docs: otp example

examples/ortho-terphenyl/1-create-config-right-density/create-initial-config.py

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+# /// script
+# requires-python = ">=3.13"
+# dependencies = [
+#     "numpy>=2.4.1",
+# ]
+# ///
+import itertools
+
+import numpy as np
+
+M = 1000
+N = M * 3
+number_density = 0.2  # This is per particle, not per molecule
+# rho = N/V
+V = N / number_density
+L = V ** (1 / 3)
+
+sigmas = [0.9, 1, 1.1]
+
+
+def main(output_file_name: str) -> None:
+    """Create a regular lattice of molecules. These planar molecules are in the x-y plane."""
+
+    number_in_each_direction = round(M ** (1 / 3))
+    dxdydz = L / number_in_each_direction
+    assert number_in_each_direction**3 == M, "M is not an int to power 3"
+
+    r_ab = (sigmas[0] + sigmas[1]) / 2
+    r_ac = (sigmas[0] + sigmas[2]) / 2
+    cos_alpha = np.cos(60 / 180)
+    sin_alpha = np.sin(60 / 180)
+
+    f = open(output_file_name, "w")
+
+    f.write(f"{N}\n")
+    f.write(f"columns:molecule,species,position cell:{L},{L},{L}\n")
+
+    counter = 1
+    for i, j, k in itertools.product(
+        range(number_in_each_direction),
+        range(number_in_each_direction),
+        range(number_in_each_direction),
+    ):
+        r_a = (i * dxdydz, j * dxdydz, k * dxdydz)
+        r_b = (i * dxdydz, j * dxdydz + r_ab, k * dxdydz)
+        r_c = (i * dxdydz + r_ac * cos_alpha, j * dxdydz + r_ac * sin_alpha, k * dxdydz)
+
+        f.write(f"{counter} 1 {r_a[0]} {r_a[1]} {r_a[2]}\n")
+        f.write(f"{counter} 2 {r_b[0]} {r_b[1]} {r_b[2]}\n")
+        f.write(f"{counter} 3 {r_c[0]} {r_c[1]} {r_c[2]}\n")
+
+        counter += 1
+
+    number_of_bonds = M * 3
+    f.write(f"{number_of_bonds}\n")
+    f.write("columns:bond\n")
+    for i in range(M):
+        index_of_a = 1 + i * 3
+        # AB
+        f.write(f"{index_of_a} {index_of_a + 1}\n")
+        # BC
+        f.write(f"{index_of_a + 1} {index_of_a + 2}\n")
+        # AC
+        f.write(f"{index_of_a} {index_of_a + 2}\n")
+
+
+if __name__ == "__main__":
+    output_file_name = "inputframe.xyz"
+    main(output_file_name)

examples/ortho-terphenyl/1-create-config-right-density/params-template.toml

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+[system]
+config = "./inputframe.xyz"
+temperature = 2.0
+density = DENSITY
+list_type = "LinkedList"
+
+[model]
+
+[model."1-1"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 0.9
+k = 37.03703703703703
+r0 = 1.35
+
+[model."1-2"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 0.95
+k = 33.24099722991689
+r0 = 1.425
+
+[model."1-3"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 1.0
+k = 30.0
+r0 = 1.5
+
+[model."2-2"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 1.0
+k = 30.0
+r0 = 1.5
+
+[model."2-3"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 1.05
+k = 27.2108843537415
+r0 = 1.575
+
+[model."3-3"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 1.1
+k = 24.79338842975207
+r0 = 1.65
+
+
+
+[simulation]
+type = "Metropolis"
+steps = 10000
+seed = 10
+parallel = false
+
+[[simulation.move]]
+action = "Displacement"
+probability = 0.8
+policy = "SimpleGaussian"
+parameters = {sigma = 0.05}
+
+[[simulation.move]]
+action = "MoleculeFlip"
+probability = 0.2
+policy = "DoubleUniform"
+
+[[simulation.output]]
+algorithm = "StoreCallbacks"
+callbacks = ["energy", "acceptance"]
+scheduler_params = {linear_interval = 1}
+
+[[simulation.output]]
+algorithm = "StoreLastFrames"
+scheduler_params = {linear_interval = 10000}
+fmt = "XYZ"
+
+[[simulation.output]]
+algorithm = "PrintTimeSteps"
+scheduler_params = {linear_interval = 1}

examples/ortho-terphenyl/1-create-config-right-density/run.sh

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+#!/bin/bash
+
+uv run --script create-initial-config.py
+
+density=0.2
+
+while (( $(echo "$density < 1.2" | bc -l ) ))
+do
+    echo "Density" $density
+
+    sed "s/DENSITY/$density/" params-template.toml > params.toml
+    particlesmc params.toml
+    cp trajectories/1/lastframe.xyz inputframe.xyz
+
+    density=$(echo "$density" | awk '{printf "%f", $1 * 1.1}')
+done

examples/ortho-terphenyl/2-equilibrate-at-different-temperatures/create-folders.sh

