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Util_Rela4C_PC.py
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Util_Rela4C_PC.py
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from pyscf import gto, scf, lib
import numpy
from functools import reduce
from pyscf import lib
from pyscf import tools
import pyscf
import re
from pyscf import __config__
from Util_File import *
from Util_Rela4C import *
IOBLK_SIZE = getattr(__config__, 'ao2mo_outcore_ioblk_size', 256) # 256 MB
IOBUF_WORDS = getattr(__config__, 'ao2mo_outcore_iobuf_words', 1e8) # 1.6 GB
IOBUF_ROW_MIN = getattr(__config__, 'ao2mo_outcore_row_min', 160)
MAX_MEMORY = getattr(__config__, 'ao2mo_outcore_max_memory', 4000) # 4GB
def _pair_correction(mol, pes_dm1, pes_dm2, mo_ene, U_mo, g_ppnp, g_pppn):
n2c = mol.nao_2c()
n4c = n2c * 2
assert pes_dm1.shape == (n2c, n2c)
assert pes_dm2.shape == (n2c, n2c, n2c, n2c)
assert mo_ene.shape == (n4c,)
assert U_mo.shape == (n4c, n4c)
assert g_ppnp.shape == (n2c, n2c, n2c, n2c)
assert g_pppn.shape == (n2c, n2c, n2c, n2c)
res = 0.0
### the first term ###
term1 = numpy.einsum("is,ti,ts->it", U_mo[:n2c, n2c:], U_mo[n2c:, :n2c], pes_dm1, optimize=True)
for i in range(n2c):
for t in range(n2c):
res += -term1[i, t] / (mo_ene[i] - mo_ene[t+n2c])
#print("term = ", term1[i, t])
#print("ene_diff = ", (mo_ene[i] - mo_ene[t+n2c]))
#print("res = ", res)
### the second term ###
term2 = numpy.einsum("pris,ti,prts->it", g_ppnp, U_mo[n2c:, :n2c], pes_dm2, optimize=True)
for i in range(n2c):
for t in range(n2c):
res += term2[i, t] / (mo_ene[i] - mo_ene[t+n2c])
### the third term ###
term3 = numpy.einsum("it,prsi,prst->rips", U_mo[:n2c, n2c:], g_pppn, pes_dm2, optimize=True)
for r in range(n2c):
for i in range(n2c):
for p in range(n2c):
for s in range(n2c):
res += term3[r, i, p, s] / (mo_ene[r+n2c] + mo_ene[i] - mo_ene[p+n2c] - mo_ene[s+n2c])
return res
def _r_outcore_Coulomb_g(mol, my_RDHF, prefix, mo_coeffs, max_memory=MAX_MEMORY, ioblk_size=IOBLK_SIZE):
from pyscf.ao2mo import r_outcore
n2c = mol.nao_2c()
#mo_coeff = my_RDHF.mo_coeff
#mo_coeff_mat = numpy.matrix(mo_coeff)
#mo_coeff_pes = mo_coeff_mat[:, n2c:]
#mo_coeff_L = mo_coeff_pes[:n2c, :]
#mo_coeff_S = mo_coeff_pes[n2c:, :]
r_outcore.general(mol, (
mo_coeffs[0][:n2c, :],
mo_coeffs[1][:n2c, :],
mo_coeffs[2][:n2c, :],
mo_coeffs[3][:n2c, :]), coulomb_LLLL %
prefix, intor="int2e_spinor", max_memory=max_memory, ioblk_size=ioblk_size, aosym='s1')
