Merge pull request #13 from zhcui/main

add example NiO FM phase

examples/dmet/04-dmet-nio-fm/NiO-AFM-417

@@ -0,0 +1,13 @@
+POSCAR generated from libdmet_solid 
+1.0 
+   4.170000000000000    2.085000000000000    2.085000000000000 
+   2.085000000000000    4.170000000000000    2.085000000000000 
+   2.085000000000000    2.085000000000000    4.170000000000000 
+  Ni    O 
+   2    2 
+Direct 
+   0.000000000000000    0.000000000000000    0.000000000000000 
+   0.500000000000000    0.500000000000000    0.500000000000000 
+   0.250000000000000    0.250000000000000    0.250000000000000 
+   0.750000000000000    0.750000000000000    0.750000000000000 
+

examples/dmet/04-dmet-nio-fm/nio_fm.py

@@ -0,0 +1,339 @@
+#!/usr/bin/env python
+
+"""
+DMET for NiO in FM phase with gth-dzvp basis.
+"""
+
+import os, sys
+import numpy as np
+import scipy.linalg as la
+
+from pyscf import lib, fci, ao2mo
+from pyscf.pbc.lib import chkfile
+from pyscf.pbc import scf, gto, df, dft, cc, tools
+
+from libdmet.system import lattice
+from libdmet.basis_transform import make_basis
+from libdmet.basis_transform import eri_transform
+from libdmet.lo.iao import reference_mol, get_labels, get_idx
+from libdmet.basis_transform.make_basis import symmetrize_kmf
+from libdmet.utils.misc import max_abs, mdot, kdot, read_poscar
+
+import libdmet.utils.logger as log
+import libdmet.dmet.Hubbard as dmet
+
+log.verbose = "DEBUG1"
+np.set_printoptions(4, linewidth=1000, suppress=True)
+
+max_memory = 110000
+exxdiv = None
+
+### ************************************************************
+### System settings
+### ************************************************************
+
+cell = read_poscar("./NiO-AFM-417")
+cell.spin = 0
+cell.basis   = 'gth-dzvp-molopt-sr'
+cell.pseudo  = 'gth-pade'
+cell.verbose = 5
+cell.precision = 1e-12
+cell.max_memory = max_memory
+kmesh = [2, 2, 2]
+cell.spin = 4 * np.prod(kmesh)
+cell.build()
+
+Ni3d = cell.search_ao_label("Ni 3d.*")
+Ni0_3d = Ni3d[[2, 4]]
+Ni1_3d = Ni3d[[2+5, 4+5]]
+
+Lat = lattice.Lattice(cell, kmesh)
+kpts = Lat.kpts
+nao = Lat.nao
+nkpts = Lat.nkpts
+
+minao = 'gth-szv-molopt-sr'
+pmol = reference_mol(cell, minao=minao)
+ncore = 0
+nval = pmol.nao_nr()
+nvirt = cell.nao_nr() - ncore - nval
+Lat.set_val_virt_core(nval, nvirt, ncore)
+
+kmf_conv_tol = 1e-11
+kmf_max_cycle = 100
+
+gdf_fname = '../03-dmet-nio-afm/gdf_ints_222.h5'
+chkfname = './nio_222.chk'
+
+### ************************************************************
+### DMET settings 
+### ************************************************************
