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pyscf converter for molecules
This commit is contained in:
Kevin Gasperich
parent
3806554438
commit
239c581073
66
src/utils_complex/Gen_Ezfio_from_pyscf_mol.sh
Executable file
66
src/utils_complex/Gen_Ezfio_from_pyscf_mol.sh
Executable file
@ -0,0 +1,66 @@
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#!/bin/bash
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ezfio=$1
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h5file=$2
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# Create the integral
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echo 'Create Integral'
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echo 'Create EZFIO'
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#read nel nmo natom <<< $(cat param)
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#read e_nucl <<< $(cat e_nuc)
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#read nao <<< $(cat num_ao)
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#read nkpts <<< $(cat kpt_num)
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#read ndf <<< $(cat num_df)
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##./create_ezfio_complex_4idx.py $ezfio $nel $natom $nmo $e_nucl $nao $nkpts
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./create_ezfio_pyscf_mol.py $ezfio $h5file #$nel $natom $nmo $e_nucl $nao $nkpts $ndf
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#Handle the orbital consitensy check
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#qp_edit -c $ezfio &> /dev/null
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#cp $ezfio/{ao,mo}_basis/ao_md5
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#qp_run import_ao_2e_complex $ezfio
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#qp_run dump_ao_2e_from_df $ezfio
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#Read the integral
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#echo 'Read Integral'
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################################################
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## using AO mono, 4-idx from pyscf ##
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################################################
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#qp_run import_integrals_ao_periodic $ezfio
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################################################
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## using AO mono, 3-idx, mo coef from pyscf ##
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################################################
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#qp_run read_ao_mono_complex $ezfio
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#qp_run read_kconserv $ezfio
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#qp_run read_ao_df_complex $ezfio
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#qp_run read_mo_coef_complex $ezfio #start from converged pyscf MOs
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#
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#qp_run save_mo_df_to_disk $ezfio
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#qp_run save_mo_bielec_to_disk $ezfio
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#qp_run mo_from_ao_orth $ezfio #use canonical orthonormalized AOs as initial MO guess
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#qp_run print_H_matrix_restart $ezfio > hmat.out
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###############################################################
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## using AO mono, full 4-idx AO bielec, mo coef from pyscf ##
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###############################################################
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#qp_run read_ao_mono_complex $ezfio
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#qp_run read_kconserv $ezfio
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#qp_run read_ao_eri_chunk_complex $ezfio
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#qp_run read_mo_coef_complex $ezfio #start from converged pyscf MOs
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##qp_run mo_from_ao_orth $ezfio #use canonical orthonormalized AOs as initial MO guess
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######################################################
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## using MO mono, full 4-idx MO bielec from pyscf ##
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######################################################
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#qp_run read_mo_mono_complex $ezfio
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#qp_run read_kconserv $ezfio
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#qp_run read_mo_eri_chunk_complex $ezfio
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@ -835,6 +835,8 @@ def pyscf2QP2_mol(mf, cas_idx=None, int_threshold = 1E-8,
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qph5.create_group('electrons')
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qph5.create_group('ao_basis')
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qph5.create_group('mo_basis')
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qph5.create_group('pseudo')
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qph5['pseudo'].attrs['do_pseudo']=False
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if mf.mol.cart:
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mo_coeff = mf.mo_coeff.copy()
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@ -951,6 +953,83 @@ def pyscf2QP2_mol(mf, cas_idx=None, int_threshold = 1E-8,
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for i in range(natom):
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atom_dset[i] = mol.atom_pure_symbol(i)
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##########################################
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# #
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# ECP #
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# #
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##########################################
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if (mol.has_ecp()):
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#atsymb = [mol.atom_pure_symbol(i) for i in range(natom)]
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#pyecp = mol._ecp
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## nelec to remove for each atom
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#nuc_z_remov = [pyecp[i][0] for i in atsymb]
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#nl_per_atom = [len(pyecp[i][1]) for i in atsymb]
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## list of l-values for channels of each atom
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#ecp_l = [[pyecp[i][1][j][0] for j in range(len(pyecp[i][1]))] for i in atsymb]
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## list of [exp,coef] for each channel (r**0,1,2,3,4,5,)
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#ecp_ac = [[pyecp[i][1][j][1] for j in range(len(pyecp[i][1]))] for i in atsymb]
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pyecp = [mol._ecp[mol.atom_pure_symbol(i)] for i in range(natom)]
