + 1.5010477020626976, + 1.471857229868571, + 1.376666750226702, + 1.287809621720087, + 1.2509046963282995 + ] + }, + { + "line": { + "color": "RoyalBlue", + "dash": "dot", + "width": 3 + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 11 + ], + "y": [ + 0, + 0 + ] + } + ], + "layout": { + "height": 650, + "plot_bgcolor": "white", + "template": { + "data": { + "bar": [ + { + "error_x": { + "color": "#2a3f5f" + }, + "error_y": { + "color": "#2a3f5f" + }, + "marker": { + "line": { + "color": "#E5ECF6", + "width": 0.5 + } + }, + "type": "bar" + } + ], + "barpolar": [ + { + "marker": { + "line": { + "color": "#E5ECF6", + "width": 0.5 + } + }, + "type": "barpolar" + } + ], + "carpet": [ + { + "aaxis": { + "endlinecolor": "#2a3f5f", + "gridcolor": "white", + "linecolor": "white", + "minorgridcolor": "white", + "startlinecolor": "#2a3f5f" + }, + "baxis": { + "endlinecolor": "#2a3f5f", + "gridcolor": "white", + "linecolor": "white", + "minorgridcolor": "white", + "startlinecolor": "#2a3f5f" + }, + "type": "carpet" + } + ], + "choropleth": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "type": "choropleth" + } + ], + "contour": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "contour" + } + ], + "contourcarpet": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "type": "contourcarpet" + } + ], + "heatmap": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "heatmap" + } + ], + "heatmapgl": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "heatmapgl" + } + ], + "histogram": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "histogram" + } + ], + "histogram2d": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "histogram2d" + } + ], + "histogram2dcontour": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "histogram2dcontour" + } + ], + "mesh3d": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "type": "mesh3d" + } + ], + "parcoords": [ + { + "line": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "parcoords" + } + ], + "pie": [ + { + "automargin": true, + "type": "pie" + } + ], + "scatter": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatter" + } + ], + "scatter3d": [ + { + "line": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatter3d" + } + ], + "scattercarpet": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scattercarpet" + } + ], + "scattergeo": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scattergeo" + } + ], + "scattergl": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scattergl" + } + ], + "scattermapbox": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scattermapbox" + } + ], + "scatterpolar": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatterpolar" + } + ], + "scatterpolargl": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatterpolargl" + } + ], + "scatterternary": [ + { + "marker": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "type": "scatterternary" + } + ], + "surface": [ + { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + }, + "colorscale": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "type": "surface" + } + ], + "table": [ + { + "cells": { + "fill": { + "color": "#EBF0F8" + }, + "line": { + "color": "white" + } + }, + "header": { + "fill": { + "color": "#C8D4E3" + }, + "line": { + "color": "white" + } + }, + "type": "table" + } + ] + }, + "layout": { + "annotationdefaults": { + "arrowcolor": "#2a3f5f", + "arrowhead": 0, + "arrowwidth": 1 + }, + "coloraxis": { + "colorbar": { + "outlinewidth": 0, + "ticks": "" + } + }, + "colorscale": { + "diverging": [ + [ + 0, + "#8e0152" + ], + [ + 0.1, + "#c51b7d" + ], + [ + 0.2, + "#de77ae" + ], + [ + 0.3, + "#f1b6da" + ], + [ + 0.4, + "#fde0ef" + ], + [ + 0.5, + "#f7f7f7" + ], + [ + 0.6, + "#e6f5d0" + ], + [ + 0.7, + "#b8e186" + ], + [ + 0.8, + "#7fbc41" + ], + [ + 0.9, + "#4d9221" + ], + [ + 1, + "#276419" + ] + ], + "sequential": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ], + "sequentialminus": [ + [ + 0, + "#0d0887" + ], + [ + 0.1111111111111111, + "#46039f" + ], + [ + 0.2222222222222222, + "#7201a8" + ], + [ + 0.3333333333333333, + "#9c179e" + ], + [ + 0.4444444444444444, + "#bd3786" + ], + [ + 0.5555555555555556, + "#d8576b" + ], + [ + 0.6666666666666666, + "#ed7953" + ], + [ + 0.7777777777777778, + "#fb9f3a" + ], + [ + 0.8888888888888888, + "#fdca26" + ], + [ + 1, + "#f0f921" + ] + ] + }, + "colorway": [ + "#636efa", + "#EF553B", + "#00cc96", + "#ab63fa", + "#FFA15A", + "#19d3f3", + "#FF6692", + "#B6E880", + "#FF97FF", + "#FECB52" + ], + "font": { + "color": "#2a3f5f" + }, + "geo": { + "bgcolor": "white", + "lakecolor": "white", + "landcolor": "#E5ECF6", + "showlakes": true, + "showland": true, + "subunitcolor": "white" + }, + "hoverlabel": { + "align": "left" + }, + "hovermode": "closest", + "mapbox": { + "style": "light" + }, + "paper_bgcolor": "white", + "plot_bgcolor": "#E5ECF6", + "polar": { + "angularaxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + }, + "bgcolor": "#E5ECF6", + "radialaxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + } + }, + "scene": { + "xaxis": { + "backgroundcolor": "#E5ECF6", + "gridcolor": "white", + "gridwidth": 2, + "linecolor": "white", + "showbackground": true, + "ticks": "", + "zerolinecolor": "white" + }, + "yaxis": { + "backgroundcolor": "#E5ECF6", + "gridcolor": "white", + "gridwidth": 2, + "linecolor": "white", + "showbackground": true, + "ticks": "", + "zerolinecolor": "white" + }, + "zaxis": { + "backgroundcolor": "#E5ECF6", + "gridcolor": "white", + "gridwidth": 2, + "linecolor": "white", + "showbackground": true, + "ticks": "", + "zerolinecolor": "white" + } + }, + "shapedefaults": { + "line": { + "color": "#2a3f5f" + } + }, + "ternary": { + "aaxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + }, + "baxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + }, + "bgcolor": "#E5ECF6", + "caxis": { + "gridcolor": "white", + "linecolor": "white", + "ticks": "" + } + }, + "title": { + "x": 0.05 + }, + "xaxis": { + "automargin": true, + "gridcolor": "white", + "linecolor": "white", + "ticks": "", + "title": { + "standoff": 15 + }, + "zerolinecolor": "white", + "zerolinewidth": 2 + }, + "yaxis": { + "automargin": true, + "gridcolor": "white", + "linecolor": "white", + "ticks": "", + "title": { + "standoff": 15 + }, + "zerolinecolor": "white", + "zerolinewidth": 2 + } + } + }, + "title": { + "text": "Si2Ge2 relaxed" + }, + "width": 450, + "xaxis": { + "gridcolor": "lightgrey", + "gridwidth": 0.5, + "linecolor": "black", + "linewidth": 1, + "mirror": true, + "range": [ + 1, + 11 + ], + "showgrid": true, + "ticks": "inside", + "ticktext": [ + "G", + "Z" + ], + "tickvals": [ + 1, + 11 + ] + }, + "yaxis": { + "gridcolor": "lightgrey", + "gridwidth": 0.5, + "linecolor": "black", + "linewidth": 1, + "mirror": true, + "showgrid": true, + "ticks": "inside", + "title": { + "text": "Energy, eV" + } + } + } + }, + "text/html": [ + "
\n", + " \n", + " \n", + "
\n", + " \n", + "
" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "# let's plot predicted bands vs calculated bands\n", + "#reading calculated bands:\n", + "data=read_data('bands/bands_relax.dat')\n", + "bands=data.read_bands_ml(fermi=5.75, bands_num=4)\n", + "bands=bands.reshape(8,11)\n", + "#predicted bands\n", + "bands_RF=y_predict_RF.reshape(4,11)\n", + "#bands_XG=y_predict_XG.reshape(4,11)\n", + "\n", + "import plotly.graph_objects as go\n", + "fig = go.Figure()\n", + "\n", + "for i in range(bands.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'))\n", + " \n", + "for i in range(bands_RF.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_RF[i],\n", + " mode='markers', marker=dict(color='red'), showlegend=False, \n", + " name='markers'))\n", + "fig.add_trace(go.Scatter(x=[1,11], y=[0,0],\n", + " mode='lines', line=dict(color= \"RoyalBlue\",width=3, dash='dot'), showlegend=False, \n", + " name='markers')) \n", + "\n", + "fig.update_xaxes(showgrid=True, \n", + " gridwidth=0.5, \n", + " gridcolor='lightgrey', \n", + " ticks='inside' , \n", + " linecolor= 'black', \n", + " linewidth= 1,\n", + " mirror= True,\n", + " ticktext=['G', 'Z'],\n", + " tickvals=[1,11],\n", + " range=[1,11]\n", + " )\n", + "fig.update_yaxes(title='Energy, eV', \n", + " showgrid=True, \n", + " gridwidth=0.5, \n", + " gridcolor='lightgrey', \n", + " ticks='inside' , \n", + " linecolor= 'black',\n", + " linewidth= 1,\n", + " mirror= True,\n", + " )\n", + "fig.update_layout(title='Si2Ge2 relaxed', width=450, height=650, plot_bgcolor='white')\n", + "fig.show()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# example of solving reverse problem " + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-28T00:13:54.951932Z", + "start_time": "2021-10-28T00:13:42.105295Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Lattice parameters:[10.58181053 10.62970763]\n", + "MSE: 0.0006365325686575999\n" + ] + } + ], + "source": [ + "# in this example we predict lattice constants for a given bandstructure (lattice constants are in bohr)\n", + "\n", + "import GPyOpt\n", + "from GPyOpt.methods import BayesianOptimization\n", + "from sklearn.metrics import mean_squared_error\n", + "\n", + "data=read_data('bands/bands_relax.dat')\n", + "bands=data.read_bands_ml(fermi=5.75, bands_num=2)\n", + "\n", + "\n", + "def objfunc(x):\n", + "\n", + " x1 = float(x[0,0])\n", + " x2 = float(x[0,1])\n", + "\n", + " return mean_squared_error(regressorRF.predict([[x1,x2]]).reshape(1,44), bands.reshape(1,44))\n", + "\n", + "maxiter = 40\n", + "domain = [\n", + " {'name': 'a_paral', 'type': 'continuous', 'domain': (10.3, 10.8)},\n", + " {'name': 'a_perp', 'type': 'continuous', 'domain': (10.3, 10.8)}\n", + " ]\n", + "\n", + "\n", + "\n", + "Bopt = GPyOpt.methods.BayesianOptimization(objfunc, domain=domain)\n", + "Bopt.run_optimization(max_iter = maxiter)\n", + "\n", + "print(\"Lattice parameters:\"+str(Bopt.x_opt)) \n", + "print(\"MSE: \"+str(Bopt.fx_opt)) " + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.10" + }, + "varInspector": { + "cols": { + "lenName": 16, + "lenType": 16, + "lenVar": 40 + }, + "kernels_config": { + "python": { + "delete_cmd_postfix": "", + "delete_cmd_prefix": "del ", + "library": "var_list.py", + "varRefreshCmd": "print(var_dic_list())" + }, + "r": { + "delete_cmd_postfix": ") ", + "delete_cmd_prefix": "rm(", + "library": "var_list.r", + "varRefreshCmd": "cat(var_dic_list()) " + } + }, + "types_to_exclude": [ + "module", + "function", + "builtin_function_or_method", + "instance", + "_Feature" + ], + "window_display": false + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/vitalypro/ml_modeling_module.py b/vitalypro/ml_modeling_module.py index bdd63db1..019a14ee 100644 --- a/vitalypro/ml_modeling_module.py +++ b/vitalypro/ml_modeling_module.py @@ -18,7 +18,103 @@ 3. Add class for ML modeling with RF, XGB (more ML algorithms -?) 4. If time permitted, add class to solve reverse problems (e.g. for known bandstructure, find SL structure) """ +class read_data: + + """ + In this module we read data from QE output and build dataset for ML modeling + 1. read energy band data from output produced by bands.x + 2. read structure parameters and fermi level from scf.out + In future work this module can be improved to read data from VASP and other modeling software + """ + def __init__(self, file): + self.file = file + + def read_bands_ml(self, fermi=0, bands_num=2, npl=10): + """ + This function reads energy bands from QE output file produced by band.x. + I found this code here https://github.com/yyyu200/QEbandplot/blob/master/pw_band_plot.py + Modifications I made to the code: + - bands get adjusted with respect to the fermi level + - print only first n valence and n conduction bands near the fermi level + :fermi - fermi level (eV) + :bands_num - number of valence/conduction bands near fermi level to print + + """ + # feig : filband in bands.x input file + # npl : number per line, 10 for bands.x, 6 for phonon + import re + f=open(self.file,'r') + lines = f.readlines() + + header = lines[0].strip() + line = header.strip('\n') + shape = re.split('[,=/]', line) + nbnd = int(shape[1]) + nks = int(shape[3]) + eig = np.zeros((nks, nbnd+1), dtype=np.float32) + + dividend = nbnd + divisor = npl + div = nbnd // npl + 1 if nbnd % npl == 0 else nbnd // npl + 2 + kinfo=[] + for index, value in enumerate(lines[1:]): + value = value.strip(' \n') + quotient = index // div + remainder = index % div + + if remainder == 0: + kinfo.append(value) + else: + value = re.split('[ ]+', value) + a = (remainder - 1) * npl + b = a + len(value) + eig[quotient][a:b] = value + + f.close() + eig = eig -fermi + cond_bands=[] + val_bands=[] + for i in range(eig.shape[0]): + cond_bands=np.append(cond_bands, eig[i][eig[i]>0][:bands_num]) + val_bands =np.append(val_bands,eig[i][eig[i]<0][-bands_num-1:-1]) + + cond_bands=cond_bands.reshape(11,bands_num).swapaxes(0,1) + val_bands=val_bands.reshape(11,bands_num).swapaxes(0,1) + bands=np.append(val_bands,cond_bands) + return bands + +class data_preparation: + + """ + Here we prepare data collected from QE output files for modeling. The following functions split the data into training / testing sets. + """ + def __init__(self, X, Y): + self.X = X + self.Y = Y + + def random_split(self, train_split=0.8, seed=42): + """ + random_split function allows to randomly select training and testing sets from the data. + :train_split - shows the ratio of train set to to the whole set in the split. Can be from 0 to 1. Defauls is 0.8 + :seed is a random state for reproducibility + """ + from sklearn.model_selection import train_test_split + X_train, X_test, Y_train, Y_test = train_test_split(self.X, self.Y, test_size=float(1-train_split), random_state=seed) + return X_train, X_test, Y_train, Y_test + + def select_train_test(self, test_row_number=[5,6]): + """ + select_train_test function allows to manually specify training and testing sets from the data. + :test_row_number is the number of rows that will be used for testing. The rest is training data + + """ + X_test = self.X[test_row_number] + Y_test = self.Y[test_row_number] + X_train = np.delete(self.X, test_row_number, 0) + Y_train = np.delete(self.Y, test_row_number, 0) + return X_train, X_test, Y_train, Y_test + class modeling: def __init__(self, X_train, Y_train, X_test, Y_test, scaler= 'None'): """ @@ -55,8 +151,8 @@ def RandomForest(self, max_evals=40, timeout=600, loss_threshold=0.5, init_val Random Forest Regressor with Sequential Model-based Optimization with Tree-Parzen estimators (Bayesian optimization) The idea is to build a probability model of the objective function and use it to select the most promising hyperparameters to evaluate in the true objective function - :max_evals - number of max evaluation in hyperparameter search algorithm. the search will stop when number of max itteration is reached. Can be any integer number. Default value is 40, - :timeout - search time. the search will stop when the time is out. Can be any integer number. Default value is 600 sec + :max_evals - number of max evaluation in hyperparameter search algorithm. The search will stop when the number of max itteration is reached. Can be any integer number. Default value is 40, + :timeout - search time. The search will stop when the time is out. Can be any integer number. Default value is 600 sec :loss_threshold - the search will stop when the loss threshold is achieved. (in our case loss function is MSE). Can be any float number. :init_vals - initial guess for the hyperparameter optimization search. Default - 'None'. Can be list of parameters such as n_estimators, max_depth etc. :n_jobs - number of CPUs for parallelization = 10, @@ -82,7 +178,7 @@ def objective(space): return {'loss': -mse_scr, 'status': STATUS_OK } """Here we define the space for Random Forest model - More hyperparameters to build the sapce can also be used """ + More hyperparameters to build the space can be added in the future work """ space ={'max_depth': hp.quniform('max_depth', 1, 18, 1), 'random_state' : hp.quniform('random_state', 1, 18, 1), @@ -134,8 +230,86 @@ def objective(space): + def XGB(self, max_evals=40, timeout=600, loss_threshold=0.5, init_vals='None' , n_jobs=10, cv=5, verbose=1): + + + """ + XGBoost does not support multi-output predictions. In this example I wanted to demonstrate one of the possible solutions + for energy bands prediction with ML methods like XGB. + For XGB model we wil use the same strategy as we used for Random forest model. In addtion we will apply sklearn MultiOutputRegressor + for multioutput predictions + + """ + + + import xgboost as xgb + from sklearn.multioutput import MultiOutputRegressor + + startTime = datetime.now() + + def objective(space): + + clf = MultiOutputRegressor(xgb.XGBRegressor(n_estimators =int(space['n_estimators']), + learning_rate = .25, + max_depth = int(space['max_depth']), + subsample = space['x_subsample'], + alpha = space['alpha'], + reg_lambda = space['x_reg_lambda'], + min_split_loss = space['min_split_loss'], + objective='reg:squarederror')) + - ####### later def XGB(self,...): + mse_scr = cross_val_score(clf, self.X_train, self.Y_train, scoring='neg_root_mean_squared_error', cv=5,verbose=0,n_jobs=n_jobs).mean() + + return {'loss': -mse_scr, 'status': STATUS_OK } + + + space ={ + 'max_depth': hp.quniform('max_depth', 1, 18, 1), + 'x_subsample': hp.quniform ('x_subsample', 0.2, 1, 0.02), + 'alpha' : hp.quniform ('alpha', 0.0, 0.6, 0.02), + 'x_reg_lambda' : hp.quniform ('x_reg_lambda', 0, 1, 0.02), + 'min_split_loss' : hp.quniform ('min_split_loss', 0, 8, 0.02), + 'n_estimators' : hp.quniform('n_estimators', 40, 800, 10) + } + + if init_vals=='None': + trials = Trials() + random=8 + else: + trials = generate_trials_to_calculate(init_vals) + random=4 + + + best = fmin(fn=objective, + space=space, + algo=partial(tpe.suggest,n_startup_jobs=random), + max_evals=max_evals, + timeout=timeout, + loss_threshold=loss_threshold, + trials=trials, + show_progressbar=False) + + best_space=space_eval(space, best) + + + + regressorXGB = MultiOutputRegressor(xgb.XGBRegressor(**{'max_depth': int(best_space['max_depth']), + 'n_estimators': int(best_space['n_estimators']), + 'x_subsample': float(best_space['x_subsample']), + 'alpha': float(best_space['alpha']), + 'x_reg_lambda': float(best_space['x_reg_lambda']), + 'min_split_loss': float(best_space['min_split_loss']) }, + objective='reg:squarederror')).fit(self.X_train, self.Y_train) + + y_fit = regressorXGB.predict(self.X_train) + y_predict = regressorXGB.predict(self.X_test) + + text=str("Time taken for XGB: " + str(datetime.now() - startTime) ) + if verbose==1: + text=str("Time taken for XGB: " + str(datetime.now() - startTime) ) + str(modeling.verbose_output(self, regressorXGB, y_fit, y_predict)) + + return y_fit, y_predict, trials.trials, best_space, regressorXGB, text From 4b248842116fb3a0b82b92187def9283259fe725 Mon Sep 17 00:00:00 2001 From: vitaly Date: Thu, 28 Oct 2021 18:26:03 -0600 Subject: [PATCH 09/15] ML module: read lattice param and E_fermi from QE xlm file --- .../ml_modeling_module.cpython-36.pyc | Bin 10234 -> 11451 bytes vitalypro/bands/{bands_0.dat => si2ge2_0.dat} | 0 vitalypro/bands/{bands_1.dat => si2ge2_1.dat} | 0 vitalypro/bands/{bands_2.dat => si2ge2_2.dat} | 0 vitalypro/bands/{bands_3.dat => si2ge2_3.dat} | 0 vitalypro/bands/{bands_4.dat => si2ge2_4.dat} | 0 vitalypro/bands/{bands_5.dat => si2ge2_5.dat} | 0 .../{bands_relax.dat => si2ge2_relax.dat} | 0 vitalypro/cell_param/si2ge2_0.xml | 474 ++++++++++++++++++ vitalypro/cell_param/si2ge2_1.xml | 474 ++++++++++++++++++ vitalypro/cell_param/si2ge2_2.xml | 474 ++++++++++++++++++ vitalypro/cell_param/si2ge2_3.xml | 474 ++++++++++++++++++ vitalypro/cell_param/si2ge2_4.xml | 474 ++++++++++++++++++ vitalypro/cell_param/si2ge2_5.xml | 474 ++++++++++++++++++ vitalypro/cell_param/si2ge2_relax.xml | 474 ++++++++++++++++++ vitalypro/code_implementation_example.ipynb | 327 +++++------- vitalypro/ml_modeling_module.py | 36 ++ 17 files changed, 3481 insertions(+), 200 deletions(-) rename vitalypro/bands/{bands_0.dat => si2ge2_0.dat} (100%) rename vitalypro/bands/{bands_1.dat => si2ge2_1.dat} (100%) rename vitalypro/bands/{bands_2.dat => si2ge2_2.dat} (100%) rename vitalypro/bands/{bands_3.dat => si2ge2_3.dat} (100%) rename vitalypro/bands/{bands_4.dat => si2ge2_4.dat} (100%) rename vitalypro/bands/{bands_5.dat => si2ge2_5.dat} (100%) rename vitalypro/bands/{bands_relax.dat => si2ge2_relax.dat} (100%) create mode 100644 vitalypro/cell_param/si2ge2_0.xml create mode 100644 vitalypro/cell_param/si2ge2_1.xml create mode 100644 vitalypro/cell_param/si2ge2_2.xml create mode 100644 vitalypro/cell_param/si2ge2_3.xml create mode 100644 vitalypro/cell_param/si2ge2_4.xml create mode 100644 vitalypro/cell_param/si2ge2_5.xml create mode 100644 vitalypro/cell_param/si2ge2_relax.xml diff --git a/vitalypro/__pycache__/ml_modeling_module.cpython-36.pyc b/vitalypro/__pycache__/ml_modeling_module.cpython-36.pyc index c031464c0c5b7c6c62a9b9cf1a97763d8cc0592c..7da5052b5920a4772ec1445474d49ca873e0095d 100644 GIT binary patch delta 3057 zcmbVOU2Ggz6`ni4JL}!G)7`{zo!H~lu`{$-(8^V)k~m3|rcEPPiVaD(b=}#W@piYf zJIm<8uTRWwN#!0ySNh#3q_ke_iV4or+B>DzV<$;%ZfCt1w1VTbWJmjI`oI9@9 zSV2^*b-y`t?!D*#oblafe)Vknk!