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jthorton/Running_QCEngine.ipynb

Created November 19, 2020 16:01
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Running QCEngine from OFFTK
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Running_QCEngine.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "4f22109bec46497e915c15b59d07ca97",
"version_major": 2,
"version_minor": 0
},
"text/plain": []
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"from openforcefield.topology import Molecule\n",
"import qcengine\n",
"from qcelemental.models import AtomicInput, OptimizationInput\n",
"from qcelemental.models.common_models import Model\n",
"from qcelemental.models.procedures import QCInputSpecification\n",
"from qcfractal.interface import FractalClient"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "5899acad2f72462791f8542c620bab66",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"NGLWidget()"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"# make a off toolkit molecule\n",
"molecule = Molecule.from_smiles(\"CCO\")\n",
"molecule.generate_conformers()\n",
"molecule"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'schema_name': 'qcschema_molecule',\n",
" 'schema_version': 2,\n",
" 'validated': True,\n",
" 'symbols': array(['C', 'C', 'O', 'H', 'H', 'H', 'H', 'H', 'H'], dtype='<U1'),\n",
" 'geometry': array([[ 2.00615820e+00, -5.06711540e-01, -1.09933000e-03],\n",
" [ 3.60951268e+00, 1.72458306e+00, -7.97534580e-01],\n",
" [ 2.86671423e+00, 2.50130220e+00, -3.25568170e+00],\n",
" [ 2.53095194e+00, -1.15425288e+00, 1.88985926e+00],\n",
" [-8.14200000e-05, -3.21260000e-04, -1.06395000e-03],\n",
" [ 2.23006866e+00, -2.07682879e+00, -1.33038667e+00],\n",
" [ 5.60946348e+00, 1.20201873e+00, -8.40105250e-01],\n",
" [ 3.35055854e+00, 3.30692363e+00, 5.07723010e-01],\n",
" [ 3.92823645e+00, 3.92941102e+00, -3.70622143e+00]]),\n",
" 'name': 'C2H6O',\n",
" 'molecular_charge': 0.0,\n",
" 'molecular_multiplicity': 1,\n",
" 'connectivity': [(0, 1, 1.0),\n",
" (0, 3, 1.0),\n",
" (0, 4, 1.0),\n",
" (0, 5, 1.0),\n",
" (1, 2, 1.0),\n",
" (1, 6, 1.0),\n",
" (1, 7, 1.0),\n",
" (2, 8, 1.0)],\n",
" 'fix_com': False,\n",
" 'fix_orientation': False,\n",
" 'provenance': {'creator': 'QCElemental',\n",
" 'version': 'v0.17.0',\n",
" 'routine': 'qcelemental.molparse.from_schema'},\n",
" 'extras': None}"
]
},
"execution_count": 23,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# generate the qcelemental molecule\n",
"qcel_mol = molecule.to_qcschema()\n",
"qcel_mol.dict()"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"AtomicInput(driver='energy', model={'method': 'openff-1.0.0', 'basis': 'smirnoff'}, molecule_hash='c6f0b48')"
]
},
"execution_count": 24,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# generate the qcengine input to compute the energy using a range of programs and methods\n",
"# openff-1.0.0 program=\"openmm\"\n",
"openff_model = Model(method=\"openff-1.0.0\", basis=\"smirnoff\")\n",
"# gaff-2.11 program=\"openmm\"\n",
"gaff_model = Model(method=\"gaff-2.11\", basis=\"antechamber\")\n",
"# DFT with D3 program=\"psi4\"\n",
"psi4_model = Model(method=\"B3LYP-D3BJ\", basis=\"DZVP\")\n",
"# torchani ani2x program=\"torchani\"\n",
"ani_model = Model(method=\"ani2x\", basis=None)\n",
"# gfn method program=\"xtb\"\n",
"xtb_model = Model(method=\"gfn2-xtb\", basis=None)\n",
"\n",
"qc_task = AtomicInput(molecule=qcel_mol, driver=\"energy\", model=openff_model)\n",
"qc_task"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {},
"outputs": [],
"source": [
"# compute the energy\n",
"result = qcengine.compute(input_data=qc_task, program=\"openmm\")"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'id': None,\n",
" 'schema_name': 'qcschema_output',\n",
" 'schema_version': 1,\n",
" 'molecule': {'schema_name': 'qcschema_molecule',\n",
" 'schema_version': 2,\n",
" 'validated': True,\n",
" 'symbols': array(['C', 'C', 'O', 'H', 'H', 'H', 'H', 'H', 'H'], dtype='<U1'),\n",
" 'geometry': array([[ 2.00615820e+00, -5.06711540e-01, -1.09933000e-03],\n",
" [ 3.60951268e+00, 1.72458306e+00, -7.97534580e-01],\n",
" [ 2.86671423e+00, 2.50130220e+00, -3.25568170e+00],\n",
" [ 2.53095194e+00, -1.15425288e+00, 1.88985926e+00],\n",
