Adds tutorial for using Psi4's SADGuess class

Self-Consistent-Field/RHF_libSADGuess.py

@@ -0,0 +1,161 @@
+"""
+A restricted Hartree-Fock script using the Psi4NumPy Formalism
+"""
+
+__authors__ = "Daniel G. A. Smith"
+__credits__ = ["Daniel G. A. Smith"]
+
+__copyright__ = "(c) 2014-2017, The Psi4NumPy Developers"
+__license__ = "BSD-3-Clause"
+__date__ = "2017-9-30"
+
+import time
+import numpy as np
+np.set_printoptions(precision=5, linewidth=200, suppress=True)
+import psi4
+
+# Memory for Psi4 in GB
+psi4.set_memory('500 MB')
+psi4.core.set_output_file("output.dat", False)
+
+# Memory for numpy in GB
+numpy_memory = 2
+
+mol = psi4.geometry("""
+O
+H 1 1.1
+H 1 1.1 2 104
+symmetry c1
+""")
+
+psi4.set_options({'basis': 'cc-pvdz',
+                  'scf_type': 'pk',
+                  'e_convergence': 1e-8})
+
+# Set defaults
+maxiter = 40
+E_conv = 1.0E-6
+D_conv = 1.0E-3
+
+# Initial guess toggle. True for SAD, False for CORE
+SAD_Guess = True
+
+# Integral generation from Psi4's MintsHelper
+wfn = psi4.core.Wavefunction.build(mol, psi4.core.get_global_option('BASIS'))
+t = time.time()
+mints = psi4.core.MintsHelper(wfn.basisset())
+S = np.asarray(mints.ao_overlap())
+
+# Get nbf and ndocc for closed shell molecules
+nbf = S.shape[0]
+ndocc = wfn.nalpha()
+
+print('\nNumber of occupied orbitals: %d' % ndocc)
+print('Number of basis functions: %d' % nbf)
+
+# Run a quick check to make sure everything will fit into memory
+I_Size = (nbf**4) * 8.e-9
+print("\nSize of the ERI tensor will be %4.2f GB." % I_Size)
+
+# Estimate memory usage
+memory_footprint = I_Size * 1.5
+if I_Size > numpy_memory:
+    psi4.core.clean()
+    raise Exception("Estimated memory utilization (%4.2f GB) exceeds numpy_memory \
+                    limit of %4.2f GB." % (memory_footprint, numpy_memory))
+
+# Compute required quantities for SCF
+V = np.asarray(mints.ao_potential())
+T = np.asarray(mints.ao_kinetic())
+I = np.asarray(mints.ao_eri())
+
+print('\nTotal time taken for integrals: %.3f seconds.' % (time.time() - t))
+t = time.time()
+
+# Construct Hamiltonian
+H = T + V
+
+# Get guess, specified by SAD_Guess toggle
+if(SAD_Guess):
+    # Set SAD basis sets
+    nbeta = wfn.nbeta()
+    psi4.core.prepare_options_for_module("SCF")
+    sad_basis_list = psi4.core.BasisSet.build(wfn.molecule(), "ORBITAL",
+        psi4.core.get_global_option("BASIS"), puream=wfn.basisset().has_puream(),
+                                         return_atomlist=True)
+
+    sad_fitting_list = psi4.core.BasisSet.build(wfn.molecule(), "DF_BASIS_SAD",
+        psi4.core.get_option("SCF", "DF_BASIS_SAD"), puream=wfn.basisset().has_puream(),
+                                           return_atomlist=True)
+
+    # Use Psi4 SADGuess object to build the SAD Guess
+    SAD = psi4.core.SADGuess.build_SAD(wfn.basisset(), sad_basis_list, ndocc, nbeta)
+    SAD.set_atomic_fit_bases(sad_fitting_list)
