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 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..fa1e208f --- /dev/null +++ b/vitalypro/.ipynb_checkpoints/code_implementation_example-checkpoint.ipynb @@ -0,0 +1,7053 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T20:09:03.115197Z", + "start_time": "2021-10-29T20:09:01.575710Z" + } + }, + "outputs": [], + "source": [ + "#load some modules \n", + "from ml_modeling_module import *\n", + "from os import walk\n", + "import plotly.graph_objects as go\n", + "from plotly.subplots import make_subplots" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# first let's plot some sige bandstructures calculated with DFT" + ] + }, + { + "cell_type": "code", + "execution_count": 2, 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" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "### EXAMPLE OF READING DATA WITH MODE=\"FERMI\" ###\n", + "\n", + "\"\"\"\n", + "read QE output file with bands for 0% and 5% strain \n", + "reshape data: 8 bands 11 k-points\n", + "fermi level is manually specified \n", + "\"\"\"\n", + "data=read_data('bands/si2ge2_0.dat')\n", + "si2ge2_0=data.read_bands_ml(mode='Fermi',fermi=6.18, bands_num=4)\n", + "si2ge2_0=si2ge2_0.reshape(8,11)\n", + "\n", + "data=read_data('bands/si2ge2_5.dat')\n", + "si2ge2_5=data.read_bands_ml(mode='Fermi',fermi=5.60, bands_num=4)\n", + "si2ge2_5=si2ge2_5.reshape(8,11)\n", + "\n", + "fig = make_subplots(rows=1, cols=2,subplot_titles=(\"Si2Ge strain 0%\", \"Si2Ge2 strain 5%\"))\n", + "\n", + "for i in range(si2ge2_0.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si2ge2_0[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), col=1, row=1) \n", + "for i in range(si2ge2_5.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si2ge2_5[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), col=2, row=1) \n", + "\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.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", + "\"\"\"\n", + "I used only 11 k-points to produce these bandstructures,\n", + "therefore, the bandstructures look a bit ugly\n", + "We can see how conduction bands shift with applied strain\n", + "\"\"\"" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T20:09:08.040635Z", + "start_time": "2021-10-29T20:09:07.941613Z" + }, + "scrolled": false + }, + "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": [ + 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"si3ge1_5=si3ge1_5.reshape(8,11)\n", + "\n", + "\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", + "\"\"\"\n", + "I used only 11 k-points to produce these bandstructures,\n", + "therefore, the bandstructures look a bit ugly\n", + "We can see how conduction bands shift with applied strain\n", + "\"\"\"" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T20:09:11.732047Z", + "start_time": "2021-10-29T20:09:11.692038Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "array([[10.34568286, 11.02820471, 0.25 ],\n", + " 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"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", + "\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": 5, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T20:09:14.289238Z", + "start_time": "2021-10-29T20:09:14.260232Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "(19, 44)" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "''' \n", + "reading bands from all QE output files \n", + "(output files are produced with band.x module)\n", + "'''\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": 8, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T20:09:53.539674Z", + "start_time": "2021-10-29T20:09:47.109225Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Time taken for RF: 0:00:06.364436\n", + "Train:\n", + "R^2:0.96 RMSE:0.02\n", + "Test:\n", + "R^2:1.0 RMSE: 0.02\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" + ] + } + ], + "source": [ + "my_data=data_preparation(X,y)\n", + "\n", + "#to manually specify testing set, use the following:\n", + "(X_train, X_test, Y_train, Y_test)=my_data.select_train_test(test_row_number=[12,16])\n", + "# for a random split use function:\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=12, timeout=150*60,loss_threshold=0.01, cv=5, verbose=1)\n", + "\n", + "print(text_RF)\n", + "\n", + "\n", + "#" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T20:28:55.380238Z", + "start_time": "2021-10-29T20:10:22.332765Z" + } + }, + "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: 0:18:31.542898\n", + "Train:\n", + "R^2:0.2 RMSE:0.1\n", + "Test:\n", + "R^2:1.0 RMSE: 0.06\n" + ] + } + ], + "source": [ + "## MultiOutputRegressor is VERY SLOW!\n", + "## need more time to better understand MultiOutputRegressor\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,cv=5, verbose=1, init_vals=[best_space])\n", + "print(text_XG)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# let's plot predicted bands vs calculated bands" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T20:30:04.049798Z", + "start_time": "2021-10-29T20:30:03.958778Z" + } + }, + "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, + 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marker=dict(color='black'), showlegend=False, \n", + " name='markers'), row=1, col=1)\n", + " \n", + "for i in range(bands_RF_1.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_RF_1[i],\n", + " mode='markers', marker=dict(color='red'), showlegend=False, \n", + " name='markers'), row=1, col=1)\n", + "for i in range(bands_XG_1.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_XG_1[i],\n", + " mode='markers', marker=dict(color='blue'), showlegend=False, \n", + " name='markers'), row=1, col=1)\n", + "for i in range(bands_si3ge1_3.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_si3ge1_3[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), row=1, col=2)\n", + " \n", + "for i in range(bands_RF_2.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_RF_2[i],\n", + " mode='markers', marker=dict(color='red'), showlegend=False, \n", + " name='markers'), row=1, col=2) \n", + "for i in range(bands_XG_2.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_XG_2[i],\n", + " mode='markers', marker=dict(color='blue'), showlegend=False, \n", + " name='markers'), row=1, col=2) \n", + " \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", + "\n", + "fig.add_trace(go.Scatter(x=[12,13], y=[0,0],\n", + " mode='lines', line=dict(color= \"black\"), showlegend=True, name='DFT-PBE', \n", + " ),col=1, row=1) \n", + "fig.add_trace(go.Scatter(x=[12], y=[0],\n", + " mode='markers', line=dict(color= \"red\"), showlegend=True, name='RandomForest', \n", + " ),col=1, row=1) \n", + "fig.add_trace(go.Scatter(x=[12], y=[0],\n", + " mode='markers', line=dict(color= \"blue\"), showlegend=True, name='MultiOutputRegressor-XGBoost', \n", + " ),col=1, row=1) \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=1000, height=650, plot_bgcolor='white')\n", + "fig.show()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# example of solving reverse problem " + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T01:59:48.099554Z", + "start_time": "2021-10-29T01:59:31.248745Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Lattice