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Merge pull request #121 from kgasperich/dev-real-kpts

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Kevin Gasperich 2020-07-29 12:27:23 -05:00 committed by GitHub
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4 changed files with 505 additions and 4 deletions

159
bin/qp_convert_h5_to_ezfio Executable file
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@ -0,0 +1,159 @@
#!/usr/bin/env python3
"""
convert hdf5 output (e.g. from PySCF) to ezfio
Usage:
qp_convert_h5_to_ezfio [-o EZFIO_DIR] FILE
Options:
-o --output=EZFIO_DIR Produced directory
by default is FILE.ezfio
"""
from ezfio import ezfio
import h5py
import sys
import numpy as np
import os
from docopt import docopt
#fname = sys.argv[1]
#qph5name = sys.argv[2]
def get_full_path(file_path):
file_path = os.path.expanduser(file_path)
file_path = os.path.expandvars(file_path)
# file_path = os.path.abspath(file_path)
return file_path
def convert_mol(filename,qph5path):
ezfio.set_file(filename)
ezfio.set_nuclei_is_complex(False)
with h5py.File(qph5path,'r') as qph5:
nucl_num = qph5['nuclei'].attrs['nucl_num']
ao_num = qph5['ao_basis'].attrs['ao_num']
mo_num = qph5['mo_basis'].attrs['mo_num']
elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num']
elec_beta_num = qph5['electrons'].attrs['elec_beta_num']
ezfio.set_nuclei_nucl_num(nucl_num)
ezfio.set_ao_basis_ao_num(ao_num)
ezfio.set_mo_basis_mo_num(mo_num)
ezfio.electrons_elec_alpha_num = elec_alpha_num
ezfio.electrons_elec_beta_num = elec_beta_num
##ao_num = mo_num
##Important !
#import math
#nelec_per_kpt = num_elec // n_kpts
#nelec_alpha_per_kpt = int(math.ceil(nelec_per_kpt / 2.))
#nelec_beta_per_kpt = int(math.floor(nelec_per_kpt / 2.))
#
#ezfio.electrons_elec_alpha_num = int(nelec_alpha_per_kpt * n_kpts)
#ezfio.electrons_elec_beta_num = int(nelec_beta_per_kpt * n_kpts)
#ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.))
#ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.))
#ezfio.set_utils_num_kpts(n_kpts)
#ezfio.set_integrals_bielec_df_num(n_aux)
#(old)Important
#ezfio.set_nuclei_nucl_num(nucl_num)
#ezfio.set_nuclei_nucl_charge([0.]*nucl_num)
#ezfio.set_nuclei_nucl_coord( [ [0.], [0.], [0.] ]*nucl_num )
#ezfio.set_nuclei_nucl_label( ['He'] * nucl_num )
with h5py.File(qph5path,'r') as qph5:
nucl_charge=qph5['nuclei/nucl_charge'][()].tolist()
nucl_coord=qph5['nuclei/nucl_coord'][()].T.tolist()
nucl_label=qph5['nuclei/nucl_label'][()].tolist()
nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion']
ezfio.set_nuclei_nucl_charge(nucl_charge)
ezfio.set_nuclei_nucl_coord(nucl_coord)
ezfio.set_nuclei_nucl_label(nucl_label)
ezfio.set_nuclei_io_nuclear_repulsion('Read')
ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
##########################################
