Hamiltonian module (#10)

* made code compatible with hamiltonians module

* moved atoms example

Author: babbush

NOTICE

@@ -12,7 +12,7 @@ This plugin library allows the electronic structure package `PySCF <http://githu
 Installation
 ------------
 
-To install the latest versions of OpenFermion, PySCF and OpenFermion-PySCF in development mode:
+To install the latest versions of OpenFermion, PySCF and OpenFermion-PySCF in (development mode):
 
 .. code-block:: bash
 

README.rst

@@ -13,9 +13,7 @@
 """This is a simple script for generating data."""
 import os
 
-from openfermion.utils import (make_atomic_ring,
-                               make_atom,
-                               periodic_table)
+from openfermion.hamiltonians import make_atomic_ring
 
 from openfermionpyscf import run_pyscf
 
@@ -26,7 +24,6 @@
     basis = 'sto-3g'
     max_electrons = 10
     spacing = 0.7414
-    compute_elements = 0
 
     # Select calculations.
     force_recompute = 1
@@ -41,11 +38,7 @@
     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)
+        molecule = make_atomic_ring(n_electrons, spacing, basis)
         if os.path.exists(molecule.filename + '.hdf5'):
             molecule.load()
 

examples/generate_data.py

@@ -13,7 +13,7 @@
 """This is a simple script for generating data."""
 import os
 
-from openfermion.utils import MolecularData
+from openfermion.hamiltonians import MolecularData
 
 from openfermionpyscf import run_pyscf
 

examples/generate_diatomic.py

@@ -15,8 +15,8 @@
 import numpy
 import warnings
 
-from openfermion.utils import (make_atom, make_atomic_ring,
-                               MolecularData, periodic_table)
+from openfermion.hamiltonians import (make_atom, make_atomic_ring,
+                                      MolecularData, periodic_table)
 
 
 def latex_name(molecule):
@@ -55,19 +55,14 @@ def latex_name(molecule):
     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 = make_atomic_ring(n_electrons, spacing, basis)
         molecule.load()
         molecular_series += [molecule]
 

examples/openfermionpyscf_demo.ipynb

@@ -11,4 +11,4 @@
 #   limitations under the License.
 
 """Define version number here and read it from setup.py automatically"""
-__version__ = "0.1a1"
+__version__ = "0.1a2"

examples/plotter.py

@@ -1,2 +1,2 @@
-openfermion>=0.1a0
+openfermion>=0.1a2
 pyscf