parameters:[10.65961975 10.68515307 0.5 ]\n", + "MSE: 0.0007605645516181882\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/si2ge2_relax.dat')\n", + "bands=data.read_bands_ml(mode='Auto', bands_num=2)\n", + "\n", + "\n", + "def objfunc(x):\n", + "\n", + " x1 = float(x[0,0])\n", + " x2 = float(x[0,1])\n", + " x3 = float(x[0,2])\n", + "\n", + " return mean_squared_error(regressorRF.predict([[x1,x2,x3]]).reshape(1,44), bands.reshape(1,44))\n", + "\n", + "maxiter = 40\n", + "domain = [\n", + " {'name': 'a_paral', 'type': 'continuous', 'domain': (10, 11)},\n", + " {'name': 'a_perp', 'type': 'continuous', 'domain': (10, 11)},\n", + " {'name': 'composition', 'type': 'discrete', 'domain': (0.25,0.5,0.75)}\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)) \n", + "\n", + "\"\"\"\n", + "I will explain this part on Monaday \n", + "\"\"\"" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Example with random split 80/20" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T20:31:04.464351Z", + "start_time": "2021-10-29T20:30:58.797072Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Time taken for RF: 0:00:05.627278\n", + "Train:\n", + "R^2:0.91 RMSE:0.03\n", + "Test:\n", + "R^2:0.99 RMSE: 0.07\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" + ] + } + ], + "source": [ + "# one more example to train model with a random split 80/20\n", + "my_data=data_preparation(X,y)\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=12, timeout=150*60,loss_threshold=0.01, cv=5, verbose=1)\n", + "\n", + "print(text_RF)\n", + "\n", + "# 20% of structures are predicted with a high accuracy\n" + ] + } + ], + "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/README.md b/vitalypro/README.md new file mode 100644 index 00000000..ea166158 --- /dev/null +++ b/vitalypro/README.md @@ -0,0 +1,43 @@ +**Prediction of Electronic Band-structure in Ultra-thin SiGe Superlattices with Tree-Based Machine Learning Models** + +**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=(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 can be significantly 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: +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 (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 only. +5. I will predict bandstructure along a short path (e.g. Gamma -Z) with a small number of K-points +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. +7. To build a good ML model we need to provide both global and local properties of the system. Global properties are lattice constants, compositions, number of atoms (if not a constant) etc. Local properties are such as local strain, nearest neighbor environment etc. In this work I will only use global properties to build an ML model + + +**Project details** + +1. **Step 1: DFT calculations** + +In the first step I performed DFT calculations of ultra-thin SixGe1-x superlattices at different external strain (x=1,2,3 is the number of monolayers). I will provide more details on this step during our Monday call. + +2. **Step 2: Develop a module for ML modeling** + +This module consist of 3 classes: *read_data*, *data_preparation*, and *modeling*. The first class is written to get all necessary data for modeling from QE output files. This includes lattice constants, compositions, fermi level (read from xlm file) and band energies (read from bands.x output). The *data_preparation* module can be used to split the data into training / testing sets. Options with manual or random selection are included. The final module consist of two tree-based ML models: Random forest and XGboost. Random forest suppots multioutput regression, however, for XGboost I had to use sklearn MultiOutputRegressor to make predictions (see https://github.com/dmlc/xgboost/issues/2087). The modeling is perfromed with automatic hyperparameter search using Bayesian optimization. To reduce possibility of overfitting, an option for n-fold cross validation is added. More details will be provided on Monday + +3. **Step 3: Predict a SL bandstructure with the ML model** + +Finaly, when the structures are calculated, the data is extracted and prepared, we test the model performance. In the figure below, I present the final results for two SiGe SL bandstructures predicted with tree-based ML models. The black curves show the bands calculated with the DFT method, the predictions with random forest and XGboost models are shown with the red and blue dots, respectively. In general, both methods provide with good predictions, however, random forest model outperfroms the XGBoost one. I believe this mostly happens due to inability for XGBoost to deal with multioutputs. We will discuss this on Monday as well. + +![ml model performance](https://user-images.githubusercontent.com/64281595/139505384-c190b36a-62a3-48ee-9360-b1d56e0efeea.png) + + 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 00000000..a54996ce Binary files /dev/null and b/vitalypro/__pycache__/ml_modeling_module.cpython-36.pyc differ diff --git a/vitalypro/bands/si1ge3_0.dat b/vitalypro/bands/si1ge3_0.dat new file mode 100644 index 00000000..0c500f78 --- /dev/null +++ b/vitalypro/bands/si1ge3_0.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.556 -3.007 -2.690 -2.689 -2.613 -2.610 -1.918 2.801 2.872 2.873 + 2.951 3.318 3.320 5.665 6.219 6.227 6.330 6.538 6.540 6.886 + 0.000001 0.000001 0.046906 + -6.547 -3.210 -2.688 -2.687 -2.608 -2.395 -1.915 2.782 2.849 2.850 + 2.923 3.327 3.329 5.496 6.168 6.175 6.387 6.588 6.591 6.927 + 0.000003 0.000003 0.093811 + -6.518 -3.521 -2.683 -2.681 -2.601 -2.042 -1.908 2.726 2.784 2.785 + 2.844 3.356 3.358 5.125 6.029 6.036 6.551 6.736 6.738 6.931 + 0.000004 0.000004 0.140717 + -6.470 -3.831 -2.675 -2.673 -2.591 -1.897 -1.661 2.643 2.690 2.691 + 2.730 3.404 3.406 4.686 5.835 5.841 6.806 6.929 6.968 6.971 + 0.000005 0.000005 0.187622 + -6.403 -4.130 -2.664 -2.663 -2.579 -1.883 -1.264 2.544 2.579 2.580 + 2.599 3.470 3.472 4.223 5.613 5.618 6.940 7.136 7.271 7.274 + 0.000007 0.000007 0.234528 + -6.317 -4.413 -2.653 -2.651 -2.564 -1.867 -0.854 2.441 2.466 2.467 + 2.467 3.555 3.557 3.751 5.379 5.384 6.967 7.525 7.634 7.636 + 0.000008 0.000008 0.281433 + -6.213 -4.680 -2.641 -2.639 -2.550 -1.851 -0.434 2.342 2.345 2.361 + 2.362 3.279 3.657 3.659 5.146 5.150 7.011 7.920 7.963 8.044 + 0.000009 0.000009 0.328339 + -6.091 -4.929 -2.630 -2.628 -2.536 -1.836 -0.007 2.242 2.258 2.271 + 2.272 2.809 3.776 3.778 4.922 4.926 7.070 7.908 8.382 8.441 + 0.000011 0.000011 0.375244 + -5.953 -5.158 -2.621 -2.619 -2.525 -1.824 0.423 2.164 2.193 2.204 + 2.204 2.349 3.908 3.910 4.713 4.716 7.138 7.807 8.577 8.953 + 0.000012 0.000012 0.422150 + -5.807 -5.360 -2.615 -2.614 -2.518 -1.816 0.838 1.915 2.116 2.152 + 2.161 2.162 4.041 4.042 4.532 4.536 7.201 7.711 8.800 9.230 + 0.000013 0.000013 0.469056 + -5.710 -5.474 -2.613 -2.612 -2.516 -1.814 1.096 1.651 2.100 2.139 + 2.147 2.147 4.117 4.118 4.441 4.445 7.230 7.670 8.970 9.099 diff --git a/vitalypro/bands/si1ge3_1.dat b/vitalypro/bands/si1ge3_1.dat new file mode 100644 index 00000000..9285e92f --- /dev/null +++ b/vitalypro/bands/si1ge3_1.