Merge branch 'master' into for_CCSDt

examples/ewf/molecules/62-external-solver.py

@@ -0,0 +1,137 @@
+'''Use the cluster dump functionality (see 20-dump-clusters.py) to dump the clusters,
+read them back in, solve them with pyscf's FCI solver, and show that the same result
+is achieved as Vayesta's internal functionality. Note that this just computes the
+'projected' energy estimator over the clusters, from the C2 amplitudes.'''
+import numpy as np
+import pyscf
+import pyscf.gto
+import pyscf.scf
+import pyscf.fci
+import vayesta
+import vayesta.ewf
+from vayesta.misc.molecules import ring
+from vayesta.core.types import Orbitals, FCI_WaveFunction, CISD_WaveFunction
+import h5py
+
+# Create natom ring of minimal basis hydrogen atoms
+natom = 6
+mol = pyscf.gto.Mole()
+mol.atom = ring("H", natom, 1.5)
+mol.basis = "sto-3g"
+mol.output = "pyscf.out"
+mol.verbose = 5
+mol.symmetry = True
+mol.build()
+
+# Hartree-Fock
+mf = pyscf.scf.RHF(mol)
+mf.kernel()
+print('Mean-Field (Hartree--Fock) energy = {}'.format(mf.e_tot))
+assert mf.converged
+
+# Full-system FCI for comparison
+ci = pyscf.fci.FCI(mf)
+ci.kernel()
+print('FCI total energy: {}'.format(ci.e_tot))
+
+# Full-system coupled cluster
+cc = pyscf.cc.CCSD(mf)
+cc.kernel()
+print('CCSD total energy: {}'.format(cc.e_tot))
+
+# Vayesta options
+use_sym = True
+nfrag = 1 # When using symmetry, we have to specify the number of atoms in the fragment in this case.
+#bath_opts = dict(bathtype="full")  # This is a complete bath space (should be exact)
+bath_opts = dict(bathtype="dmet")   # This is the smallest bath size
+# bath_opts = dict(bathtype='mp2', threshold=1.e-6)
+
+# Run vayesta for comparison with FCI solver
+emb = vayesta.ewf.EWF(mf, solver="FCI", bath_options=bath_opts, solver_options=dict(conv_tol=1.e-14)
+# Set up fragments
+with emb.iao_fragmentation() as f:
+    if use_sym:
+        # Add rotational symmetry
+        # Set order of rotation (2: 180 degrees, 3: 120 degrees, 4: 90: degrees,...),
+        # axis along which to rotate and center of rotation (default units for axis and center are Angstroms):
+        with f.rotational_symmetry(order=natom//nfrag, axis=[0, 0, 1]):
+            f.add_atomic_fragment(range(nfrag))
+    else:
+        # Add all atoms as separate fragments 
+        f.add_all_atomic_fragments()
+emb.kernel()
+
+# Run vayesta again, but just dump clusters, rather than solve them
+emb_dump = vayesta.ewf.EWF(mf, solver="DUMP", bath_options=bath_opts, solver_options=dict(dumpfile="clusters-rhf.h5"))
+# Set up fragments
+with emb_dump.iao_fragmentation() as f:
+    if use_sym:
+        # Add rotational symmetry
+        # Set order of rotation (2: 180 degrees, 3: 120 degrees, 4: 90: degrees,...),
+        # axis along which to rotate and center of rotation (default units for axis and center are Angstroms):
+        with f.rotational_symmetry(order=natom//nfrag, axis=[0, 0, 1]):
+            f.add_atomic_fragment(range(nfrag))
+    else:
+        # Add all atoms as separate fragments 
+        f.add_all_atomic_fragments()
+print('Total number of fragments (inc. sym related): {}'.format(len(emb_dump.fragments)))
+emb_dump.kernel()
+
+class Cluster(object):
+
+    def __init__(self, key, cluster):
+