r_outcore.general(mol, (
mo_coeffs[0][n2c:, :],
mo_coeffs[1][n2c:, :],
mo_coeffs[2][n2c:, :],
mo_coeffs[3][n2c:, :]), coulomb_SSSS %
prefix, intor="int2e_spsp1spsp2_spinor", max_memory=max_memory, ioblk_size=ioblk_size, aosym='s1')
r_outcore.general(mol, (
mo_coeffs[0][:n2c, :],
mo_coeffs[1][:n2c, :],
mo_coeffs[2][n2c:, :],
mo_coeffs[3][n2c:, :]), coulomb_LLSS %
prefix, intor="int2e_spsp2_spinor", max_memory=max_memory, ioblk_size=ioblk_size, aosym='s1')
r_outcore.general(mol, (
mo_coeffs[0][n2c:, :],
mo_coeffs[1][n2c:, :],
mo_coeffs[2][:n2c, :],
mo_coeffs[3][:n2c, :]), coulomb_SSLL %
prefix, intor="int2e_spsp1_spinor", max_memory=max_memory, ioblk_size=ioblk_size, aosym='s1')
def _r_outcore_Breit_g(mol, my_RDHF, prefix, mo_coeffs, max_memory=MAX_MEMORY, ioblk_size=IOBLK_SIZE):
from pyscf.ao2mo import r_outcore
n2c = mol.nao_2c()
#mo_coeff = my_RDHF.mo_coeff
#mo_coeff_mat = numpy.matrix(mo_coeff)
#mo_coeff_pes = mo_coeff_mat[:, n2c:]
#mo_coeff_L = mo_coeff_pes[:n2c, :]
#mo_coeff_S = mo_coeff_pes[n2c:, :]
r_outcore.general(mol, (
mo_coeffs[0][:n2c, :],
mo_coeffs[1][n2c:, :],
mo_coeffs[2][:n2c, :],
mo_coeffs[3][n2c:, :]), breit_LSLS %
prefix, intor="int2e_breit_ssp1ssp2_spinor", max_memory=max_memory, ioblk_size=ioblk_size, aosym='s1')
r_outcore.general(mol, (
mo_coeffs[0][n2c:, :],
mo_coeffs[1][:n2c, :],
mo_coeffs[2][n2c:, :],
mo_coeffs[3][:n2c, :]), breit_SLSL %
prefix, intor="int2e_breit_sps1sps2_spinor", max_memory=max_memory, ioblk_size=ioblk_size, aosym='s1')
r_outcore.general(mol, (
mo_coeffs[0][:n2c, :],
mo_coeffs[1][n2c:, :],
mo_coeffs[2][n2c:, :],
mo_coeffs[3][:n2c, :]), breit_LSSL %
prefix, intor="int2e_breit_ssp1sps2_spinor", max_memory=max_memory, ioblk_size=ioblk_size, aosym='s1')
r_outcore.general(mol, (
mo_coeffs[0][n2c:, :],
mo_coeffs[1][:n2c, :],
mo_coeffs[2][:n2c, :],
mo_coeffs[3][n2c:, :]), breit_SLLS %
prefix, intor="int2e_breit_sps1ssp2_spinor", max_memory=max_memory, ioblk_size=ioblk_size, aosym='s1')
def _get_g(mol, my_RDHF, mo_coeff, type, incore=True):
assert type in ["ppnp", "pppn"]
n2c = mol.nao_2c()
n4c = n2c * 2
assert mo_coeff.shape == (n4c, n4c)
mo_coeffs = []
if type == "ppnp":
mo_coeffs.append(mo_coeff[:, n2c:])
mo_coeffs.append(mo_coeff[:, n2c:])
mo_coeffs.append(mo_coeff[:, :n2c])
mo_coeffs.append(mo_coeff[:, n2c:])
else:
mo_coeffs.append(mo_coeff[:, n2c:])
mo_coeffs.append(mo_coeff[:, n2c:])
mo_coeffs.append(mo_coeff[:, n2c:])
mo_coeffs.append(mo_coeff[:, :n2c])