# #
# Basis #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
do_pseudo = qph5['pseudo'].attrs['do_pseudo']
ezfio.set_pseudo_do_pseudo(do_pseudo)
if (do_pseudo):
ezfio.set_pseudo_pseudo_lmax(qph5['pseudo'].attrs['pseudo_lmax'])
ezfio.set_pseudo_pseudo_klocmax(qph5['pseudo'].attrs['pseudo_klocmax'])
ezfio.set_pseudo_pseudo_kmax(qph5['pseudo'].attrs['pseudo_kmax'])
ezfio.set_pseudo_nucl_charge_remove(qph5['pseudo/nucl_charge_remove'][()].tolist())
ezfio.set_pseudo_pseudo_n_k(qph5['pseudo/pseudo_n_k'][()].tolist())
ezfio.set_pseudo_pseudo_n_kl(qph5['pseudo/pseudo_n_kl'][()].tolist())
ezfio.set_pseudo_pseudo_v_k(qph5['pseudo/pseudo_v_k'][()].tolist())
ezfio.set_pseudo_pseudo_v_kl(qph5['pseudo/pseudo_v_kl'][()].tolist())
ezfio.set_pseudo_pseudo_dz_k(qph5['pseudo/pseudo_dz_k'][()].tolist())
ezfio.set_pseudo_pseudo_dz_kl(qph5['pseudo/pseudo_dz_kl'][()].tolist())
##########################################
# #
# Basis #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
#coeftmp = qph5['ao_basis/ao_coef'][()]
#expotmp = qph5['ao_basis/ao_expo'][()]
ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
ezfio.set_ao_basis_ao_prim_num(qph5['ao_basis/ao_prim_num'][()].tolist())
ezfio.set_ao_basis_ao_power(qph5['ao_basis/ao_power'][()].tolist())
ezfio.set_ao_basis_ao_coef(qph5['ao_basis/ao_coef'][()].tolist())
ezfio.set_ao_basis_ao_expo(qph5['ao_basis/ao_expo'][()].tolist())
##########################################
# #
# MO Coef #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
mo_coef = qph5['mo_basis/mo_coef'][()].tolist()
ezfio.set_mo_basis_mo_coef(mo_coef)
#maybe fix qp so we don't need this?
#ezfio.set_mo_basis_mo_coef([[i for i in range(mo_num)] * ao_num])
return
if __name__ == '__main__':
ARGUMENTS = docopt(__doc__)
FILE = get_full_path(ARGUMENTS['FILE'])
if ARGUMENTS["--output"]:
EZFIO_FILE = get_full_path(ARGUMENTS["--output"])
else:
EZFIO_FILE = "{0}.ezfio".format(FILE)
convert_mol(EZFIO_FILE,FILE)
sys.stdout.flush()
if os.system("qp_run save_ortho_mos "+EZFIO_FILE) != 0:
print("""Warning: You need to run
qp run save_ortho_mos
to be sure your MOs will be orthogonal, which is not the case when
the MOs are read from output files (not enough precision in output).""")

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@ -0,0 +1,66 @@
#!/bin/bash
ezfio=$1
h5file=$2
# Create the integral
echo 'Create Integral'
echo 'Create EZFIO'
#read nel nmo natom <<< $(cat param)
#read e_nucl <<< $(cat e_nuc)
#read nao <<< $(cat num_ao)
#read nkpts <<< $(cat kpt_num)
#read ndf <<< $(cat num_df)
##./create_ezfio_complex_4idx.py $ezfio $nel $natom $nmo $e_nucl $nao $nkpts
./create_ezfio_pyscf_mol.py $ezfio $h5file #$nel $natom $nmo $e_nucl $nao $nkpts $ndf
#Handle the orbital consitensy check
#qp_edit -c $ezfio &> /dev/null
#cp $ezfio/{ao,mo}_basis/ao_md5
#qp_run import_ao_2e_complex $ezfio
#qp_run dump_ao_2e_from_df $ezfio
#Read the integral
#echo 'Read Integral'