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nzrmv=[0]*natom
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lmax=0
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klocmax=0
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knlmax=0
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for i,(nz,dat) in enumerate(pyecp):
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nzrmv[i]=nz
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for lval,ac in dat:
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if (lval==-1):
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klocmax=max(sum(len(j) for j in ac),klocmax)
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else:
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lmax=max(lval,lmax)
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knlmax=max(sum(len(j) for j in ac),knlmax)
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#psd_nk = np.zeros((natom,klocmax),dtype=int)
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#psd_vk = np.zeros((natom,klocmax),dtype=float)
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#psd_dzk = np.zeros((natom,klocmax),dtype=float)
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#psd_nkl = np.zeros((natom,knlmax,lmax+1),dtype=int)
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#psd_vkl = np.zeros((natom,knlmax,lmax+1),dtype=float)
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#psd_dzkl = np.zeros((natom,knlmax,lmax+1),dtype=float)
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klnlmax=max(klocmax,knlmax)
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psd_n = np.zeros((lmax+2,klnlmax,natom),dtype=int)
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psd_v = np.zeros((lmax+2,klnlmax,natom),dtype=float)
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psd_dz = np.zeros((lmax+2,klnlmax,natom),dtype=float)
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for i,(_,dat) in enumerate(pyecp):
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for lval,ac in dat:
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count=0
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for ri,aici in enumerate(ac):
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for ai,ci in aici:
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psd_n[lval+1,count,i] = ri-2
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psd_v[lval+1,count,i] = ci
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psd_dz[lval+1,count,i] = ai
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count += 1
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psd_nk = psd_n[0,:klocmax]
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psd_vk = psd_v[0,:klocmax]
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psd_dzk = psd_dz[0,:klocmax]
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psd_nkl = psd_n[1:,:knlmax]
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psd_vkl = psd_v[1:,:knlmax]
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psd_dzkl = psd_dz[1:,:knlmax]
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with h5py.File(qph5path,'a') as qph5:
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qph5['pseudo'].attrs['do_pseudo']=True
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qph5['pseudo'].attrs['pseudo_lmax']=lmax
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qph5['pseudo'].attrs['pseudo_klocmax']=klocmax
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qph5['pseudo'].attrs['pseudo_kmax']=knlmax
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qph5.create_dataset('pseudo/nucl_charge_remove',data=nzrmv)
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qph5.create_dataset('pseudo/pseudo_n_k',data=psd_nk)
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qph5.create_dataset('pseudo/pseudo_n_kl',data=psd_nkl)
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qph5.create_dataset('pseudo/pseudo_v_k',data=psd_vk)
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qph5.create_dataset('pseudo/pseudo_v_kl',data=psd_vkl)
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qph5.create_dataset('pseudo/pseudo_dz_k',data=psd_dzk)
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qph5.create_dataset('pseudo/pseudo_dz_kl',data=psd_dzkl)
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## nelec to remove for each atom
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#nuc_z_remov = [i[0] for i in pyecp]
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#nl_per_atom = [len(i[1]) for i in pyecp]
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## list of l-values for channels of each atom
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#ecp_l = [[ j[0] for j in i[1] ] for i in pyecp]
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#lmax = max(map(max,ecp_l))
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## list of [exp,coef] for each channel (r**0,1,2,3,4,5,)
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#ecp_ac = [[ j[1] for j in i[1] ] for i in pyecp]
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##########################################
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# #
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# Basis #
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124
src/utils_complex/create_ezfio_pyscf_mol.py
Executable file
124
src/utils_complex/create_ezfio_pyscf_mol.py
Executable file
@ -0,0 +1,124 @@
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#!/usr/bin/env python
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from ezfio import ezfio
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import h5py
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import sys
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import numpy as np
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fname = sys.argv[1]
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qph5name = sys.argv[2]
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#qph5=h5py.File(qph5path,'r')
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def convert_mol(filename,qph5path):
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ezfio.set_file(filename)
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ezfio.set_nuclei_is_complex(False)
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with h5py.File(qph5path,'r') as qph5:
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nucl_num = qph5['nuclei'].attrs['nucl_num']
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ao_num = qph5['ao_basis'].attrs['ao_num']
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mo_num = qph5['mo_basis'].attrs['mo_num']
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elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num']
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elec_beta_num = qph5['electrons'].attrs['elec_beta_num']
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ezfio.set_nuclei_nucl_num(nucl_num)
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ezfio.set_ao_basis_ao_num(ao_num)
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ezfio.set_mo_basis_mo_num(mo_num)
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ezfio.electrons_elec_alpha_num = elec_alpha_num
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ezfio.electrons_elec_beta_num = elec_beta_num
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##ao_num = mo_num
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##Important !
