Basic example added (issue #58)

gabrielasd · Jul 13, 2021 · eab5ea6 · eab5ea6
1 parent 00b9a93
commit eab5ea6
Show file tree

Hide file tree

Showing 8 changed files with 101 additions and 9 deletions.
diff --git a/docs/source/examples.rst b/docs/source/examples.rst
@@ -17,4 +17,50 @@
 Examples
 ########
 
-To be completed.
+EOMEE computes excited states energies though the implementation of the equation-of-motion
+formalism. 
+
+Some example scripts showcasing the supported features can be found inside the project's *examples* folder.
+These assume the package has been installed following the instructions in :ref:`Installation
+<installation>`.
+
+To run particle-hole RPA for Hellium with EOMEE do:
+
+    .. code-block:: python
+
+        from eomee import EOMExc
+
+        from eomee.tools import (
+            find_datafiles,
+            spinize,
+            hartreefock_rdms,
+        )
+
+        import numpy as np
+
+        # System He
+        nalpha = 1
+        nbeta = 1
+        # Load one- and two-electron integrals (in molecular orbitals basis)
+        one_mo = np.load(find_datafiles("he_ccpvdz_oneint.npy"))
+        two_mo = np.load(find_datafiles("he_ccpvdz_twoint.npy"))
+
+        # Make spin-resolved one- and two-particle density matrices for Hartree-Fock slater determinant
+        nbasis = one_mo.shape[0] # Number of molecular orbitals in the basis set
+        one_dm, two_dm = hartreefock_rdms(nbasis, nalpha, nbeta)
+
+        # Transform electron integrlas from spatial to spin-resolved representation
+        one_mo = spinize(one_mo)
+        two_mo = spinize(two_mo)
+
+        # Solve particle-hole EOM
+        pheom = EOMExc(one_mo, two_mo, one_dm, two_dm)
+        ev, cv = pheom.solve_dense(orthog="asymmetric")
+
+        print("Number of eigenvalues: ", pheom.neigs)
+        print("Left-hand-side matrix: ", pheom.lhs, "\n")
+        print("Right-hand-side matrix: ", pheom.rhs, "\n")
+
+        print("Transition energies: ", ev)
+
+One can get the electron integrals required as input in above's example thorugh a mean-field calculation using an external package (e.g. PySCF). 
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -14,6 +14,8 @@
     : You should have received a copy of the GNU General Public License
     : along with EOMEE. If not, see <http://www.gnu.org/licenses/>.
 
+.. _installation:
+
 Installation
 ############
 

diff --git a/examples/be_sto3g_onedm_spino.npy b/examples/be_sto3g_onedm_spino.npy
diff --git a/examples/be_sto3g_oneint_spino.npy b/examples/be_sto3g_oneint_spino.npy
diff --git a/examples/be_sto3g_twodm_spino.npy b/examples/be_sto3g_twodm_spino.npy
diff --git a/examples/be_sto3g_twoint_spino.npy b/examples/be_sto3g_twoint_spino.npy
diff --git a/examples/example_exceom.txt b/examples/example_exceom.txt
diff --git a/examples/he_ccpvdz_exc.py b/examples/he_ccpvdz_exc.py
@@ -0,0 +1,52 @@
+# This file is part of EOMEE.
+#
+# EOMEE is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+#
+# EOMEE is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+# for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EOMEE. If not, see <http://www.gnu.org/licenses/>.
+
+r"""Example excited state calculation for the particle-hole operator."""
+
+
+from eomee import EOMExc
+
+from eomee.tools import (
+    find_datafiles,
+    spinize,
+    hartreefock_rdms,
+)
+
+import numpy as np
+
+# System He
+nalpha = 1
+nbeta = 1
+# Load one- and two-electron integrals (in molecular orbitals basis)
+one_mo = np.load(find_datafiles("he_ccpvdz_oneint.npy"))
+two_mo = np.load(find_datafiles("he_ccpvdz_twoint.npy"))
+
+# Make spin-resolved one- and two-particle density matrices for Hartree-Fock slater determinant
+nbasis = one_mo.shape[0] # Number of molecular orbitals in the basis set
+one_dm, two_dm = hartreefock_rdms(nbasis, nalpha, nbeta)
+
+# Transform electron integrlas from spatial to spin-resolved representation
+one_mo = spinize(one_mo)
+two_mo = spinize(two_mo)
+
+# Solve particle-hole EOM
+pheom = EOMExc(one_mo, two_mo, one_dm, two_dm)
+ev, cv = pheom.solve_dense(orthog="asymmetric")
+
+print("Number of eigenvalues: ", pheom.neigs)
+print("Left-hand-side matrix: ", pheom.lhs, "\n")
+print("Right-hand-side matrix: ", pheom.rhs, "\n")
+
+print("Transition energies: ", ev)