&`d|Ma4B^YAaybBr75f#IBMxT!T()Lhd|uSrGS z?Qt{sG~DcrWcPNiv41MEBJ(TS--k<1!ws#97g>&5TM8r3wO*-4FInJ)i(WbEysqDn z**;z{y>^*N$uEr$4cFti!apLo%$0np#%gklAuan#U2VxsYO{VuShLp<>4sp znybi}8*8Pao?519Y!Qo!nkf{Ub<+dVs@yUzte=yjTvKiutIX{|9&^n>sbw}bGODSQ ziA{4s!H{L9fk|yivRQ0A9xOE?58yuZ8+IXVhDF8~71s=|uz*mJn$ldR#Uc#ED!UG*>WsTdhMBHW8|79l}My<9CMgYdIOJL!PorWAfV)^83B1|PC zVwGgTLE2&ESaqVH4v*nm5w+JBgRn~Kx5Yp1|1Z%!Px{0A5hOXo=r6@~;a`Cj6qV)J z7%Rw^M*e4#HnTyEL{%f2=}9EEHWN0Gf(@i%-OEk6reOmq?MRP|rsB%oE~=%lc(sD$ z>bNv4ZtOBFTZ76Ljyz3p2BFxq;6c4Q?|aLhzde?HA{?6seD7tv5z-iuk_e_p*`@op z#ca#*XDf@Drt~C&1C5!;h5~YRZ z0K6??M~JJ27a#(c|0O?~+q@-m&UY7v+0XdF!g03Hxm>u)nA^0Js)eehkOq=)48c|tmEA*P>t+7lo_*{JzrE*lpAgrz zu*vg#zsN4~V|%CDiHRsCHWtBitK}#OdO+f91WN=r5bS(n_Bt`H5nM-z&1$0>%`f8w z2H~1;@>Q`DMh--?)w&07((x+x@ zm!H6#hSBZLi$e!w_6C2;dT!eF>Nr>nHN?|zGsDjza(a_m9{p1 z3jtVO!-L92EBW7GBMLYoxizxL{Lb}}JnN<4RdC_&lPS2&f4T2;n|Q^n?>W$@HY)R^ zRb--QhD)W;sV`zJ-=Z^V@GA4ZQ!lv={16#QG+IP05HJLE`0GS(Mo$D2KSi$-ca=^U zapwG~<7d4J`W*(qFF(-p^k({Cjn3(GPDuj&1~I-t3>Cglw8)P5U??kXOh3hg& z;sn?_61>CD?BCmdmq?mN@FN0?fCePIN8k{Y3En3t5q$2ZfSYvuHG*zJKcLrcBb=j7 zfbS4|Nbp^RVg^ekNiU`v?%f#wnN0XGT^5a@;GHbvQ)7=ZnJ2%0kdw*eXXzcOY6vyZ8k6~G0p)61^G|XbDJ7t^3U~DxY6bm)9g%r@%Ras_thVA0AyFD}f zsy|jO)mGXnz4jUP!NkNDvnD?1OaB4mgHMwfH9VL;sEPW-llOZESu{L!lKJeJbI&<5 z=f}PK&5PR;4Sfv_;ld}Y#`;M`+2S8ZTEFZbVexK7Q7k3NOeN_vS<-L%O#hma447fF z#tf~oWYDagQuMmYCi~m(`-|~=!QUGVbAHiwa)qpxHVUR)`BdHTu^4}%)@m8o{lr8} zY6hYLy2_75PV#GsXb07c=T>pssz9hFz(N73;}_WR%6AdQ)Kg-ChWTdOLH2Uxw?@_X z_y{zfT1akiE?+bpJwy@ll&o{e$Q4p{DW7xPfNfbOjqvW~VK&RH=8xEqe7ku_)ua(0 zj&A-N{@1A9bQW>X17pBBuC?^Ac|O|mbnmlJoEFe)s2}nG@C+~r9010FNnTDIY^Nb1 zUlg|;5(ov5S2#>V6}RO&8=4lnaXsj&cE-qCwDUTlq}@-@RhiCyOZ2=f#&YHBw$EAL z3vk1mT)*v*8>Hf5!E}RmrbyNv?-(os_7!sIJl|+Pe7x!xaI6)F8WBgL38s-Hi_%5g zN);EK(xP*NZ?zAziOP|V+l(2NuO7L@n8QzXcJLW-FLlnyr$d!LJAd)9QT{{M;U)_K zM}avY%R^dP-6?EIi|Zz|^FSUz^Y*;IwwRu`GEQ#E`i$S#22aZvZNlb(93vT5z5xT3 z)BM6Yi&d0c4|uPv8exg1`RQ0UEAeb>tVxEeeqom1j~!zs|06bD_C8TKxHToR%v{Ft zx^f9Irhr-C4FNssefCu-UIShiaBFjgoReBI^0t?nO!8H^Vmk&o)42tUY?zk-L~>OU z`=+?y2Kcw#tpl$>KLexyv_&MfU&Umz>L;c1sA#$E+^a+$jr*9*PxQRhZ(lAhYq)cc zmN5!i+R{oz+s>u)mgW?-odh+jU{Q9}+q+s=^Dh2#PpNX@NR&0AP$;3ez8|DHZa+3w zhA!EVw+t$XZJ#2;v1HYgwf17#HWo@^uy4U8Ojb6PHx|;SL3f10%ltB=2>@q9PJ|U{&?Nl-BwW%b}H=rUQw?=K~MzfeaO2*=K5E% z>FT7(&)HV^-S~hv6&NydfOY;;yseBRc9IuDpS-pP={786K8uj#EEz)bX3;z5yfIwI zI->0Hk>)rCXh}e4v@Cu`#Tm8&og9l*NLLkcHdjYW&I-K=7u5?c1MT+)n}4C7Yn7?{ z5UC7^ZKBXyyy57f^4k!xTj&Eo1D*rk0jia~hDUiUJ@f{kHTcMa&qKoK({-Ra^cOMp z^e*roa6=$jFGj^{uV^*xzX|@^O!^ScaufK4&jaOd?~}~WPxL0rsIEAz(GyAo89>$? z-SLJG&3;&;|DF5t$e%@|o4^Kujk*JVClTtB=LI_K{SC12flxzuT59zc8sxQ!5q5@8 TB#x>>@SGC=9Z&g(BVGRhkJG8p diff --git a/vitalypro/bands/bands_0.dat b/vitalypro/bands/si2ge2_0.dat similarity index 100% rename from vitalypro/bands/bands_0.dat rename to vitalypro/bands/si2ge2_0.dat diff --git a/vitalypro/bands/bands_1.dat b/vitalypro/bands/si2ge2_1.dat similarity index 100% rename from vitalypro/bands/bands_1.dat rename to vitalypro/bands/si2ge2_1.dat diff --git a/vitalypro/bands/bands_2.dat b/vitalypro/bands/si2ge2_2.dat similarity index 100% rename from vitalypro/bands/bands_2.dat rename to vitalypro/bands/si2ge2_2.dat diff --git a/vitalypro/bands/bands_3.dat b/vitalypro/bands/si2ge2_3.dat similarity index 100% rename from vitalypro/bands/bands_3.dat rename to vitalypro/bands/si2ge2_3.dat diff --git a/vitalypro/bands/bands_4.dat b/vitalypro/bands/si2ge2_4.dat similarity index 100% rename from vitalypro/bands/bands_4.dat rename to vitalypro/bands/si2ge2_4.dat diff --git a/vitalypro/bands/bands_5.dat b/vitalypro/bands/si2ge2_5.dat similarity index 100% rename from vitalypro/bands/bands_5.dat rename to vitalypro/bands/si2ge2_5.dat diff --git a/vitalypro/bands/bands_relax.dat b/vitalypro/bands/si2ge2_relax.dat similarity index 100% rename from vitalypro/bands/bands_relax.dat rename to vitalypro/bands/si2ge2_relax.dat diff --git a/vitalypro/cell_param/si2ge2_0.xml b/vitalypro/cell_param/si2ge2_0.xml new file mode 100644 index 00000000..f8ad3b4c --- /dev/null +++ b/vitalypro/cell_param/si2ge2_0.xml @@ -0,0 +1,474 @@ + + + + + QEXSD_19.03 + XML file generated by PWSCF + This run was terminated on: 18:16:23 26 Oct 2021 + + + + 1 + 1 + 1 + 1 + 1 + 1 + + + + + bands + from_scratch + Si_cubic + ../../pseudo + ./ + false + false + true + low + 10000000 + 1 + 5.000000000000000e-5 + 5.000000000000000e-4 + 5.000000000000000e-1 + high + 100000 + + + + Si.pbe-rrkj.UPF + + + 7.264000000000000e1 + Ge.pbe-kjpaw.UPF + + + + + 1.404406667437952e-3 1.404406667437952e-3 -4.473343261149537e-2 + 2.587760345251342e0 2.587760345251342e0 2.517347977909821e0 + 5.174096277304679e0 1.115990995858547e-3 5.217030514893136e0 + 1.115990995858547e-3 5.174096277304679e0 5.217030514893136e0 + 5.174106810638142e0 5.174106810638142e0 -4.501924801991594e-2 + 7.760456065260715e0 2.587475826195049e0 8.047598618895766e0 + 2.587475826195049e0 7.760456065260715e0 8.047598618895766e0 + 7.760462539462447e0 7.760462539462447e0 2.517063043113779e0 + + + 1.034568286400000e1 -2.734100000000000e-4 -2.808260000000000e-4 + -2.734100000000000e-4 1.034568286400000e1 -2.808260000000000e-4 + -2.734100000000000e-4 -2.734100000000000e-4 1.079211782200000e1 + + + + pbe + + + false + false + false + + + gaussian + 0.000000000000000e0 + smearing + + + false + 1.500000000000000e1 + 6.000000000000000e1 + + + davidson + plain + 7.000000000000000e-1 + 5.000000000000000e-9 + 8 + 100 + false + false + false + false + 0.000000000000000e0 + false + 20 + 20 + + + 11 + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 1.301104319514717e-6 1.301104319514717e-6 4.793166205318520e-2 + 2.602208639029433e-6 2.602208639029433e-6 9.586332410637040e-2 + 3.903312958544150e-6 3.903312958544150e-6 1.437949861595556e-1 + 5.204417278058867e-6 5.204417278058867e-6 1.917266482127408e-1 + 6.505521597573583e-6 6.505521597573583e-6 2.396583102659259e-1 + 7.806625917088300e-6 7.806625917088300e-6 2.875899723191112e-1 + 9.107730236603016e-6 9.107730236603016e-6 3.355216343722964e-1 + 1.040883455611773e-5 1.040883455611773e-5 3.834532964254816e-1 + 1.170993887563245e-5 1.170993887563245e-5 4.313849584786667e-1 + 1.301104319514717e-5 1.301104319514717e-5 4.793166205318519e-1 + + + none + 1.000000000000000e2 + false + false + + + none + 0.000000000000000e0 + 3.672227080435770e5 + 0.000000000000000e0 + false + false + false + + + false + false + false + false + false + false + + + + + + false + 1 + 0.000000000000000e0 + + + + false + false + true + true + + + + 2.808550000000000e1 + Si.pbe-rrkj.UPF + + + 7.264000000000000e1 + Ge.pbe-kjpaw.UPF + + + + + 1.404406667437952e-3 1.404406667437952e-3 -4.473343261149537e-2 + 2.587760345251342e0 2.587760345251342e0 2.517347977909821e0 + 5.174096277304679e0 1.115990995858547e-3 5.217030514893136e0 + 1.115990995858547e-3 5.174096277304679e0 5.217030514893136e0 + 5.174106810638142e0 5.174106810638142e0 -4.501924801991594e-2 + 7.760456065260715e0 2.587475826195049e0 8.047598618895766e0 + 2.587475826195049e0 7.760456065260715e0 8.047598618895766e0 + 7.760462539462447e0 7.760462539462447e0 2.517063043113779e0 + + + 1.034568286400000e1 -2.734100000000000e-4 -2.808260000000000e-4 + -2.734100000000000e-4 1.034568286400000e1 -2.808260000000000e-4 + -2.734100000000000e-4 -2.734100000000000e-4 1.079211782200000e1 + + + + 2 + 4 + 0 + + crystal_symmetry + + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 1.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 1.000000000000000e0 + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + 1 2 3 4 5 6 7 8 + + + + crystal_symmetry + + 0.000000000000000e0 1.000000000000000e0 0.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 1.000000000000000e0 + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + 1 2 4 3 5 7 6 8 + + + + lattice_symmetry + + -1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 -1.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 -1.000000000000000e0 + + + + lattice_symmetry + + 0.000000000000000e0 -1.000000000000000e0 0.000000000000000e0 + -1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 -1.000000000000000e0 + + + + + false + 1.500000000000000e1 + 6.000000000000000e1 + + + + 25689 + 25689 + 3210 + + 1.000000002103333e0 2.642813614798932e-5 2.533490004477236e-5 + 2.642813614798932e-5 1.000000002103333e0 2.533490004477236e-5 + 2.602208639030483e-5 2.602208639030483e-5 9.586332410640907e-1 + + + + PBE + + + false + false + false + 0.000000000000000e0 + 0.000000000000000e0 + false + + + 0.000000000000000e0 + 0.000000000000000e0 + 2.251969856583011e0 + -1.298952906283941e1 + -3.712800683609099e1 + 0.000000000000000e0 + -4.563800771351229e-7 + + + false + false + false + 20 + 3.200000000000000e1 + 32 + true + 2.270846378623998e-1 + + 11 + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 1.301104319515242e-6 1.301104319515242e-6 4.793166205320453e-2 + 2.602208639030483e-6 2.602208639030483e-6 9.586332410640907e-2 + 3.903312958545725e-6 3.903312958545725e-6 1.437949861596136e-1 + 5.204417278060967e-6 5.204417278060967e-6 1.917266482128182e-1 + 6.505521597576208e-6 6.505521597576208e-6 2.396583102660227e-1 + 7.806625917091450e-6 7.806625917091450e-6 2.875899723192272e-1 + 9.107730236606692e-6 9.107730236606692e-6 3.355216343724318e-1 + 1.040883455612193e-5 1.040883455612193e-5 3.834532964256363e-1 + 1.170993887563717e-5 1.170993887563717e-5 4.313849584788408e-1 + 1.301104319515242e-5 1.301104319515242e-5 4.793166205320453e-1 + + 11 + smearing + gaussian + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 3191 + + -2.319080972063870e-1 -9.437828602437987e-2 -9.436889465634197e-2 -9.127162250651935e-2 -8.849752214327854e-2 + -6.874854793055469e-2 -6.873993815420531e-2 1.070571896662729e-1 1.070805442909951e-1 1.121170303071959e-1 + 1.121410158977077e-1 1.188585119058203e-1 1.205559930369458e-1 2.111985507269512e-1 2.255366958983164e-1 + 2.266280451817555e-1 2.323838775826039e-1 2.324129399916517e-1 2.512797131317772e-1 2.573078495752736e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 9.951010053080854e-1 9.779643546434960e-198 6.946406609177071e-200 0.000000000000000e0 0.000000000000000e0 + + + + 1.301104319515242e-6 1.301104319515242e-6 4.793166205320453e-2 + 3171 + + -2.315463695622637e-1 -1.030499222321178e-1 -9.429214111377753e-2 -9.428257287992528e-2 -7.620950381365709e-2 + -6.865368868420076e-2 -6.864491520406657e-2 1.062595464523755e-1 1.062825371208069e-1 1.109734426522158e-1 + 1.109969483640989e-1 1.191977013071949e-1 1.209139254866793e-1 2.069701451413852e-1 2.237277447597195e-1 + 2.248316570850509e-1 2.345742975664123e-1 2.346038394527454e-1 2.505728831946326e-1 2.590806541582831e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 2.602208639030483e-6 2.602208639030483e-6 9.586332410640907e-2 + 3187 + + -2.304634367101751e-1 -1.155668169173707e-1 -9.404258835329626e-2 -9.403251932686672e-2 -6.837941860428729e-2 + -6.837018252160241e-2 -6.216903701762987e-2 1.040074714253695e-1 1.040294253020853e-1 1.078157364791493e-1 + 1.078379226798121e-1 1.202111249078253e-1 1.219817971248194e-1 1.963108570011089e-1 2.188032273995119e-1 + 2.199429704124943e-1 2.408665284390867e-1 2.408973624969112e-1 2.495744505396194e-1 2.642393996105772e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 3.903312958545725e-6 3.903312958545725e-6 1.437949861596136e-1 + 3183 + + -2.286628887911030e-1 -1.275346099066048e-1 -9.364864386056439e-2 -9.363782578405324e-2 -6.794582799807719e-2 + -6.793589900152691e-2 -4.767039933500766e-2 1.006714207467200e-1 1.006917994134431e-1 1.032968929402156e-1 + 1.033171795315675e-1 1.218895539957412e-1 1.237586810967027e-1 1.823149065558355e-1 2.118288624989489e-1 + 2.130515938680579e-1 2.491078743001141e-1 2.506355822251014e-1 2.506682131049003e-1 2.698175877765149e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 5.204417278060967e-6 5.204417278060967e-6 1.917266482128182e-1 + 3207 + + -2.261527496084643e-1 -1.389056213183417e-1 -9.314608776267953e-2 -9.313436867085445e-2 -6.739162012109073e-2 + -6.738085706718694e-2 -3.277751534582288e-2 9.671658928359925e-2 9.673500753994016e-2 9.813829096198457e-2 + 9.815633809550825e-2 1.242113587075041e-1 1.262384540303622e-1 1.667641432379452e-1 2.037584626703977e-1 + 2.051264515951960e-1 2.493116415868800e-1 2.631642453210016e-1 2.631989143921860e-1 2.751962972222455e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 6.505521597576208e-6 6.505521597576208e-6 2.396583102660227e-1 + 3191 + + -2.229463340284238e-1 -1.496418406523093e-1 -9.257852624788612e-2 -9.256585084737758e-2 -6.676371880528889e-2 + -6.675207022383375e-2 -1.754645635925853e-2 9.260267087100347e-2 9.261888002184502e-2 9.295060227744395e-2 + 9.296623850619914e-2 1.271460725655555e-1 1.294120497122050e-1 1.505084880139808e-1 1.952399810939945e-1 + 1.968487735040394e-1 2.501850069052853e-1 2.778846986056168e-1 2.779214868296196e-1 2.806989956223863e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 7.806625917091450e-6 7.806625917091450e-6 2.875899723192272e-1 + 3195 + + -2.190696929609750e-1 -1.597015014762939e-1 -9.200147288104581e-2 -9.198787447707346e-2 -6.612329138346526e-2 + -6.611078757730010e-2 -2.052023865288311e-3 8.819016798124535e-2 8.820333788035251e-2 8.872040297033507e-2 + 8.873427450117257e-2 1.306306690427517e-1 1.332682386463006e-1 1.339645806073340e-1 1.866785847679295e-1 + 1.886627301514089e-1 2.516715436980879e-1 2.847655379713160e-1 2.943451274334167e-1 2.943840152242505e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 9.107730236606692e-6 9.107730236606692e-6 3.355216343724318e-1 + 3185 + + -2.145775583957843e-1 -1.690159441236538e-1 -9.147176362524888e-2 -9.145735387856019e-2 -6.553368072406811e-2 + -6.552042398847936e-2 1.358689659643953e-2 8.418750042063476e-2 8.419825743837063e-2 8.538469778021383e-2 + 8.539623116162932e-2 1.174201558749696e-1 1.345431034598574e-1 1.377831101168359e-1 1.783366616254070e-1 + 1.809285676431074e-1 2.536427845322046e-1 2.851210756744533e-1 3.097208182335413e-1 3.122293894786926e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.040883455612193e-5 1.040883455612193e-5 3.834532964256363e-1 + 3199 + + -2.096113741403771e-1 -1.774338007713554e-1 -9.104559757227076e-2 -9.103055560274052e-2 -6.505819845941925e-2 + -6.504435434029911e-2 2.910887189146690e-2 8.117449839799512e-2 8.118305744327936e-2 8.283289516895264e-2 + 8.284227799342098e-2 1.012169494549989e-1 1.386108214630957e-1 1.429224295186018e-1 1.703832038581047e-1 + 1.740499139945319e-1 2.558464571219833e-1 2.826621134842740e-1 3.167529696990210e-1 3.312575036844862e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.170993887563717e-5 1.170993887563717e-5 4.313849584788408e-1 + 3202 + + -2.046696929913427e-1 -1.844491267136382e-1 -9.076915472366947e-2 -9.075371002812428e-2 -6.474896995211788e-2 + -6.473475186525012e-2 4.359340860288929e-2 7.930665983135342e-2 7.931353748466558e-2 8.123566255254744e-2 + 8.124340910259081e-2 8.631370514862198e-2 1.421619283933808e-1 1.485505860887775e-1 1.630386932912088e-1 + 1.687867086665964e-1 2.577738736667350e-1 2.799941396944813e-1 3.255706528240428e-1 3.453403429953790e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.301104319515242e-5 1.301104319515242e-5 4.793166205320453e-1 + 3210 + + -2.019703413879465e-1 -1.878402040582997e-1 -9.067364994770017e-2 -9.065806698961067e-2 -6.464217657608002e-2 + -6.462782989455079e-2 5.169122701952142e-2 7.807465387032985e-2 7.867420612641114e-2 7.868041678487017e-2 + 8.069204302107924e-2 8.069914860837292e-2 1.437307677472610e-1 1.529117447651394e-1 1.581006266030402e-1 + 1.666420982596487e-1 2.585906744676688e-1 2.788590507259447e-1 3.325145543293302e-1 3.389982539886054e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + + 0 + + + 1.785568700000000e1 + 1.788387989997864e1 + + + 1.651095500000000e1 + 1.652714109420776e1 + + + + diff --git a/vitalypro/cell_param/si2ge2_1.xml b/vitalypro/cell_param/si2ge2_1.xml new file mode 100644 index 00000000..6fc14900 --- /dev/null +++ b/vitalypro/cell_param/si2ge2_1.xml @@ -0,0 +1,474 @@ + + + + + QEXSD_19.03 + XML file generated by PWSCF + This run was terminated on: 18:24:21 26 Oct 2021 + + + + 1 + 1 + 1 + 1 + 1 + 1 + + + + + bands + from_scratch + Si_cubic + ../../pseudo + ./ + false + false + true + low + 10000000 + 1 + 5.000000000000000e-5 + 5.000000000000000e-4 + 5.000000000000000e-1 + high + 100000 + + + + Si.pbe-rrkj.UPF + + + 7.264000000000000e1 + Ge.pbe-kjpaw.UPF + + + + + -4.084677807193163e-2 -4.084677807193163e-2 -4.452252405725629e-2 + 2.573268640250605e0 2.573268640250605e0 2.497030763136631e0 + 5.187694406406219e0 -4.008572299725620e-2 5.177595192167118e0 + -4.008572299725620e-2 5.187694406406219e0 5.177595192167118e0 + 5.188247359169963e0 5.188247359169963e0 -4.300854162000296e-2 + 7.801772901369843e0 2.574675987331906e0 7.989440715455436e0 + 2.574675987331906e0 7.801772901369843e0 7.989440715455436e0 + 7.802151470206048e0 7.802151470206048e0 2.498598619776207e0 + + + 1.045682864000000e1 -2.734100000000000e-4 -2.768190000000000e-4 + -2.734100000000000e-4 1.045682864000000e1 -2.768190000000000e-4 + -2.734100000000000e-4 -2.734100000000000e-4 1.071265005100000e1 + + + + pbe + + + false + false + false + + + gaussian + 0.000000000000000e0 + smearing + + + false + 1.500000000000000e1 + 6.000000000000000e1 + + + davidson + plain + 7.000000000000000e-1 + 5.000000000000000e-9 + 8 + 100 + false + false + false + false + 0.000000000000000e0 + false + 20 + 20 + + + 11 + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 1.292053027491588e-6 1.292053027491588e-6 4.880598456773017e-2 + 2.584106054983176e-6 2.584106054983176e-6 9.761196913546033e-2 + 3.876159082474764e-6 3.876159082474764e-6 1.464179537031905e-1 + 5.168212109966353e-6 5.168212109966353e-6 1.952239382709207e-1 + 6.460265137457938e-6 6.460265137457938e-6 2.440299228386508e-1 + 7.752318164949528e-6 7.752318164949528e-6 2.928359074063811e-1 + 9.044371192441114e-6 9.044371192441114e-6 3.416418919741111e-1 + 1.033642421993270e-5 1.033642421993270e-5 3.904478765418413e-1 + 1.162847724742429e-5 1.162847724742429e-5 4.392538611095715e-1 + 1.292053027491588e-5 1.292053027491588e-5 4.880598456773016e-1 + + + none + 1.000000000000000e2 + false + false + + + none + 0.000000000000000e0 + 3.672227080435770e5 + 0.000000000000000e0 + false + false + false + + + false + false + false + false + false + false + + + + + + false + 1 + 0.000000000000000e0 + + + + false + false + true + true + + + + 2.808550000000000e1 + Si.pbe-rrkj.UPF + + + 7.264000000000000e1 + Ge.pbe-kjpaw.UPF + + + + + -4.084677807193163e-2 -4.084677807193163e-2 -4.452252405725629e-2 + 2.573268640250605e0 2.573268640250605e0 2.497030763136631e0 + 5.187694406406219e0 -4.008572299725620e-2 5.177595192167118e0 + -4.008572299725620e-2 5.187694406406219e0 5.177595192167118e0 + 5.188247359169963e0 5.188247359169963e0 -4.300854162000296e-2 + 7.801772901369843e0 2.574675987331906e0 7.989440715455436e0 + 2.574675987331906e0 7.801772901369843e0 7.989440715455436e0 + 7.802151470206048e0 7.802151470206048e0 2.498598619776207e0 + + + 1.045682864000000e1 -2.734100000000000e-4 -2.768190000000000e-4 + -2.734100000000000e-4 1.045682864000000e1 -2.768190000000000e-4 + -2.734100000000000e-4 -2.734100000000000e-4 1.071265005100000e1 + + + + 2 + 4 + 0 + + crystal_symmetry + + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 1.