################################################
## using AO mono, 4-idx from pyscf ##
################################################
#qp_run import_integrals_ao_periodic $ezfio
################################################
## using AO mono, 3-idx, mo coef from pyscf ##
################################################
#qp_run read_ao_mono_complex $ezfio
#qp_run read_kconserv $ezfio
#qp_run read_ao_df_complex $ezfio
#qp_run read_mo_coef_complex $ezfio #start from converged pyscf MOs
#
#qp_run save_mo_df_to_disk $ezfio
#qp_run save_mo_bielec_to_disk $ezfio
#qp_run mo_from_ao_orth $ezfio #use canonical orthonormalized AOs as initial MO guess
#qp_run print_H_matrix_restart $ezfio > hmat.out
###############################################################
## using AO mono, full 4-idx AO bielec, mo coef from pyscf ##
###############################################################
#qp_run read_ao_mono_complex $ezfio
#qp_run read_kconserv $ezfio
#qp_run read_ao_eri_chunk_complex $ezfio
#qp_run read_mo_coef_complex $ezfio #start from converged pyscf MOs
##qp_run mo_from_ao_orth $ezfio #use canonical orthonormalized AOs as initial MO guess
######################################################
## using MO mono, full 4-idx MO bielec from pyscf ##
######################################################
#qp_run read_mo_mono_complex $ezfio
#qp_run read_kconserv $ezfio
#qp_run read_mo_eri_chunk_complex $ezfio

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@ -807,7 +807,6 @@ def xyzcount(s):
def pyscf2QP2_mol(mf, cas_idx=None, int_threshold = 1E-8,
qph5path = 'qpdat.h5',
norm='sp',
print_debug=False):
'''
cas_idx = List of active MOs. If not specified all MOs are actives
@ -817,6 +816,7 @@ def pyscf2QP2_mol(mf, cas_idx=None, int_threshold = 1E-8,
import h5py
norm='sp'
mol = mf.mol
nao_c = mol.nao_cart()
@ -835,15 +835,90 @@ def pyscf2QP2_mol(mf, cas_idx=None, int_threshold = 1E-8,
qph5.create_group('electrons')
qph5.create_group('ao_basis')
qph5.create_group('mo_basis')
qph5.create_group('pseudo')
qph5['pseudo'].attrs['do_pseudo']=False
if mf.mol.cart:
mo_coeff = mf.mo_coeff
mo_coeff = mf.mo_coeff.copy()
else:
c2s = mol.cart2sph_coeff(normalized=norm)
#c2s = mol.cart2sph_coeff(normalized='sp')
#c2s = mol.cart2sph_coeff(normalized=norm)
c2s = mol.cart2sph_coeff(normalized='sp')
#c2s = mol.cart2sph_coeff(normalized='all')
#c2s = mol.cart2sph_coeff(normalized=None)
mo_coeff = np.dot(c2s,mf.mo_coeff)
#TODO: clean this up; use mol.cart_labels(fmt=False)
dnormlbl1=["dxx","dyy","dzz"]
dnormfac1 = 2.0*np.sqrt(np.pi/5)
dnormlbl2=["dxy","dxz","dyz"]
dnormfac2 = 2.0*np.sqrt(np.pi/15)
fnormlbl1=["fxxx","fyyy","fzzz"]
fnormfac1 = 2.0*np.sqrt(np.pi/7)
fnormlbl2=["fxxy","fxxz","fxyy","fxzz","fyyz","fyzz"]
fnormfac2 = 2.0*np.sqrt(np.pi/35)
fnormlbl3=["fxyz"]
fnormfac3 = 2.0*np.sqrt(np.pi/105)
gnormlbl1=["gxxxx","gyyyy","gzzzz"]
