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python: doc and example updates

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This commit is contained in:
Richard Berger
2024-11-24 01:36:01 -07:00
committed by Richard Berger
parent e45ef5adc0
commit 754aa1c73f
16 changed files with 206 additions and 466 deletions
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253
python/examples/ipython/atoms.ipynb
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@ -4,7 +4,14 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Example 3: Example 3: Using Atom Data"
"<div style=\"text-align: center\"><a href=\"index.ipynb\">LAMMPS Python Tutorials</a></div>"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Example 3: Working with Per-Atom Data"
]
},
{
@ -133,248 +140,6 @@
"L.ipython.image(zoom=1.8)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Queries about LAMMPS simulation"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.system"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.system.natoms"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.system.nbonds"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.system.nbondtypes"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.communication"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.fixes"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.computes"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.dumps"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.groups"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Working with LAMMPS Variables"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.variable(\"a index 2\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.variables"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.variable(\"t equal temp\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.variables"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import sys\n",
"\n",
"if sys.version_info < (3, 0):\n",
" # In Python 2 'print' is a restricted keyword, which is why you have to use the lmp_print function instead.\n",
" x = float(L.lmp_print('\"${a}\"'))\n",
"else:\n",
" # In Python 3 the print function can be redefined.\n",
" # x = float(L.print('\"${a}\"')\")\n",
" \n",
" # To avoid a syntax error in Python 2 executions of this notebook, this line is packed into an eval statement\n",
" x = float(eval(\"L.print('\\\"${a}\\\"')\"))\n",
"x"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.variables['t'].value"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.eval(\"v_t/2.0\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.variable(\"b index a b c\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.variables['b'].value"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.eval(\"v_b\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.variables['b'].definition"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.variable(\"i loop 10\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.variables['i'].value"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.next(\"i\")\n",
"L.variables['i'].value"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.expand(\"ke\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
@ -451,7 +216,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.6"
"version": "3.12.7"
}
},
"nbformat": 4,

11
python/examples/ipython/dihedrals/dihedral.ipynb
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@ -4,7 +4,14 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Validating a dihedral potential"
"<div style=\"text-align: center\"><a href=\"../index.ipynb\">LAMMPS Python Tutorials</a></div>"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Example 4: Validating a dihedral potential"
]
},
{
@ -232,7 +239,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.6"
"version": "3.12.7"
}
},
"nbformat": 4,

8
python/examples/ipython/index.ipynb
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@ -5,7 +5,7 @@
"id": "666d3036-47d5-44d2-bc1a-ca4b00a9e9b8",
"metadata": {},
"source": [
"# LAMMPS IPython Tutorial"
"# LAMMPS Python Tutorials"
]
},
{
@ -25,7 +25,9 @@
"\n",
"- [Example 1: Using LAMMPS with Python](simple.ipynb)\n",
"- [Example 2: Analyzing LAMMPS thermodynamic data](thermo.ipynb)\n",
"- [Example 3: Using Atom Data](atom.ipynb)"
"- [Example 3: Using Atom Data](atoms.ipynb)\n",
"- [Example 4: Validating a dihedral potential](dihedrals/dihedral.ipynb)\n",
"- [Example 5: Running a Monte Carlo relaxation](montecarlo/mc.ipynb)"
]
},
{
@ -53,7 +55,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.6"
"version": "3.12.7"
}
},
"nbformat": 4,

11
python/examples/ipython/montecarlo/mc.ipynb
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@ -4,7 +4,14 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Monte Carlo Relaxation"
"<div style=\"text-align: center\"><a href=\"../index.ipynb\">LAMMPS Python Tutorials</a></div>"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Example 5: Monte Carlo Relaxation"
]
},
{
@ -343,7 +350,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.6"
"version": "3.12.7"
}
},
"nbformat": 4,

2
python/examples/ipython/simple.ipynb
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@ -298,7 +298,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.6"
"version": "3.12.7"
}
},
"nbformat": 4,

20
python/examples/ipython/thermo.ipynb
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@ -279,6 +279,24 @@
"source": [
"current_run.plot(x='Step', y='TotEng')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Conclusion\n",
"\n",
"The Python interface gives you a powerful way of invoking and extracting simulation data while the simulation is running. Next we'll look at how to extract information about the atoms in your system.\n",
"\n",
"<div style=\"text-align:right\"><a href=\"atoms.ipynb\">Next</a>"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
@ -297,7 +315,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.6"
"version": "3.12.7"
}
},
"nbformat": 4,