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 1.000000000000000e0 + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + 1 2 3 4 5 6 7 8 + + + + crystal_symmetry + + 0.000000000000000e0 1.000000000000000e0 0.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 1.000000000000000e0 + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + 1 2 4 3 5 7 6 8 + + + + lattice_symmetry + + -1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 -1.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 -1.000000000000000e0 + + + + lattice_symmetry + + 0.000000000000000e0 -1.000000000000000e0 0.000000000000000e0 + -1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 -1.000000000000000e0 + + + + + false + 1.500000000000000e1 + 6.000000000000000e1 + + + + 25973 + 25973 + 3263 + + 1.000000002051685e0 2.614722638940713e-5 2.552283031485711e-5 + 2.614722638940713e-5 1.000000002051685e0 2.552283031485711e-5 + 2.584106054982784e-5 2.584106054982784e-5 9.761196913544554e-1 + + + + PBE + + + false + false + false + 0.000000000000000e0 + 0.000000000000000e0 + false + + + 0.000000000000000e0 + 0.000000000000000e0 + 2.281308557767477e0 + -1.295324602550547e1 + -3.710009274633742e1 + 0.000000000000000e0 + -6.531958529780458e-35 + + + false + false + false + 20 + 3.200000000000000e1 + 32 + true + 2.215001966798720e-1 + + 11 + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 1.292053027491392e-6 1.292053027491392e-6 4.880598456772278e-2 + 2.584106054982784e-6 2.584106054982784e-6 9.761196913544556e-2 + 3.876159082474178e-6 3.876159082474178e-6 1.464179537031684e-1 + 5.168212109965569e-6 5.168212109965569e-6 1.952239382708911e-1 + 6.460265137456961e-6 6.460265137456961e-6 2.440299228386138e-1 + 7.752318164948355e-6 7.752318164948355e-6 2.928359074063367e-1 + 9.044371192439748e-6 9.044371192439748e-6 3.416418919740594e-1 + 1.033642421993114e-5 1.033642421993114e-5 3.904478765417822e-1 + 1.162847724742253e-5 1.162847724742253e-5 4.392538611095049e-1 + 1.292053027491392e-5 1.292053027491392e-5 4.880598456772277e-1 + + 11 + smearing + gaussian + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 3239 + + -2.336800865926448e-1 -9.923666054816399e-2 -9.920355378641489e-2 -9.255817292601629e-2 -8.974910754969525e-2 + -7.377282762729189e-2 -7.374205109365562e-2 1.046030267328790e-1 1.046219350572613e-1 1.097957784044024e-1 + 1.098357553858738e-1 1.115858936493853e-1 1.132304439203501e-1 2.090668211981953e-1 2.182775239027698e-1 + 2.194470061508925e-1 2.296109417993862e-1 2.296415717784883e-1 2.432520276791203e-1 2.517591674947259e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.292053027491392e-6 1.292053027491392e-6 4.880598456772278e-2 + 3255 + + -2.333156674043261e-1 -1.043129250089002e-1 -9.914899030962999e-2 -9.911604413231824e-2 -7.750179612510011e-2 + -7.367677820692920e-2 -7.364595049921897e-2 1.037729022100601e-1 1.037920653073255e-1 1.086101070963893e-1 + 1.086495839352915e-1 1.119276314535057e-1 1.135894953577324e-1 2.045727387978558e-1 2.165043709877229e-1 + 2.176808101251799e-1 2.318443147627065e-1 2.318766070370096e-1 2.423848215427270e-1 2.534790189782474e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 2.584106054982784e-6 2.584106054982784e-6 9.761196913544556e-2 + 3231 + + -2.322231658633386e-1 -1.168328874227150e-1 -9.889059897612512e-2 -9.885813572168898e-2 -7.339372710112501e-2 + -7.336278073398949e-2 -6.350381916719744e-2 1.014356655765711e-1 1.014554475465725e-1 1.053435562529287e-1 + 1.053815354970241e-1 1.129508411378489e-1 1.146670988286889e-1 1.934959892778217e-1 2.116638570405573e-1 + 2.128697441460180e-1 2.382789278267701e-1 2.383151531456740e-1 2.411973246341384e-1 2.572679073704597e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 3.876159082474178e-6 3.876159082474178e-6 1.464179537031684e-1 + 3227 + + -2.304071947576340e-1 -1.288176415736294e-1 -9.848447548167329e-2 -9.845280487683086e-2 -7.294784724676227e-2 + -7.291668542485214e-2 -4.906852300763692e-2 9.797796953692384e-2 9.799844643771669e-2 1.006794822828921e-1 + 1.007150092711222e-1 1.146444556228594e-1 1.164593960872528e-1 1.792477691934769e-1 2.047694983055341e-1 + 2.060477651062044e-1 2.405949949343104e-1 2.482341563896972e-1 2.482749031618839e-1 2.621507381535037e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 5.168212109965569e-6 5.168212109965569e-6 1.952239382708911e-1 + 3249 + + -2.278753128343769e-1 -1.402153425308277e-1 -9.796661492787701e-2 -9.793602212901497e-2 -7.237794608429362e-2 + -7.234650772358969e-2 -3.426133063594252e-2 9.388676179485406e-2 9.390779714731062e-2 9.536761265755821e-2 + 9.539983978871309e-2 1.169900542854619e-1 1.189603968924908e-1 1.636270557636152e-1 1.967575322851616e-1 + 1.981773665241261e-1 2.406971825201127e-1 2.609732024272556e-1 2.610181553697483e-1 2.677611986696280e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 6.460265137456961e-6 6.460265137456961e-6 2.440299228386138e-1 + 3255 + + -2.246415557277445e-1 -1.509869405068593e-1 -9.738169267504816e-2 -9.735241374161612e-2 -7.173262148324251e-2 + -7.170086711467858e-2 -1.914111234152953e-2 8.963763673718343e-2 8.965901887455983e-2 9.003657728934657e-2 + 9.006478192545758e-2 1.199522163756185e-1 1.221595722754407e-1 1.474158532473860e-1 1.882698786638228e-1 + 1.899196533596740e-1 2.415083114980525e-1 2.734278328307969e-1 2.759106728187329e-1 2.759593103495658e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 7.752318164948355e-6 7.752318164948355e-6 2.928359074063367e-1 + 3263 + + -2.207316318157857e-1 -1.610885119562723e-1 -9.678577982392945e-2 -9.675796303264416e-2 -7.107277010020413e-2 + -7.104068817108439e-2 -3.785431024843785e-3 8.515276633315533e-2 8.517634477709766e-2 8.563447095570437e-2 + 8.565600742203699e-2 1.234694402052971e-1 1.260404602517729e-1 1.309959846029243e-1 1.797096038117094e-1 + 1.817256638576314e-1 2.429688580368693e-1 2.773336041018442e-1 2.925976926852991e-1 2.926495078336986e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 9.044371192439748e-6 9.044371192439748e-6 3.416418919740594e-1 + 3242 + + -2.161987913988419e-1 -1.704512461980118e-1 -9.623829993202609e-2 -9.621195771279258e-2 -7.046500809741030e-2 + -7.043262109556546e-2 1.168436995197904e-2 8.105095772708495e-2 8.106943197710509e-2 8.219853429623930e-2 + 8.222009434315201e-2 1.146361943810119e-1 1.274202923180274e-1 1.305907811619386e-1 1.713576313120979e-1 + 1.739716455595841e-1 2.449593484943549e-1 2.771117808383313e-1 3.022731185751679e-1 3.107087172977718e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.033642421993114e-5 1.033642421993114e-5 3.904478765417822e-1 + 3238 + + -2.111824037743890e-1 -1.789252504442567e-1 -9.579799424074009e-2 -9.577295036125914e-2 -6.997490461642739e-2 + -6.994226913370005e-2 2.699508336209557e-2 7.796551695832694e-2 7.797858985609495e-2 7.957386935949455e-2 + 7.959538954884220e-2 9.866535868733095e-2 1.315310488753741e-1 1.357639373924494e-1 1.633843536746098e-1 + 1.670641917725922e-1 2.472212759597618e-1 2.741933036469205e-1 3.098401573194759e-1 3.299596678172706e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.162847724742253e-5 1.162847724742253e-5 4.392538611095049e-1 + 3242 + + -2.061755936469521e-1 -1.860096721776962e-1 -9.551208115207967e-2 -9.548793986326654e-2 -6.965643382863700e-2 + -6.962363444392762e-2 4.119493594458046e-2 7.605429084771988e-2 7.606210923636292e-2 7.793030439021163e-2 + 7.795177728106363e-2 8.406564374602894e-2 1.351255999850779e-1 1.414234090382723e-1 1.560165830325427e-1 + 1.617619257304654e-1 2.492277075514701e-1 2.712606107678340e-1 3.189094823509283e-1 3.385381121636111e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.292053027491392e-5 1.292053027491392e-5 4.880598456772277e-1 + 3242 + + -2.034205958498218e-1 -1.894576898038480e-1 -9.541329265287096e-2 -9.538947776808385e-2 -6.954631463979457e-2 + -6.951345837819312e-2 4.900899933248148e-2 7.540782361216760e-2 7.541264007542637e-2 7.611641641667868e-2 + 7.737178136972442e-2 7.739320610704750e-2 1.367169065108563e-1 1.457878802856605e-1 1.510784017675544e-1 + 1.595980442662650e-1 2.500895305432226e-1 2.700272463402190e-1 3.258132495659668e-1 3.325372298069440e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + + 0 + + + 1.848316900000000e1 + 1.855565404891968e1 + + + 1.666781200000000e1 + 1.670562005043030e1 + + + + diff --git a/vitalypro/cell_param/si2ge2_2.xml b/vitalypro/cell_param/si2ge2_2.xml new file mode 100644 index 00000000..b72ccc46 --- /dev/null +++ b/vitalypro/cell_param/si2ge2_2.xml @@ -0,0 +1,474 @@ + + + + + QEXSD_19.03 + XML file generated by PWSCF + This run was terminated on: 18:27:12 26 Oct 2021 + + + + 1 + 1 + 1 + 1 + 1 + 1 + + + + + bands + from_scratch + Si_cubic + ../../pseudo + ./ + false + false + true + low + 10000000 + 1 + 5.000000000000000e-5 + 5.000000000000000e-4 + 5.000000000000000e-1 + high + 100000 + + + + Si.pbe-rrkj.UPF + + + 7.264000000000000e1 + Ge.pbe-kjpaw.UPF + + + + + -8.029057999910789e-2 -8.029057999910789e-2 -4.465005789451247e-2 + 2.559540010441779e0 2.559540010441779e0 2.479762154716498e0 + 5.200464204293028e0 -7.883500332744369e-2 5.145037008027051e0 + -7.883500332744369e-2 5.200464204293028e0 5.145037008027051e0 + 5.201780946565162e0 5.201780946565162e0 -4.121450554930824e-2 + 7.840458240926599e0 2.562462131755583e0 7.940498486690504e0 + 2.562462131755583e0 7.840458240926599e0 7.940498486690504e0 + 7.841298311120071e0 7.841298311120071e0 2.483294084984205e0 + + + 1.056082864000000e1 -2.734100000000000e-4 -2.734340000000000e-4 + -2.734100000000000e-4 1.056082864000000e1 -2.734340000000000e-4 + -2.734100000000000e-4 -2.734100000000000e-4 1.064615758800000e1 + + + + pbe + + + false + false + false + + + gaussian + 0.000000000000000e0 + smearing + + + false + 1.500000000000000e1 + 6.000000000000000e1 + + + davidson + plain + 7.000000000000000e-1 + 5.000000000000000e-9 + 8 + 100 + false + false + false + false + 0.000000000000000e0 + false + 20 + 20 + + + 11 + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 1.284224272565796e-6 1.284224272565796e-6 4.959925012301931e-2 + 2.568448545131592e-6 2.568448545131592e-6 9.919850024603862e-2 + 3.852672817697389e-6 3.852672817697389e-6 1.487977503690580e-1 + 5.136897090263184e-6 5.136897090263184e-6 1.983970004920772e-1 + 6.421121362828980e-6 6.421121362828980e-6 2.479962506150966e-1 + 7.705345635394778e-6 7.705345635394778e-6 2.975955007381159e-1 + 8.989569907960572e-6 8.989569907960572e-6 3.471947508611353e-1 + 1.027379418052637e-5 1.027379418052637e-5 3.967940009841545e-1 + 1.155801845309216e-5 1.155801845309216e-5 4.463932511071738e-1 + 1.284224272565796e-5 1.284224272565796e-5 4.959925012301932e-1 + + + none + 1.000000000000000e2 + false + false + + + none + 0.000000000000000e0 + 3.672227080435770e5 + 0.000000000000000e0 + false + false + false + + + false + false + false + false + false + false + + + + + + false + 1 + 0.000000000000000e0 + + + + false + false + true + true + + + + 2.808550000000000e1 + Si.pbe-rrkj.UPF + + + 7.264000000000000e1 + Ge.pbe-kjpaw.UPF + + + + + -8.029057999910789e-2 -8.029057999910789e-2 -4.465005789451247e-2 + 2.559540010441779e0 2.559540010441779e0 2.479762154716498e0 + 5.200464204293028e0 -7.883500332744369e-2 5.145037008027051e0 + -7.883500332744369e-2 5.200464204293028e0 5.145037008027051e0 + 5.201780946565162e0 5.201780946565162e0 -4.121450554930824e-2 + 7.840458240926599e0 2.562462131755583e0 7.940498486690504e0 + 2.562462131755583e0 7.840458240926599e0 7.940498486690504e0 + 7.841298311120071e0 7.841298311120071e0 2.483294084984205e0 + + + 1.056082864000000e1 -2.734100000000000e-4 -2.734340000000000e-4 + -2.734100000000000e-4 1.056082864000000e1 -2.734340000000000e-4 + -2.734100000000000e-4 -2.734100000000000e-4 1.064615758800000e1 + + + + 2 + 4 + 0 + + crystal_symmetry + + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 1.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 1.000000000000000e0 + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + 1 2 3 4 5 6 7 8 + + + + crystal_symmetry + + 0.000000000000000e0 1.000000000000000e0 0.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 1.000000000000000e0 + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + 1 2 4 3 5 7 6 8 + + + + lattice_symmetry + + -1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 -1.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 -1.000000000000000e0 + + + + lattice_symmetry + + 0.000000000000000e0 -1.000000000000000e0 0.000000000000000e0 + -1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 -1.000000000000000e0 + + + + + false + 1.500000000000000e1 + 6.000000000000000e1 + + + + 26369 + 26369 + 3294 + + 1.000000002005610e0 2.588973197689545e-5 2.568223105847696e-5 + 2.588973197689545e-5 1.000000002005610e0 2.568223105847696e-5 + 2.568448545131337e-5 2.568448545131337e-5 9.919850024602878e-1 + + + + PBE + + + false + false + false + 0.000000000000000e0 + 0.000000000000000e0 + false + + + 0.000000000000000e0 + 0.000000000000000e0 + 2.307564727246630e0 + -1.291754253138696e1 + -3.707265859643593e1 + 0.000000000000000e0 + -5.965930672780756e-27 + + + false + false + false + 20 + 3.200000000000000e1 + 32 + true + 2.145200714993164e-1 + + 11 + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 1.284224272565669e-6 1.284224272565669e-6 4.959925012301439e-2 + 2.568448545131337e-6 2.568448545131337e-6 9.919850024602878e-2 + 3.852672817697007e-6 3.852672817697007e-6 1.487977503690432e-1 + 5.136897090262675e-6 5.136897090262675e-6 1.983970004920576e-1 + 6.421121362828344e-6 6.421121362828344e-6 2.479962506150720e-1 + 7.705345635394014e-6 7.705345635394014e-6 2.975955007380864e-1 + 8.989569907959682e-6 8.989569907959682e-6 3.471947508611008e-1 + 1.027379418052535e-5 1.027379418052535e-5 3.967940009841151e-1 + 1.155801845309102e-5 1.155801845309102e-5 4.463932511071295e-1 + 1.284224272565669e-5 1.284224272565669e-5 4.959925012301439e-1 + + 11 + smearing + gaussian + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 3279 + + -2.353426365966560e-1 -1.037374195497185e-1 -1.036655546361904e-1 -9.397535479226622e-2 -9.117851878736587e-2 + -7.840430483986649e-2 -7.832107126649717e-2 1.022320929952983e-1 1.022433818765262e-1 1.050111735436868e-1 + 1.066228661642317e-1 1.075324766197091e-1 1.075845394179033e-1 2.066688292199538e-1 2.116039512094630e-1 + 2.127679402508547e-1 2.268752398403722e-1 2.269115657213571e-1 2.358401547152006e-1 2.443893265734669e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.284224272565669e-6 1.284224272565669e-6 4.959925012301439e-2 + 3275 + + -2.349759114493857e-1 -1.057023608369042e-1 -1.036469316618630e-1 -1.035753135417348e-1 -7.897548833984080e-2 + -7.830545098056918e-2 -7.822171529602834e-2 1.013739643324245e-1 1.013880252341582e-1 1.053559501038103e-1 + 1.063108981865275e-1 1.063634492056357e-1 1.069856051819082e-1 2.018591918214892e-1 2.098660137191339e-1 + 2.110372976530375e-1 2.291543406660307e-1 2.291945470808691e-1 2.348429988116531e-1 2.461723508358901e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 2.568448545131337e-6 2.568448545131337e-6 9.919850024602878e-2 + 3291 + + -2.338771157583729e-1 -1.182045668235591e-1 -1.033831926975808e-1 -1.033123035638094e-1 -7.801636631987602e-2 + -7.793329078829786e-2 -6.504584766642076e-2 9.895941004985078e-2 9.897872970024711e-2 1.029499187379393e-1 + 1.030017231987906e-1 1.063863130537686e-1 1.080688314059526e-1 1.903098436175068e-1 2.051003576481237e-1 + 2.062991757532518e-1 2.334945401859750e-1 2.356938847947068e-1 2.357423941970674e-1 2.500769910734418e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 3.852672817697007e-6 3.852672817697007e-6 1.487977503690432e-1 + 3275 + + -2.320500843638141e-1 -1.301824175585848e-1 -1.029676336786440e-1 -1.028979337945747e-1 -7.756026395947623e-2 + -7.747726507959376e-2 -5.069830822468205e-2 9.539456985333716e-2 9.541863162387488e-2 9.816236608603720e-2 + 9.821243114294429e-2 1.080932856576097e-1 1.098734939860841e-1 1.758036503618680e-1 1.982924934945842e-1 + 1.995617187202390e-1 2.327727786501567e-1 2.458019077645145e-1 2.458589368075148e-1 2.551489839365559e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 