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.607 -3.052 -2.828 -2.827 -2.751 -2.654 -2.057 2.726 2.799 2.799 + 2.876 3.115 3.116 5.605 6.013 6.013 6.247 6.448 6.449 6.620 + 0.000001 0.000001 0.047724 + -6.598 -3.254 -2.826 -2.826 -2.748 -2.438 -2.055 2.705 2.775 2.775 + 2.847 3.125 3.125 5.417 5.963 5.963 6.305 6.500 6.500 6.683 + 0.000003 0.000003 0.095449 + -6.569 -3.564 -2.820 -2.820 -2.742 -2.087 -2.048 2.648 2.708 2.708 + 2.766 3.154 3.154 5.028 5.827 5.827 6.471 6.649 6.650 6.691 + 0.000004 0.000004 0.143173 + -6.521 -3.874 -2.812 -2.812 -2.732 -2.036 -1.708 2.562 2.611 2.611 + 2.649 3.202 3.202 4.583 5.635 5.635 6.686 6.730 6.886 6.886 + 0.000005 0.000005 0.190897 + -6.453 -4.172 -2.801 -2.801 -2.719 -2.022 -1.313 2.460 2.497 2.497 + 2.515 3.269 3.269 4.119 5.414 5.414 6.695 7.065 7.194 7.195 + 0.000007 0.000007 0.238622 + -6.367 -4.456 -2.789 -2.789 -2.704 -2.006 -0.907 2.353 2.380 2.381 + 2.381 3.354 3.354 3.651 5.182 5.182 6.720 7.458 7.561 7.562 + 0.000008 0.000008 0.286346 + -6.263 -4.724 -2.777 -2.777 -2.689 -1.989 -0.490 2.252 2.256 2.272 + 2.272 3.183 3.457 3.458 4.949 4.949 6.764 7.701 7.901 7.977 + 0.000009 0.000009 0.334070 + -6.140 -4.973 -2.766 -2.765 -2.676 -1.974 -0.067 2.151 2.166 2.181 + 2.181 2.720 3.577 3.577 4.725 4.725 6.823 7.671 8.166 8.383 + 0.000011 0.000011 0.381795 + -6.002 -5.203 -2.757 -2.756 -2.665 -1.962 0.357 2.072 2.099 2.111 + 2.111 2.266 3.710 3.710 4.515 4.515 6.892 7.559 8.371 8.900 + 0.000012 0.000012 0.429519 + -5.854 -5.405 -2.751 -2.751 -2.658 -1.954 0.766 1.839 2.023 2.057 + 2.068 2.068 3.844 3.844 4.333 4.333 6.957 7.457 8.599 9.019 + 0.000013 0.000013 0.477243 + -5.758 -5.520 -2.749 -2.749 -2.655 -1.951 1.017 1.583 2.006 2.043 + 2.053 2.053 3.921 3.921 4.240 4.241 6.988 7.414 8.768 8.895 diff --git a/vitalypro/bands/si1ge3_2.dat b/vitalypro/bands/si1ge3_2.dat new file mode 100644 index 00000000..6d364f1b --- /dev/null +++ b/vitalypro/bands/si1ge3_2.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.651 -3.088 -2.948 -2.948 -2.871 -2.686 -2.182 2.664 2.741 2.741 + 2.817 2.935 2.935 5.556 5.829 5.830 6.175 6.373 6.373 6.382 + 0.000001 0.000001 0.048528 + -6.641 -3.288 -2.947 -2.946 -2.869 -2.472 -2.179 2.643 2.716 2.716 + 2.787 2.944 2.944 5.345 5.780 5.781 6.234 6.425 6.426 6.466 + 0.000003 0.000003 0.097055 + -6.612 -3.597 -2.941 -2.941 -2.862 -2.172 -2.123 2.583 2.647 2.647 + 2.703 2.973 2.974 4.940 5.647 5.647 6.403 6.476 6.578 6.579 + 0.000004 0.000004 0.145583 + -6.564 -3.908 -2.932 -2.932 -2.852 -2.160 -1.746 2.494 2.546 2.546 + 2.583 3.022 3.022 4.489 5.457 5.457 6.468 6.667 6.819 6.819 + 0.000005 0.000005 0.194110 + -6.496 -4.206 -2.921 -2.921 -2.839 -2.146 -1.353 2.389 2.429 2.429 + 2.446 3.089 3.089 4.027 5.238 5.238 6.474 7.006 7.133 7.133 + 0.000007 0.000007 0.242638 + -6.409 -4.491 -2.909 -2.909 -2.824 -2.129 -0.950 2.280 2.307 2.309 + 2.309 3.175 3.175 3.562 5.006 5.007 6.498 7.390 7.405 7.506 + 0.000008 0.000008 0.291166 + -6.304 -4.759 -2.896 -2.896 -2.808 -2.112 -0.537 2.176 2.180 2.197 + 2.197 3.099 3.279 3.279 4.775 4.775 6.540 7.507 7.852 7.863 + 0.000009 0.000009 0.339693 + -6.181 -5.009 -2.885 -2.885 -2.795 -2.097 -0.118 2.073 2.087 2.103 + 2.103 2.641 3.399 3.399 4.550 4.550 6.599 7.458 7.982 8.340 + 0.000010 0.000010 0.388221 + -6.041 -5.240 -2.875 -2.875 -2.783 -2.084 0.301 1.992 2.019 2.032 + 2.032 2.193 3.532 3.532 4.340 4.340 6.669 7.338 8.197 8.861 + 0.000012 0.000012 0.436748 + -5.893 -5.443 -2.869 -2.869 -2.776 -2.076 0.703 1.774 1.942 1.976 + 1.987 1.987 3.667 3.667 4.158 4.158 6.737 7.231 8.427 8.840 + 0.000013 0.000013 0.485276 + -5.795 -5.559 -2.867 -2.867 -2.773 -2.073 0.947 1.525 1.925 1.961 + 1.972 1.972 3.745 3.745 4.065 4.065 6.769 7.185 8.593 8.724 diff --git a/vitalypro/bands/si1ge3_3.dat b/vitalypro/bands/si1ge3_3.dat new file mode 100644 index 00000000..cdb48b25 --- /dev/null +++ b/vitalypro/bands/si1ge3_3.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.691 -3.124 -3.061 -3.061 -2.984 -2.719 -2.297 2.606 2.686 2.686 + 2.762 2.768 2.768 5.506 5.658 5.659 6.107 6.150 6.301 6.301 + 0.000001 0.000001 0.049295 + -6.682 -3.323 -3.059 -3.059 -2.982 -2.507 -2.294 2.584 2.661 2.661 + 2.731 2.777 2.778 5.266 5.610 5.611 6.167 6.263 6.354 6.355 + 0.000003 0.000003 0.098591 + -6.652 -3.631 -3.053 -3.053 -2.975 -2.287 -2.159 2.523 2.589 2.589 + 2.645 2.807 2.807 4.844 5.479 5.479 6.275 6.339 6.510 6.510 + 0.000004 0.000004 0.147886 + -6.604 -3.941 -3.044 -3.044 -2.964 -2.275 -1.785 2.432 2.485 2.485 + 2.522 2.855 2.856 4.390 5.292 5.292 6.264 6.607 6.755 6.755 + 0.000005 0.000005 0.197182 + -6.536 -4.239 -3.033 -3.033 -2.951 -2.260 -1.395 2.324 2.365 2.365 + 2.381 2.923 2.923 3.929 5.074 5.074 6.267 6.950 7.043 7.073 + 0.000007 0.000007 0.246477 + -6.448 -4.524 -3.020 -3.020 -2.935 -2.243 -0.995 2.211 2.240 2.241 + 2.241 3.009 3.010 3.468 4.844 4.844 6.290 7.216 7.354 7.451 + 0.000008 0.000008 0.295773 + -6.343 -4.792 -3.007 -3.007 -2.920 -2.226 -0.586 2.105 2.110 2.127 + 2.127 3.010 3.114 3.114 4.613 4.613 6.331 7.324 7.674 7.806 + 0.000009 0.000009 0.345068 + -6.219 -5.043 -2.995 -2.995 -2.906 -2.210 -0.172 2.000 2.013 2.030 + 2.030 2.558 3.235 3.235 4.388 4.389 6.390 7.258 7.813 8.297 + 0.000010 0.000010 0.394363 + -6.078 -5.275 -2.985 -2.985 -2.894 -2.197 0.242 1.918 1.943 1.957 + 1.957 2.116 3.369 3.369 4.178 4.178 6.461 7.130 8.036 8.728 + 0.000012 0.000012 0.443659 + -5.929 -5.479 -2.979 -2.979 -2.887 -2.189 0.637 1.705 1.867 1.899 + 1.912 1.912 3.505 3.505 3.995 3.995 6.530 7.018 8.269 8.672 + 0.000013 0.000013 0.492954 + -5.830 -5.596 -2.977 -2.977 -2.884 -2.186 0.874 1.463 1.850 1.885 + 1.896 1.896 3.583 3.583 3.901 3.902 6.563 6.970 8.433 8.564 diff --git a/vitalypro/bands/si1ge3_4.dat b/vitalypro/bands/si1ge3_4.dat new file mode 100644 index 00000000..bf58f5e7 --- /dev/null +++ b/vitalypro/bands/si1ge3_4.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.731 -3.172 -3.170 -3.163 -3.095 -2.756 -2.410 2.548 2.606 2.606 + 2.631 2.631 2.706 5.447 5.490 5.491 5.909 6.036 6.218 6.226 + 0.000001 0.000001 0.050050 + -6.722 -3.361 -3.170 -3.168 -3.092 -2.546 -2.407 2.526 2.604 2.605 + 2.616 2.616 2.674 5.169 5.442 5.443 6.062 6.097 6.279 6.282 + 0.000003 0.000003 0.100100 + -6.692 -3.667 -3.164 -3.162 -3.086 -2.400 -2.201 2.462 2.531 2.531 + 2.586 2.645 2.646 4.733 5.313 5.314 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0.000012 0.450452 + -5.966 -5.515 -3.088 -3.087 -2.996 -2.300 0.562 1.625 1.792 1.823 + 1.837 1.837 3.346 3.347 3.837 3.838 6.327 6.809 8.114 8.503 + 0.000013 0.000013 0.500502 + -5.866 -5.633 -3.086 -3.085 -2.993 -2.297 0.792 1.391 1.775 1.808 + 1.821 1.821 3.425 3.427 3.742 3.744 6.361 6.760 8.274 8.404 diff --git a/vitalypro/bands/si1ge3_5.dat b/vitalypro/bands/si1ge3_5.dat new file mode 100644 index 00000000..025ece8c --- /dev/null +++ b/vitalypro/bands/si1ge3_5.