Merge pull request #5 from ProjectQ-Framework/develop

First pre-release

README.rst

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

examples/generate_diatomic.py

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

examples/plotter.py

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