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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "94cda45d-8d84-4270-8635-99672fad15d8",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"></pre>\n"
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},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"from pyiron import Project\n",
"import pandas as pd"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "a815efef-461e-4797-ba33-85fb5794a46a",
"metadata": {},
"outputs": [],
"source": [
"pr = Project(\"AlLiMEAM\")"
]
},
{
"cell_type": "markdown",
"id": "972d60b9-b4c9-4533-b90f-6c9d3d55e564",
"metadata": {},
"source": [
"Using openkim potentials requires a kim init command, which has to be placed before the structure. This is not directly possible in pyiron due to the order in the control file.\n",
"\n",
"A somewhat hacky workaround is to place the read_data command into the potential file and delete it from the original control.inp file."
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "41d45117-b80c-4d61-9800-ec432e614a06",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Parameter</th>\n",
" <th>Value</th>\n",
" <th>Comment</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>units</td>\n",
" <td>metal</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>dimension</td>\n",
" <td>3</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>boundary</td>\n",
" <td>p p p</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>atom_style</td>\n",
" <td>atomic</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>include</td>\n",
" <td>potential.inp</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>fix___ensemble</td>\n",
" <td>all nve</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>variable___dumptime</td>\n",
" <td>equal 100</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>variable___thermotime</td>\n",
" <td>equal 100</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>dump___1</td>\n",
" <td>all custom ${dumptime} dump.out id type xsu ys...</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>dump_modify___1</td>\n",
" <td>sort id format line \"%d %d %20.15g %20.15g %20...</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>thermo_style</td>\n",
" <td>custom step temp pe etotal pxx pxy pxz pyy pyz...</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>thermo_modify</td>\n",
" <td>format float %20.15g</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>thermo</td>\n",
" <td>${thermotime}</td>\n",
" <td></td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>run</td>\n",
" <td>0</td>\n",
" <td></td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" Parameter Value \\\n",
"0 units metal \n",
"1 dimension 3 \n",
"2 boundary p p p \n",
"3 atom_style atomic \n",
"4 include potential.inp \n",
"5 fix___ensemble all nve \n",
"6 variable___dumptime equal 100 \n",
"7 variable___thermotime equal 100 \n",
"8 dump___1 all custom ${dumptime} dump.out id type xsu ys... \n",
"9 dump_modify___1 sort id format line \"%d %d %20.15g %20.15g %20... \n",
"10 thermo_style custom step temp pe etotal pxx pxy pxz pyy pyz... \n",
"11 thermo_modify format float %20.15g \n",
"12 thermo ${thermotime} \n",
"13 run 0 \n",
"\n",
" Comment \n",
"0 \n",
"1 \n",
"2 \n",
"3 \n",
"4 \n",
"5 \n",
"6 \n",
"7 \n",
"8 \n",
"9 \n",
"10 \n",
"11 \n",
"12 \n",
"13 "
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"s = pr.create.structure.ase.bulk(\"Al\", cubic=True)\n",
"s[1] = \"Li\"\n",
"job = pr.create.job.Lammps(\"PotDF\", delete_existing_job=True)\n",
"job.structure = s\n",
"\n",
"pot = pd.DataFrame(\n",
" {\n",
" \"Name\": \"KIM MEAM\",\n",
" \"Filename\": [[]],\n",
" \"Model\": [\"Custom\"],\n",
" \"Species\": [[\"Al\", \"Li\"]],\n",
" \"Config\": [\n",
" [\n",
" 'kim init MEAM_LAMMPS_RoyDuttaChakraborti_2021_AlLi__MO_971738391444_000 metal\\n',\n",
" 'read_data structure.inp\\n', # This is a really dirty fix for the kim init problem\n",
" 'kim interactions Al Li\\n',\n",
" ]\n",
" ],\n",
" }\n",
")\n",
"\n",
"job.potential = pot\n",
"del job.input.control[\"read_data\"]\n",
"job.input.control"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "342e2237-afe9-4664-944b-2883b3807f3c",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"The job PotDF was saved and received the ID: 648448\n"
]
}
],
"source": [
"job.run()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "7c153be5-2c4c-4678-8f54-a184e5f46e8b",
"metadata": {},
"outputs": [],
"source": []
}
],
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"file_extension": ".py",
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