" [-8.14200000e-05, -3.21260000e-04, -1.06395000e-03],\n",
" [ 2.23006866e+00, -2.07682879e+00, -1.33038667e+00],\n",
" [ 5.60946348e+00, 1.20201873e+00, -8.40105250e-01],\n",
" [ 3.35055854e+00, 3.30692363e+00, 5.07723010e-01],\n",
" [ 3.92823645e+00, 3.92941102e+00, -3.70622143e+00]]),\n",
" 'name': 'C2H6O',\n",
" 'molecular_charge': 0.0,\n",
" 'molecular_multiplicity': 1,\n",
" 'connectivity': [(0, 1, 1.0),\n",
" (0, 3, 1.0),\n",
" (0, 4, 1.0),\n",
" (0, 5, 1.0),\n",
" (1, 2, 1.0),\n",
" (1, 6, 1.0),\n",
" (1, 7, 1.0),\n",
" (2, 8, 1.0)],\n",
" 'fix_com': False,\n",
" 'fix_orientation': False,\n",
" 'provenance': {'creator': 'QCElemental',\n",
" 'version': 'v0.17.0',\n",
" 'routine': 'qcelemental.molparse.from_schema'},\n",
" 'extras': None},\n",
" 'driver': <DriverEnum.energy: 'energy'>,\n",
" 'model': {'method': 'openff-1.0.0', 'basis': 'smirnoff'},\n",
" 'keywords': {},\n",
" 'protocols': {},\n",
" 'extras': {},\n",
" 'provenance': {'creator': 'openmm',\n",
" 'version': '7.4.2',\n",
" 'routine': None,\n",
" 'nthreads': 5,\n",
" 'cpu': 'Intel(R) Core(TM) i9-10910 CPU @ 3.60GHz',\n",
" 'qcengine_version': 'v0.17.0',\n",
" 'hostname': 'Joshuas-iMac',\n",
" 'wall_time': 0.2566111087799072,\n",
" 'username': 'joshua'},\n",
" 'properties': {'return_energy': -0.0070563665201323015},\n",
" 'wavefunction': None,\n",
" 'return_result': -0.0070563665201323015,\n",
" 'stdout': None,\n",
" 'stderr': None,\n",
" 'success': True,\n",
" 'error': None}"
]
},
"execution_count": 26,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"result.dict()"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"OptimizationInput(model={'method': 'openff-1.0.0', 'basis': 'smirnoff'}, molecule_hash='c6f0b48')"
]
},
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# now perform an optimization using geometric\n",
"# make sure to change the model and program here\n",
"geometric_input = OptimizationInput(initial_molecule=qcel_mol, input_specification=QCInputSpecification(model=openff_model), keywords={\"coordsys\": \"tric\", \"maxiter\": 300, \"program\": \"openmm\"})\n",
"geometric_input"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {},
"outputs": [],
"source": [
"opt_result = qcengine.compute_procedure(input_data=geometric_input, procedure=\"geometric\")"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "21e57dbfebd248af9c9525c8ba46e691",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"NGLWidget()"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"initial_mol = opt_result.initial_molecule\n",
"initial_mol"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "61da33603f4f48419bc9839d2c314fb5",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"NGLWidget()"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"final_mol = opt_result.final_molecule\n",
"final_mol"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"2.873823736800184"
]
},
"execution_count": 31,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# measure a bond on the molecule in Bohr\n",
"final_mol.measure((0,1))"
]
},
{
"cell_type": "code",
"execution_count": 32,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"2.8607219871857166"
]
},
"execution_count": 32,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"initial_mol.measure((0,1))"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[AtomicResult(driver='gradient', model={'method': 'openff-1.0.0', 'basis': 'smirnoff'}, molecule_hash='c6f0b48'),\n",
" AtomicResult(driver='gradient', model={'method': 'openff-1.0.0', 'basis': 'smirnoff'}, molecule_hash='385d605'),\n",
" AtomicResult(driver='gradient', model={'method': 'openff-1.0.0', 'basis': 'smirnoff'}, molecule_hash='eb2dd28'),\n",
" AtomicResult(driver='gradient', model={'method': 'openff-1.0.0', 'basis': 'smirnoff'}, molecule_hash='73b4c38')]"
]
},
"execution_count": 33,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"opt_result.trajectory"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
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"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
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"version": "3.7.8"
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"nbformat_minor": 4
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