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.772 -3.285 -3.285 -3.210 -3.203 -2.792 -2.527 2.437 2.437 2.492 + 2.578 2.578 2.653 5.314 5.314 5.385 5.651 5.966 6.028 6.151 + 0.000001 0.000001 0.050911 + -6.762 -3.398 -3.283 -3.283 -3.207 -2.585 -2.525 2.447 2.447 2.469 + 2.551 2.551 2.620 5.054 5.268 5.269 5.854 6.028 6.124 6.207 + 0.000003 0.000003 0.101822 + -6.733 -3.703 -3.277 -3.277 -3.200 -2.517 -2.243 2.403 2.474 2.474 + 2.476 2.477 2.529 4.607 5.142 5.142 5.871 6.206 6.352 6.368 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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/si2ge2_1.dat b/vitalypro/bands/si2ge2_1.dat new file mode 100644 index 00000000..7f9bcb77 --- /dev/null +++ b/vitalypro/bands/si2ge2_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 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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/si2ge2_2.dat b/vitalypro/bands/si2ge2_2.dat new file mode 100644 index 00000000..e776d146 --- /dev/null +++ b/vitalypro/bands/si2ge2_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 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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/si2ge2_4.dat b/vitalypro/bands/si2ge2_4.dat new file mode 100644 index 00000000..4e77074a --- /dev/null +++ b/vitalypro/bands/si2ge2_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 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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/si2ge2_5.dat b/vitalypro/bands/si2ge2_5.dat new file mode 100644 index 00000000..e1c156d3 --- /dev/null +++ b/vitalypro/bands/si2ge2_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 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-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/si2ge2_relax.dat b/vitalypro/bands/si2ge2_relax.dat new file mode 100644 index 00000000..b137e447 --- /dev/null +++ b/vitalypro/bands/si2ge2_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/bands/si3ge1_0.dat b/vitalypro/bands/si3ge1_0.dat new file mode 100644 index 00000000..d6201d72 --- /dev/null +++ b/vitalypro/bands/si3ge1_0.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.045 -2.521 -2.284 -1.873 -1.820 -1.756 -1.754 3.017 3.088 3.088 + 3.145 3.225 3.225 5.862 6.063 6.063 6.312 6.787 6.789 6.790 + 0.000001 0.000001 0.048948 + -6.034 -2.519 -2.496 -1.818 -1.752 -1.751 -1.648 2.993 3.059 3.059 + 3.111 3.234 3.234 5.772 6.016 6.016 6.375 6.759 6.844 6.846 + 0.000003 0.000003 0.097896 + -6.004 -2.821 -2.511 -1.810 -1.743 -1.742 -1.284 2.927 2.979 2.979 + 3.018 3.263 3.263 5.531 5.887 5.887 6.554 6.723 7.006 7.007 + 0.000004 0.000004 0.146844 + -5.953 -3.146 -2.500 -1.797 -1.728 -1.726 -0.892 2.828 2.862 2.862 + 2.886 3.310 3.311 5.195 5.703 5.703 6.705 6.830 7.252 7.258 + 0.000005 0.000005 0.195793 + -5.882 -3.459 -2.485 -1.781 -1.708 -1.707 -0.485 2.712 2.726 2.726 + 2.736 3.377 3.377 4.805 5.489 5.490 6.710 7.182 7.415 7.586 + 0.000006 0.000006 0.244741 + -5.790 -3.758 -2.469 -1.763 -1.686 -1.685 -0.068 2.586 2.587 2.587 + 2.592 3.461 3.462 4.386 5.263 5.264 6.738 7.584 7.593 7.973 + 0.000008 0.000008 0.293689 + -5.680 -4.039 -2.452 -1.744 -1.663 -1.662 0.357 2.449 2.457 2.457 + 2.479 3.564 3.564 3.953 5.036 5.036 6.786 7.699 8.051 8.183 + 0.000009 0.000009 0.342637 + -5.551 -4.301 -2.436 -1.727 -1.642 -1.641 0.787 2.334 2.346 2.346 + 2.382 3.513 3.682 3.682 4.815 4.816 6.853 7.669 8.310 8.546 + 0.000010 0.000010 0.391585 + -5.407 -4.541 -2.424 -1.713 -1.625 -1.624 1.218 2.248 2.262 2.262 + 2.308 3.074 3.814 3.814 4.609 4.610 6.933 7.559 8.554 9.071 + 0.000011 0.000011 0.440533 + -5.258 -4.748 -2.416 -1.704 -1.614 -1.613 1.637 2.194 2.209 2.209 + 2.262 2.650 3.946 3.947 4.430 4.431 7.012 7.449 8.845 9.476 + 0.000013 0.000013 0.489481 + -5.168 -4.857 -2.413 -1.700 -1.610 -1.609 1.909 2.176 2.191 2.191 + 2.246 2.376 4.022 4.023 4.338 4.340 7.052 7.397 9.114 9.209 diff --git a/vitalypro/bands/si3ge1_1.dat b/vitalypro/bands/si3ge1_1.dat new file mode 100644 index 00000000..0e28ede6 --- /dev/null +++ b/vitalypro/bands/si3ge1_1.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.093 -2.651 -2.319 -1.954 -1.903 -1.889 -1.888 2.954 3.024 3.025 + 3.029 3.029 3.086 5.802 5.873 5.874 6.242 6.574 6.715 6.718 + 0.000001 0.000001 0.049843 + -6.083 -2.648 -2.529 -1.951 -1.886 -1.884 -1.680 2.929 2.994 2.995 + 3.039 3.039 3.051 5.708 5.826 5.828 6.306 6.542 6.772 6.775 + 0.000003 0.000003 0.099686 + -6.052 -2.853 -2.641 -1.943 -1.876 -1.875 -1.317 2.860 2.912 2.912 + 2.954 3.068 3.068 5.459 5.700 5.701 6.489 6.499 6.906 6.937 + 0.000004 0.000004 0.149529 + -6.000 -3.179 -2.629 -1.930 -1.861 -1.859 -0.927 2.758 2.791 2.792 + 2.818 3.116 3.116 5.115 5.518 5.519 6.478 6.771 7.054 7.195 + 0.000005 0.000005 0.199371 + -5.928 -3.493 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2.102 2.102 + 2.157 2.319 3.834 3.837 4.150 4.151 6.824 7.167 8.952 9.058 diff --git a/vitalypro/bands/si3ge1_2.dat b/vitalypro/bands/si3ge1_2.dat new file mode 100644 index 00000000..df554fc8 --- /dev/null +++ b/vitalypro/bands/si3ge1_2.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.135 -2.766 -2.349 -2.073 -2.008 -2.007 -1.929 2.854 2.855 2.901 + 2.971 2.971 3.037 5.704 5.707 5.748 6.181 6.383 6.543 6.654 + 0.000001 0.000001 0.050700 + -6.125 -2.763 -2.557 -2.070 -2.004 -2.003 -1.707 2.864 2.865 2.875 + 2.940 2.941 3.000 5.649 5.659 5.661 6.246 6.346 6.602 6.712 + 0.000003 0.000003 0.101399 + -6.094 -2.881 -2.756 -2.062 -1.994 -1.993 -1.346 2.803 2.855 2.855 + 2.893 2.894 2.901 5.391 5.533 5.536 6.298 6.433 6.723 6.880 + 0.000004 0.000004 0.152099 + -6.042 -3.207 -2.743 -2.048 -1.978 -1.977 -0.959 2.697 2.731 2.731 + 2.759 2.942 2.943 5.040 5.353 5.355 6.272 6.721 6.878 7.142 + 0.000005 0.000005 0.202798 + -5.969 -3.522 -2.728 -2.031 -1.958 -1.957 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3.670 3.983 3.983 6.617 6.958 8.811 8.925 diff --git a/vitalypro/bands/si3ge1_3.dat b/vitalypro/bands/si3ge1_3.dat new file mode 100644 index 00000000..306fe54c --- /dev/null +++ b/vitalypro/bands/si3ge1_3.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.173 -2.870 -2.374 -2.181 -2.115 -2.115 -1.950 2.695 2.695 2.857 + 2.927 2.927 2.996 5.552 5.553 5.698 6.127 6.207 6.368 6.600 + 0.000001 0.000001 0.051544 + -6.163 -2.867 -2.581 -2.178 -2.112 -2.111 -1.730 2.705 2.705 2.830 + 2.895 2.895 2.958 5.507 5.508 5.595 6.165 6.194 6.429 6.659 + 0.000002 0.000002 0.103088 + -6.131 -2.904 -2.859 -2.170 -2.101 -2.101 -1.372 2.734 2.735 2.755 + 2.806 2.807 2.855 5.327 5.383 5.384 6.111 6.386 6.556 6.831 + 0.000004 0.000004 0.154631 + -6.079 -3.230 -2.847 -2.156 -2.085 -2.085 -0.987 2.645 2.678 2.679 + 2.709 2.784 2.784 4.968 5.205 5.205 6.081 6.678 6.717 7.098 + 0.000005 0.000005 0.206175 + -6.006 -3.546 -2.831 -2.138 -2.064 -2.064 -0.589 2.517 2.530 2.530 + 2.546 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8.686 8.807 diff --git a/vitalypro/bands/si3ge1_4.dat b/vitalypro/bands/si3ge1_4.dat new file mode 100644 index 00000000..61ac3ad5 --- /dev/null +++ b/vitalypro/bands/si3ge1_4.