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Merge pull request #5 from ProjectQ-Framework/develop
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‎README.rst

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FermiLib Plugin to interface with PySCF
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=======================================
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This repository contains a plugin which allows `FermiLib <http://github.com/ProjectQ-Framework/FermiLib>`__ (licensed under Apache 2) to interface with the open-source quantum chemistry package `PySCF <https://github.com/sunqm/pyscf>`__ (licensed under BSD-2-Clause).
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License
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-------
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This plugin is released under the Apache 2 license.

‎examples/generate_data.py

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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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"""This is a simple script for generating data."""
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import os
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from fermilib.utils import (make_atomic_ring,
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make_atom,
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periodic_table)
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from fermilibpluginpyscf import run_pyscf
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if __name__ == '__main__':
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# Set chemical parameters.
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basis = 'sto-3g'
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max_electrons = 10
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spacing = 0.7414
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compute_elements = 0
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# Select calculations.
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force_recompute = 1
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run_scf = 1
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run_mp2 = 1
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run_cisd = 1
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run_ccsd = 1
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run_fci = 1
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verbose = 1
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# Generate data.
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for n_electrons in range(2, max_electrons + 1):
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# Initialize.
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if compute_elements:
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atomic_symbol = periodic_table[n_electrons]
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molecule = make_atom(atomic_symbol, basis)
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else:
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molecule = make_atomic_ring(n_electrons, spacing, basis)
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if os.path.exists(molecule.filename + '.hdf5'):
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molecule.load()
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# To run or not to run.
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if run_scf and not molecule.hf_energy:
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run_job = 1
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elif run_mp2 and not molecule.mp2_energy:
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run_job = 1
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elif run_cisd and not molecule.cisd_energy:
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run_job = 1
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elif run_ccsd and not molecule.ccsd_energy:
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run_job = 1
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elif run_fci and not molecule.fci_energy:
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run_job = 1
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else:
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run_job = force_recompute
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# Run.
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if run_job:
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molecule = run_pyscf(molecule,
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run_scf=run_scf,
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run_mp2=run_mp2,
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run_cisd=run_cisd,
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run_ccsd=run_ccsd,
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run_fci=run_fci,
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verbose=verbose)
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molecule.save()

‎examples/generate_diatomic.py

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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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"""This is a simple script for generating data."""
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import os
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from fermilib.utils import MolecularData
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from fermilibpluginpyscf import run_pyscf
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if __name__ == '__main__':
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# Set chemical parameters.
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element_names = ['H', 'H']
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basis = 'sto-3g'
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charge = 0
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multiplicity = 1
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# Single point at equilibrium for testing
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spacings = [0.7414]
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# Add points for a full dissociation curve from 0.1 to 3.0 angstroms
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spacings += [0.1 * r for r in range(1, 31)]
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# Set run options
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run_scf = 1
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run_mp2 = 1
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run_cisd = 1
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run_ccsd = 1
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run_fci = 1
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verbose = 1
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# Run Diatomic Curve
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for spacing in spacings:
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description = "{}".format(spacing)
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geometry = [[element_names[0], [0, 0, 0]],
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[element_names[1], [0, 0, spacing]]]
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molecule = MolecularData(geometry,
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basis,
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multiplicity,
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charge,
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description)
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molecule = run_pyscf(molecule,
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run_scf=run_scf,
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run_mp2=run_mp2,
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run_cisd=run_cisd,
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run_ccsd=run_ccsd,
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run_fci=run_fci,
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verbose=verbose)
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molecule.save()
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# Run Li H single point
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description = "1.45"
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geometry = [['Li', [0, 0, 0]],
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['H', [0, 0, 1.45]]]
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molecule = MolecularData(geometry,
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basis,
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multiplicity,
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charge,
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description)
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molecule = run_pyscf(molecule,
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run_scf=run_scf,
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run_mp2=run_mp2,
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run_cisd=run_cisd,
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run_ccsd=run_ccsd,
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run_fci=run_fci,
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verbose=verbose)
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molecule.save()

‎examples/plotter.py

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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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"""These functions compare properties of different molecules."""
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import matplotlib.pyplot
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import numpy
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import warnings
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from fermilib.utils import (make_atom, make_atomic_ring,
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MolecularData, periodic_table)
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def latex_name(molecule):
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"""Write the name of the molecule in LaTeX.
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Returns:
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name: A string giving the name in LaTeX.
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"""
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# Get sorted atom vector.
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atoms = [item[0] for item in molecule.geometry]
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atom_charge_info = [(atom, atoms.count(atom)) for atom in set(atoms)]
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sorted_info = sorted(atom_charge_info,
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key=lambda atom: molecular_data.
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_PERIODIC_HASH_TABLE[atom[0]])
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# Name molecule and return.
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name = '{}$_{}$'.format(sorted_info[0][0], sorted_info[0][1])
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for info in sorted_info[1::]:
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name += '{}$_{}$'.format(info[0], info[1])
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return name
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# Run.
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if __name__ == '__main__':
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# Set plot parameters.
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matplotlib.pyplot.rcParams['text.usetex'] = True
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matplotlib.pyplot.rcParams['text.latex.unicode'] = True
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matplotlib.pyplot.rc('text', usetex=True)
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matplotlib.pyplot.rc('font', family='sans=serif')
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marker_size = 6
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line_width = 2
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axis_size = 12
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font_size = 16
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x_log = 0
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y_log = 0
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# Set chemical series parameters.
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plot_elements = 0
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max_electrons = 10
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spacing = 0.7414
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basis = 'sto-3g'
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# Get chemical series.
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molecular_series = []
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for n_electrons in range(2, max_electrons + 1):
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if plot_elements:
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atomic_symbol = periodic_table[n_electrons]
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molecule = make_atom(atomic_symbol, basis)
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else:
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molecule = make_atomic_ring(n_electrons, spacing, basis)
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molecule.load()
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molecular_series += [molecule]
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# Get plot data.
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x_values = []
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y_values = []
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for molecule in molecular_series:
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# x-axis.
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x_label = 'Number of Electrons'
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x_values += [molecule.n_electrons]
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# y-axis.
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y_label = 'MP2 Energy'
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y_values += [molecule.mp2_energy]
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# Print.
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print('\n{} for {} = {}.'.format(x_label, molecule.name, x_values[-1]))
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print('{} for {} = {}.'.format(y_label, molecule.name, y_values[-1]))
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# Plot.
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matplotlib.pyplot.figure(0)
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matplotlib.pyplot.plot(x_values, y_values, lw=0, marker='o')
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# Set log scales.
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if y_log:
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matplotlib.pyplot.yscale('log')
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if x_log:
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matplotlib.pyplot.xscale('log')
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# Finish making the plot.
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matplotlib.pyplot.xticks(size=axis_size)
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matplotlib.pyplot.yticks(size=axis_size)
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matplotlib.pyplot.xlabel(r'%s' % x_label, fontsize=font_size)
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matplotlib.pyplot.ylabel(r'%s' % y_label, fontsize=font_size)
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matplotlib.pyplot.show()

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