5.136897090262675e-6 5.136897090262675e-6 1.983970004920576e-1 + 3259 + + -2.295025382345815e-1 -1.415836439902149e-1 -1.024365159036108e-1 -1.023684148316443e-1 -7.697602207513209e-2 + -7.689314405768290e-2 -3.599870150175952e-2 9.118569906949046e-2 9.121312363736877e-2 9.272243867880920e-2 + 9.276925945649278e-2 1.104566474285063e-1 1.123907295616766e-1 1.601100273638638e-1 1.903430446507572e-1 + 1.917516146163224e-1 2.327955386768937e-1 2.587221813195772e-1 2.587863796637937e-1 2.609792821208938e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 6.421121362828344e-6 6.421121362828344e-6 2.479962506150720e-1 + 3267 + + -2.262489327535124e-1 -1.523678754486706e-1 -1.018384001274685e-1 -1.017722181804078e-1 -7.631626191384945e-2 + -7.623353373855267e-2 -2.101098973096626e-2 8.682006690270873e-2 8.684946781481457e-2 8.727098110166908e-2 + 8.731312326848904e-2 1.134422776844953e-1 1.156080502827566e-1 1.439447419367222e-1 1.818930865815913e-1 + 1.835268614652059e-1 2.335507861477552e-1 2.667868765599674e-1 2.738335510783198e-1 2.739034366472570e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 7.705345635394014e-6 7.705345635394014e-6 2.975955007380864e-1 + 3282 + + -2.223148191843393e-1 -1.624897725925576e-1 -1.012282531736393e-1 -1.011641679608426e-1 -7.564111443740444e-2 + -7.555855371554793e-2 -5.812960095238452e-3 8.228354785237070e-2 8.231981480783578e-2 8.271303278717602e-2 + 8.274330348203168e-2 1.169861245219266e-1 1.195137668058927e-1 1.276535781165950e-1 1.733512071123601e-1 + 1.753483539872438e-1 2.349865519507000e-1 2.704816569083836e-1 2.906946158817209e-1 2.907689791730085e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 8.989569907959682e-6 8.989569907959682e-6 3.471947508611008e-1 + 3294 + + -2.177532646040730e-1 -1.718789953406297e-1 -1.006691798603407e-1 -1.006071634060000e-1 -7.502053184393222e-2 + -7.493813983500379e-2 9.471850538897892e-3 7.809768728522838e-2 7.812721219869635e-2 7.919117247809902e-2 + 7.922156459155046e-2 1.114760240160040e-1 1.209693000891922e-1 1.240889958266807e-1 1.650002776548988e-1 + 1.675883330911687e-1 2.369892895651847e-1 2.696968780742890e-1 2.955329509634202e-1 3.089570303568441e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.027379418052535e-5 1.027379418052535e-5 3.967940009841151e-1 + 3285 + + -2.127025801077359e-1 -1.803868792067958e-1 -1.002174819644354e-1 -1.001572413628761e-1 -7.451777933586612e-2 + -7.443553057623825e-2 2.455836513997590e-2 7.495175952510660e-2 7.497419904855304e-2 7.650250727494868e-2 + 7.653263174326385e-2 9.573201442167932e-2 1.251168789180418e-1 1.292867487250118e-1 1.570165096120228e-1 + 1.606590762742946e-1 2.392922142417516e-1 2.663840151768264e-1 3.035348309733974e-1 3.283772645996939e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.155801845309102e-5 1.155801845309102e-5 4.463932511071295e-1 + 3290 + + -2.076521567165375e-1 -1.875150289132363e-1 -9.992428097411212e-2 -9.986525287570009e-2 -7.419073572022219e-2 + -7.410858520981045e-2 3.847055105513746e-2 7.300356672397225e-2 7.301969201896840e-2 7.482007321916875e-2 + 7.484984102318315e-2 8.142232183613418e-2 1.287495856555439e-1 1.349669534179876e-1 1.496333956637528e-1 + 1.553245953698204e-1 2.413631544718802e-1 2.632277462108901e-1 3.127755277990951e-1 3.320786321979358e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.284224272565669e-5 1.284224272565669e-5 4.959925012301439e-1 + 3282 + + -2.048605310530762e-1 -1.909997586970178e-1 -9.982231400566006e-2 -9.976371711419935e-2 -7.407713859361537e-2 + -7.399502473217245e-2 4.601932147976274e-2 7.234483438735129e-2 7.235805848296586e-2 7.373912369106530e-2 + 7.424995766763670e-2 7.428048238095725e-2 1.303622299087112e-1 1.393336258448811e-1 1.446945955879623e-1 + 1.531404668231060e-1 2.422634793190984e-1 2.619105855472961e-1 3.196140304385565e-1 3.264332898187799e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + + 0 + + + 1.922289400000000e1 + 1.929700088500977e1 + + + 1.802030900000000e1 + 1.806570601463318e1 + + + + diff --git a/vitalypro/cell_param/si2ge2_3.xml b/vitalypro/cell_param/si2ge2_3.xml new file mode 100644 index 00000000..7908fd5d --- /dev/null +++ b/vitalypro/cell_param/si2ge2_3.xml @@ -0,0 +1,474 @@ + + + + + QEXSD_19.03 + XML file generated by PWSCF + This run was terminated on: 18:29: 0 26 Oct 2021 + + + + 1 + 1 + 1 + 1 + 1 + 1 + + + + + bands + from_scratch + Si_cubic + ../../pseudo + ./ + false + false + true + low + 10000000 + 1 + 5.000000000000000e-5 + 5.000000000000000e-4 + 5.000000000000000e-1 + high + 100000 + + + + Si.pbe-rrkj.UPF + + + 7.264000000000000e1 + Ge.pbe-kjpaw.UPF + + + + + -1.179300733043311e-1 -1.179300733043311e-1 -4.426832187731278e-2 + 2.546666457141644e0 2.546666457141644e0 2.462997566491623e0 + 5.212952663532625e0 -1.150077667973663e-1 5.110870334356099e0 + -1.150077667973663e-1 5.212952663532625e0 5.110870334356099e0 + 5.214279706701909e0 5.214279706701909e0 -3.951375202971117e-2 + 7.877300366179780e0 2.549586688729315e0 7.888231670298891e0 + 2.549586688729315e0 7.877300366179780e0 7.888231670298891e0 + 7.879030215812644e0 7.879030215812644e0 2.466929816343321e0 + + + 1.066056828600000e1 -2.734100000000000e-4 -2.698399999999999e-4 + -2.734100000000000e-4 1.066056828600000e1 -2.698399999999999e-4 + -2.734100000000000e-4 -2.734100000000000e-4 1.057623402600000e1 + + + + pbe + + + false + false + false + + + gaussian + 0.000000000000000e0 + smearing + + + false + 1.500000000000000e1 + 6.000000000000000e1 + + + davidson + plain + 7.000000000000000e-1 + 5.000000000000000e-9 + 8 + 100 + false + false + false + false + 0.000000000000000e0 + false + 20 + 20 + + + 11 + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 1.275723100436894e-6 1.275723100436894e-6 5.039869711970894e-2 + 2.551446200873789e-6 2.551446200873789e-6 1.007973942394179e-1 + 3.827169301310684e-6 3.827169301310684e-6 1.511960913591268e-1 + 5.102892401747577e-6 5.102892401747577e-6 2.015947884788358e-1 + 6.378615502184472e-6 6.378615502184472e-6 2.519934855985447e-1 + 7.654338602621368e-6 7.654338602621368e-6 3.023921827182537e-1 + 8.930061703058261e-6 8.930061703058261e-6 3.527908798379626e-1 + 1.020578480349515e-5 1.020578480349515e-5 4.031895769576716e-1 + 1.148150790393205e-5 1.148150790393205e-5 4.535882740773805e-1 + 1.275723100436894e-5 1.275723100436894e-5 5.039869711970894e-1 + + + none + 1.000000000000000e2 + false + false + + + none + 0.000000000000000e0 + 3.672227080435770e5 + 0.000000000000000e0 + false + false + false + + + false + false + false + false + false + false + + + + + + false + 1 + 0.000000000000000e0 + + + + false + false + true + true + + + + 2.808550000000000e1 + Si.pbe-rrkj.UPF + + + 7.264000000000000e1 + Ge.pbe-kjpaw.UPF + + + + + -1.179300733043311e-1 -1.179300733043311e-1 -4.426832187731278e-2 + 2.546666457141644e0 2.546666457141644e0 2.462997566491623e0 + 5.212952663532625e0 -1.150077667973663e-1 5.110870334356099e0 + -1.150077667973663e-1 5.212952663532625e0 5.110870334356099e0 + 5.214279706701909e0 5.214279706701909e0 -3.951375202971117e-2 + 7.877300366179780e0 2.549586688729315e0 7.888231670298891e0 + 2.549586688729315e0 7.877300366179780e0 7.888231670298891e0 + 7.879030215812644e0 7.879030215812644e0 2.466929816343321e0 + + + 1.066056828600000e1 -2.734100000000000e-4 -2.698399999999999e-4 + -2.734100000000000e-4 1.066056828600000e1 -2.698399999999999e-4 + -2.734100000000000e-4 -2.734100000000000e-4 1.057623402600000e1 + + + + 2 + 4 + 0 + + crystal_symmetry + + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 1.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 1.000000000000000e0 + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + 1 2 3 4 5 6 7 8 + + + + crystal_symmetry + + 0.000000000000000e0 1.000000000000000e0 0.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 1.000000000000000e0 + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + 1 2 4 3 5 7 6 8 + + + + lattice_symmetry + + -1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 -1.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 -1.000000000000000e0 + + + + lattice_symmetry + + 0.000000000000000e0 -1.000000000000000e0 0.000000000000000e0 + -1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 -1.000000000000000e0 + + + + + false + 1.500000000000000e1 + 6.000000000000000e1 + + + + 26737 + 26737 + 3362 + + 1.000000001961264e0 2.564750481494990e-5 2.585201992962412e-5 + 2.564750481494990e-5 1.000000001961264e0 2.585201992962412e-5 + 2.551446200874063e-5 2.551446200874063e-5 1.007973942394287e0 + + + + PBE + + + false + false + false + 0.000000000000000e0 + 0.000000000000000e0 + false + + + 0.000000000000000e0 + 0.000000000000000e0 + 2.329478910724486e0 + -1.288505146816536e1 + -3.704771912388927e1 + 0.000000000000000e0 + -1.901210228201247e-70 + + + false + false + false + 20 + 3.200000000000000e1 + 32 + true + 2.097970187526756e-1 + + 11 + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 1.275723100437031e-6 1.275723100437031e-6 5.039869711971434e-2 + 2.551446200874063e-6 2.551446200874063e-6 1.007973942394287e-1 + 3.827169301311093e-6 3.827169301311093e-6 1.511960913591430e-1 + 5.102892401748125e-6 5.102892401748125e-6 2.015947884788574e-1 + 6.378615502185156e-6 6.378615502185156e-6 2.519934855985717e-1 + 7.654338602622185e-6 7.654338602622185e-6 3.023921827182861e-1 + 8.930061703059218e-6 8.930061703059218e-6 3.527908798380004e-1 + 1.020578480349625e-5 1.020578480349625e-5 4.031895769577147e-1 + 1.148150790393328e-5 1.148150790393328e-5 4.535882740774291e-1 + 1.275723100437031e-5 1.275723100437031e-5 5.039869711971434e-1 + + 11 + smearing + gaussian + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 3335 + + -2.367986473280816e-1 -1.077761801938808e-1 -1.076844763204535e-1 -9.506553025867188e-2 -9.231224576618430e-2 + -8.249311792227619e-2 -8.243452069393451e-2 9.903141233046908e-2 1.003232341650422e-1 1.003290989103366e-1 + 1.006161042159648e-1 1.057205409920674e-1 1.057390307098922e-1 2.046443056406355e-1 2.056437580148942e-1 + 2.067425736720580e-1 2.246391876834594e-1 2.246664223747588e-1 2.290703136368283e-1 2.377256895498293e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.275723100437031e-6 1.275723100437031e-6 5.039869711971434e-2 + 3355 + + -2.364294675171112e-1 -1.076843241248575e-1 -1.075924640287125e-1 -1.067835576689542e-1 -8.239242343273991e-2 + -8.233343568930529e-2 -8.013461232149101e-2 9.937874013390079e-2 9.943470419791664e-2 9.944245883302703e-2 + 1.009804145593882e-1 1.044597302340057e-1 1.044787084639935e-1 1.994815219575566e-1 2.039317086703659e-1 + 2.050378703835880e-1 2.269597029528834e-1 2.269865020821471e-1 2.279316263471753e-1 2.395379676212314e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 2.551446200874063e-6 2.551446200874063e-6 1.007973942394287e-1 + 3343 + + -2.353229783608665e-1 -1.192726684458729e-1 -1.074138026094098e-1 -1.073214887080988e-1 -8.209535007465693e-2 + -8.203562758335924e-2 -6.626923478855823e-2 9.693730558259761e-2 9.694905515264068e-2 1.004190309708176e-1 + 1.009974586830899e-1 1.010178960374903e-1 1.020736129608660e-1 1.874484174878915e-1 1.992446817069524e-1 + 2.003812967281589e-1 2.264245528032344e-1 2.336256252629355e-1 2.336512821059430e-1 2.435612976571976e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 3.827169301311093e-6 3.827169301311093e-6 1.511960913591430e-1 + 3339 + + -2.334834707366926e-1 -1.312499483154482e-1 -1.069882353851584e-1 -1.068951973232911e-1 -8.162757452749593e-2 + -8.156657699339256e-2 -5.200719795474945e-2 9.325537726262167e-2 9.327165754387048e-2 9.607524837763732e-2 + 9.609757326072568e-2 1.021412050255294e-1 1.038902296916301e-1 1.726911615705071e-1 1.925066493085806e-1 + 1.937188353797233e-1 2.255754048095644e-1 2.439040038427993e-1 2.439281641702426e-1 2.488423230021478e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 5.102892401748125e-6 5.102892401748125e-6 2.015947884788574e-1 + 3319 + + -2.309189350636769e-1 -1.426609728514386e-1 -1.064440968519786e-1 -1.063501181413061e-1 -8.102798639256585e-2 + -8.096533876754254e-2 -3.741729314668680e-2 8.891640225093072e-2 8.893724228630996e-2 9.049436616519042e-2 + 9.051891580133709e-2 1.045259229717685e-1 1.064236153485260e-1 1.569301954365853e-1 1.846050131033196e-1 + 1.859570900119777e-1 2.255004754351968e-1 2.548923222937765e-1 2.570191816919676e-1 2.570418168539796e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 6.378615502185156e-6 6.378615502185156e-6 2.519934855985717e-1 + 3342 + + -2.276437173415002e-1 -1.534640611648467e-1 -1.058311334973120e-1 -1.057360734811222e-1 -8.035090380932264e-2 + -8.028637150978547e-2 -2.256175231473310e-2 8.442199274433953e-2 8.444715428592605e-2 8.490921356545725e-2 + 8.493603624077997e-2 1.075389522501172e-1 1.096644887974434e-1 1.408131370052954e-1 1.761818767782423e-1 + 1.777570265799569e-1 2.261938801837576e-1 2.608394531164016e-1 2.723214102359843e-1 2.723426600583508e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 7.654338602622185e-6 7.654338602622185e-6 3.023921827182861e-1 + 3334 + + -2.236831525394527e-1 -1.636109574416009e-1 -1.052065910822382e-1 -1.051104079433304e-1 -7.965851355092889e-2 + -7.959203185400777e-2 -7.518898914142160e-3 7.980454634073087e-2 7.983350539060561e-2 8.019915073015698e-2 + 8.022820170610576e-2 1.111179862540935e-1 1.135999684203959e-1 1.246474915571334e-1 1.676541080483632e-1 + 1.695874852441494e-1 2.276102131169150e-1 2.642654211794666e-1 2.846517922889920e-1 2.893660642726431e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 8.930061703059218e-6 8.930061703059218e-6 3.527908798380004e-1 + 3346 + + -2.190914502823090e-1 -1.730314561063130e-1 -1.046331760311106e-1 -1.045359392345892e-1 -7.902067281373211e-2 + -7.895237337676010e-2 7.579766510113992e-3 7.552305646872597e-2 7.555386797634255e-2 7.658096661002523e-2 + 7.661330262264494e-2 1.086434999432395e-1 1.151404359093958e-1 1.182040490267790e-1 1.592942783179246e-1 + 1.618104619743840e-1 2.296206802926633e-1 2.628691386847067e-1 2.895748628034168e-1 3.078091100968315e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.020578480349625e-5 1.020578480349625e-5 4.031895769577147e-1 + 3346 + + -2.140064344313975e-1 -1.815747763606733e-1 -1.041704895896685e-1 -1.040723867110657e-1 -7.850478537238036e-2 + -7.843500002366151e-2 2.244751280509848e-2 7.230541015890688e-2 7.233765893484301e-2 7.381936382837910e-2 + 7.385421937691085e-2 9.312193277482274e-2 1.193370066411118e-1 1.234354833354786e-1 1.512913902621840e-1 + 1.548453292131194e-1 2.319707453867732e-1 2.591686094302460e-1 2.980091120545214e-1 3.273966459730372e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.148150790393328e-5 1.148150790393328e-5 4.535882740774291e-1 + 3362 + + -2.089172750821011e-1 -1.887425030518432e-1 -1.038706958244445e-1 -1.037720237386111e-1 -7.816952035805958e-2 + -7.809875903380701e-2 3.608429448844324e-2 7.031239114580884e-2 7.034555232740197e-2 7.209111761178497e-2 + 7.212764237197009e-2 7.909210370950217e-2 1.230247767176584e-1 1.291508811906336e-1 1.438812953049234e-1 + 1.494649650617445e-1 2.341144753052558e-1 2.557895366083605e-1 3.074320806141485e-1 3.264004657149547e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.275723100437031e-5 1.275723100437031e-5 5.039869711971434e-1 + 3362 + + -2.060974579590212e-1 -1.922556245869665e-1 -1.037666684881354e-1 -1.036677993432719e-1 -7.805289736551564e-2 + -7.798179455161423e-2 4.339054305607027e-2 6.963790396415982e-2 6.967137807662928e-2 7.149652358030524e-2 + 7.154079207357954e-2 7.166346145953979e-2 1.246686455545688e-1 1.335462923640341e-1 1.389155797854031e-1 + 1.472528349970398e-1 2.350586224700414e-1 2.543834654154531e-1 3.142364521249157e-1 3.210653178792273e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + + 0 + + + 1.832985300000000e1 + 1.838387989997864e1 + + + 1.711017500000000e1 + 1.713861680030823e1 + + + + diff --git a/vitalypro/cell_param/si2ge2_4.xml b/vitalypro/cell_param/si2ge2_4.xml new file mode 100644 index 00000000..1948cd9e --- /dev/null +++ b/vitalypro/cell_param/si2ge2_4.xml @@ -0,0 +1,474 @@ + + + + + QEXSD_19.03 + XML file generated by PWSCF + This run was terminated on: 18:30:44 26 Oct 2021 + + + + 1 + 1 + 1 + 1 + 1 + 1 + + + + + bands + from_scratch + Si_cubic + ../../pseudo + ./ + false + false + true + low + 10000000 + 1 + 5.000000000000000e-5 + 5.000000000000000e-4 + 5.000000000000000e-1 + high + 100000 + + + + Si.pbe-rrkj.UPF + + + 7.264000000000000e1 + Ge.pbe-kjpaw.UPF + + + + + -1.560260658617494e-1 -1.560260658617494e-1 -4.374094844650385e-2 + 2.534046040215914e0 2.534046040215914e0 2.445373542159869e0 + 5.225299865743789e0 -1.518648473431602e-1 5.074713295297327e0 + -1.518648473431602e-1 5.225299865743789e0 5.074713295297327e0 + 5.226368347134941e0 5.226368347134941e0 -3.812297595686972e-2 + 7.914746444125576e0 2.537383294676864e0 7.834752904508117e0 + 2.537383294676864e0 7.914746444125576e0 7.834752904508117e0 + 7.916925181193773e0 7.916925181193773e0 2.449578897122018e0 + + + 1.076056828600000e1 -2.734100000000000e-4 -2.660640000000000e-4 + -2.734100000000000e-4 1.076056828600000e1 -2.660640000000000e-4 + -2.734100000000000e-4 -2.734100000000000e-4 1.050342487000000e1 + + + + pbe + + + false + false + false + + + gaussian + 0.000000000000000e0 + smearing + + + false + 1.500000000000000e1 + 6.000000000000000e1 + + + davidson + plain + 7.000000000000000e-1 + 5.000000000000000e-9 + 8 + 100 + false + false + false + false + 0.000000000000000e0 + false + 20 + 20 + + + 11 + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 1.266590489598078e-6 1.266590489598078e-6 5.122409328286625e-2 + 2.533180979196156e-6 2.533180979196156e-6 1.024481865657325e-1 + 3.799771468794233e-6 3.799771468794233e-6 1.536722798485988e-1 + 5.066361958392312e-6 5.066361958392312e-6 2.048963731314650e-1 + 6.332952447990390e-6 6.332952447990390e-6 2.561204664143312e-1 + 7.599542937588466e-6 7.599542937588466e-6 3.073445596971975e-1 + 8.866133427186542e-6 8.866133427186542e-6 3.585686529800638e-1 + 1.013272391678462e-5 1.013272391678462e-5 4.097927462629300e-1 + 1.139931440638270e-5 1.139931440638270e-5 4.610168395457962e-1 + 1.266590489598078e-5 1.266590489598078e-5 5.122409328286625e-1 + + + none + 1.000000000000000e2 + false + false + + + none + 0.000000000000000e0 + 3.672227080435770e5 + 0.000000000000000e0 + false + false + false + + + false + false + false + false + false + false + + + + + + false + 1 + 0.000000000000000e0 + + + + false + false + true + true + + + + 2.808550000000000e1 + Si.pbe-rrkj.UPF + + + 7.264000000000000e1 + Ge.pbe-kjpaw.UPF + + + + + -1.560260658617494e-1 -1.560260658617494e-1 -4.374094844650385e-2 + 2.534046040215914e0 2.534046040215914e0 2.445373542159869e0 + 5.225299865743789e0 -1.518648473431602e-1 5.074713295297327e0 + -1.518648473431602e-1 5.225299865743789e0 5.074713295297327e0 + 5.226368347134941e0 5.226368347134941e0 -3.812297595686972e-2 + 7.914746444125576e0 2.537383294676864e0 7.834752904508117e0 + 2.537383294676864e0 7.914746444125576e0 7.834752904508117e0 + 7.916925181193773e0 7.916925181193773e0 2.449578897122018e0 + + + 1.076056828600000e1 -2.734100000000000e-4 -2.660640000000000e-4 + -2.734100000000000e-4 1.076056828600000e1 -2.660640000000000e-4 + -2.734100000000000e-4 -2.734100000000000e-4 1.050342487000000e1 + + + + 2 + 4 + 0 + + crystal_symmetry + + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 1.