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.210 -2.972 -2.403 -2.287 -2.221 -2.220 -1.974 2.540 2.541 2.812 + 2.882 2.882 2.955 5.401 5.403 5.640 6.035 6.073 6.200 6.544 + 0.000001 0.000001 0.052382 + -6.200 -2.969 -2.608 -2.284 -2.218 -2.216 -1.758 2.550 2.551 2.784 + 2.849 2.849 2.916 5.357 5.359 5.533 5.988 6.141 6.262 6.605 + 0.000002 0.000002 0.104763 + -6.168 -2.961 -2.930 -2.275 -2.207 -2.206 -1.402 2.580 2.581 2.707 + 2.758 2.758 2.809 5.235 5.237 5.254 5.928 6.336 6.393 6.779 + 0.000004 0.000004 0.157145 + -6.115 -3.256 -2.948 -2.261 -2.190 -2.189 -1.020 2.593 2.626 2.627 + 2.630 2.630 2.659 4.887 5.058 5.060 5.894 6.562 6.634 7.051 + 0.000005 0.000005 0.209526 + -6.042 -3.571 -2.931 -2.243 -2.169 -2.168 -0.626 2.461 2.474 2.474 + 2.491 2.699 2.699 4.483 4.849 4.851 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a/vitalypro/bands/si3ge1_5.dat b/vitalypro/bands/si3ge1_5.dat new file mode 100644 index 00000000..fe8c6d9e --- /dev/null +++ b/vitalypro/bands/si3ge1_5.dat @@ -0,0 +1,34 @@ + &plot nbnd= 20, nks= 11 / + 0.000000 0.000000 0.000000 + -6.247 -3.076 -2.429 -2.397 -2.330 -2.329 -1.995 2.380 2.380 2.772 + 2.843 2.843 2.920 5.248 5.248 5.578 5.856 6.021 6.030 6.494 + 0.000001 0.000001 0.053344 + -6.237 -3.073 -2.632 -2.394 -2.326 -2.325 -1.781 2.390 2.390 2.743 + 2.808 2.809 2.879 5.205 5.205 5.467 5.803 6.089 6.091 6.555 + 0.000002 0.000002 0.106688 + -6.205 -3.065 -2.953 -2.384 -2.315 -2.314 -1.429 2.420 2.420 2.663 + 2.714 2.714 2.768 5.085 5.085 5.178 5.735 6.224 6.291 6.734 + 0.000004 0.000004 0.160031 + -6.151 -3.278 -3.051 -2.369 -2.298 -2.297 -1.051 2.470 2.470 2.545 + 2.578 2.578 2.613 4.802 4.910 4.910 5.696 6.402 6.595 7.012 + 0.000005 0.000005 0.213375 + -6.077 -3.593 -3.034 -2.350 -2.275 -2.275 -0.661 2.407 2.421 2.421 + 2.439 2.540 2.540 4.393 4.702 4.702 5.686 6.604 6.977 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a/vitalypro/bandstructures.png b/vitalypro/bandstructures.png new file mode 100644 index 00000000..845b522d Binary files /dev/null and b/vitalypro/bandstructures.png differ diff --git a/vitalypro/cell_param/si1ge3_0.xml b/vitalypro/cell_param/si1ge3_0.xml new file mode 100644 index 00000000..edfa1fea --- /dev/null +++ b/vitalypro/cell_param/si1ge3_0.xml @@ -0,0 +1,474 @@ + + + + + QEXSD_19.03 + XML file generated by PWSCF + This run was terminated on: 19: 0:31 27 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 + + + + + 1.405111535285519e-3 1.405111535285519e-3 -1.147601786588879e-1 + 2.587762405052827e0 2.587762405052827e0 2.572383108915556e0 + 5.174093333111363e0 1.114382838919461e-3 5.400151413576964e0 + 1.114382838919461e-3 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a/vitalypro/cell_param/si1ge3_3.xml b/vitalypro/cell_param/si1ge3_3.xml new file mode 100644 index 00000000..769d0b12 --- /dev/null +++ b/vitalypro/cell_param/si1ge3_3.xml @@ -0,0 +1,474 @@ + + + + + QEXSD_19.03 + XML file generated by PWSCF + This run was terminated on: 19: 8:30 27 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 + + + + + -1.187566357354030e-1 -1.187566357354030e-1 -1.137914823664572e-1 + 2.546995286496302e0 2.546995286496302e0 2.520027377129939e0 + 5.213349437990391e0 -1.148688001170062e-1 5.293635747208438e0 + -1.148688001170062e-1 5.213349437990391e0 5.293635747208438e0 + 5.214012344469177e0 5.214012344469177e0 -1.121683285607809e-1 + 7.878763103023761e0 2.549538383549906e0 8.064382586262134e0 + 2.549538383549906e0 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plotly.subplots import make_subplots" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# first let's plot some sige bandstructures calculated with DFT" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T20:09:05.156811Z", + "start_time": "2021-10-29T20:09:03.685480Z" + }, + "scrolled": false + }, + "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, 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" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "### EXAMPLE OF READING DATA WITH MODE=\"FERMI\" ###\n", + "\n", + "\"\"\"\n", + "read QE output file with bands for 0% and 5% strain \n", + "reshape data: 8 bands 11 k-points\n", + "fermi level is manually specified \n", + "\"\"\"\n", + "data=read_data('bands/si2ge2_0.dat')\n", + "si2ge2_0=data.read_bands_ml(mode='Fermi',fermi=6.18, bands_num=4)\n", + "si2ge2_0=si2ge2_0.reshape(8,11)\n", + "\n", + "data=read_data('bands/si2ge2_5.dat')\n", + "si2ge2_5=data.read_bands_ml(mode='Fermi',fermi=5.60, bands_num=4)\n", + "si2ge2_5=si2ge2_5.reshape(8,11)\n", + "\n", + "fig = make_subplots(rows=1, cols=2,subplot_titles=(\"Si2Ge strain 0%\", \"Si2Ge2 strain 5%\"))\n", + "\n", + "for i in range(si2ge2_0.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si2ge2_0[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), col=1, row=1) \n", + "for i in range(si2ge2_5.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si2ge2_5[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), col=2, row=1) \n", + "\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.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", + "\"\"\"\n", + "I used only 11 k-points to produce these bandstructures,\n", + "therefore, the bandstructures look a bit ugly\n", + "We can see how conduction bands shift with applied strain\n", + "\"\"\"" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T20:09:08.040635Z", + "start_time": "2021-10-29T20:09:07.941613Z" + }, + "scrolled": false + }, + "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": [ + 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" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "### EXAMPLE OF READING DAT WITH MODE=\"Auto\" ###\n", + "\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", + "In this case the fermi level is not specified,\n", + "it is automatically placed at the top of the valence zone\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", + "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", + "\"\"\"\n", + "I used only 11 k-points to produce these bandstructures,\n", + "therefore, the bandstructures look a bit ugly\n", + "We can see how conduction bands shift with applied strain\n", + "\"\"\"" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T20:09:11.732047Z", + "start_time": "2021-10-29T20:09:11.692038Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "array([[10.34568286, 11.02820471, 0.25 ],\n", + " 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"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", + "\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": 5, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T20:09:14.289238Z", + "start_time": "2021-10-29T20:09:14.260232Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "(19, 44)" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "''' \n", + "reading bands from all QE output files \n", + "(output files are produced with band.x module)\n", + "'''\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": 8, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T20:09:53.539674Z", + "start_time": "2021-10-29T20:09:47.109225Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Time taken for RF: 0:00:06.364436\n", + "Train:\n", + "R^2:0.96 RMSE:0.02\n", + "Test:\n", + "R^2:1.0 RMSE: 0.02\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" + ] + } + ], + "source": [ + "my_data=data_preparation(X,y)\n", + "\n", + "#to manually specify testing set, use the following:\n", + "(X_train, X_test, Y_train, Y_test)=my_data.select_train_test(test_row_number=[12,16])\n", + "# for a random split use function:\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=12, timeout=150*60,loss_threshold=0.01, cv=5, verbose=1)\n", + "\n", + "print(text_RF)\n", + "\n", + "\n", + "#" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T20:28:55.380238Z", + "start_time": "2021-10-29T20:10:22.332765Z" + } + }, + "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: 0:18:31.542898\n", + "Train:\n", + "R^2:0.2 RMSE:0.1\n", + "Test:\n", + "R^2:1.0 RMSE: 0.06\n" + ] + } + ], + "source": [ + "## MultiOutputRegressor is VERY SLOW!