gnormfac1 = 2.0*np.sqrt(np.pi/9)
gnormlbl2=["gxxxy","gxxxz","gxyyy","gxzzz","gyyyz","gyzzz"]
gnormfac2 = 2.0*np.sqrt(np.pi/63)
gnormlbl3=["gxxyy","gxxzz","gyyzz"]
gnormfac3 = 2.0*np.sqrt(np.pi/105)
gnormlbl4=["gxxyz","gxyyz","gxyzz"]
gnormfac4 = 2.0*np.sqrt(np.pi/315)
hnormlbl1=["hxxxxx","hyyyyy","hzzzzz"]
hnormfac1 = 2.0*np.sqrt(np.pi/11)
hnormlbl2=["hxxxxy","hxxxxz","hxyyyy","hxzzzz","hyyyyz","hyzzzz"]
hnormfac2 = 2.0*np.sqrt(np.pi/99)
hnormlbl3=["hxxxyy","hxxxzz","hxxyyy","hxxzzz","hyyyzz","hyyzzz"]
hnormfac3 = 2.0*np.sqrt(np.pi/231)
hnormlbl4=["hxxxyz","hxyyyz","hxyzzz"]
hnormfac4 = 2.0*np.sqrt(np.pi/693)
hnormlbl5=["hxxyyz","hxxyzz","hxyyzz"]
hnormfac5 = 2.0*np.sqrt(np.pi/1155)
for i_lbl,mo_lbl in enumerate(mol.cart_labels()):
if any(i in mo_lbl for i in dnormlbl1):
mo_coeff[i_lbl,:] *= dnormfac1
elif any(i in mo_lbl for i in dnormlbl2):
mo_coeff[i_lbl,:] *= dnormfac2
elif any(i in mo_lbl for i in fnormlbl1):
mo_coeff[i_lbl,:] *= fnormfac1
elif any(i in mo_lbl for i in fnormlbl2):
mo_coeff[i_lbl,:] *= fnormfac2
elif any(i in mo_lbl for i in fnormlbl3):
mo_coeff[i_lbl,:] *= fnormfac3
elif any(i in mo_lbl for i in gnormlbl1):
mo_coeff[i_lbl,:] *= gnormfac1
elif any(i in mo_lbl for i in gnormlbl2):
mo_coeff[i_lbl,:] *= gnormfac2
elif any(i in mo_lbl for i in gnormlbl3):
mo_coeff[i_lbl,:] *= gnormfac3
elif any(i in mo_lbl for i in gnormlbl4):
mo_coeff[i_lbl,:] *= gnormfac4
elif any(i in mo_lbl for i in hnormlbl1):
mo_coeff[i_lbl,:] *= hnormfac1
elif any(i in mo_lbl for i in hnormlbl2):
mo_coeff[i_lbl,:] *= hnormfac2
elif any(i in mo_lbl for i in hnormlbl3):
mo_coeff[i_lbl,:] *= hnormfac3
elif any(i in mo_lbl for i in hnormlbl4):
mo_coeff[i_lbl,:] *= hnormfac4
elif any(i in mo_lbl for i in hnormlbl5):
mo_coeff[i_lbl,:] *= hnormfac5
# Mo_coeff actif
mo_c = np.array([c[:,cas_idx] for c in mo_coeff] if cas_idx is not None else mo_coeff)
e_c = np.array([e[cas_idx] for e in mf.mo_energy] if cas_idx is not None else mf.mo_energy)
@ -878,6 +953,83 @@ def pyscf2QP2_mol(mf, cas_idx=None, int_threshold = 1E-8,
for i in range(natom):
atom_dset[i] = mol.atom_pure_symbol(i)
##########################################
# #
# ECP #
# #
##########################################
if (mol.has_ecp()):
#atsymb = [mol.atom_pure_symbol(i) for i in range(natom)]
#pyecp = mol._ecp
## nelec to remove for each atom
#nuc_z_remov = [pyecp[i][0] for i in atsymb]
#nl_per_atom = [len(pyecp[i][1]) for i in atsymb]
## list of l-values for channels of each atom
#ecp_l = [[pyecp[i][1][j][0] for j in range(len(pyecp[i][1]))] for i in atsymb]
## list of [exp,coef] for each channel (r**0,1,2,3,4,5,)
#ecp_ac = [[pyecp[i][1][j][1] for j in range(len(pyecp[i][1]))] for i in atsymb]
pyecp = [mol._ecp[mol.atom_pure_symbol(i)] for i in range(natom)]
nzrmv=[0]*natom
lmax=0
klocmax=0
knlmax=0
for i,(nz,dat) in enumerate(pyecp):
nzrmv[i]=nz