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 1.000000000000000e0 + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + 1 2 3 4 5 6 7 8 + + + + crystal_symmetry + + 0.000000000000000e0 1.000000000000000e0 0.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 1.000000000000000e0 + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + 1 2 4 3 5 7 6 8 + + + + lattice_symmetry + + -1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 -1.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 -1.000000000000000e0 + + + + lattice_symmetry + + 0.000000000000000e0 -1.000000000000000e0 0.000000000000000e0 + -1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 -1.000000000000000e0 + + + + + false + 1.500000000000000e1 + 6.000000000000000e1 + + + + 27009 + 27009 + 3428 + + 1.000000001917472e0 2.540915305096845e-5 2.603121848586057e-5 + 2.540915305096845e-5 1.000000001917472e0 2.603121848586057e-5 + 2.533180979196814e-5 2.533180979196814e-5 1.024481865657591e0 + + + + PBE + + + false + false + false + 0.000000000000000e0 + 0.000000000000000e0 + false + + + 0.000000000000000e0 + 0.000000000000000e0 + 2.348805869411177e0 + -1.285325547642020e1 + -3.702334362938325e1 + 0.000000000000000e0 + -3.903900025463921e-90 + + + false + false + false + 20 + 3.200000000000000e1 + 32 + true + 2.079751307152457e-1 + + 11 + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 1.266590489598407e-6 1.266590489598407e-6 5.122409328287956e-2 + 2.533180979196814e-6 2.533180979196814e-6 1.024481865657591e-1 + 3.799771468795221e-6 3.799771468795221e-6 1.536722798486387e-1 + 5.066361958393627e-6 5.066361958393627e-6 2.048963731315182e-1 + 6.332952447992034e-6 6.332952447992034e-6 2.561204664143978e-1 + 7.599542937590442e-6 7.599542937590442e-6 3.073445596972774e-1 + 8.866133427188847e-6 8.866133427188847e-6 3.585686529801570e-1 + 1.013272391678725e-5 1.013272391678725e-5 4.097927462630365e-1 + 1.139931440638566e-5 1.139931440638566e-5 4.610168395459160e-1 + 1.266590489598407e-5 1.266590489598407e-5 5.122409328287956e-1 + + 11 + smearing + gaussian + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 3367 + + -2.381481259439597e-1 -1.115860412003840e-1 -1.114688053608287e-1 -9.608484951935615e-2 -9.328397628042650e-2 + -8.640359563591536e-2 -8.636336133407001e-2 9.331487560754397e-2 9.484181728830537e-2 9.861635104571871e-2 + 9.864640018028837e-2 1.041427376920228e-1 1.041665363626857e-1 1.999050809126587e-1 2.010702366031041e-1 + 2.026586139836778e-1 2.225579654246689e-1 2.225595328859189e-1 2.225930073330868e-1 2.314004830378831e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.266590489598407e-6 1.266590489598407e-6 5.122409328287956e-2 + 3351 + + -2.377759409527282e-1 -1.114909813656233e-1 -1.113737467105988e-1 -1.077485108856249e-1 -8.629953620964294e-2 + -8.625946277350756e-2 -8.117832099132183e-2 9.366645561099347e-2 9.521063800084740e-2 9.769589650485287e-2 + 9.772689804599793e-2 1.028392710765074e-1 1.028645621319983e-1 1.970963298242284e-1 1.982390939645908e-1 + 1.994102755145138e-1 2.212612007003497e-1 2.249301970528302e-1 2.249668005224393e-1 2.331746680502824e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 2.533180979196814e-6 2.533180979196814e-6 1.024481865657591e-1 + 3343 + + -2.366611189603925e-1 -1.202201824152866e-1 -1.112116235357896e-1 -1.110943975677000e-1 -8.599285888854286e-2 + -8.595337562020537e-2 -6.738694451080198e-2 9.471591244722548e-2 9.511129797666493e-2 9.514442391723319e-2 + 9.631147591090038e-2 9.926516303704588e-2 9.929311607635107e-2 1.845483117895577e-1 1.936225861930219e-1 + 1.948193518007533e-1 2.195679314015258e-1 2.317289712513948e-1 2.317723068743263e-1 2.373014100216639e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 3.799771468795221e-6 3.799771468795221e-6 1.536722798486387e-1 + 3355 + + -2.348078782693361e-1 -1.321949145299133e-1 -1.107732004212829e-1 -1.106559867143471e-1 -8.551033433669584e-2 + -8.547181008257814e-2 -5.322050226899083e-2 9.130640974994362e-2 9.134178433781164e-2 9.419543738441039e-2 + 9.422516939360037e-2 9.645385627912674e-2 9.814092259130957e-2 1.695471431425284e-1 1.869574230561242e-1 + 1.882212113868599e-1 2.185772378703380e-1 2.421820322776815e-1 2.422321988217883e-1 2.427994493288582e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 5.066361958393627e-6 5.066361958393627e-6 2.048963731315182e-1 + 3342 + + -2.322236832729158e-1 -1.436154470190607e-1 -1.102124063214495e-1 -1.100952137702693e-1 -8.489184635534675e-2 + -8.485463261021129e-2 -3.874798538350216e-2 8.683015755144384e-2 8.686698188712359e-2 8.846099485947702e-2 + 8.849034759582434e-2 9.886104488137857e-2 1.006954441219217e-1 1.537377885970461e-1 1.791196308679650e-1 + 1.805133238607180e-1 2.184045314367882e-1 2.490943772555315e-1 2.554860556425242e-1 2.555418275315402e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 6.332952447992034e-6 6.332952447992034e-6 2.561204664143978e-1 + 3370 + + -2.289237540288471e-1 -1.544382134095186e-1 -1.095801451067146e-1 -1.094629876404322e-1 -8.419262879835378e-2 + -8.415702395376009e-2 -2.403533719787229e-2 8.220202553686406e-2 8.223940167660539e-2 8.273443248501597e-2 + 8.276164501821169e-2 1.019019286804900e-1 1.039608899040300e-1 1.376800963017948e-1 1.707270881186876e-1 + 1.723373946646649e-1 2.190327195104845e-1 2.551587182624178e-1 2.709905371155829e-1 2.710505856305887e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 7.599542937590442e-6 7.599542937590442e-6 3.073445596972774e-1 + 3382 + + -2.249333610948700e-1 -1.646137328388880e-1 -1.089360154612505e-1 -1.088188990456727e-1 -8.347789345932345e-2 + -8.344409754725021e-2 -9.162657772828942e-3 7.750795470819584e-2 7.753156625243021e-2 7.785849980138451e-2 + 7.789567664226404e-2 1.055150053454721e-1 1.079243286529199e-1 1.216450796515087e-1 1.622122439184806e-1 + 1.641696972354759e-1 2.204177912686702e-1 2.582190347651863e-1 2.784394698577819e-1 2.882197944890274e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 8.866133427188847e-6 8.866133427188847e-6 3.585686529801570e-1 + 3428 + + -2.203063565648425e-1 -1.740697696394675e-1 -1.083452630242659e-1 -1.082281938488177e-1 -8.281969478248030e-2 + -8.278774250762220e-2 5.739331496408479e-3 7.312809753023273e-2 7.314697497009109e-2 7.413858876406612e-2 + 7.417509538580990e-2 1.058205898385510e-1 1.095782702980034e-1 1.125610242150883e-1 1.538448010505495e-1 + 1.563747065755039e-1 2.224342505446474e-1 2.561958961803747e-1 2.840917657059147e-1 3.068321485774699e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.013272391678725e-5 1.013272391678725e-5 4.097927462630365e-1 + 3418 + + -2.151792191315744e-1 -1.826560528151303e-1 -1.078674110360100e-1 -1.077506004349688e-1 -8.228590949839411e-2 + -8.225552200142381e-2 2.037516707813063e-2 6.984032851071822e-2 6.985375268537462e-2 7.130415459515747e-2 + 7.133994591787074e-2 9.052541139790021e-2 1.138195361609816e-1 1.178266089053402e-1 1.458247157495848e-1 + 1.493777679991330e-1 2.248261875122872e-1 2.521369635780646e-1 2.929229092806949e-1 3.250593075831030e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.139931440638566e-5 1.139931440638566e-5 4.610168395459160e-1 + 3418 + + -2.100377864017308e-1 -1.898769495987056e-1 -1.075571176583719e-1 -1.074401211307078e-1 -8.193818299059375e-2 + -8.190901794291172e-2 3.372332337230520e-2 6.780586415780951e-2 6.781335229156848e-2 6.953118432427336e-2 + 6.956634033800910e-2 7.678389823323234e-2 1.175547846583486e-1 1.235737795067999e-1 1.383911025084658e-1 + 1.439571890486547e-1 2.270394241573144e-1 2.485477585803934e-1 3.024987938496736e-1 3.210789494508171e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.266590489598407e-5 1.266590489598407e-5 5.122409328287956e-1 + 3402 + + -2.071748640792528e-1 -1.934336791403292e-1 -1.074489011671514e-1 -1.073319154906091e-1 -8.181643011266058e-2 + -8.178768061960005e-2 4.078019957586494e-2 6.711831059591409e-2 6.712188688282572e-2 6.892671523289212e-2 + 6.896353892758464e-2 6.959835912680385e-2 1.192243988958350e-1 1.279822205947322e-1 1.334153177841487e-1 + 1.417206817293754e-1 2.280256660698821e-1 2.470598095674909e-1 3.092300222935751e-1 3.160953996103452e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + + 0 + + + 2.435240400000000e1 + 2.442502093315125e1 + + + 2.227762300000000e1 + 2.232217407226563e1 + + + + diff --git a/vitalypro/cell_param/si2ge2_5.xml b/vitalypro/cell_param/si2ge2_5.xml new file mode 100644 index 00000000..ad566ff9 --- /dev/null +++ b/vitalypro/cell_param/si2ge2_5.xml @@ -0,0 +1,474 @@ + + + + + QEXSD_19.03 + XML file generated by PWSCF + This run was terminated on: 18:32:47 26 Oct 2021 + + + + 1 + 1 + 1 + 1 + 1 + 1 + + + + + bands + from_scratch + Si_cubic + ../../pseudo + ./ + false + false + true + low + 10000000 + 1 + 5.000000000000000e-5 + 5.000000000000000e-4 + 5.000000000000000e-1 + high + 100000 + + + + Si.pbe-rrkj.UPF + + + 7.264000000000000e1 + Ge.pbe-kjpaw.UPF + + + + + -1.979232236382058e-1 -1.979232236382058e-1 -4.308317446389514e-2 + 2.519955510845105e0 2.519955510845105e0 2.425692894862625e0 + 5.238968502417075e0 -1.929164263744695e-1 5.035420503275157e0 + -1.929164263744695e-1 5.238968502417075e0 5.035420503275157e0 + 5.239959161106622e0 5.239959161106622e0 -3.652913180351451e-2 + 7.956189430792432e0 2.524185165795596e0 7.776967220424183e0 + 2.524185165795596e0 7.956189430792432e0 7.776967220424183e0 + 7.958460138941791e0 7.958460138941791e0 2.430562998786539e0 + + + 1.087056828600000e1 -2.734100000000000e-4 -2.619210000000000e-4 + -2.734100000000000e-4 1.087056828600000e1 -2.619210000000000e-4 + -2.734100000000000e-4 -2.734100000000000e-4 1.042434959100000e1 + + + + pbe + + + false + false + false + + + gaussian + 0.000000000000000e0 + smearing + + + false + 1.500000000000000e1 + 6.000000000000000e1 + + + davidson + plain + 7.000000000000000e-1 + 5.000000000000000e-9 + 8 + 100 + false + false + false + false + 0.000000000000000e0 + false + 20 + 20 + + + 11 + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 1.256325807420914e-6 1.256325807420914e-6 5.214027125352347e-2 + 2.512651614841828e-6 2.512651614841828e-6 1.042805425070469e-1 + 3.768977422262743e-6 3.768977422262743e-6 1.564208137605704e-1 + 5.025303229683655e-6 5.025303229683655e-6 2.085610850140939e-1 + 6.281629037104569e-6 6.281629037104569e-6 2.607013562676173e-1 + 7.537954844525485e-6 7.537954844525485e-6 3.128416275211409e-1 + 8.794280651946398e-6 8.794280651946398e-6 3.649818987746643e-1 + 1.005060645936731e-5 1.005060645936731e-5 4.171221700281878e-1 + 1.130693226678823e-5 1.130693226678823e-5 4.692624412817113e-1 + 1.256325807420914e-5 1.256325807420914e-5 5.214027125352347e-1 + + + none + 1.000000000000000e2 + false + false + + + none + 0.000000000000000e0 + 3.672227080435770e5 + 0.000000000000000e0 + false + false + false + + + false + false + false + false + false + false + + + + + + false + 1 + 0.000000000000000e0 + + + + false + false + true + true + + + + 2.808550000000000e1 + Si.pbe-rrkj.UPF + + + 7.264000000000000e1 + Ge.pbe-kjpaw.UPF + + + + + -1.979232236382058e-1 -1.979232236382058e-1 -4.308317446389514e-2 + 2.519955510845105e0 2.519955510845105e0 2.425692894862625e0 + 5.238968502417075e0 -1.929164263744695e-1 5.035420503275157e0 + -1.929164263744695e-1 5.238968502417075e0 5.035420503275157e0 + 5.239959161106622e0 5.239959161106622e0 -3.652913180351451e-2 + 7.956189430792432e0 2.524185165795596e0 7.776967220424183e0 + 2.524185165795596e0 7.956189430792432e0 7.776967220424183e0 + 7.958460138941791e0 7.958460138941791e0 2.430562998786539e0 + + + 1.087056828600000e1 -2.734100000000000e-4 -2.619210000000000e-4 + -2.734100000000000e-4 1.087056828600000e1 -2.619210000000000e-4 + -2.734100000000000e-4 -2.734100000000000e-4 1.042434959100000e1 + + + + 2 + 4 + 0 + + crystal_symmetry + + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 1.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 1.000000000000000e0 + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + 1 2 3 4 5 6 7 8 + + + + crystal_symmetry + + 0.000000000000000e0 1.000000000000000e0 0.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 1.000000000000000e0 + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + 1 2 4 3 5 7 6 8 + + + + lattice_symmetry + + -1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 -1.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 -1.000000000000000e0 + + + + lattice_symmetry + + 0.000000000000000e0 -1.000000000000000e0 0.000000000000000e0 + -1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 -1.000000000000000e0 + + + + + false + 1.500000000000000e1 + 6.000000000000000e1 + + + + 27337 + 27337 + 3466 + + 1.000000001870800e0 2.515203098483858e-5 2.622867498269100e-5 + 2.515203098483858e-5 1.000000001870800e0 2.622867498269100e-5 + 2.512651614842695e-5 2.512651614842695e-5 1.042805425070829e0 + + + + PBE + + + false + false + false + 0.000000000000000e0 + 0.000000000000000e0 + false + + + 0.000000000000000e0 + 0.000000000000000e0 + 2.367669476956909e0 + -1.281816744178155e1 + -3.699647162258770e1 + 0.000000000000000e0 + -3.903900025463921e-90 + + + false + false + false + 20 + 3.200000000000000e1 + 32 + true + 2.058027199080325e-1 + + 11 + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 1.256325807421348e-6 1.256325807421348e-6 5.214027125354146e-2 + 2.512651614842695e-6 2.512651614842695e-6 1.042805425070829e-1 + 3.768977422264042e-6 3.768977422264042e-6 1.564208137606244e-1 + 5.025303229685391e-6 5.025303229685391e-6 2.085610850141658e-1 + 6.281629037106738e-6 6.281629037106738e-6 2.607013562677073e-1 + 7.537954844528084e-6 7.537954844528084e-6 3.128416275212488e-1 + 8.794280651949432e-6 8.794280651949432e-6 3.649818987747903e-1 + 1.005060645937078e-5 1.005060645937078e-5 4.171221700283317e-1 + 1.130693226679212e-5 1.130693226679212e-5 4.692624412818732e-1 + 1.256325807421347e-5 1.256325807421347e-5 5.214027125354146e-1 + + 11 + smearing + gaussian + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 3423 + + -2.395598763338620e-1 -1.155669543573564e-1 -1.154924572214776e-1 -9.721194816729881e-2 -9.436613507919386e-2 + -9.057388117471390e-2 -9.048763000233285e-2 8.728790997474206e-2 8.876151969986521e-2 9.687087379289924e-2 + 9.691979479953574e-2 1.025522184594578e-1 1.025576457103074e-1 1.938394906362968e-1 1.950719655350952e-1 + 2.002975105748776e-1 2.156156778492821e-1 2.203314260727441e-1 2.203940671337137e-1 2.248269118915438e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.256325807421348e-6 1.256325807421348e-6 5.214027125354146e-2 + 3395 + + -2.391845139283090e-1 -1.154687072122075e-1 -1.153942563984997e-1 -1.088058718360499e-1 -9.046641386770069e-2 + -9.038035464670630e-2 -8.235095640549975e-2 8.764328071176747e-2 8.913370947741427e-2 9.591409574045656e-2 + 9.596316312359694e-2 1.011964924394591e-1 1.012099614617073e-1 1.922145160514690e-1 1.934476249376864e-1 + 1.942266420727309e-1 2.141312096571894e-1 2.227600415998710e-1 2.228241328887050e-1 2.264281124396048e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 2.512651614842695e-6 2.512651614842695e-6 1.042805425070829e-1 + 3398 + + -2.380604211541292e-1 -1.212462895007941e-1 -1.151809165341621e-1 -1.151064509158584e-1 -9.015058285754808e-2 + -9.006497787962097e-2 -6.865589388279480e-2 8.870337577587367e-2 9.024443102192945e-2 9.322943157186396e-2 + 9.327856668641743e-2 9.749025462282690e-2 9.751293803735352e-2 1.810908016435792e-1 1.876845966089082e-1 + 1.889383508483505e-1 2.122416870395236e-1 2.297014676298732e-1 2.297675608048361e-1 2.306797156016017e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 8.780835722023596e-291 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 3.768977422264042e-6 3.768977422264042e-6 1.564208137606244e-1 + 3394 + + -2.361919523868524e-1 -1.332080512779842e-1 -1.147267547526692e-1 -1.146526678994205e-1 -8.965127209428591e-2 + -8.956693649001668e-2 -5.461121106023529e-2 8.928656590766975e-2 8.933482206880964e-2 9.045845919612045e-2 + 9.208698876682789e-2 9.225430365774207e-2 9.228282784217628e-2 1.658440699352130e-1 1.811086779756900e-1 + 1.824208347313881e-1 2.110978634512700e-1 2.364424780845032e-1 2.403571530285486e-1 2.404285847970244e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.959781530291091e-197 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 5.025303229685391e-6 5.025303229685391e-6 2.085610850141658e-1 + 3406 + + -2.335868718243551e-1 -1.446307841968770e-1 -1.141474120846017e-1 -1.140736260319665e-1 -8.901293338334792e-2 + -8.893004623323289e-2 -4.028833555472197e-2 8.465677561312024e-2 8.470255182772970e-2 8.634304359819783e-2 + 8.637610234416826e-2 9.288924558645263e-2 9.466517375755663e-2 1.499935259429280e-1 1.733367391845312e-1 + 1.747699522339140e-1 2.108069562204332e-1 2.430042027064198e-1 2.538737374651433e-1 2.539487015312270e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.368265562926709e-176 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 6.281629037106738e-6 6.281629037106738e-6 2.607013562677073e-1 + 3426 + + -2.302600015612736e-1 -1.554680065103559e-1 -1.134938742121400e-1 -1.134204448967775e-1 -8.829052185215641e-2 + -8.820938796706606e-2 -2.575204616630727e-2 7.987892763217158e-2 7.992065532823569e-2 8.045357519911732e-2 + 8.048822881962412e-2 9.596069153425821e-2 9.795803601316601e-2 1.340205811717134e-1 1.649875302078734e-1 + 1.666295701702690e-1 2.113625292541562e-1 2.491754319283530e-1 2.695862087823715e-1 2.696641953745300e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 2.031769371349541e-217 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 7.537954844528084e-6 7.537954844528084e-6 3.128416275212488e-1 + 3434 + + -2.262373037221815e-1 -1.656684095157991e-1 -1.128274326239050e-1 -1.127543886111025e-1 -8.755152387096793e-2 + -8.747231940840541e-2 -1.108405777810170e-2 7.508588576860145e-2 7.512079029936302e-2 7.540203306318583e-2 + 7.543819001778242e-2 9.961026238593579e-2 1.019532257198777e-1 1.181393867601630e-1 1.564906909359732e-1 + 1.584683846864254e-1 2.127097580707631e-1 2.517215617825699e-1 2.720167559295603e-1 2.870172185753359e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 8.794280651949432e-6 8.794280651949432e-6 3.649818987747903e-1 + 3462 + + -2.215719886323395e-1 -1.751595614650777e-1 -1.122148390205891e-1 -1.121421702389648e-1 -8.686961491965794e-2 + -8.679232734515825e-2 3.582521501280738e-3 7.059243628838994e-2 7.062683177651452e-2 