with_breit = my_RDHF.with_breit
with_gaunt = my_RDHF.with_gaunt
if with_breit:
INT_LSLS_name = "int2e_breit_ssp1ssp2_spinor"
INT_SLSL_name = "int2e_breit_sps1sps2_spinor"
INT_LSSL_name = "int2e_breit_ssp1sps2_spinor"
INT_SLLS_name = "int2e_breit_sps1ssp2_spinor"
else:
if with_gaunt:
INT_LSLS_name = "int2e_ssp1ssp2_spinor"
INT_SLSL_name = "int2e_sps1sps2_spinor"
INT_LSSL_name = "int2e_ssp1sps2_spinor"
INT_SLLS_name = "int2e_sps1ssp2_spinor"
if incore:
int2e_res = numpy.zeros((n4c, n4c, n4c, n4c), dtype=numpy.complex128)
c1 = .5 / lib.param.LIGHT_SPEED
int2e_res[:n2c, :n2c, :n2c, :n2c] = mol.intor("int2e_spinor") # LL LL
tmp = mol.intor("int2e_spsp1_spinor") * c1**2
int2e_res[n2c:, n2c:, :n2c, :n2c] = tmp # SS LL
int2e_res[:n2c, :n2c, n2c:, n2c:] = tmp.transpose(2, 3, 0, 1) # LL SS
int2e_res[n2c:, n2c:, n2c:, n2c:] = mol.intor("int2e_spsp1spsp2_spinor") * c1**4 # SS SS
int2e_res = lib.einsum("ijkl,ip->pjkl", int2e_res, mo_coeffs[0].conj())
int2e_res = lib.einsum("pjkl,jq->pqkl", int2e_res, mo_coeffs[1])
int2e_res = lib.einsum("pqkl,kr->pqrl", int2e_res, mo_coeffs[2].conj())
int2e_res = lib.einsum("pqrl,ls->pqrs", int2e_res, mo_coeffs[3])
if with_breit or with_gaunt:
int2e_bg = numpy.zeros((n4c, n4c, n4c, n4c), dtype=numpy.complex128)
##### (LS|LS) and (SL|SL) #####
tmp = mol.intor(INT_LSLS_name) * c1**2
int2e_bg[:n2c, n2c:, :n2c, n2c:] = tmp
tmp = mol.intor(INT_SLSL_name) * c1**2
int2e_bg[n2c:, :n2c, n2c:, :n2c] = tmp
##### (LS|SL) and (SL|LS) #####
tmp2 = mol.intor(INT_LSSL_name) * c1**2
int2e_bg[:n2c, n2c:, n2c:, :n2c] = tmp2 # (LS|SL)
tmp2 = mol.intor(INT_SLLS_name) * c1**2
int2e_bg[n2c:, :n2c, :n2c, n2c:] = tmp2 # (SL|LS)
###############################
int2e_bg = lib.einsum("ijkl,ip->pjkl", int2e_bg, mo_coeffs[0].conj())
int2e_bg = lib.einsum("pjkl,jq->pqkl", int2e_bg, mo_coeffs[1])
int2e_bg = lib.einsum("pqkl,kr->pqrl", int2e_bg, mo_coeffs[2].conj())
int2e_bg = lib.einsum("pqrl,ls->pqrs", int2e_bg, mo_coeffs[3])
int2e_res += int2e_bg
else:
PREFIX = "RELA_4C_%d" % (numpy.random.randint(1, 19951201+1))
_r_outcore_Coulomb_g(mol, my_RDHF, PREFIX, mo_coeffs)
import h5py, os
c1 = .5 / lib.param.LIGHT_SPEED
feri_coulomb_LLLL = h5py.File(coulomb_LLLL % PREFIX, 'r')
feri_coulomb_LLSS = h5py.File(coulomb_LLSS % PREFIX, 'r')
feri_coulomb_SSLL = h5py.File(coulomb_SSLL % PREFIX, 'r')
feri_coulomb_SSSS = h5py.File(coulomb_SSSS % PREFIX, 'r')
int2e_res = numpy.array(feri_coulomb_LLLL['eri_mo'])
