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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,