for lval,ac in dat:
if (lval==-1):
klocmax=max(sum(len(j) for j in ac),klocmax)
else:
lmax=max(lval,lmax)
knlmax=max(sum(len(j) for j in ac),knlmax)
#psd_nk = np.zeros((natom,klocmax),dtype=int)
#psd_vk = np.zeros((natom,klocmax),dtype=float)
#psd_dzk = np.zeros((natom,klocmax),dtype=float)
#psd_nkl = np.zeros((natom,knlmax,lmax+1),dtype=int)
#psd_vkl = np.zeros((natom,knlmax,lmax+1),dtype=float)
#psd_dzkl = np.zeros((natom,knlmax,lmax+1),dtype=float)
klnlmax=max(klocmax,knlmax)
psd_n = np.zeros((lmax+2,klnlmax,natom),dtype=int)
psd_v = np.zeros((lmax+2,klnlmax,natom),dtype=float)
psd_dz = np.zeros((lmax+2,klnlmax,natom),dtype=float)
for i,(_,dat) in enumerate(pyecp):
for lval,ac in dat:
count=0
for ri,aici in enumerate(ac):
for ai,ci in aici:
psd_n[lval+1,count,i] = ri-2
psd_v[lval+1,count,i] = ci
psd_dz[lval+1,count,i] = ai
count += 1
psd_nk = psd_n[0,:klocmax]
psd_vk = psd_v[0,:klocmax]
psd_dzk = psd_dz[0,:klocmax]
psd_nkl = psd_n[1:,:knlmax]
psd_vkl = psd_v[1:,:knlmax]
psd_dzkl = psd_dz[1:,:knlmax]
with h5py.File(qph5path,'a') as qph5:
qph5['pseudo'].attrs['do_pseudo']=True
qph5['pseudo'].attrs['pseudo_lmax']=lmax
qph5['pseudo'].attrs['pseudo_klocmax']=klocmax
qph5['pseudo'].attrs['pseudo_kmax']=knlmax
qph5.create_dataset('pseudo/nucl_charge_remove',data=nzrmv)
qph5.create_dataset('pseudo/pseudo_n_k',data=psd_nk)
qph5.create_dataset('pseudo/pseudo_n_kl',data=psd_nkl)
qph5.create_dataset('pseudo/pseudo_v_k',data=psd_vk)
qph5.create_dataset('pseudo/pseudo_v_kl',data=psd_vkl)
qph5.create_dataset('pseudo/pseudo_dz_k',data=psd_dzk)
qph5.create_dataset('pseudo/pseudo_dz_kl',data=psd_dzkl)
## nelec to remove for each atom
#nuc_z_remov = [i[0] for i in pyecp]
#nl_per_atom = [len(i[1]) for i in pyecp]
## list of l-values for channels of each atom
#ecp_l = [[ j[0] for j in i[1] ] for i in pyecp]
#lmax = max(map(max,ecp_l))
## list of [exp,coef] for each channel (r**0,1,2,3,4,5,)
#ecp_ac = [[ j[1] for j in i[1] ] for i in pyecp]
##########################################
# #
# Basis #

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@ -0,0 +1,124 @@
#!/usr/bin/env python
from ezfio import ezfio
import h5py
import sys
import numpy as np
fname = sys.argv[1]
qph5name = sys.argv[2]
#qph5=h5py.File(qph5path,'r')
def convert_mol(filename,qph5path):
ezfio.set_file(filename)
ezfio.set_nuclei_is_complex(False)
with h5py.File(qph5path,'r') as qph5:
nucl_num = qph5['nuclei'].attrs['nucl_num']
ao_num = qph5['ao_basis'].attrs['ao_num']
mo_num = qph5['mo_basis'].attrs['mo_num']
elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num']
elec_beta_num = qph5['electrons'].attrs['elec_beta_num']
ezfio.set_nuclei_nucl_num(nucl_num)
ezfio.set_ao_basis_ao_num(ao_num)
ezfio.set_mo_basis_mo_num(mo_num)
ezfio.electrons_elec_alpha_num = elec_alpha_num
ezfio.electrons_elec_beta_num = elec_beta_num
##ao_num = mo_num
##Important !