7.157553549882721e-2 + 7.160487094214357e-2 1.025233823046320e-1 1.037145944177273e-1 1.066227013218326e-1 1.481157018288198e-1 + 1.506579610871007e-1 2.147227452068944e-1 2.490275919267174e-1 2.784507248446753e-1 3.058236693269187e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.005060645937078e-5 1.005060645937078e-5 4.171221700283317e-1 + 3466 + + -2.163989746353370e-1 -1.837899428171752e-1 -1.117204394053901e-1 -1.116480874529011e-1 -8.631755297242806e-2 + -8.624192371645462e-2 1.794571601845080e-2 6.721949608738786e-2 6.725310874967974e-2 6.866054386099695e-2 + 6.868229993001739e-2 8.748807419260729e-2 1.080026436390960e-1 1.119234485305129e-1 1.400785502837000e-1 + 1.436318558614194e-1 2.171555078969526e-1 2.446053507709161e-1 2.876897340750628e-1 3.187344761916488e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.130693226679212e-5 1.130693226679212e-5 4.692624412818732e-1 + 3450 + + -2.111996447550353e-1 -1.910677736960730e-1 -1.113985246747767e-1 -1.113263853980260e-1 -8.595710098315179e-2 + -8.588260792720325e-2 3.096529160766408e-2 6.513198435086078e-2 6.516493898664903e-2 6.683995036164243e-2 + 6.685460302493724e-2 7.406923969725487e-2 1.117853550086024e-1 1.177025339665033e-1 1.326230041412457e-1 + 1.381737156216278e-1 2.194391465983887e-1 2.408028954808747e-1 2.973856958920828e-1 3.154259966674537e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + 1.256325807421347e-5 1.256325807421347e-5 5.214027125354146e-1 + 3434 + + -2.082875932856379e-1 -1.946733691237101e-1 -1.112867009825660e-1 -1.112146364174962e-1 -8.583167321479220e-2 + -8.575758431149982e-2 3.775180559607239e-2 6.442552279610848e-2 6.445822391818381e-2 6.621875181895335e-2 + 6.623277826665537e-2 6.715371025031551e-2 1.134809889089343e-1 1.221189069316305e-1 1.276440228327017e-1 + 1.359144708265725e-1 2.204701985154919e-1 2.392294172045331e-1 3.040172886878048e-1 3.108452834735412e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + + 0 + + + 1.865847300000000e1 + 1.868454289436341e1 + + + 1.740882200000000e1 + 1.743066692352295e1 + + + + diff --git a/vitalypro/cell_param/si2ge2_relax.xml b/vitalypro/cell_param/si2ge2_relax.xml new file mode 100644 index 00000000..6e1b3aaa --- /dev/null +++ b/vitalypro/cell_param/si2ge2_relax.xml @@ -0,0 +1,474 @@ + + + + + QEXSD_19.03 + XML file generated by PWSCF + This run was terminated on: 16:42:53 26 Oct 2021 + + + + 1 + 1 + 1 + 1 + 1 + 1 + + + + + bands + from_scratch + Si_cubic + ../../pseudo + ./ + false + false + true + low + 10000000 + 1 + 5.000000000000000e-5 + 5.000000000000000e-4 + 5.000000000000000e-1 + high + 100000 + + + + Si.pbe-rrkj.UPF + + + 7.264000000000000e1 + Ge.pbe-kjpaw.UPF + + + + + -1.116822494254278e-1 -1.116822494254278e-1 -4.531905307089824e-2 + 2.537649205599927e0 2.537649205599927e0 2.471288055818799e0 + 5.195656355506836e0 -1.097133059730516e-1 5.129356561353791e0 + -1.097133059730516e-1 5.195656355506836e0 5.129356561353791e0 + 5.192711844717810e0 5.192711844717810e0 -3.628744716947523e-2 + 7.844766699346559e0 2.541009059295700e0 7.917876352166046e0 + 2.541009059295700e0 7.844766699346559e0 7.917876352166046e0 + 7.841797128899285e0 7.841797128899285e0 2.480371544151200e0 + + + 1.060789756200000e1 -5.460376000000000e-3 3.338752000000000e-3 + -5.460376000000000e-3 1.060789756200000e1 3.338752000000000e-3 + 3.376974000000000e-3 3.376974000000000e-3 1.061021974900000e1 + + + + pbe + + + false + false + false + + + gaussian + 0.000000000000000e0 + smearing + + + false + 1.500000000000000e1 + 6.000000000000000e1 + + + davidson + plain + 7.000000000000000e-1 + 5.000000000000000e-9 + 8 + 100 + false + false + false + false + 0.000000000000000e0 + false + 20 + 20 + + + 11 + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + -1.574176997262032e-5 -1.574176997262032e-5 4.998907595747389e-2 + -3.148353994524064e-5 -3.148353994524064e-5 9.997815191494778e-2 + -4.722530991786096e-5 -4.722530991786096e-5 1.499672278724217e-1 + -6.296707989048128e-5 -6.296707989048128e-5 1.999563038298956e-1 + -7.870884986310158e-5 -7.870884986310158e-5 2.499453797873695e-1 + -9.445061983572192e-5 -9.445061983572192e-5 2.999344557448433e-1 + -1.101923898083422e-4 -1.101923898083422e-4 3.499235317023173e-1 + -1.259341597809626e-4 -1.259341597809626e-4 3.999126076597912e-1 + -1.416759297535829e-4 -1.416759297535829e-4 4.499016836172650e-1 + -1.574176997262032e-4 -1.574176997262032e-4 4.998907595747389e-1 + + + none + 1.000000000000000e2 + false + false + + + none + 0.000000000000000e0 + 3.672227080435770e5 + 0.000000000000000e0 + false + false + false + + + false + false + false + false + false + false + + + + + + false + 1 + 0.000000000000000e0 + + + + false + false + true + true + + + + 2.808550000000000e1 + Si.pbe-rrkj.UPF + + + 7.264000000000000e1 + Ge.pbe-kjpaw.UPF + + + + + -1.116822494254278e-1 -1.116822494254278e-1 -4.531905307089824e-2 + 2.537649205599927e0 2.537649205599927e0 2.471288055818799e0 + 5.195656355506836e0 -1.097133059730516e-1 5.129356561353791e0 + -1.097133059730516e-1 5.195656355506836e0 5.129356561353791e0 + 5.192711844717810e0 5.192711844717810e0 -3.628744716947523e-2 + 7.844766699346559e0 2.541009059295700e0 7.917876352166046e0 + 2.541009059295700e0 7.844766699346559e0 7.917876352166046e0 + 7.841797128899285e0 7.841797128899285e0 2.480371544151200e0 + + + 1.060789756200000e1 -5.460376000000000e-3 3.338752000000000e-3 + -5.460376000000000e-3 1.060789756200000e1 3.338752000000000e-3 + 3.376974000000000e-3 3.376974000000000e-3 1.061021974900000e1 + + + + 2 + 4 + 0 + + crystal_symmetry + + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 1.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 1.000000000000000e0 + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + 1 2 3 4 5 6 7 8 + + + + crystal_symmetry + + 0.000000000000000e0 1.000000000000000e0 0.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 1.000000000000000e0 + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + 1 2 4 3 5 7 6 8 + + + + lattice_symmetry + + -1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 -1.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 -1.000000000000000e0 + + + + lattice_symmetry + + 0.000000000000000e0 -1.000000000000000e0 0.000000000000000e0 + -1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 0.000000000000000e0 0.000000000000000e0 -1.000000000000000e0 + + + + + false + 1.500000000000000e1 + 6.000000000000000e1 + + + + 26675 + 26675 + 3362 + + 1.000000547255294e0 5.148468060949311e-4 -3.184396320032397e-4 + 5.148468060949311e-4 1.000000547255294e0 -3.184396320032397e-4 + -3.148353994523145e-4 -3.148353994523145e-4 9.997815191491862e-1 + + + + PBE + + + false + false + false + 0.000000000000000e0 + 0.000000000000000e0 + false + + + 0.000000000000000e0 + 0.000000000000000e0 + 2.317767674798253e0 + -1.290294254499129e1 + -3.706143484789722e1 + 0.000000000000000e0 + -1.389488622288629e-16 + + + false + false + false + 20 + 3.200000000000000e1 + 32 + true + 2.112843663136382e-1 + + 11 + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + -1.574176997261572e-5 -1.574176997261572e-5 4.998907595745931e-2 + -3.148353994523145e-5 -3.148353994523145e-5 9.997815191491862e-2 + -4.722530991784718e-5 -4.722530991784718e-5 1.499672278723779e-1 + -6.296707989046290e-5 -6.296707989046290e-5 1.999563038298372e-1 + -7.870884986307862e-5 -7.870884986307862e-5 2.499453797872965e-1 + -9.445061983569436e-5 -9.445061983569436e-5 2.999344557447559e-1 + -1.101923898083101e-4 -1.101923898083101e-4 3.499235317022152e-1 + -1.259341597809258e-4 -1.259341597809258e-4 3.999126076596744e-1 + -1.416759297535415e-4 -1.416759297535415e-4 4.499016836171338e-1 + -1.574176997261572e-4 -1.574176997261572e-4 4.998907595745931e-1 + + 11 + smearing + gaussian + + 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + 3287 + + -2.360037729934431e-1 -1.055815977626925e-1 -1.055171771154544e-1 -9.422575779794894e-2 -9.178171732762932e-2 + -8.034821856026792e-2 -8.023697944339393e-2 1.012360833291221e-1 1.015880665986117e-1 1.023392147878309e-1 + 1.036069767911211e-1 1.066149128170949e-1 1.069487004687656e-1 2.058219161581937e-1 2.088120563372507e-1 + 2.100281787318490e-1 2.256741547328115e-1 2.261590593097602e-1 2.327887437003423e-1 2.410743074335393e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 9.999999999994030e-1 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + -1.574176997261572e-5 -1.574176997261572e-5 4.998907595745931e-2 + 3308 + + -2.356356946296370e-1 -1.061051446754427e-1 -1.054912808205307e-1 -1.054254213351245e-1 -8.024818217117790e-2 + -8.013924875503459e-2 -7.943176154080810e-2 1.003660598795161e-1 1.007136232126581e-1 1.026847564208284e-1 + 1.039701203093822e-1 1.053751274033971e-1 1.057046508994087e-1 2.008711053086214e-1 2.070764764397808e-1 + 2.083084186228176e-1 2.279724505069295e-1 2.284591276352343e-1 2.316648711793021e-1 2.429425593891004e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + -3.148353994523145e-5 -3.148353994523145e-5 9.997815191491862e-2 + 3303 + + -2.345324850031125e-1 -1.186158598622496e-1 -1.052258783844039e-1 -1.051558468208168e-1 -7.995389494289390e-2 + -7.984509069745118e-2 -6.551968909109602e-2 9.791908353042203e-2 9.825364241828007e-2 1.019677964408280e-1 + 1.022831988267132e-1 1.037192896326081e-1 1.050603281977079e-1 1.891175504787660e-1 2.023332293817635e-1 + 2.036196531912908e-1 2.301958904463084e-1 2.345746077710591e-1 2.350743659065577e-1 2.469534226711331e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + -4.722530991784718e-5 -4.722530991784718e-5 1.499672278723779e-1 + 3303 + + -2.326983723555330e-1 -1.306028692724669e-1 -1.048077815070237e-1 -1.047317023633492e-1 -7.948996203743328e-2 + -7.938397055628505e-2 -5.120343563263087e-2 9.430835590011689e-2 9.462277221888515e-2 9.711894422060377e-2 + 9.741499893846949e-2 1.054322005075583e-1 1.068716291452198e-1 1.745010280341417e-1 1.955350720973294e-1 + 1.969320919512050e-1 2.293942232150065e-1 2.447676661918344e-1 2.452832005949517e-1 2.521431242120245e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + -6.296707989046290e-5 -6.296707989046290e-5 1.999563038298372e-1 + 3287 + + -2.301409835461588e-1 -1.420167345940553e-1 -1.042731222962680e-1 -1.041899580807253e-1 -7.889548733542656e-2 + -7.879360739961458e-2 -3.654785358835221e-2 9.004875143578207e-2 9.033758023037286e-2 9.161520825612913e-2 + 9.188827954289494e-2 1.078039748843522e-1 1.094008137509050e-1 1.587799730281368e-1 1.875891992618503e-1 + 1.891612387499479e-1 2.293597841144518e-1 2.577835656904934e-1 2.580811035946787e-1 2.583179682699721e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + -7.870884986307862e-5 -7.870884986307862e-5 2.499453797872965e-1 + 3306 + + -2.268749221200832e-1 -1.528167518512299e-1 -1.036704941145733e-1 -1.035801425211779e-1 -7.822379441470112e-2 + -7.812736769989312e-2 -2.161551373066657e-2 8.563474232237919e-2 8.589404982196900e-2 8.610446703968588e-2 + 8.635278858281250e-2 1.107999594882803e-1 1.126320938783947e-1 1.426387364477657e-1 1.791312743724609e-1 + 1.809601459331495e-1 2.300851583860919e-1 2.639579750339402e-1 2.729854711470943e-1 2.735410755379601e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + -9.445061983569436e-5 -9.445061983569436e-5 2.999344557447559e-1 + 3320 + + -2.229254643782340e-1 -1.629571886158972e-1 -1.030561212116172e-1 -1.029587300695107e-1 -7.753646216280298e-2 + -7.744640025652274e-2 -6.485354939957306e-3 8.106617927866342e-2 8.128969585125212e-2 8.148546022248169e-2 + 8.171303916343822e-2 1.143567214056841e-1 1.165561100189624e-1 1.264069817444402e-1 1.705793911412089e-1 + 1.727969940993087e-1 2.315123614394052e-1 2.675341772653987e-1 2.882346694164382e-1 2.899351714187878e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + -1.101923898083101e-4 -1.101923898083101e-4 3.499235317022152e-1 + 3336 + + -2.183461374676089e-1 -1.723678459148631e-1 -1.024921155157767e-1 -1.023888318554553e-1 -7.690281316025688e-2 + -7.682003812768134e-2 8.714803944044871e-3 7.684000763098214e-2 7.703975469769237e-2 7.793121989761059e-2 + 7.812691363728621e-2 1.103068187967227e-1 1.183526943811107e-1 1.211490010012970e-1 1.622087723223473e-1 + 1.650398462488165e-1 2.335195386947439e-1 2.664692857439530e-1 2.927837709964247e-1 3.082832395609447e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + -1.259341597809258e-4 -1.259341597809258e-4 3.999126076596744e-1 + 3326 + + -2.132743451893724e-1 -1.808992808622119e-1 -1.020365634375873e-1 -1.019288186143333e-1 -7.638936881067284e-2 + -7.631338973931562e-2 2.370441988574847e-2 7.366431117461519e-2 7.384455203372359e-2 7.522124002523683e-2 + 7.538750073913708e-2 9.467123486795142e-2 1.225134468393501e-1 1.263679643392285e-1 1.542039774439689e-1 + 1.581062912941528e-1 2.358473323381765e-1 2.629812083044742e-1 3.009921737429695e-1 3.277811600427565e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + -1.416759297535415e-4 -1.416759297535415e-4 4.499016836171338e-1 + 3322 + + -2.081984787428685e-1 -1.880541075131277e-1 -1.017407931432552e-1 -1.016302253787053e-1 -7.605496449587321e-2 + -7.598408123056908e-2 3.748679782978592e-2 7.169787167686090e-2 7.186456869863167e-2 7.352715066273680e-2 + 7.367192332930925e-2 8.049765889017548e-2 1.261588498135318e-1 1.320692872307658e-1 1.468004541709949e-1 + 1.527664599365442e-1 2.379569617175389e-1 2.597272989707609e-1 3.103154677988798e-1 3.295366444233414e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + -1.574176997261572e-4 -1.574176997261572e-4 4.998907595745931e-1 + 3362 + + -2.053869842641341e-1 -1.915593004695142e-1 -1.016398478568590e-1 -1.015283164331424e-1 -7.594114527794986e-2 + -7.587217495245486e-2 4.491490393148154e-2 7.103187836799597e-2 7.119370921999497e-2 7.287712336613205e-2 + 7.300800391180752e-2 7.308821655502634e-2 1.277771882872673e-1 1.364429102566429e-1 1.418544509906449e-1 + 1.505784297957828e-1 2.388784457384820e-1 2.583689123142609e-1 3.171003195237713e-1 3.240738971414058e-1 + + + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 1.000000000000000e0 + 1.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 0.000000000000000e0 + + + + + 0 + + + 1.918452400000000e1 + 1.925226998329163e1 + + + 1.796744400000000e1 + 1.801732301712036e1 + + + + diff --git a/vitalypro/code_implementation_example.ipynb b/vitalypro/code_implementation_example.ipynb index a1258ac9..bc9111ba 100644 --- a/vitalypro/code_implementation_example.ipynb +++ b/vitalypro/code_implementation_example.ipynb @@ -2,96 +2,14 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": 18, "metadata": { "ExecuteTime": { - "end_time": "2021-10-27T18:59:04.286973Z", - "start_time": "2021-10-27T18:59:01.347246Z" + "end_time": "2021-10-29T00:22:54.876849Z", + "start_time": "2021-10-29T00:22:54.815867Z" } }, "outputs": [ - { - "data": { - "text/html": [ - " \n", - " " - ] - }, - "metadata": {}, - "output_type": "display_data" - }, { "data": { "application/vnd.plotly.v1+json": { @@ -1663,20 +1581,20 @@ "
\n", " \n", " \n", - "
\n", + "
\n", " \n", + "
" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "### EXAMPLE WITH MODE=\"Auto\" ###\n", + "\n", + "#read QE output file with bands for 0% and 5% strain and different composition\n", + "# reshape data: 8 bands 11 k-points\n", + "\n", + "\n", + "data=read_data('bands/si1ge3_0.dat')\n", + "si1ge3_0=data.read_bands_ml(mode='Auto', bands_num=4)\n", + "si1ge3_0=si1ge3_0.reshape(8,11)\n", + "\n", + "data=read_data('bands/si1ge3_5.dat')\n", + "si1ge3_5=data.read_bands_ml(mode='Auto', bands_num=4)\n", + "si1ge3_5=si1ge3_5.reshape(8,11)\n", + "\n", + "data=read_data('bands/si3ge1_0.dat')\n", + "si3ge1_0=data.read_bands_ml(mode='Auto', bands_num=4)\n", + "si3ge1_0=si3ge1_0.reshape(8,11)\n", + "\n", + "data=read_data('bands/si3ge1_5.dat')\n", + "si3ge1_5=data.read_bands_ml(mode='Auto', bands_num=4)\n", + "si3ge1_5=si3ge1_5.reshape(8,11)\n", + "\n", + "\n", + "\n", + "import plotly.graph_objects as go\n", + "from plotly.subplots import make_subplots\n", + "fig = make_subplots(rows=2, cols=2,\n", + " subplot_titles=(\"Si1Ge3 strain 0%\", \" Si1G3 strain 5%\", 'S3Ge1 strain 0%', 'Si3Ge1 strain 5%'),\n", + " vertical_spacing=0.04)\n", + "\n", + "for i in range(si3ge1_0.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si3ge1_0[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), col=1, row=1) \n", + "for i in range(si3ge1_5.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si3ge1_5[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), col=2, row=1) \n", + "for i in range(si1ge3_0.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si1ge3_0[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), col=1, row=2) \n", + "for i in range(si1ge3_5.