ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

python: doc and example updates

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

253
python/examples/ipython/atoms.ipynb
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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,