#import math
#nelec_per_kpt = num_elec // n_kpts
#nelec_alpha_per_kpt = int(math.ceil(nelec_per_kpt / 2.))
#nelec_beta_per_kpt = int(math.floor(nelec_per_kpt / 2.))
#
#ezfio.electrons_elec_alpha_num = int(nelec_alpha_per_kpt * n_kpts)
#ezfio.electrons_elec_beta_num = int(nelec_beta_per_kpt * n_kpts)
#ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.))
#ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.))
#ezfio.set_utils_num_kpts(n_kpts)
#ezfio.set_integrals_bielec_df_num(n_aux)
#(old)Important
#ezfio.set_nuclei_nucl_num(nucl_num)
#ezfio.set_nuclei_nucl_charge([0.]*nucl_num)
#ezfio.set_nuclei_nucl_coord( [ [0.], [0.], [0.] ]*nucl_num )
#ezfio.set_nuclei_nucl_label( ['He'] * nucl_num )
with h5py.File(qph5path,'r') as qph5:
nucl_charge=qph5['nuclei/nucl_charge'][()].tolist()
nucl_coord=qph5['nuclei/nucl_coord'][()].T.tolist()
nucl_label=qph5['nuclei/nucl_label'][()].tolist()
nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion']
ezfio.set_nuclei_nucl_charge(nucl_charge)
ezfio.set_nuclei_nucl_coord(nucl_coord)
ezfio.set_nuclei_nucl_label(nucl_label)
ezfio.set_nuclei_io_nuclear_repulsion('Read')
ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
##########################################
# #
# Basis #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
do_pseudo = qph5['pseudo'].attrs['do_pseudo']
ezfio.set_pseudo_do_pseudo(do_pseudo)
if (do_pseudo):
ezfio.set_pseudo_pseudo_lmax(qph5['pseudo'].attrs['pseudo_lmax'])
ezfio.set_pseudo_pseudo_klocmax(qph5['pseudo'].attrs['pseudo_klocmax'])
ezfio.set_pseudo_pseudo_kmax(qph5['pseudo'].attrs['pseudo_kmax'])
ezfio.set_pseudo_nucl_charge_remove(qph5['pseudo/nucl_charge_remove'][()].tolist())
ezfio.set_pseudo_pseudo_n_k(qph5['pseudo/pseudo_n_k'][()].tolist())
ezfio.set_pseudo_pseudo_n_kl(qph5['pseudo/pseudo_n_kl'][()].tolist())
ezfio.set_pseudo_pseudo_v_k(qph5['pseudo/pseudo_v_k'][()].tolist())
ezfio.set_pseudo_pseudo_v_kl(qph5['pseudo/pseudo_v_kl'][()].tolist())
ezfio.set_pseudo_pseudo_dz_k(qph5['pseudo/pseudo_dz_k'][()].tolist())
ezfio.set_pseudo_pseudo_dz_kl(qph5['pseudo/pseudo_dz_kl'][()].tolist())
##########################################
# #
# Basis #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
coeftmp = qph5['ao_basis/ao_coef'][()]
expotmp = qph5['ao_basis/ao_expo'][()]
ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
ezfio.set_ao_basis_ao_prim_num(qph5['ao_basis/ao_prim_num'][()].tolist())
ezfio.set_ao_basis_ao_power(qph5['ao_basis/ao_power'][()].tolist())
ezfio.set_ao_basis_ao_coef(qph5['ao_basis/ao_coef'][()].tolist())
ezfio.set_ao_basis_ao_expo(qph5['ao_basis/ao_expo'][()].tolist())
print(coeftmp)
print(expotmp)
##########################################
# #
# MO Coef #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
mo_coef = qph5['mo_basis/mo_coef'][()].tolist()
ezfio.set_mo_basis_mo_coef(mo_coef)
#maybe fix qp so we don't need this?
#ezfio.set_mo_basis_mo_coef([[i for i in range(mo_num)] * ao_num])
return
convert_mol(fname,qph5name)