+    SAD.compute_guess();
+    D = SAD.Da()
+else: 
+    # Orthogonalizer A = S^(-1/2) using Psi4's matrix power.
+    A = mints.ao_overlap()
+    A.power(-0.5, 1.e-16)
+    A = np.asarray(A)
+
+    # Calculate initial core guess
+    Hp = A.dot(H).dot(A)
+    e, C2 = np.linalg.eigh(Hp)
+    C = A.dot(C2)
+    Cocc = C[:, :ndocc]
+    D = np.einsum('pi,qi->pq', Cocc, Cocc)
+
+# Orthogonalizer A = S^(-1/2) using Psi4's matrix power.
+A = mints.ao_overlap()
+A.power(-0.5, 1.e-16)
+A = np.asarray(A)
+
+print('\nTotal time taken for setup: %.3f seconds' % (time.time() - t))
+
+print('\nStart SCF iterations:\n')
+t = time.time()
+E = 0.0
+Enuc = mol.nuclear_repulsion_energy()
+Eold = 0.0
+Dold = np.zeros_like(D)
+
+for SCF_ITER in range(1, maxiter + 1):
+
+    # Build fock matrix
+    J = np.einsum('pqrs,rs->pq', I, D)
+    K = np.einsum('prqs,rs->pq', I, D)
+    F = H + J * 2 - K
+
+    diis_e = np.einsum('ij,jk,kl->il', F, D, S) - np.einsum('ij,jk,kl->il', S, D, F)
+    diis_e = A.dot(diis_e).dot(A)
+
+    # SCF energy and update
+    SCF_E = np.einsum('pq,pq->', F + H, D) + Enuc
+    dRMS = np.mean(diis_e**2)**0.5
+
+    print('SCF Iteration %3d: Energy = %4.16f   dE = % 1.5E   dRMS = %1.5E' % (SCF_ITER, SCF_E, (SCF_E - Eold), dRMS))
+    if (abs(SCF_E - Eold) < E_conv) and (dRMS < D_conv):
+        break
+
+    Eold = SCF_E
+    Dold = D
+
+    # Diagonalize Fock matrix
+    Fp = A.dot(F).dot(A)
+    e, C2 = np.linalg.eigh(Fp)
+    C = A.dot(C2)
+    Cocc = C[:, :ndocc]
+    D = np.einsum('pi,qi->pq', Cocc, Cocc)
+
+    if SCF_ITER == maxiter:
+        clean()
+        raise Exception("Maximum number of SCF cycles exceeded.")
+
+print('Total time for SCF iterations: %.3f seconds \n' % (time.time() - t))
+
+print('Final SCF energy: %.8f hartree' % SCF_E)
+SCF_E_psi = psi4.energy('SCF')
+psi4.compare_values(SCF_E_psi, SCF_E, 6, 'SCF Energy')
+psi4.compare_values(SCF_ITER, 14, 6, 'SAD Iterations')
+

tests/addons.py

@@ -40,6 +40,9 @@ def is_numpy_new_enough(version_feature_introduced):
 using_psi4_efpmints = pytest.mark.skipif(is_psi4_new_enough("1.2a1.dev507") is False,
                                 reason="Psi4 does not include EFP integrals in mints. Update to development head")
 
+using_psi4_sadpy = pytest.mark.skipif(is_psi4_new_enough("1.2a1.dev600") is False,
+                                reason="Psi4 does not include SADGuess bindings. Update to development head")
+
 using_numpy_113 = pytest.mark.skipif(is_numpy_new_enough("1.13.0") is False,
                                 reason='NumPy does not include 1.13 features. Update package and add to envvar PYTHONPATH')
 

tests/test_RI_SCF.py

@@ -20,6 +20,10 @@ def test_RHF_libJK(workspace):
 def test_RHF(workspace):
     exe_py(workspace, tdir, 'RHF')
 
+@using_psi4_sadpy
+def test_RHF_libSADGuess(workspace):
+    exe_py(workspace, tdir, 'RHF_libSADGuess')
+
 
 @using_psi4_efpmints
 @using_pylibefp