+
+# system
+#Filling = [(cell.nelectron + 4) / float(Lat.nscsites*2.0),
+#           (cell.nelectron - 4) / float(Lat.nscsites*2.0)]
+Filling = (cell.nelectron) / float(Lat.nscsites*2.0)
+restricted = False
+bogoliubov = False
+int_bath = True
+nscsites = Lat.nscsites
+Mu = 0.0
+last_dmu = 0.0
+#beta = np.inf
+beta = 1000.0
+
+# DMET SCF control
+MaxIter = 100
+u_tol = 1.0e-4
+E_tol = 5.0e-5
+iter_tol = 4
+
+# DIIS
+adiis = lib.diis.DIIS()
+adiis.space = 4
+diis_start = 4
+dc = dmet.FDiisContext(adiis.space)
+
+# solver and mu fit
+ncas = nscsites + nval
+nelecas = (Lat.ncore + Lat.nval) * 2
+cisolver = dmet.impurity_solver.CCSD(restricted=restricted, tol=5e-7, tol_normt=5e-5, max_memory=max_memory)
+solver = cisolver
+nelec_tol = 1.0e-5
+delta = 0.01
+step = 0.1
+load_frecord = False
+
+# vcor fit
+imp_fit = False
+emb_fit_iter = 2000 # embedding fitting
+full_fit_iter = 0
+ytol = 1e-7
+gtol = 1e-3 
+CG_check = False
+
+### ************************************************************
+### SCF Mean-field calculation
+### ************************************************************
+
+log.section("\nSolving SCF mean-field problem\n")
+
+# idx of orbitals 
+aoind = cell.aoslice_by_atom()
+ao_labels = cell.ao_labels()
+
+idx_Ni0 = list(range(aoind[0][2], aoind[0][3]))
+idx_Ni1 = list(range(aoind[1][2], aoind[1][3]))
+idx_O0 = list(range(aoind[2][2], aoind[2][3]))
+idx_O1 = list(range(aoind[3][2], aoind[3][3]))
+
+labels, B2_labels, virt_labels = get_labels(cell, minao=minao)
+iao_Ni0 = get_idx(labels, 0)
+iao_Ni1 = get_idx(labels, 1)
+iao_O0 = get_idx(labels, 2)
+iao_O1 = get_idx(labels, 3)
+
+iao_Ni0_val = get_idx(B2_labels, 0)
+iao_Ni1_val = get_idx(B2_labels, 1)
+iao_O0_val = get_idx(B2_labels, 2)
+iao_O1_val = get_idx(B2_labels, 3)
+
+iao_Ni0_virt = get_idx(virt_labels, 0, offset=len(B2_labels))
+iao_Ni1_virt = get_idx(virt_labels, 1, offset=len(B2_labels))
+iao_O0_virt = get_idx(virt_labels, 2, offset=len(B2_labels))
+iao_O1_virt = get_idx(virt_labels, 3, offset=len(B2_labels))
+
+iao_Ni0_3d = (5, 6, 7, 8, 9) # 3d
+iao_Ni1_3d = (15, 16, 17, 18, 19) # 3d
+iao_Ni0_t2g = (5, 6, 8)
+iao_Ni0_eg = (7, 9)
+iao_Ni1_t2g = (15, 16, 18)
+iao_Ni1_eg = (17, 19)
+
+sl_Ni0 = slice(aoind[0][2], aoind[0][3])
+sl_Ni1 = slice(aoind[1][2], aoind[1][3])
+sl_O0 = slice(aoind[2][2], aoind[2][3])
+sl_O1 = slice(aoind[3][2], aoind[3][3])
+sl = [[sl_Ni0, sl_O0], [sl_Ni1, sl_O1]]
+
+gdf = df.GDF(cell, kpts)
+gdf.mesh = np.asarray([18,18,18])
+gdf._cderi_to_save = gdf_fname
+gdf.auxbasis = df.aug_etb(cell, beta=2.3)
+gdf.linear_dep_threshold = 0.