\n", + "## need more time to better understand MultiOutputRegressor\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,cv=5, verbose=1, init_vals=[best_space])\n", + "print(text_XG)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# let's plot predicted bands vs calculated bands" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T20:30:04.049798Z", + "start_time": "2021-10-29T20:30:03.958778Z" + } + }, + "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, + 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" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "#reading calculated bands:\n", + "data=read_data('bands/si2ge2_relax.dat')\n", + "bands_si2ge2_relaxed=data.read_bands_ml(mode='Auto', bands_num=4)\n", + "bands_si2ge2_relaxed=bands_si2ge2_relaxed.reshape(8,11)\n", + "\n", + "data=read_data('bands/si3ge1_3.dat')\n", + "bands_si3ge1_3=data.read_bands_ml(mode='Auto', bands_num=4)\n", + "bands_si3ge1_3=bands_si3ge1_3.reshape(8,11)\n", + "\n", + "#predicted bands\n", + "bands_RF_1=y_predict_RF[0].reshape(4,11)\n", + "bands_RF_2=y_predict_RF[1].reshape(4,11)\n", + "\n", + "bands_XG_1=y_predict_XG[0].reshape(4,11)\n", + "bands_XG_2=y_predict_XG[0].reshape(4,11)\n", + "\n", + "fig = make_subplots(rows=1, cols=2,subplot_titles=(\"Si2Ge2 strain 2.5%\", \"Si3Ge1 strain 3%\"))\n", + "\n", + "for i in range(bands_si2ge2_relaxed.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_si2ge2_relaxed[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), row=1, col=1)\n", + " \n", + "for i in range(bands_RF_1.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_RF_1[i],\n", + " mode='markers', marker=dict(color='red'), showlegend=False, \n", + " name='markers'), row=1, col=1)\n", + "for i in range(bands_XG_1.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_XG_1[i],\n", + " mode='markers', marker=dict(color='blue'), showlegend=False, \n", + " name='markers'), row=1, col=1)\n", + "for i in range(bands_si3ge1_3.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_si3ge1_3[i],\n", + " mode='lines', marker=dict(color='black'), showlegend=False, \n", + " name='markers'), row=1, col=2)\n", + " \n", + "for i in range(bands_RF_2.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_RF_2[i],\n", + " mode='markers', marker=dict(color='red'), showlegend=False, \n", + " name='markers'), row=1, col=2) \n", + "for i in range(bands_XG_2.shape[0]):\n", + " fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_XG_2[i],\n", + " mode='markers', marker=dict(color='blue'), showlegend=False, \n", + " name='markers'), row=1, col=2) \n", + " \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", + "\n", + "fig.add_trace(go.Scatter(x=[12,13], y=[0,0],\n", + " mode='lines', line=dict(color= \"black\"), showlegend=True, name='DFT-PBE', \n", + " ),col=1, row=1) \n", + "fig.add_trace(go.Scatter(x=[12], y=[0],\n", + " mode='markers', line=dict(color= \"red\"), showlegend=True, name='RandomForest', \n", + " ),col=1, row=1) \n", + "fig.add_trace(go.Scatter(x=[12], y=[0],\n", + " mode='markers', line=dict(color= \"blue\"), showlegend=True, name='MultiOutputRegressor-XGBoost', \n", + " ),col=1, row=1) \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=1000, height=650, plot_bgcolor='white')\n", + "fig.show()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# example of solving reverse problem " + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T01:59:48.099554Z", + "start_time": "2021-10-29T01:59:31.248745Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Lattice parameters:[10.65961975 10.68515307 0.5 ]\n", + "MSE: 0.0007605645516181882\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/si2ge2_relax.dat')\n", + "bands=data.read_bands_ml(mode='Auto', bands_num=2)\n", + "\n", + "\n", + "def objfunc(x):\n", + "\n", + " x1 = float(x[0,0])\n", + " x2 = float(x[0,1])\n", + " x3 = float(x[0,2])\n", + "\n", + " return mean_squared_error(regressorRF.predict([[x1,x2,x3]]).reshape(1,44), bands.reshape(1,44))\n", + "\n", + "maxiter = 40\n", + "domain = [\n", + " {'name': 'a_paral', 'type': 'continuous', 'domain': (10, 11)},\n", + " {'name': 'a_perp', 'type': 'continuous', 'domain': (10, 11)},\n", + " {'name': 'composition', 'type': 'discrete', 'domain': (0.25,0.5,0.75)}\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)) \n", + "\n", + "\"\"\"\n", + "I will explain this part on Monaday \n", + "\"\"\"" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Example with random split 80/20" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": { + "ExecuteTime": { + "end_time": "2021-10-29T20:31:04.464351Z", + "start_time": "2021-10-29T20:30:58.797072Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Time taken for RF: 0:00:05.627278\n", + "Train:\n", + "R^2:0.91 RMSE:0.03\n", + "Test:\n", + "R^2:0.99 RMSE: 0.07\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" + ] + } + ], + "source": [ + "# one more example to train model with a random split 80/20\n", + "my_data=data_preparation(X,y)\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=12, timeout=150*60,loss_threshold=0.01, cv=5, verbose=1)\n", + "\n", + "print(text_RF)\n", + "\n", + "# 20% of structures are predicted with a high accuracy\n" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": 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100644 index 00000000..c3fe7636 --- /dev/null +++ b/vitalypro/code_implementation_example.py @@ -0,0 +1,415 @@ +#!/usr/bin/env python +# coding: utf-8 + +# In[1]: + + +#load some modules +from ml_modeling_module import * +from os import walk +import plotly.graph_objects as go +from plotly.subplots import make_subplots + + +# # first let's plot some sige bandstructures calculated with DFT + +# In[2]: + + +### EXAMPLE OF READING DATA WITH MODE="FERMI" ### + +""" +read QE output file with bands for 0% and 5% strain +reshape data: 8 bands 11 k-points +fermi level is manually specified +""" +data=read_data('bands/si2ge2_0.dat') +si2ge2_0=data.read_bands_ml(mode='Fermi',fermi=6.18, bands_num=4) +si2ge2_0=si2ge2_0.reshape(8,11) + +data=read_data('bands/si2ge2_5.dat') +si2ge2_5=data.read_bands_ml(mode='Fermi',fermi=5.60, bands_num=4) +si2ge2_5=si2ge2_5.reshape(8,11) + +fig = make_subplots(rows=1, cols=2,subplot_titles=("Si2Ge strain 0%", "Si2Ge2 strain 5%")) + +for i in range(si2ge2_0.shape[0]): + fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si2ge2_0[i], + mode='lines', marker=dict(color='black'), showlegend=False, + name='markers'), col=1, row=1) +for i in range(si2ge2_5.shape[0]): + fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si2ge2_5[i], + mode='lines', marker=dict(color='black'), showlegend=False, + name='markers'), col=2, row=1) + + +fig.add_trace(go.Scatter(x=[1,11], y=[0,0], + mode='lines', line=dict(color= "RoyalBlue",width=3, dash='dot'), showlegend=False, + name='markers'), col=1, row=1) +fig.add_trace(go.Scatter(x=[1,11], y=[0,0], + mode='lines', line=dict(color= "RoyalBlue",width=3, dash='dot'), showlegend=False, + name='markers'), col=2, row=1) +fig.update_xaxes(showgrid=True, + gridwidth=0.5, + gridcolor='lightgrey', + ticks='inside' , + linecolor= 'black', + linewidth= 1, + mirror= True, + ticktext=['G', 