int2e_res+= numpy.array(feri_coulomb_LLSS['eri_mo']) * c1**2
int2e_res+= numpy.array(feri_coulomb_SSLL['eri_mo']) * c1**2
int2e_res+= numpy.array(feri_coulomb_SSSS['eri_mo']) * c1**4
#print("int2e_res.shape = ", int2e_res.shape)
os.remove(coulomb_LLLL % PREFIX)
os.remove(coulomb_LLSS % PREFIX)
os.remove(coulomb_SSLL % PREFIX)
os.remove(coulomb_SSSS % PREFIX)
if with_breit:
_r_outcore_Breit_g(mol, my_RDHF, PREFIX, mo_coeffs)
feri_breit_LSLS = h5py.File(breit_LSLS % PREFIX, 'r')
feri_breit_SLSL = h5py.File(breit_SLSL % PREFIX, 'r')
feri_breit_LSSL = h5py.File(breit_LSSL % PREFIX, 'r')
feri_breit_SLLS = h5py.File(breit_SLLS % PREFIX, 'r')
int2e_res += numpy.array(feri_breit_LSLS['eri_mo']) * c1**2
int2e_res += numpy.array(feri_breit_SLSL['eri_mo']) * c1**2
int2e_res += numpy.array(feri_breit_LSSL['eri_mo']) * c1**2
int2e_res += numpy.array(feri_breit_SLLS['eri_mo']) * c1**2
os.remove(breit_LSLS % PREFIX)
os.remove(breit_SLSL % PREFIX)
os.remove(breit_LSSL % PREFIX)
os.remove(breit_SLLS % PREFIX)
else:
if with_gaunt:
raise NotImplementedError
#print("int2e_res.shape = ", int2e_res.shape)
int2e_res = int2e_res.reshape((n2c, n2c, n2c, n2c))
return int2e_res
def _Generate_InputFile_SiCI(File,
Segment,
nelec_val,
cmin=0.0,
perturbation=1,
Task=None,
tol=1e-8,
selection=1,
dumprdm=0
):
"""Generate the input file
"""
with open(File, "w") as f:
f.write("nsegment=%s\n" % Segment)
f.write("nvalelec=%d\n" % nelec_val)
f.write("rotatemo=%d\n" % 0)
f.write("cmin=%s\n" % cmin)
f.write("perturbation=%d 0\n" % perturbation)
f.write("dumprdm=%d\n" % dumprdm)
f.write("task=%s\n" % Task)
f.write("etol=%e\n" % tol)
f.write("selection=%d\n" % selection)
f.write("print=12\n")
APP = "/home/ningzhangcaltech/Github_Repo/iCIPT2_CXX/bin/iCIPT2_Spinor.exe"
def _pack_fzc(dm1, dm2, norb, nfzc):
### rdm1 ###
for i in range(2*nfzc):
dm1[i,i] = 1.0
### rdm2 pure core ###
### iiii
for i in range(nfzc):
dm2[2*i,2*i,2*i+1,2*i+1] = 1.0
dm2[2*i,2*i+1,2*i+1,2*i] = 1.0
dm2[2*i+1,2*i,2*i,2*i+1] = 1.0
dm2[2*i+1,2*i+1,2*i,2*i] = 1.0
### iijj
for i in range(nfzc):
for j in range(nfzc):
if i == j:
continue
dm2[2*i,2*i,2*j,2*j] = 1.0
dm2[2*i,2*i,2*j+1,2*j+1] = 1.0
dm2[2*i+1,2*i+1,2*j,2*j] = 1.0
dm2[2*i+1,2*i+1,2*j+1,2*j+1] = 1.0
dm2[2*i,2*j,2*j,2*i] = -1.0
dm2[2*i,2*j+1,2*j+1,2*i] = -1.0
dm2[2*i+1,2*j,2*j,2*i+1] = -1.0
dm2[2*i+1,2*j+1,2*j+1,2*i+1] = -1.0
### rdm2 semicore
for i in range(2*nfzc):
dm2[i,i,2*nfzc:2*norb,2*nfzc:2*norb] = dm1[2*nfzc:2*norb,2*nfzc:2*norb]