+if not os.path.isfile(gdf_fname):
+    gdf.build()
+
+chkfname = chkfname
+#if False:
+if os.path.isfile(chkfname):
+    kmf = scf.KUHF(cell, kpts, exxdiv=exxdiv).density_fit()
+    kmf.with_df = gdf
+    kmf.with_df._cderi = gdf_fname
+    data = chkfile.load(chkfname, 'scf')
+    kmf.__dict__.update(data)
+else:
+    kmf = scf.KUHF(cell, kpts, exxdiv=exxdiv).density_fit()
+    kmf.with_df = gdf
+    kmf.with_df._cderi = gdf_fname
+    kmf.conv_tol = 1e-11
+    kmf.chkfile = chkfname
+    aoind = cell.aoslice_by_atom()
+
+    dm = kmf.get_init_guess()
+    dm[1] = dm[0]
+
+    dm[0, :, Ni0_3d, Ni0_3d] *= 2.0
+    dm[0, :, Ni1_3d, Ni1_3d] *= 2.0
+    dm[1, :, Ni0_3d, Ni0_3d] = 0.0
+    dm[1, :, Ni1_3d, Ni1_3d] = 0.0
+
+    kmf.max_cycle = 50
+
+    Lat.mulliken_lo_R0(Lat.k2R(dm)[:, 0], labels=cell.ao_labels())
+
+    #from libdmet.routine import pbc_helper as pbc_hp
+    #kmf = pbc_hp.smearing_(kmf, sigma=(1.0/beta))
+
+    kmf.kernel(dm0=dm)
+
+log.result("kmf electronic energy: %20.12f", kmf.e_tot - kmf.energy_nuc())
+
+### ************************************************************
+### Pre-processing, LO and subspace partition
+### ************************************************************
+
+log.section("\nPre-process, orbital localization and subspace partition\n")
+# IAO
+from libdmet.lo.iao import reference_mol, get_labels, get_idx_each
+S_ao_ao = kmf.get_ovlp()
+C_ao_iao, C_ao_iao_val, C_ao_iao_virt = make_basis.get_C_ao_lo_iao(Lat, kmf, minao=minao, full_return=True)
+lo_labels = get_labels(cell, minao=minao)[0]
+
+assert(nval == C_ao_iao_val.shape[-1])
+
+# use IAO
+C_ao_lo = C_ao_iao
+Lat.set_Ham(kmf, gdf, C_ao_lo, eri_symmetry=4)
+
+# vcor initialization
+idx_range = list(range(ncore, ncore+nval))
+vcor = dmet.VcorLocal_new(restricted, bogoliubov, nscsites, idx_range=idx_range)
+vcor.update(np.zeros(vcor.length()))
+
+### ************************************************************
+### DMET procedure
+### ************************************************************
+
+# DMET main loop
+E_old = 0.0
+conv = False
+history = dmet.IterHistory()
+dVcor_per_ele = None
+if load_frecord:
+    dmet.SolveImpHam_with_fitting.load("./frecord")
+
+for iter in range(MaxIter):
+    log.section("\nDMET Iteration %d\n", iter)
+
+    log.section("\nSolving mean-field problem\n")
+    log.result("Vcor =\n%s", vcor.get())
+    log.result("Mu (guess) = %s", Mu)
+
+    rho, Mu, res = dmet.HartreeFock(Lat, vcor, Filling, Mu, beta=beta, ires=True, symm=True)
+    rho = rho.real
+    rho_k = Lat.R2k(rho)
+
+    Lat.mulliken_lo_R0(rho[:, 0], labels=np.asarray(lo_labels))
+
+    print ("mf rho alpha")
+    dm_Ni0_3d_a = rho[0,0][np.ix_(iao_Ni0_3d, iao_Ni0_3d)]
+    dm_Ni1_3d_a = rho[0,0][np.ix_(iao_Ni1_3d, iao_Ni1_3d)]
+    print (dm_Ni0_3d_a)
+    print (dm_Ni1_3d_a)
+
+    print ("mf rho beta")
+    dm_Ni0_3d_b = rho[1,0][np.ix_(iao_Ni0_3d, iao_Ni0_3d)]
+    dm_Ni1_3d_b = rho[1,0][np.ix_(iao_Ni1_3d, iao_Ni1_3d)]
+    print (dm_Ni0_3d_b)
