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python: update examples and docs

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This commit is contained in:
Richard Berger
2024-11-04 09:19:38 -07:00
committed by Richard Berger
parent 9da58b3ffc
commit 24a4ff78b6
31 changed files with 1608 additions and 1730 deletions
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240
python/examples/ipython/dihedrals/dihedral.ipynb Normal file
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Validating a dihedral potential"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import matplotlib.pyplot as plt\n",
"from lammps import lammps"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L = lammps()\n",
"cmd = L.cmd"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import math\n",
"\n",
"cmd.units(\"real\")\n",
"cmd.atom_style(\"molecular\")\n",
"\n",
"cmd.boundary(\"f f f\")\n",
"cmd.neighbor(0.3, \"bin\")\n",
"\n",
"cmd.dihedral_style(\"harmonic\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"cmd.read_data(\"data.dihedral\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"cmd.pair_style(\"zero\", 5)\n",
"cmd.pair_coeff(\"*\", \"*\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"cmd.mass(1, 1.0)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"cmd.velocity(\"all\", \"set\", 0.0, 0.0, 0.0)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"cmd.run(0);"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.ipython.image(zoom=1.0,size=[320,320])"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"x = L.numpy.extract_atom(\"x\")\n",
"print(x[3])"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"x[3] = (1.0, 0.0, 1.0)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.ipython.image(zoom=1.0,size=[320,320])"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.get_thermo(\"pe\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"x[3] = (1.0, 0.0, -1.0)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"cmd.run(0)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"phi = [d * math.pi / 180 for d in range(360)]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"pos = [(1.0, math.cos(p), math.sin(p)) for p in phi]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"K = 80.0\n",
"d = 1\n",
"n = 2\n",
"E_analytical = [K * (1 + d * math.cos(n*p)) for p in phi]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"pe = []\n",
"for p in pos:\n",
" x[3] = p\n",
" cmd.run(0);\n",
" pe.append(L.get_thermo(\"pe\"))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"plt.plot(range(360), pe, range(360), E_analytical)\n",
"plt.xlabel('angle')\n",
"plt.ylabel('E')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"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": "3.9.6"
}
},
"nbformat": 4,
"nbformat_minor": 4
}