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+#!/bin/bash
+
+for temperature in 3.0 2.0 1.6 1.4 1.25 1.2 1.15 1.1 1.05 1.0
+do
+    mkdir -p $temperature
+    sed "s/TEMPERATURE/$temperature/" params-template.toml > $temperature/params.toml
+done

examples/ortho-terphenyl/2-equilibrate-at-different-temperatures/params-template.toml

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+[system]
+config = "../../1-create-config-right-density/inputframe.xyz"
+temperature = TEMPERATURE
+density = 1.2
+list_type = "LinkedList"
+
+[model]
+
+[model."1-1"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 0.9
+k = 37.03703703703703
+r0 = 1.35
+
+[model."1-2"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 0.95
+k = 33.24099722991689
+r0 = 1.425
+
+[model."1-3"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 1.0
+k = 30.0
+r0 = 1.5
+
+[model."2-2"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 1.0
+k = 30.0
+r0 = 1.5
+
+[model."2-3"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 1.05
+k = 27.2108843537415
+r0 = 1.575
+
+[model."3-3"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 1.1
+k = 24.79338842975207
+r0 = 1.65
+
+
+
+[simulation]
+type = "Metropolis"
+steps = 5000000
+seed = 10
+parallel = false
+
+[[simulation.move]]
+action = "Displacement"
+probability = 0.8
+policy = "SimpleGaussian"
+parameters = {sigma = 0.05}
+
+[[simulation.move]]
+action = "MoleculeFlip"
+probability = 0.2
+policy = "DoubleUniform"
+
+[[simulation.output]]
+algorithm = "StoreCallbacks"
+callbacks = ["energy", "acceptance"]
+scheduler_params = {linear_interval = 1000}
+
+[[simulation.output]]
+algorithm = "StoreLastFrames"
+scheduler_params = {linear_interval = 10000}
+fmt = "XYZ"
+
+[[simulation.output]]
+algorithm = "StoreTrajectories"
+scheduler_params = {linear_interval = 1000}
+fmt = "XYZ"
+
+[[simulation.output]]
+algorithm = "PrintTimeSteps"
+scheduler_params = {linear_interval = 1000}

examples/ortho-terphenyl/3-run-production/create-folders.sh

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+#!/bin/bash
+
+for temperature in 3.0 2.0 1.6 1.4 1.25 1.2 1.15 1.1 1.05 1.0
+do
+    mkdir -p $temperature
+    sed "s/TEMPERATURE/$temperature/" params-template.toml > $temperature/params.toml
+done

examples/ortho-terphenyl/3-run-production/params-template.toml

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+[system]
+config = "../../2-equilibrate-at-different-temperatures/TEMPERATURE/trajectories/1/lastframe.xyz"
+temperature = TEMPERATURE
+density = 1.2
+list_type = "LinkedList"
+
+[model]
+
+[model."1-1"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 0.9
+k = 37.03703703703703
+r0 = 1.35
+
+[model."1-2"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 0.95
+k = 33.24099722991689
+r0 = 1.425
+
+[model."1-3"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 1.0
+k = 30.0
+r0 = 1.5
+
+[model."2-2"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 1.0
+k = 30.0
+r0 = 1.5
+
+[model."2-3"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 1.05
+k = 27.2108843537415
+r0 = 1.575
+
+[model."3-3"]
+name = "GeneralKG"
+epsilon = 1.0
+sigma = 1.1
+k = 24.79338842975207
+r0 = 1.65
+
+
+
+[simulation]
+type = "Metropolis"
+steps = 5000000
+seed = 10
+parallel = false
+
+[[simulation.move]]
+action = "Displacement"
+probability = 0.8
+policy = "SimpleGaussian"
+parameters = {sigma = 0.05}
+
+[[simulation.move]]
+action = "MoleculeFlip"
+probability = 0.2
+policy = "DoubleUniform"
+
+[[simulation.output]]
+algorithm = "StoreCallbacks"
+callbacks = ["energy", "acceptance"]
+scheduler_params = {linear_interval = 1000}
+
+[[simulation.output]]
+algorithm = "StoreLastFrames"
+scheduler_params = {linear_interval = 10000}
+fmt = "XYZ"
+
+[[simulation.output]]
+algorithm = "StoreTrajectories"
+scheduler_params = {linear_interval = 4096, log_base=2.0}
+fmt = "XYZ"
+
+[[simulation.output]]
+algorithm = "PrintTimeSteps"
+scheduler_params = {linear_interval = 1000}