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#import math
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#nelec_per_kpt = num_elec // n_kpts
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#nelec_alpha_per_kpt = int(math.ceil(nelec_per_kpt / 2.))
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#nelec_beta_per_kpt = int(math.floor(nelec_per_kpt / 2.))
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#
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#ezfio.electrons_elec_alpha_num = int(nelec_alpha_per_kpt * n_kpts)
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#ezfio.electrons_elec_beta_num = int(nelec_beta_per_kpt * n_kpts)
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#ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.))
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#ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.))
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#ezfio.set_utils_num_kpts(n_kpts)
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#ezfio.set_integrals_bielec_df_num(n_aux)
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#(old)Important
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#ezfio.set_nuclei_nucl_num(nucl_num)
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#ezfio.set_nuclei_nucl_charge([0.]*nucl_num)
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#ezfio.set_nuclei_nucl_coord( [ [0.], [0.], [0.] ]*nucl_num )
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#ezfio.set_nuclei_nucl_label( ['He'] * nucl_num )
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with h5py.File(qph5path,'r') as qph5:
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nucl_charge=qph5['nuclei/nucl_charge'][()].tolist()
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nucl_coord=qph5['nuclei/nucl_coord'][()].T.tolist()
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nucl_label=qph5['nuclei/nucl_label'][()].tolist()
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nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion']
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ezfio.set_nuclei_nucl_charge(nucl_charge)
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ezfio.set_nuclei_nucl_coord(nucl_coord)
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ezfio.set_nuclei_nucl_label(nucl_label)
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ezfio.set_nuclei_io_nuclear_repulsion('Read')
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ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
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##########################################
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# #
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# Basis #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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do_pseudo = qph5['pseudo'].attrs['do_pseudo']
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ezfio.set_pseudo_do_pseudo(do_pseudo)
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if (do_pseudo):
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ezfio.set_pseudo_pseudo_lmax(qph5['pseudo'].attrs['pseudo_lmax'])
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ezfio.set_pseudo_pseudo_klocmax(qph5['pseudo'].attrs['pseudo_klocmax'])
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ezfio.set_pseudo_pseudo_kmax(qph5['pseudo'].attrs['pseudo_kmax'])
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ezfio.set_pseudo_nucl_charge_remove(qph5['pseudo/nucl_charge_remove'][()].tolist())
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ezfio.set_pseudo_pseudo_n_k(qph5['pseudo/pseudo_n_k'][()].tolist())
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ezfio.set_pseudo_pseudo_n_kl(qph5['pseudo/pseudo_n_kl'][()].tolist())
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ezfio.set_pseudo_pseudo_v_k(qph5['pseudo/pseudo_v_k'][()].tolist())
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ezfio.set_pseudo_pseudo_v_kl(qph5['pseudo/pseudo_v_kl'][()].tolist())
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ezfio.set_pseudo_pseudo_dz_k(qph5['pseudo/pseudo_dz_k'][()].tolist())
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ezfio.set_pseudo_pseudo_dz_kl(qph5['pseudo/pseudo_dz_kl'][()].tolist())
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##########################################
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# #
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# Basis #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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coeftmp = qph5['ao_basis/ao_coef'][()]
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expotmp = qph5['ao_basis/ao_expo'][()]
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ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
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ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
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ezfio.set_ao_basis_ao_prim_num(qph5['ao_basis/ao_prim_num'][()].tolist())
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ezfio.set_ao_basis_ao_power(qph5['ao_basis/ao_power'][()].tolist())
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ezfio.set_ao_basis_ao_coef(qph5['ao_basis/ao_coef'][()].tolist())
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ezfio.set_ao_basis_ao_expo(qph5['ao_basis/ao_expo'][()].tolist())
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print(coeftmp)
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print(expotmp)
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##########################################
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# #
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# MO Coef #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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mo_coef = qph5['mo_basis/mo_coef'][()].tolist()
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ezfio.set_mo_basis_mo_coef(mo_coef)
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#maybe fix qp so we don't need this?
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#ezfio.set_mo_basis_mo_coef([[i for i in range(mo_num)] * ao_num])
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return
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convert_mol(fname,qph5name)
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