'Z'], + tickvals=[1,11], + range=[1,11], + ) +fig.update_yaxes(title='Energy, eV', + showgrid=True, + gridwidth=0.5, + gridcolor='lightgrey', + ticks='inside' , + linecolor= 'black', + linewidth= 1, + mirror= True, + ) + +fig.update_layout(width=900, height=650, plot_bgcolor='white') +fig.show() + +""" +I used only 11 k-points to produce these bandstructures, +therefore, the bandstructures look a bit ugly +We can see how conduction bands shift with applied strain +""" + + +# In[3]: + + +### EXAMPLE OF READING DAT WITH MODE="Auto" ### + +""" +read QE output file with bands for 0% and 5% strain and different composition +reshape data: 8 bands 11 k-points +In this case the fermi level is not specified, +it is automatically placed at the top of the valence zone +""" + +data=read_data('bands/si1ge3_0.dat') +si1ge3_0=data.read_bands_ml(mode='Auto', bands_num=4) +si1ge3_0=si1ge3_0.reshape(8,11) + +data=read_data('bands/si1ge3_5.dat') +si1ge3_5=data.read_bands_ml(mode='Auto', bands_num=4) +si1ge3_5=si1ge3_5.reshape(8,11) + +data=read_data('bands/si3ge1_0.dat') +si3ge1_0=data.read_bands_ml(mode='Auto', bands_num=4) +si3ge1_0=si3ge1_0.reshape(8,11) + +data=read_data('bands/si3ge1_5.dat') +si3ge1_5=data.read_bands_ml(mode='Auto', bands_num=4) +si3ge1_5=si3ge1_5.reshape(8,11) + + +fig = make_subplots(rows=2, cols=2, + subplot_titles=("Si1Ge3 strain 0%", " Si1G3 strain 5%", 'S3Ge1 strain 0%', 'Si3Ge1 strain 5%'), + vertical_spacing=0.04) + +for i in range(si3ge1_0.shape[0]): + fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si3ge1_0[i], + mode='lines', marker=dict(color='black'), showlegend=False, + name='markers'), col=1, row=1) +for i in range(si3ge1_5.shape[0]): + fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si3ge1_5[i], + mode='lines', marker=dict(color='black'), showlegend=False, + name='markers'), col=2, row=1) +for i in range(si1ge3_0.shape[0]): + fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si1ge3_0[i], + mode='lines', marker=dict(color='black'), showlegend=False, + name='markers'), col=1, row=2) +for i in range(si1ge3_5.shape[0]): + fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=si1ge3_5[i], + mode='lines', marker=dict(color='black'), showlegend=False, + name='markers'), col=2, row=2) + +fig.add_trace(go.Scatter(x=[1,11], y=[0,0], + mode='lines', line=dict(color= "RoyalBlue",width=3, dash='dot'), showlegend=False, + name='markers'), col=1, row=1) +fig.add_trace(go.Scatter(x=[1,11], y=[0,0], + mode='lines', line=dict(color= "RoyalBlue",width=3, dash='dot'), showlegend=False, + name='markers'), col=2, row=1) +fig.add_trace(go.Scatter(x=[1,11], y=[0,0], + mode='lines', line=dict(color= "RoyalBlue",width=3, dash='dot'), showlegend=False, + name='markers'), col=1, row=2) +fig.add_trace(go.Scatter(x=[1,11], y=[0,0], + mode='lines', line=dict(color= "RoyalBlue",width=3, dash='dot'), showlegend=False, + name='markers'), col=2, row=2) +fig.update_xaxes(showgrid=True, + gridwidth=0.5, + gridcolor='lightgrey', + ticks='inside' , + linecolor= 'black', + linewidth= 1, + mirror= True, + ticktext=['G', 'Z'], + tickvals=[1,11], + range=[1,11], + ) +fig.update_yaxes(title='Energy, eV', + showgrid=True, + gridwidth=0.5, + gridcolor='lightgrey', + ticks='inside' , + linecolor= 'black', + linewidth= 1, + mirror= True, + ) + +fig.update_layout(width=900, height=1450, plot_bgcolor='white') +fig.show() + +""" +I used only 11 k-points to produce these bandstructures, +therefore, the bandstructures look a bit ugly +We can see how conduction bands shift with applied strain +""" + + +# In[4]: + + +""" +reading cell parameters from all QE output xlm files +""" + +mypath='cell_param/' +filenames = next(walk(mypath), (None, None, []))[2] + +lattice=[] +fermi=[] +for file in filenames: + data=read_data(mypath+file) + (a, c, composition) = data.read_lattice_parameters() + lattice.append ([a, c, composition]) +# Fermi energy could be obtained with: +# fermi_level = data.read_fermi_levle() +# fermi.append(fermi_level) + +X=lattice=np.array(lattice) + +X + + +# In[36]: + + +filenames + + +# In[5]: + + +''' +reading bands from all QE output files +(output files are produced with band.x module) +''' + +mypath='bands/' +filenames = next(walk(mypath), (None, None, []))[2] + +y=[] +for i in range(len(filenames)): + data=read_data(mypath+filenames[i]) + bands_ml=data.read_bands_ml(mode='Auto', bands_num=2) + y= np.append(y, bands_ml) +y=y.reshape(len(filenames),44) +y.shape + + +# # prepare data for modeling: split for training and testig sets + +# In[8]: + + +my_data=data_preparation(X,y) + +#to manually specify testing set, use the following: +(X_train, X_test, Y_train, Y_test)=my_data.select_train_test(test_row_number=[12,16]) +# for a random split use function: +#(X_train, X_test, Y_train, Y_test)=my_data.random_split(train_split=0.8, seed=42) + +my_model=modeling(X_train, Y_train, X_test, Y_test, scaler='None') + +#train Random forest model with No initial guess +(y_fit_RF, y_predict_RF, trials_RF, best_space_RF, regressorRF, text_RF)=my_model.RandomForest( max_evals=12, timeout=150*60,loss_threshold=0.01, cv=5, verbose=1) + +print(text_RF) + + +# + + +# In[9]: + + +## MultiOutputRegressor is VERY SLOW! +## need more time to better understand MultiOutputRegressor + +#train XGboost model with initial guess +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} +(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,cv=5, verbose=1, init_vals=[best_space]) +print(text_XG) + + +# # let's plot predicted bands vs calculated bands + +# In[11]: + + +#reading calculated bands: +data=read_data('bands/si2ge2_relax.dat') +bands_si2ge2_relaxed=data.read_bands_ml(mode='Auto', bands_num=4) +bands_si2ge2_relaxed=bands_si2ge2_relaxed.reshape(8,11) + +data=read_data('bands/si3ge1_3.dat') +bands_si3ge1_3=data.read_bands_ml(mode='Auto', bands_num=4) +bands_si3ge1_3=bands_si3ge1_3.reshape(8,11) + +#predicted bands +bands_RF_1=y_predict_RF[0].reshape(4,11) +bands_RF_2=y_predict_RF[1].reshape(4,11) + +bands_XG_1=y_predict_XG[0].reshape(4,11) +bands_XG_2=y_predict_XG[0].reshape(4,11) + +fig = make_subplots(rows=1, cols=2,subplot_titles=("Si2Ge2 strain 2.5%", "Si3Ge1 strain 3%")) + +for i in range(bands_si2ge2_relaxed.shape[0]): + fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_si2ge2_relaxed[i], + mode='lines', marker=dict(color='black'), showlegend=False, + name='markers'), row=1, col=1) + +for i in range(bands_RF_1.shape[0]): + fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_RF_1[i], + mode='markers', marker=dict(color='red'), showlegend=False, + name='markers'), row=1, col=1) +for i in range(bands_XG_1.shape[0]): + fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_XG_1[i], + mode='markers', marker=dict(color='blue'), showlegend=False, + name='markers'), row=1, col=1) +for i in range(bands_si3ge1_3.shape[0]): + fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_si3ge1_3[i], + mode='lines', marker=dict(color='black'), showlegend=False, + name='markers'), row=1, col=2) + +for i in range(bands_RF_2.shape[0]): + fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_RF_2[i], + mode='markers', marker=dict(color='red'), showlegend=False, + name='markers'), row=1, col=2) +for i in