+    print (dm_Ni1_3d_b)
+
+    log.section("\nConstructing impurity problem\n")
+    ImpHam, H1e, basis = dmet.ConstructImpHam(Lat, rho, vcor, int_bath=int_bath, max_memory=max_memory)
+    ImpHam = dmet.apply_dmu(Lat, ImpHam, basis, last_dmu)
+    basis_k = Lat.R2k_basis(basis)
+
+    log.section("\nSolving impurity problem\n")
+    solver_args = {"nelec": (Lat.ncore+Lat.nval)*2, "dm0": dmet.foldRho_k(rho_k, basis_k)}
+
+    rhoEmb, EnergyEmb, ImpHam, dmu = \
+        dmet.SolveImpHam_with_fitting(Lat, Filling, ImpHam, basis, solver, \
+        solver_args=solver_args, thrnelec=nelec_tol, \
+        delta=delta, step=step)
+    dmet.SolveImpHam_with_fitting.save("./frecord")
+    last_dmu += dmu
+    rhoImp, EnergyImp, nelecImp = \
+        dmet.transformResults_new(rhoEmb, EnergyEmb, Lat, basis, ImpHam, H1e, last_dmu, \
+        int_bath=int_bath, solver=solver, solver_args=solver_args,
+        rebuild_veff=True)
+    EnergyImp *= nscsites
+    log.result("last_dmu = %20.12f", last_dmu)
+    log.result("E(DMET) = %20.12f", EnergyImp)
+
+    Lat.mulliken_lo_R0(rhoImp, labels=np.asarray(lo_labels))
+
+    print ("alpha")
+    dm_Ni0_3d_a = rhoImp[0][np.ix_(iao_Ni0_3d, iao_Ni0_3d)]
+    dm_Ni1_3d_a = rhoImp[0][np.ix_(iao_Ni1_3d, iao_Ni1_3d)]
+    print (dm_Ni0_3d_a)
+    print (dm_Ni1_3d_a)
+
+    print ("beta")
+    dm_Ni0_3d_b = rhoImp[1][np.ix_(iao_Ni0_3d, iao_Ni0_3d)]
+    dm_Ni1_3d_b = rhoImp[1][np.ix_(iao_Ni1_3d, iao_Ni1_3d)]
+    print (dm_Ni0_3d_b)
+    print (dm_Ni1_3d_b)
+
+    dm_Ni0_a = rhoImp[0][np.ix_(iao_Ni0, iao_Ni0)]
+    dm_Ni0_b = rhoImp[1][np.ix_(iao_Ni0, iao_Ni0)]
+
+    print ("magnetic order")
+    print (dm_Ni0_a.trace() + dm_Ni0_b.trace())
+    print (dm_Ni0_a.trace() - dm_Ni0_b.trace())
+
+    # DUMP results:
+    dump_res_iter = np.array([Mu, last_dmu, vcor.param, rhoEmb, basis, rhoImp, C_ao_lo, \
+            Lat.getFock(kspace=False), rho], dtype=object)
+    np.save('./dmet_iter_%s.npy'%(iter), dump_res_iter)
+
+    log.section("\nfitting correlation potential\n")
+    vcor_new, err = dmet.FitVcor(rhoEmb, Lat, basis, \
+            vcor, beta, Filling, MaxIter1=emb_fit_iter, MaxIter2=full_fit_iter, method='CG', \
+            imp_fit=imp_fit, ytol=ytol, gtol=gtol, CG_check=CG_check)
+
+    dVcor_per_ele = np.max(np.abs(vcor_new.param - vcor.param))
+    dE = EnergyImp - E_old
+    E_old = EnergyImp 
+
+    if iter >= diis_start:
+        pvcor = adiis.update(vcor_new.param)
+        dc.nDim = adiis.get_num_vec()
+    else:
+        pvcor = vcor_new.param
+
+    dVcor_per_ele = np.max(np.abs(pvcor - vcor.param))
+    vcor.update(pvcor)
+    log.result("Trace of vcor: %20.12f ", np.sum(np.diagonal((vcor.get())[:2], 0, 1, 2)))
+
+    history.update(EnergyImp, err, nelecImp, dVcor_per_ele, dc)
+    history.write_table()
+
+    if dVcor_per_ele < u_tol and abs(dE) < E_tol and iter > iter_tol :
+        conv = True
+        break
+
+if conv:
+    log.result("DMET converge.")
+else:
+    log.result("DMET does not converge.")
+