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si1ge3_5[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), col=2, row=2) \n", + " \n", + "fig.add_trace(go.Scatter(x=[1,11], y=[0,0],\n", + " mode='lines', line=dict(color= \"RoyalBlue\",width=3, dash='dot'), showlegend=False, \n", + " name='markers'), col=1, row=1) \n", + "fig.add_trace(go.Scatter(x=[1,11], y=[0,0],\n", + " mode='lines', line=dict(color= \"RoyalBlue\",width=3, dash='dot'), showlegend=False, \n", + " name='markers'), col=2, row=1) \n", + "fig.add_trace(go.Scatter(x=[1,11], y=[0,0],\n", + " mode='lines', line=dict(color= \"RoyalBlue\",width=3, dash='dot'), showlegend=False, \n", + " name='markers'), col=1, row=2) \n", + "fig.add_trace(go.Scatter(x=[1,11], y=[0,0],\n", + " mode='lines', line=dict(color= \"RoyalBlue\",width=3, dash='dot'), showlegend=False, \n", + " name='markers'), col=2, row=2) \n", + "fig.update_xaxes(showgrid=True, \n", + " gridwidth=0.5, \n", + " gridcolor='lightgrey', \n", + " ticks='inside' , \n", + " linecolor= 'black', \n", + " linewidth= 1,\n", + " mirror= True,\n", + " ticktext=['G', 'Z'],\n", + " tickvals=[1,11],\n", + " range=[1,11],\n", + " )\n", + "fig.update_yaxes(title='Energy, eV', \n", + " showgrid=True, \n", + " gridwidth=0.5, \n", + " gridcolor='lightgrey', \n", + " ticks='inside' , \n", + " linecolor= 'black',\n", + " linewidth= 1,\n", + " mirror= True,\n", + " )\n", + "\n", + "fig.update_layout(width=900, height=1450, plot_bgcolor='white')\n", + "fig.show()\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": 35, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T02:23:45.931705Z", + "start_time": "2021-10-29T02:23:45.895707Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "array([[10.34568286, 11.02820471, 0.25 ],\n", + " [10.45682864, 10.95544485, 0.25 ],\n", + " [10.56082864, 10.8812629 , 0.25 ],\n", + " [10.66056829, 10.81293885, 0.25 ],\n", + " [10.76056829, 10.74977523, 0.25 ],\n", + " [10.87056829, 10.67605785, 0.25 ],\n", + " [10.34568286, 10.79211782, 0.5 ],\n", + " [10.45682864, 10.71265005, 0.5 ],\n", + " [10.56082864, 10.64615759, 0.5 ],\n", + " [10.66056829, 10.57623403, 0.5 ],\n", + " [10.76056829, 10.50342487, 0.5 ],\n", + " [10.87056829, 10.42434959, 0.5 ],\n", + " [10.60789756, 10.61021975, 0.5 ],\n", + " [10.34568286, 10.5680025 , 0.75 ],\n", + " [10.45682864, 10.48979506, 0.75 ],\n", + " [10.56082864, 10.41511474, 0.75 ],\n", + " [10.66056829, 10.34128041, 0.75 ],\n", + " [10.76056829, 10.27133855, 0.75 ],\n", + " [10.87056829, 10.18915583, 0.75 ]])" + ] + }, + "execution_count": 35, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# reading cell parameters from all QE output file\n", + "\n", + "mypath='cell_param/'\n", + "filenames = next(walk(mypath), (None, None, []))[2]\n", + "\n", + "lattice=[]\n", + "fermi=[]\n", + "for file in filenames:\n", + " data=read_data(mypath+file)\n", + " (a, c, composition) = data.read_lattice_parameters()\n", + " lattice.append ([a, c, composition])\n", + "# Fermi energy could be obtained with: \n", + "# fermi_level = data.read_fermi_levle()\n", + "# fermi.append(fermi_level)\n", + " \n", + "X=lattice=np.array(lattice)\n", + "X\n" + ] + }, + { + "cell_type": "code", + "execution_count": 36, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T02:23:48.178246Z", + "start_time": "2021-10-29T02:23:48.159233Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "['si1ge3_0.xml',\n", + " 'si1ge3_1.xml',\n", + " 'si1ge3_2.xml',\n", + " 'si1ge3_3.xml',\n", + " 'si1ge3_4.xml',\n", + " 'si1ge3_5.xml',\n", + " 'si2ge2_0.xml',\n", + " 'si2ge2_1.xml',\n", + " 'si2ge2_2.xml',\n", + " 'si2ge2_3.xml',\n", + " 'si2ge2_4.xml',\n", + " 'si2ge2_5.xml',\n", + " 'si2ge2_relax.xml',\n", + " 'si3ge1_0.xml',\n", + " 'si3ge1_1.xml',\n", + " 'si3ge1_2.xml',\n", + " 'si3ge1_3.xml',\n", + " 'si3ge1_4.xml',\n", + " 'si3ge1_5.xml']" + ] + }, + "execution_count": 36, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "filenames" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T01:48:59.681776Z", + "start_time": "2021-10-29T01:48:59.664772Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "(19, 44)" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# reading bands from all QE output file\n", + "\n", + "mypath='bands/'\n", + "filenames = next(walk(mypath), (None, None, []))[2]\n", + "\n", + "y=[]\n", + "for i in range(len(filenames)):\n", + " data=read_data(mypath+filenames[i])\n", + " bands_ml=data.read_bands_ml(mode='Auto', bands_num=2)\n", + " y= np.append(y, bands_ml)\n", + "y=y.reshape(len(filenames),44)\n", + "y.shape" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# prepare data for modeling: split for training and testig sets" + ] + }, + { + "cell_type": "code", + "execution_count": 44, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T02:55:29.974677Z", + "start_time": "2021-10-29T02:55:22.192915Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Time taken for RF: 0:00:07.726750\n", + "Train:\n", + "R^2:0.96 RMSE:0.02\n", + "Test:\n", + "R^2:-5.14 RMSE: 0.01\n" + ] + } + ], + "source": [ + "my_data=data_preparation(X,y)\n", + "(X_train, X_test, Y_train, Y_test)=my_data.select_train_test(test_row_number=[12,16])\n", + "#random split could also be used\n", + "#(X_train, X_test, Y_train, Y_test)=my_data.random_split(train_split=0.8, seed=42)\n", + "\n", + "my_model=modeling(X_train, Y_train, X_test, Y_test, scaler='None')\n", + "\n", + "#train Random forest model with No initial guess\n", + "(y_fit_RF, y_predict_RF, trials_RF, best_space_RF, regressorRF, text_RF)=my_model.RandomForest( max_evals=15, timeout=150*60,loss_threshold=0.01, cv=5, verbose=1)\n", + "\n", + "print(text_RF)\n", + "\n", + "\n", + "#" + ] + }, + { + "cell_type": "code", + "execution_count": 45, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T03:19:50.954175Z", + "start_time": "2021-10-29T02:55:34.440216Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Time taken for XGB: 0:24:14.743505\n", + "Train:\n", + "R^2:0.64 RMSE:0.06\n", + "Test:\n", + "R^2:-31.98 RMSE: 0.04\n" + ] + } + ], + "source": [ + "## MultiOutputRegressor is VERY SLOW!\n", + "\n", + "#train XGboost model with initial guess\n", + "best_space = {'alpha': 0.0, 'max_depth': 3.0, 'min_split_loss': 5.6, 'n_estimators': 100, 'x_reg_lambda': 1.00, 'x_subsample': 1.0}\n", + "(y_fit_XG, y_predict_XG, trials_XG, best_space_XG, regressorXGB, text_XG)=my_model.XGB( max_evals=12, timeout=150*60,loss_threshold=0.01,init_vals=[best_space],cv=5, verbose=1) \n", + "print(text_XG)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# let's plot predicted bands vs calculated bands" + ] + }, + { + "cell_type": "code", + "execution_count": 46, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T03:20:03.044873Z", + "start_time": "2021-10-29T03:20:02.959854Z" + } + }, + "outputs": [ + { + "data": { + "application/vnd.plotly.v1+json": { + "config": { + "plotlyServerURL": "https://plot.ly" + }, + "data": [ + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.42599964141845703, + 0.48799991607666016, + 0.5489997863769531, + 0.5269999504089355, + 0.5260000228881836, + 0.5460000038146973, + 0.5850000381469727, + 0.6389999389648438, + 0.7030000686645508, + 0.7599997520446777, + 0.7849998474121094 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.43899965286254883, + 0.5019998550415039, + 0.6679997444152832, + 0.9449996948242188, + 1.299999713897705, + 1.4679999351501465, + 1.565000057220459, + 1.5359997749328613, + 1.440999984741211, + 1.3529996871948242, + 1.315999984741211 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.619999885559082, + 0.5889997482299805, + 0.681999683380127, + 0.9589996337890625, + 1.307999610900879, + 1.7129998207092285, + 2.127999782562256, + 2.251999855041504, + 2.47499942779541, + 2.7290000915527344, + 2.913999557495117 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.8449997901916504, + 0.8959999084472656, + 1.0049996376037598, + 1.1459999084472656, + 1.3139996528625488, + 1.7279996871948242, + 2.174999713897705, + 2.673999786376953, + 3.2039995193481445, + 3.251999855041504, + 3.102999687194824 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -2.805000066757202, + -2.8390002250671387, + -2.8560001850128174, + -2.807000160217285, + -2.7380001544952393, + -2.6500000953674316, + -2.5430002212524414, + -2.494000196456909, + -2.38100004196167, + -2.2820000648498535, + -2.2380001544952393 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -0.11400032043457031, + -0.24900007247924805, + -0.569000244140625, + -0.9670000076293945, + -1.3940000534057617, + -1.8340001106262207, + -2.2750000953674316, + -2.4180002212524414, + -2.2760002613067627, + -2.121000051498413, + -2.002000093460083 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -0.03299999237060547, + -0.07999992370605469, + -0.2090001106262207, + -0.3940000534057617, + -0.6100001335144043, + -0.8410000801086426, + -1.0729999542236328, + -1.3010001182556152, + -1.5190000534057617, + -1.7200002670288086, + -1.8550002574920654 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0, + -0.04699993133544922, + -0.17400026321411133, + -0.3559999465942383, + -0.568000316619873, + -0.7910003662109375, + -1.0130000114440918, + -1.2239999771118164, + -1.4130001068115234, + -1.558000087738037, + -1.6180000305175781 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.4163817214001295, + 0.47795961961131334, + 0.5505676203220141, + 0.5389267346349589, + 0.5391505310116466, + 0.5595778514702914, + 0.5996257496241824, + 0.6556927949830644, + 0.7209722468283324, + 0.7820150656284183, + 0.8088482954408668 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.4535879510091017, + 0.5074918206814116, + 0.6652743530032306, + 0.9371859596291022, + 1.2659557236431522, + 1.478615816263423, + 1.577445077233007, + 1.544232721726602, + 1.444608168716527, + 1.3516637938363212, + 1.312231291711858 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -0.02910236884308826, + -0.07699500745828776, + -0.20572319163383937, + -0.3902427719154792, + -0.6060936405746132, + -0.8349418694391263, + -1.0668495922112735, + -1.2931732564750122, + -1.5091252085834026, + -1.7070543416381334, + -1.8348659534671363 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0, + -0.05093044999577152, + -0.17890395949372148, + -0.3622213296130695, + -0.5744007709807, + -0.7986422386844602, + -1.0224084257325994, + -1.2357800576539166, + -1.4277962788317808, + -1.579796350710612, + -1.6455348336741837 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "blue" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.3820151686668396, + 0.4353727400302887, + 0.501971960067749, + 0.5688056945800781, + 0.5747143030166626, + 0.6009825468063354, + 0.6415016055107117, + 0.6995277404785156, + 0.7660749554634094, + 0.8433831930160522, + 0.8762089014053345 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "blue" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.4932188093662262, + 0.5469381213188171, + 0.6642600297927856, + 0.928294837474823, + 1.2238987684249878, + 1.4589495658874512, + 1.5917128324508667, + 1.5662966966629028, + 1.463591456413269, + 1.3635516166687012, + 1.3197029829025269 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "blue" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -0.03758132457733154, + -0.08677172660827637, + -0.21767783164978027, + -0.4047420620918274, + -0.6230689287185669, + -0.8520381450653076, + -1.0831680297851562, + -1.3068233728408813, + -1.5190889835357666, + -1.70831298828125, + -1.8221969604492188 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "blue" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 2.384185791015625e-07, + -0.07094085216522217, + -0.20446914434432983, + -0.39226412773132324, + -0.6083120107650757, + -0.8349472284317017, + -1.0624866485595703, + -1.2821804285049438, + -1.4831597805023193, + -1.6506619453430176, + -1.7139101028442383 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.4289999008178711, + 0.46700000762939453, + 0.41300010681152344, + 0.38299989700317383, + 0.38000011444091797, + 0.40199995040893555, + 0.4479999542236328, + 0.5149998664855957, + 0.5970001220703125, + 0.6820001602172852, + 0.7270002365112305 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.5089998245239258, + 0.495999813079834, + 0.6880002021789551, + 0.9800000190734863, + 1.2049999237060547, + 1.3910002708435059, + 1.4759998321533203, + 1.3899998664855957, + 1.250999927520752, + 1.125, + 1.065999984741211 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.6700000762939453, + 0.7309999465942383, + 0.8580002784729004, + 1.0190000534057617, + 1.3499999046325684, + 1.7800002098083496, + 1.938000202178955, + 2.135000228881836, + 2.4169998168945312, + 2.7270002365112305, + 2.98799991607666 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.9019999504089355, + 0.9609999656677246, + 1.1329998970031738, + 1.4000000953674316, + 1.744999885559082, + 1.940000057220459, + 2.25600004196167, + 2.7690000534057617, + 3.312000274658203, + 3.3439998626708984, + 3.1090002059936523 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -2.7019999027252197, + -2.740000009536743, + -2.8429999351501465, + -2.9140000343322754, + -2.8459999561309814, + -2.759000062942505, + -2.6540000438690186, + -2.5320000648498535, + -2.3969998359680176, + -2.259999990463257, + -2.180000066757202 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -0.14599990844726562, + -0.19099998474121094, + -0.370999813079834, + -0.7300000190734863, + -1.130000114440918, + -1.5500001907348633, + -1.9779999256134033, + -2.4070000648498535, + -2.3969998359680176, + -2.259000062942505, + -2.180000066757202 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -0.14499998092651367, + -0.19000005722045898, + -0.315000057220459, + -0.4930000305175781, + -0.7039999961853027, + -0.9289999008178711, + -1.1570000648498535, + -1.379000186920166, + -1.5889997482299805, + -1.7719998359680176, + -1.8659999370574951 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0, + -0.10300016403198242, + -0.31400012969970703, + -0.4930000305175781, + -0.7030000686645508, + -0.9279999732971191, + -1.1560001373291016, + -1.379000186920166, + -1.5889997482299805, + -1.7719998359680176, + -1.8659999370574951 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.41281924989220464, + 0.41825276771477893, + 0.4111516454578501, + 0.38203538262889297, + 0.3786295488118824, + 0.3999899105838819, + 0.44502530116046274, + 0.5097547590205099, + 0.5908130357600042, + 0.6727547681738544, + 0.7153199559970089 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.5252439375924401, + 0.5508154116749914, + 0.694986123351472, + 0.9464298343537881, + 1.2041430093545828, + 1.390714202306967, + 1.4729052090313282, + 1.3898533749972222, + 1.2542326616125674, + 1.1311389926712672, + 1.0736195965753645 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -0.14034649454688303, + -0.18651320569584554, + -0.3116485508895855, + -0.4913715737508009, + -0.7017306564128505, + -0.9269873821629887, + -1.1550569106293689, + -1.3781391347554781, + -1.5886258201864365, + -1.7733981796221245, + -1.872869742353707 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0, + -0.09569539674163317, + -0.2965486522872288, + -0.48596713274679654, + -0.696305946514067, + -0.9210580959633539, + -1.1484008468357862, + -1.3698254668456413, + -1.5776764050446328, + -1.7568520330146953, + -1.8481984497171589 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "blue" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.3820151686668396, + 0.4353727400302887, + 0.501971960067749, + 0.5688056945800781, + 0.5747143030166626, + 0.6009825468063354, + 0.6415016055107117, + 0.6995277404785156, + 0.7660749554634094, + 0.8433831930160522, + 0.8762089014053345 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "blue" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.4932188093662262, + 0.5469381213188171, + 0.6642600297927856, + 0.928294837474823, + 1.2238987684249878, + 1.4589495658874512, + 1.5917128324508667, + 1.5662966966629028, + 1.463591456413269, + 1.3635516166687012, + 1.3197029829025269 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "blue" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -0.03758132457733154, + -0.08677172660827637, + -0.21767783164978027, + -0.4047420620918274, + -0.6230689287185669, + -0.8520381450653076, + -1.0831680297851562, + -1.3068233728408813, + -1.5190889835357666, + -1.70831298828125, + -1.8221969604492188 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "blue" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 2.384185791015625e-07, + -0.07094085216522217, + -0.20446914434432983, + -0.39226412773132324, + -0.6083120107650757, + -0.8349472284317017, + -1.0624866485595703, + -1.2821804285049438, + -1.4831597805023193, + -1.6506619453430176, + -1.7139101028442383 + ], + "yaxis": "y2" + }, + { + "line": { + "color": "RoyalBlue", + "dash": "dot", + "width": 3 + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 11 + ], + "xaxis": "x", + "y": [ + 0, + 0 + ], + "yaxis": "y" + }, + { + "line": { + "color": "RoyalBlue", + "dash": "dot", + "width": 3 + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 11 + ], + "xaxis": "x2", + "y": [ + 0, + 0 + ], + "yaxis": "y2" + } + ], + "layout": { + "annotations": [ + { + "font": { + "size": 16 + }, + "showarrow": false, + "text": "Si2Ge2 strain 2.5%", + "x": 0.225, + "xanchor": "center", + "xref": "paper", + "y": 1, + "yanchor": "bottom", + "yref": "paper" + }, + { + "font": { + "size": 16 + }, + "showarrow": false, + "text": "Si3Ge1 strain 3%", + "x": 0.775, + "xanchor": "center", + "xref": "paper", + "y": 1, + "yanchor": "bottom", + "yref": "paper" + } + ], "height": 650, "plot_bgcolor": "white", "template": { @@ -3226,8 +6560,39 @@ "title": { "text": "Si2Ge2 relaxed" }, - "width": 450, + "width": 800, "xaxis": { + "anchor": "y", + "domain": [ + 0, + 0.45 + ], + "gridcolor": "lightgrey", + "gridwidth": 0.5, + "linecolor": "black", + "linewidth": 1, + "mirror": true, + "range": [ + 1, + 11 + ], + "showgrid": true, + "ticks": "inside", + "ticktext": [ + "G", + "Z" + ], + "tickvals": [ + 1, + 11 + ] + }, + "xaxis2": { + "anchor": "y2", + "domain": [ + 0.55, + 1 + ], "gridcolor": "lightgrey", "gridwidth": 0.5, "linecolor": "black", @@ -3249,6 +6614,28 @@ ] }, "yaxis": { + "anchor": "x", + "domain": [ + 0, + 1 + ], + "gridcolor": "lightgrey", + "gridwidth": 0.5, + "linecolor": "black", + "linewidth": 1, + "mirror": true, + "showgrid": true, + "ticks": "inside", + "title": { + "text": "Energy, eV" + } + }, + "yaxis2": { + "anchor": "x2", + "domain": [ + 0, + 1 + ], "gridcolor": "lightgrey", "gridwidth": 0.5, "linecolor": "black", @@ -3266,20 +6653,20 @@ "
\n", " \n", " \n", - "
\n", + "
\n", " \n", + " " + ] + }, + "metadata": {}, + "output_type": "display_data" + }, { "data": { "application/vnd.plotly.v1+json": { @@ -659,7 +765,7 @@ "size": 16 }, "showarrow": false, - "text": "strain 0%", + "text": "Si2Ge strain 0%", "x": 0.225, "xanchor": "center", "xref": "paper", @@ -672,7 +778,7 @@ "size": 16 }, "showarrow": false, - "text": "strain 5%", + "text": "Si2Ge2 strain 5%", "x": 0.775, "xanchor": "center", "xref": "paper", @@ -1581,20 +1687,20 @@ "
\n", " \n", " \n", - "
\n", + "
\n", " \n", + "
" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "### EXAMPLE WITH MODE=\"Auto\" ###\n", + "\n", + "#read QE output file with bands for 0% and 5% strain and different composition\n", + "# reshape data: 8 bands 11 k-points\n", + "\n", + "\n", + "data=read_data('bands/si1ge3_0.dat')\n", + "si1ge3_0=data.read_bands_ml(mode='Auto', bands_num=4)\n", + "si1ge3_0=si1ge3_0.reshape(8,11)\n", + "\n", + "data=read_data('bands/si1ge3_5.dat')\n", + "si1ge3_5=data.read_bands_ml(mode='Auto', bands_num=4)\n", + "si1ge3_5=si1ge3_5.reshape(8,11)\n", + "\n", + "data=read_data('bands/si3ge1_0.dat')\n", + "si3ge1_0=data.read_bands_ml(mode='Auto', bands_num=4)\n", + "si3ge1_0=si3ge1_0.reshape(8,11)\n", + "\n", + "data=read_data('bands/si3ge1_5.dat')\n", + "si3ge1_5=data.read_bands_ml(mode='Auto', bands_num=4)\n", + "si3ge1_5=si3ge1_5.reshape(8,11)\n", + "\n", + "\n", + "\n", + "import plotly.graph_objects as go\n", + "from plotly.subplots import make_subplots\n", + "fig = make_subplots(rows=2, cols=2,\n", + " subplot_titles=(\"Si1Ge3 strain 0%\", \" Si1G3 strain 5%\", 'S3Ge1 strain 0%', 'Si3Ge1 strain 5%'),\n", + " vertical_spacing=0.04)\n", + "\n", + "for i in range(si3ge1_0.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si3ge1_0[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), col=1, row=1) \n", + "for i in range(si3ge1_5.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si3ge1_5[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), col=2, row=1) \n", + "for i in range(si1ge3_0.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si1ge3_0[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), col=1, row=2) \n", + "for i in range(si1ge3_5.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si1ge3_5[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), col=2, row=2) \n", + " \n", + "fig.add_trace(go.Scatter(x=[1,11], y=[0,0],\n", + " mode='lines', line=dict(color= \"RoyalBlue\",width=3, dash='dot'), showlegend=False, \n", + " name='markers'), col=1, row=1) \n", + "fig.add_trace(go.Scatter(x=[1,11], y=[0,0],\n", + " mode='lines', line=dict(color= \"RoyalBlue\",width=3, dash='dot'), showlegend=False, \n", + " name='markers'), col=2, row=1) \n", + "fig.add_trace(go.Scatter(x=[1,11], y=[0,0],\n", + " mode='lines', line=dict(color= \"RoyalBlue\",width=3, dash='dot'), showlegend=False, \n", + " name='markers'), col=1, row=2) \n", + "fig.add_trace(go.Scatter(x=[1,11], y=[0,0],\n", + " mode='lines', line=dict(color= \"RoyalBlue\",width=3, dash='dot'), showlegend=False, \n", + " name='markers'), col=2, row=2) \n", + "fig.update_xaxes(showgrid=True, \n", + " gridwidth=0.5, \n", + " gridcolor='lightgrey', \n", + " ticks='inside' , \n", + " linecolor= 'black', \n", + " linewidth= 1,\n", + " mirror= True,\n", + " ticktext=['G', 'Z'],\n", + " tickvals=[1,11],\n", + " range=[1,11],\n", + " )\n", + "fig.update_yaxes(title='Energy, eV', \n", + " showgrid=True, \n", + " gridwidth=0.5, \n", + " gridcolor='lightgrey', \n", + " ticks='inside' , \n", + " linecolor= 'black',\n", + " linewidth= 1,\n", + " mirror= True,\n", + " )\n", + "\n", + "fig.update_layout(width=900, height=1450, plot_bgcolor='white')\n", + "fig.show()\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": 35, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T02:23:45.931705Z", + "start_time": "2021-10-29T02:23:45.895707Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "array([[10.34568286, 11.02820471, 0.25 ],\n", + " [10.45682864, 10.95544485, 0.25 ],\n", + " [10.56082864, 10.8812629 , 0.25 ],\n", + " [10.66056829, 10.81293885, 0.25 ],\n", + " [10.76056829, 10.74977523, 0.25 ],\n", + " [10.87056829, 10.67605785, 0.25 ],\n", + " [10.34568286, 10.79211782, 0.5 ],\n", + " [10.45682864, 10.71265005, 0.5 ],\n", + " [10.56082864, 10.64615759, 0.5 ],\n", + " [10.66056829, 10.57623403, 0.5 ],\n", + " [10.76056829, 10.50342487, 0.5 ],\n", + " [10.87056829, 10.42434959, 0.5 ],\n", + " [10.60789756, 10.61021975, 0.5 ],\n", + " [10.34568286, 10.5680025 , 0.75 ],\n", + " [10.45682864, 10.48979506, 0.75 ],\n", + " [10.56082864, 10.41511474, 0.75 ],\n", + " [10.66056829, 10.34128041, 0.75 ],\n", + " [10.76056829, 10.27133855, 0.75 ],\n", + " [10.87056829, 10.18915583, 0.75 ]])" + ] + }, + "execution_count": 35, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# reading cell parameters from all QE output file\n", + "\n", + "mypath='cell_param/'\n", + "filenames = next(walk(mypath), (None, None, []))[2]\n", + "\n", + "lattice=[]\n", + "fermi=[]\n", + "for file in filenames:\n", + " data=read_data(mypath+file)\n", + " (a, c, composition) = data.read_lattice_parameters()\n", + " lattice.append ([a, c, composition])\n", + "# Fermi energy could be obtained with: \n", + "# fermi_level = data.read_fermi_levle()\n", + "# fermi.append(fermi_level)\n", + " \n", + "X=lattice=np.array(lattice)\n", + "X\n" + ] + }, + { + "cell_type": "code", + "execution_count": 36, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T02:23:48.178246Z", + "start_time": "2021-10-29T02:23:48.159233Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "['si1ge3_0.xml',\n", + " 'si1ge3_1.xml',\n", + " 'si1ge3_2.xml',\n", + " 'si1ge3_3.xml',\n", + " 'si1ge3_4.xml',\n", + " 'si1ge3_5.xml',\n", + " 'si2ge2_0.xml',\n", + " 'si2ge2_1.xml',\n", + " 'si2ge2_2.xml',\n", + " 'si2ge2_3.xml',\n", + " 'si2ge2_4.xml',\n", + " 'si2ge2_5.xml',\n", + " 'si2ge2_relax.xml',\n", + " 'si3ge1_0.xml',\n", + " 'si3ge1_1.xml',\n", + " 'si3ge1_2.xml',\n", + " 'si3ge1_3.xml',\n", + " 'si3ge1_4.xml',\n", + " 'si3ge1_5.xml']" + ] + }, + "execution_count": 36, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "filenames" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T01:48:59.681776Z", + "start_time": "2021-10-29T01:48:59.664772Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "(19, 44)" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# reading bands from all QE output file\n", + "\n", + "mypath='bands/'\n", + "filenames = next(walk(mypath), (None, None, []))[2]\n", + "\n", + "y=[]\n", + "for i in range(len(filenames)):\n", + " data=read_data(mypath+filenames[i])\n", + " bands_ml=data.read_bands_ml(mode='Auto', bands_num=2)\n", + " y= np.append(y, bands_ml)\n", + "y=y.reshape(len(filenames),44)\n", + "y.shape" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# prepare data for modeling: split for training and testig sets" + ] + }, + { + "cell_type": "code", + "execution_count": 44, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T02:55:29.974677Z", + "start_time": "2021-10-29T02:55:22.192915Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Time taken for RF: 0:00:07.726750\n", + "Train:\n", + "R^2:0.96 RMSE:0.02\n", + "Test:\n", + "R^2:-5.14 RMSE: 0.01\n" + ] + } + ], + "source": [ + "my_data=data_preparation(X,y)\n", + "(X_train, X_test, Y_train, Y_test)=my_data.select_train_test(test_row_number=[12,16])\n", + "#random split could also be used\n", + "#(X_train, X_test, Y_train, Y_test)=my_data.random_split(train_split=0.8, seed=42)\n", + "\n", + "my_model=modeling(X_train, Y_train, X_test, Y_test, scaler='None')\n", + "\n", + "#train Random forest model with No initial guess\n", + "(y_fit_RF, y_predict_RF, trials_RF, best_space_RF, regressorRF, text_RF)=my_model.RandomForest( max_evals=15, timeout=150*60,loss_threshold=0.01, cv=5, verbose=1)\n", + "\n", + "print(text_RF)\n", + "\n", + "\n", + "#" + ] + }, + { + "cell_type": "code", + "execution_count": 45, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T03:19:50.954175Z", + "start_time": "2021-10-29T02:55:34.440216Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Time taken for XGB: 0:24:14.743505\n", + "Train:\n", + "R^2:0.64 RMSE:0.06\n", + "Test:\n", + "R^2:-31.98 RMSE: 0.04\n" + ] + } + ], + "source": [ + "## MultiOutputRegressor is VERY SLOW!\n", + "\n", + "#train XGboost model with initial guess\n", + "best_space = {'alpha': 0.0, 'max_depth': 3.0, 'min_split_loss': 5.6, 'n_estimators': 100, 'x_reg_lambda': 1.00, 'x_subsample': 1.0}\n", + "(y_fit_XG, y_predict_XG, trials_XG, best_space_XG, regressorXGB, text_XG)=my_model.XGB( max_evals=12, timeout=150*60,loss_threshold=0.01,init_vals=[best_space],cv=5, verbose=1) \n", + "print(text_XG)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# let's plot predicted bands vs calculated bands" + ] + }, + { + "cell_type": "code", + "execution_count": 46, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T03:20:03.044873Z", + "start_time": "2021-10-29T03:20:02.959854Z" + } + }, + "outputs": [ + { + "data": { + "application/vnd.plotly.v1+json": { + "config": { + "plotlyServerURL": "https://plot.ly" + }, + "data": [ + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.42599964141845703, + 0.48799991607666016, + 0.5489997863769531, + 0.5269999504089355, + 0.5260000228881836, + 0.5460000038146973, + 0.5850000381469727, + 0.6389999389648438, + 0.7030000686645508, + 0.7599997520446777, + 0.7849998474121094 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.43899965286254883, + 0.5019998550415039, + 0.6679997444152832, + 0.9449996948242188, + 1.299999713897705, + 1.4679999351501465, + 1.565000057220459, + 1.5359997749328613, + 1.440999984741211, + 1.3529996871948242, + 1.315999984741211 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.619999885559082, + 0.5889997482299805, + 0.681999683380127, + 0.9589996337890625, + 1.307999610900879, + 1.7129998207092285, + 2.127999782562256, + 2.251999855041504, + 2.47499942779541, + 2.7290000915527344, + 2.913999557495117 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.8449997901916504, + 0.8959999084472656, + 1.0049996376037598, + 1.1459999084472656, + 1.3139996528625488, + 1.7279996871948242, + 2.174999713897705, + 2.673999786376953, + 3.2039995193481445, + 3.251999855041504, + 3.102999687194824 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -2.805000066757202, + -2.8390002250671387, + -2.8560001850128174, + -2.807000160217285, + -2.7380001544952393, + -2.6500000953674316, + -2.5430002212524414, + -2.494000196456909, + -2.38100004196167, + -2.2820000648498535, + -2.2380001544952393 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -0.11400032043457031, + -0.24900007247924805, + -0.569000244140625, + -0.9670000076293945, + -1.3940000534057617, + -1.8340001106262207, + -2.2750000953674316, + -2.4180002212524414, + -2.2760002613067627, + -2.121000051498413, + -2.002000093460083 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -0.03299999237060547, + -0.07999992370605469, + -0.2090001106262207, + -0.3940000534057617, + -0.6100001335144043, + -0.8410000801086426, + -1.0729999542236328, + -1.3010001182556152, + -1.5190000534057617, + -1.7200002670288086, + -1.8550002574920654 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0, + -0.04699993133544922, + -0.17400026321411133, + -0.3559999465942383, + -0.568000316619873, + -0.7910003662109375, + -1.0130000114440918, + -1.2239999771118164, + -1.4130001068115234, + -1.558000087738037, + -1.6180000305175781 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.4163817214001295, + 0.47795961961131334, + 0.5505676203220141, + 0.5389267346349589, + 0.5391505310116466, + 0.5595778514702914, + 0.5996257496241824, + 0.6556927949830644, + 0.7209722468283324, + 0.7820150656284183, + 0.8088482954408668 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.4535879510091017, + 0.5074918206814116, + 0.6652743530032306, + 0.9371859596291022, + 1.2659557236431522, + 1.478615816263423, + 1.577445077233007, + 1.544232721726602, + 1.444608168716527, + 1.3516637938363212, + 1.312231291711858 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -0.02910236884308826, + -0.07699500745828776, + -0.20572319163383937, + -0.3902427719154792, + -0.6060936405746132, + -0.8349418694391263, + -1.0668495922112735, + -1.2931732564750122, + -1.5091252085834026, + -1.7070543416381334, + -1.8348659534671363 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0, + -0.05093044999577152, + -0.17890395949372148, + -0.3622213296130695, + -0.5744007709807, + -0.7986422386844602, + -1.0224084257325994, + -1.2357800576539166, + -1.4277962788317808, + -1.579796350710612, + -1.6455348336741837 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "blue" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.3820151686668396, + 0.4353727400302887, + 0.501971960067749, + 0.5688056945800781, + 0.5747143030166626, + 0.6009825468063354, + 0.6415016055107117, + 0.6995277404785156, + 0.7660749554634094, + 0.8433831930160522, + 0.8762089014053345 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "blue" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 0.4932188093662262, + 0.5469381213188171, + 0.6642600297927856, + 0.928294837474823, + 1.2238987684249878, + 1.4589495658874512, + 1.5917128324508667, + 1.5662966966629028, + 1.463591456413269, + 1.3635516166687012, + 1.3197029829025269 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "blue" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + -0.03758132457733154, + -0.08677172660827637, + -0.21767783164978027, + -0.4047420620918274, + -0.6230689287185669, + -0.8520381450653076, + -1.0831680297851562, + -1.3068233728408813, + -1.5190889835357666, + -1.70831298828125, + -1.8221969604492188 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "blue" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x", + "y": [ + 2.384185791015625e-07, + -0.07094085216522217, + -0.20446914434432983, + -0.39226412773132324, + -0.6083120107650757, + -0.8349472284317017, + -1.0624866485595703, + -1.2821804285049438, + -1.4831597805023193, + -1.6506619453430176, + -1.7139101028442383 + ], + "yaxis": "y" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.4289999008178711, + 0.46700000762939453, + 0.41300010681152344, + 0.38299989700317383, + 0.38000011444091797, + 0.40199995040893555, + 0.4479999542236328, + 0.5149998664855957, + 0.5970001220703125, + 0.6820001602172852, + 0.7270002365112305 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.5089998245239258, + 0.495999813079834, + 0.6880002021789551, + 0.9800000190734863, + 1.2049999237060547, + 1.3910002708435059, + 1.4759998321533203, + 1.3899998664855957, + 1.250999927520752, + 1.125, + 1.065999984741211 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.6700000762939453, + 0.7309999465942383, + 0.8580002784729004, + 1.0190000534057617, + 1.3499999046325684, + 1.7800002098083496, + 1.938000202178955, + 2.135000228881836, + 2.4169998168945312, + 2.7270002365112305, + 2.98799991607666 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.9019999504089355, + 0.9609999656677246, + 1.1329998970031738, + 1.4000000953674316, + 1.744999885559082, + 1.940000057220459, + 2.25600004196167, + 2.7690000534057617, + 3.312000274658203, + 3.3439998626708984, + 3.1090002059936523 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -2.7019999027252197, + -2.740000009536743, + -2.8429999351501465, + -2.9140000343322754, + -2.8459999561309814, + -2.759000062942505, + -2.6540000438690186, + -2.5320000648498535, + -2.3969998359680176, + -2.259999990463257, + -2.180000066757202 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -0.14599990844726562, + -0.19099998474121094, + -0.370999813079834, + -0.7300000190734863, + -1.130000114440918, + -1.5500001907348633, + -1.9779999256134033, + -2.4070000648498535, + -2.3969998359680176, + -2.259000062942505, + -2.180000066757202 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -0.14499998092651367, + -0.19000005722045898, + -0.315000057220459, + -0.4930000305175781, + -0.7039999961853027, + -0.9289999008178711, + -1.1570000648498535, + -1.379000186920166, + -1.5889997482299805, + -1.7719998359680176, + -1.8659999370574951 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "black" + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0, + -0.10300016403198242, + -0.31400012969970703, + -0.4930000305175781, + -0.7030000686645508, + -0.9279999732971191, + -1.1560001373291016, + -1.379000186920166, + -1.5889997482299805, + -1.7719998359680176, + -1.8659999370574951 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.41281924989220464, + 0.41825276771477893, + 0.4111516454578501, + 0.38203538262889297, + 0.3786295488118824, + 0.3999899105838819, + 0.44502530116046274, + 0.5097547590205099, + 0.5908130357600042, + 0.6727547681738544, + 0.7153199559970089 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.5252439375924401, + 0.5508154116749914, + 0.694986123351472, + 0.9464298343537881, + 1.2041430093545828, + 1.390714202306967, + 1.4729052090313282, + 1.3898533749972222, + 1.2542326616125674, + 1.1311389926712672, + 1.0736195965753645 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -0.14034649454688303, + -0.18651320569584554, + -0.3116485508895855, + -0.4913715737508009, + -0.7017306564128505, + -0.9269873821629887, + -1.1550569106293689, + -1.3781391347554781, + -1.5886258201864365, + -1.7733981796221245, + -1.872869742353707 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "red" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0, + -0.09569539674163317, + -0.2965486522872288, + -0.48596713274679654, + -0.696305946514067, + -0.9210580959633539, + -1.1484008468357862, + -1.3698254668456413, + -1.5776764050446328, + -1.7568520330146953, + -1.8481984497171589 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "blue" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.3820151686668396, + 0.4353727400302887, + 0.501971960067749, + 0.5688056945800781, + 0.5747143030166626, + 0.6009825468063354, + 0.6415016055107117, + 0.6995277404785156, + 0.7660749554634094, + 0.8433831930160522, + 0.8762089014053345 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "blue" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 0.4932188093662262, + 0.5469381213188171, + 0.6642600297927856, + 0.928294837474823, + 1.2238987684249878, + 1.4589495658874512, + 1.5917128324508667, + 1.5662966966629028, + 1.463591456413269, + 1.3635516166687012, + 1.3197029829025269 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "blue" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + -0.03758132457733154, + -0.08677172660827637, + -0.21767783164978027, + -0.4047420620918274, + -0.6230689287185669, + -0.8520381450653076, + -1.0831680297851562, + -1.3068233728408813, + -1.5190889835357666, + -1.70831298828125, + -1.8221969604492188 + ], + "yaxis": "y2" + }, + { + "marker": { + "color": "blue" + }, + "mode": "markers", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11 + ], + "xaxis": "x2", + "y": [ + 2.384185791015625e-07, + -0.07094085216522217, + -0.20446914434432983, + -0.39226412773132324, + -0.6083120107650757, + -0.8349472284317017, + -1.0624866485595703, + -1.2821804285049438, + -1.4831597805023193, + -1.6506619453430176, + -1.7139101028442383 + ], + "yaxis": "y2" + }, + { + "line": { + "color": "RoyalBlue", + "dash": "dot", + "width": 3 + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 11 ], + "xaxis": "x", "y": [ 0, 0 - ] + ], + "yaxis": "y" + }, + { + "line": { + "color": "RoyalBlue", + "dash": "dot", + "width": 3 + }, + "mode": "lines", + "name": "markers", + "showlegend": false, + "type": "scatter", + "x": [ + 1, + 11 + ], + "xaxis": "x2", + "y": [ + 0, + 0 + ], + "yaxis": "y2" } ], "layout": { + "annotations": [ + { + "font": { + "size": 16 + }, + "showarrow": false, + "text": "Si2Ge2 strain 2.5%", + "x": 0.225, + "xanchor": "center", + "xref": "paper", + "y": 1, + "yanchor": "bottom", + "yref": "paper" + }, + { + "font": { + "size": 16 + }, + "showarrow": false, + "text": "Si3Ge1 strain 3%", + "x": 0.775, + "xanchor": "center", + "xref": "paper", + "y": 1, + "yanchor": "bottom", + "yref": "paper" + } + ], "height": 650, "plot_bgcolor": "white", "template": { @@ -3151,8 +6560,39 @@ "title": { "text": "Si2Ge2 relaxed" }, - "width": 450, + "width": 800, "xaxis": { + "anchor": "y", + "domain": [ + 0, + 0.45 + ], + "gridcolor": "lightgrey", + "gridwidth": 0.5, + "linecolor": "black", + "linewidth": 1, + "mirror": true, + "range": [ + 1, + 11 + ], + "showgrid": true, + "ticks": "inside", + "ticktext": [ + "G", + "Z" + ], + "tickvals": [ + 1, + 11 + ] + }, + "xaxis2": { + "anchor": "y2", + "domain": [ + 0.55, + 1 + ], "gridcolor": "lightgrey", "gridwidth": 0.5, "linecolor": "black", @@ -3174,6 +6614,28 @@ ] }, "yaxis": { + "anchor": "x", + "domain": [ + 0, + 1 + ], + "gridcolor": "lightgrey", + "gridwidth": 0.5, + "linecolor": "black", + "linewidth": 1, + "mirror": true, + "showgrid": true, + "ticks": "inside", + "title": { + "text": "Energy, eV" + } + }, + "yaxis2": { + "anchor": "x2", + "domain": [ + 0, + 1 + ], "gridcolor": "lightgrey", "gridwidth": 0.5, "linecolor": "black", @@ -3191,20 +6653,20 @@ "
\n", " \n", " \n", - "
\n", + "
\n", "