+        self.key = key
+        self.c_frag = np.array(cluster["c_frag"]) # Fragment orbitals (AO,Frag)
+        self.c_cluster = np.array(cluster["c_cluster"]) # Cluster orbitals (AO,Cluster)
+
+        self.norb, self.nocc, self.nvir = cluster.attrs["norb"], cluster.attrs["nocc"], cluster.attrs["nvir"]
+        self.fock = np.array(cluster["fock"]) # Fock matrix (Cluster,Cluster)
+        self.h1e = np.array(cluster["heff"]) # 1 electron integrals (Cluster,Cluster)
+        self.h2e = np.array(cluster["eris"]) # 2 electron integrals (Cluster,Cluster,Cluster,Cluster)
+
+    def __repr__(self):
+        return self.key
+
+# Load clusters from file
+with h5py.File("clusters-rhf.h5", "r") as f:
+    clusters = [Cluster(key, cluster) for key, cluster in f.items()]
+print(clusters)
+print("Clusters loaded: %d" % len(clusters))
+
+# To complete the info we need the AO overlap matrix (also get the MO coefficients)
+mo_coeff, ovlp = mf.mo_coeff, mf.get_ovlp()
+
+# Go through each cluster, and solve it with pyscf's FCI module. Find its energy contribution by passing in the hamiltonian.
+e_corr = 0
+for ind, cluster in enumerate(clusters):
+    # Solve, and return energy and FCI wave function
+    energy, ci_vec = pyscf.fci.direct_spin0.kernel(cluster.h1e, cluster.h2e, cluster.norb, nelec=(cluster.nocc, cluster.nocc), conv_tol=1.e-14)
+    orbs = Orbitals(cluster.c_cluster, occ=cluster.nocc)
+    # Get the FCI wave function, and extract out the C0, C1 and C2 coefficients. Set C0 to 1 (intermediate normalization).
+    wf = FCI_WaveFunction(orbs, ci_vec).as_cisd(c0=1.0)
+    #assert(np.allclose(wf.c2,emb.fragments[ind].results.wf.as_cisd(c0=1.0).c2))
+    #print("Error in C2 amplitudes: ",np.linalg.norm(emb.fragments[ind].results.wf.as_cisd(c0=1.0).c2-wf.c2))
+
+    # Create a fragment projector of the occupied cluster orbitals onto the fragment space
+    proj = cluster.c_frag.T @ ovlp @ cluster.c_cluster[:,:cluster.nocc]
+    #assert(np.allclose(proj, emb.fragments[ind].get_overlap("frag|cluster-occ")))
+    # Transform the first index of the C2 and C1 amplitudes to the fragment space
+    wf_proj = wf.project(proj)
+
+    # Calculate projected correlation energy contribution
+    o, v = np.s_[:cluster.nocc], np.s_[cluster.nocc:]
+    # NOTE: Formally, we should include a C1^2 contribution to the energy too, but this is likely to be small.
+    # If using a non-canonical reference, there should also be a C1.F contribution too, which we are ignoring here.
+    e_loc = 2*np.einsum('xi,xjab,iabj', proj, wf_proj.c2, cluster.h2e[o,v,v,o]) - np.einsum('xi,xjab,ibaj', proj, wf_proj.c2, cluster.h2e[o,v,v,o])
+    #assert(np.isclose(emb.fragments[ind].get_fragment_energy(wf_proj.c1, wf_proj.c2)[2], e_loc))
+    print('From cluster {}: FCI energy = {}, local correlation energy contribution = {}'.format(cluster, energy, e_loc))
+    e_corr += e_loc
+if use_sym:
+    e_corr *= natom // nfrag
+
+print("Full system mean-field energy = %f" % mf.e_tot)
+print("Full system CCSD correlation energy = %f" % cc.e_corr)
+print("Full system FCI correlation energy: {}".format(ci.e_tot-mf.e_tot))
+print("Vayesta correlation energy = %f" % emb.e_corr)
+print("Correlation energy from external FCI solver = %f" % e_corr)