dm2[2*nfzc:2*norb,2*nfzc:2*norb,i,i] = dm1[2*nfzc:2*norb,2*nfzc:2*norb]
dm2[i,2*nfzc:2*norb,2*nfzc:2*norb,i] = -dm1[2*nfzc:2*norb,2*nfzc:2*norb].T
dm2[2*nfzc:2*norb,i,i,2*nfzc:2*norb] = -dm1[2*nfzc:2*norb,2*nfzc:2*norb].T
return dm1, dm2
if __name__ == "__main__":
# mol = gto.M(atom='H 0 0 0; H 0 0 1; O 0 1 0', basis='sto-3g', verbose=5)
mol = gto.M(atom='F 0 0 0', basis='cc-pvdz-dk', verbose=5,
charge=-1, spin=0, symmetry="d2h")
mol.build()
mf = scf.dhf.RDHF(mol)
mf.conv_tol = 1e-12
mf.kernel()
mf.with_breit = True
mf.kernel()
mo_coeff = mf.mo_coeff
print("mo_coeff.shape = ", mo_coeff.shape)
Dump_Cmoao_4C("F_4C", mo_coeff)
hcore = mf.get_hcore()
print("hcore.shape = ", hcore.shape)
dm = mf.make_rdm1()
print("dm.shape = ", dm.shape)
fock = mf.get_fock(dm=dm)
ovlp = mf.get_ovlp()
e, mo_coeff = mf._eigh(fock, ovlp)
print("mo_ene = ", e)
hcore_mo = reduce(numpy.dot, (mo_coeff.conj().T, hcore, mo_coeff))
fock_mo = reduce(numpy.dot, (mo_coeff.conj().T, fock, mo_coeff))
U_mo = fock_mo - hcore_mo
print("fock_mo[4] = ", fock_mo[4])
print("hcore_mo[4] = ", hcore_mo[4])
print("U_mo[4] = ", U_mo[4])
g_pppn = _get_g(mol, mf, mo_coeff, "pppn", incore=False)
g_ppnp = _get_g(mol, mf, mo_coeff, "ppnp", incore=False)
int2e2, breit_2 = FCIDUMP_Rela4C(
mol, mf, with_breit=None, filename="FCIDUMP_4C_incore", mode="incore", debug=False)
_Generate_InputFile_SiCI(
File="input",
Segment="1 0 4 4 0 %d" % (mol.nao-9),
nelec_val=7,
cmin="0.0",
perturbation=0,
Task="1 0 6 1 1 1 1 1 1",
dumprdm=7
)
import os
os.system("%s %s %s 1>%s.out 2>%s.err" % (APP, "input", "FCIDUMP_4C_incore", "F", "F"))
rdm1 = ReadIn_RDM1_4C("SpinTwo_%d_Irrep_%d_rdm1.csv" % (1,0), mol.nao * 2, 6)
rdm2 = ReadIn_RDM2_4C("SpinTwo_%d_Irrep_%d_rdm2.csv" % (1,0), mol.nao * 2, 6)
print("rdm1.shape = ", rdm1.shape)
print("rdm2.shape = ", rdm2.shape)
istate1 = 4
istate2 = 2
rdm1_average = (rdm1[0] + rdm1[1] + rdm1[2] + rdm1[3]) / 4
rdm2_average = (rdm2[0] + rdm2[1] + rdm2[2] + rdm2[3]) / 4
rdm1_average, rdm2_average = _pack_fzc(rdm1_average, rdm2_average, 1, 9)
print(rdm1_average[1])
print(_pair_correction(mol, rdm1_average, rdm2_average, mf.mo_energy, U_mo, g_ppnp, g_pppn))
rdm1_average = (rdm1[4] + rdm1[5]) / 2
rdm2_average = (rdm2[4] + rdm2[5]) / 2
rdm1_average, rdm2_average = _pack_fzc(rdm1_average, rdm2_average, 1, 9)
print(rdm1_average[1])
print(_pair_correction(mol, rdm1_average, rdm2_average, mf.mo_energy, U_mo, g_ppnp, g_pppn))