range(bands_XG_2.shape[0]): + fig.add_trace(go.Scatter(x=np.arange(1,12,1), y=bands_XG_2[i], + mode='markers', marker=dict(color='blue'), showlegend=False, + name='markers'), row=1, col=2) + + +fig.add_trace(go.Scatter(x=[1,11], y=[0,0], + mode='lines', line=dict(color= "RoyalBlue",width=3, dash='dot'), showlegend=False, + name='markers'), col=1, row=1) +fig.add_trace(go.Scatter(x=[1,11], y=[0,0], + mode='lines', line=dict(color= "RoyalBlue",width=3, dash='dot'), showlegend=False, + name='markers'),col=2, row=1) + +fig.add_trace(go.Scatter(x=[12,13], y=[0,0], + mode='lines', line=dict(color= "black"), showlegend=True, name='DFT-PBE', + ),col=1, row=1) +fig.add_trace(go.Scatter(x=[12], y=[0], + mode='markers', line=dict(color= "red"), showlegend=True, name='RandomForest', + ),col=1, row=1) +fig.add_trace(go.Scatter(x=[12], y=[0], + mode='markers', line=dict(color= "blue"), showlegend=True, name='MultiOutputRegressor-XGBoost', + ),col=1, row=1) + +fig.update_xaxes(showgrid=True, + gridwidth=0.5, + gridcolor='lightgrey', + ticks='inside' , + linecolor= 'black', + linewidth= 1, + mirror= True, + ticktext=['G', 'Z'], + tickvals=[1,11], + range=[1,11] + ) +fig.update_yaxes(title='Energy, eV', + showgrid=True, + gridwidth=0.5, + gridcolor='lightgrey', + ticks='inside' , + linecolor= 'black', + linewidth= 1, + mirror= True, + ) +fig.update_layout(title='Si2Ge2 relaxed', width=1000, height=650, plot_bgcolor='white') +fig.show() + + +# # example of solving reverse problem + +# In[25]: + + +# in this example we predict lattice constants for a given bandstructure (lattice constants are in bohr) + +import GPyOpt +from GPyOpt.methods import BayesianOptimization +from sklearn.metrics import mean_squared_error + +data=read_data('bands/si2ge2_relax.dat') +bands=data.read_bands_ml(mode='Auto', bands_num=2) + + +def objfunc(x): + + x1 = float(x[0,0]) + x2 = float(x[0,1]) + x3 = float(x[0,2]) + + return mean_squared_error(regressorRF.predict([[x1,x2,x3]]).reshape(1,44), bands.reshape(1,44)) + +maxiter = 40 +domain = [ + {'name': 'a_paral', 'type': 'continuous', 'domain': (10, 11)}, + {'name': 'a_perp', 'type': 'continuous', 'domain': (10, 11)}, + {'name': 'composition', 'type': 'discrete', 'domain': (0.25,0.5,0.75)} + ] + + + +Bopt = GPyOpt.methods.BayesianOptimization(objfunc, domain=domain) +Bopt.run_optimization(max_iter = maxiter) + +print("Lattice parameters:"+str(Bopt.x_opt)) +print("MSE: "+str(Bopt.fx_opt)) + +""" +I will explain this part on Monaday +""" + + +# # Example with random split 80/20 + +# In[13]: + + +# one more example to train model with a random split 80/20 +my_data=data_preparation(X,y) +#random split could also be used +(X_train, X_test, Y_train, Y_test)=my_data.random_split(train_split=0.8, seed=42) + +my_model=modeling(X_train, Y_train, X_test, Y_test, scaler='None') + +#train Random forest model with No initial guess +(y_fit_RF, y_predict_RF, trials_RF, best_space_RF, regressorRF, text_RF)=my_model.RandomForest( max_evals=12, timeout=150*60,loss_threshold=0.01, cv=5, verbose=1) + +print(text_RF) + +# 20% of structures are predicted with a high accuracy + diff --git a/vitalypro/ml model performance.png b/vitalypro/ml model performance.png new file mode 100644 index 00000000..9878eeab Binary files /dev/null and b/vitalypro/ml model performance.png differ diff --git a/vitalypro/ml_modeling_module.py b/vitalypro/ml_modeling_module.py new file mode 100644 index 00000000..4b5905b3 --- /dev/null +++ b/vitalypro/ml_modeling_module.py @@ -0,0 +1,381 @@ +# -*- 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. class for data (energy bands, cell geometry etc) extraction from QE output files +2. class for data preparation for ML modeling +3. class for ML modeling with RF and XGB + +""" +class read_data: + + """ + In this module we read data from QE output and build a dataset for ML modeling + 1. read energy band data from output produced by bands.x + 2. read structure parameters and fermi level from xlm file + 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, mode='Fermi', 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 above/below the fermi level + :mode - 'Fermi': user provides fermi level and bands get adjusted with respect to this level + - 'Auto' : the fermi level will be automatically placed at the top of the conduction zone. + this option can be useful is the fermi level is unknown or calculated on a large mesh (my case) + :fermi - fermi level (eV) (will be ignored if mode='Auto' is used. + :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() + if mode=='Fermi': + 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) + elif mode=='Auto': + """ + For a general case, i would need to read QE output file or pseudopotential file to find out + how many valence electrons each atoms has and how many atoms of each type I have to count the number + of conduction bands. It can be done in the future work. In this work I only study SiGe systems. Both Si and Ge have + 4 val electrons. All my structures contain 8 atoms, so 4*8/2=16 conduction bands + number_cnb = 16 + """ + number_cnb = 16 + cond_bands=[] + val_bands=[] + for i in range(eig.shape[0]): + cond_bands=np.append(cond_bands, eig[i][number_cnb-bands_num:number_cnb]) + val_bands =np.append(val_bands,eig[i][number_cnb: number_cnb+bands_num]) + fermi= np.max(cond_bands) + cond_bands=cond_bands-fermi + val_bands=val_bands-fermi + 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 + + def read_lattice_parameters(self): + """read lattice constants from xlm file""" + import xml.etree.ElementTree as ET + from collections import Counter + tree = ET.parse(self.file) + root = tree.getroot() + a = root[2][2][1][0].text + c = root[2][2][1][2].text + a = [float(value) for value in a.split(' ')] + c = [float(value) for value in c.split(' ')] + + #read composition SixGe1-x + atom=[] + for i in range(8): + atom=np.append(atom,root[2][2][0][i].attrib['name']) + composition = int(Counter(atom)['Si'])/8 + + return a[0], c[2], composition + + def read_fermi_levle(self): + import xml.etree.ElementTree as ET + tree = ET.parse(self.file) + root = tree.getroot() + """ + read fermi level from xlm file + convert from Ry to eV and multiply by 2!!! + I am using qe 6.4 which has a bug for fermi level: + + Fermi energy incorrectly written to xml file in 'bands' calculation + (did not affect results, just Fermi energy position in band plotting) + see for more info https://gitlab.com/QEF/q-e/-/releases + + """ + fermi_level=round(float(root[3][9][7].text)*2*13.605,2) + return fermi_level + +class data_preparation: + + """ + In this module 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'): + """ + 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.flatten(), y_predict.flatten(), 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 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, + :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 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), + '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 + + + + + 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. This method is VERY SLOW... + + """ + + + 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')) + + + 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 + + + + + +