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https://github.com/QuantumPackage/qp2.git
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updated qmcpack converter
This commit is contained in:
Kevin Gasperich
Kevin Gasperich
parent
620a9b7044
commit
9f58d723e3
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@ -3,11 +3,12 @@
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convert hdf5 output (e.g. from PySCF) to ezfio
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Usage:
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qp_convert_h5_to_ezfio [-o EZFIO_DIR] FILE
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qp_convert_h5_to_ezfio [--qmc] [-o EZFIO_DIR] FILE
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Options:
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-o --output=EZFIO_DIR Produced directory
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by default is FILE.ezfio
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--qmc include basis, cell, etc. for QMCPACK
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"""
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from ezfio import ezfio
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@ -137,7 +138,7 @@ def convert_mol(filename,qph5path):
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return
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def convert_kpts(filename,qph5path):
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def convert_kpts(filename,qph5path,qmcpack=False):
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ezfio.set_file(filename)
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ezfio.set_nuclei_is_complex(True)
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@ -210,61 +211,83 @@ def convert_kpts(filename,qph5path):
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##########################################
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# #
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# Basis #
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# Basis(Dummy) #
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# #
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##########################################
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#with h5py.File(qph5path,'r') as qph5:
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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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#
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#
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#Just need one (can clean this up later)
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# ao_prim_num_max = 5
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#
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# d = [ [0] *ao_prim_num_max]*ao_num
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# ezfio.set_ao_basis_ao_prim_num([ao_prim_num_max]*ao_num)
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# ezfio.set_ao_basis_ao_power(d)
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# ezfio.set_ao_basis_ao_coef(d)
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# ezfio.set_ao_basis_ao_expo(d)
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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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#Just need one (can clean this up later)
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ao_prim_num_max = 5
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d = [ [0] *ao_prim_num_max]*ao_num
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ezfio.set_ao_basis_ao_prim_num([ao_prim_num_max]*ao_num)
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ezfio.set_ao_basis_ao_power(d)
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ezfio.set_ao_basis_ao_coef(d)
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ezfio.set_ao_basis_ao_expo(d)
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###########################################
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## #
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## Pseudo #
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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(Dummy) #
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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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##########################################
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# #
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# Basis(QMC) #
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# #
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##########################################
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if qmcpack:
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with h5py.File(qph5path,'r') as qph5:
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ezfio.set_qmcpack_qmc_nshell(qph5['qmcpack'].attrs['qmc_nshell'])
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ezfio.set_qmcpack_qmc_prim_num_max(qph5['qmcpack'].attrs['qmc_prim_num_max'])
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ezfio.set_qmcpack_qmc_nucl(qph5['qmcpack/qmc_nucl'][()].tolist())
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ezfio.set_qmcpack_qmc_prim_num(qph5['qmcpack/qmc_prim_num'][()].tolist())
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ezfio.set_qmcpack_qmc_lbas(qph5['qmcpack/qmc_lbas'][()].tolist())
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ezfio.set_qmcpack_qmc_coef(qph5['qmcpack/qmc_coef'][()].tolist())
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ezfio.set_qmcpack_qmc_expo(qph5['qmcpack/qmc_expo'][()].tolist())
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ezfio.set_qmcpack_qmc_pbc(qph5['qmcpack'].attrs['PBC'])
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ezfio.set_qmcpack_supertwist(qph5['qmcpack/Super_Twist'][()].tolist())
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ezfio.set_qmcpack_latticevectors(qph5['qmcpack/LatticeVectors'][()].tolist())
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ezfio.set_qmcpack_qmc_mo_energy(qph5['qmcpack/eigenval'][()].tolist())
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@ -596,17 +619,19 @@ if __name__ == '__main__':
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ARGUMENTS = docopt(__doc__)
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FILE = get_full_path(ARGUMENTS['FILE'])
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qmcpack = False
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if ARGUMENTS["--output"]:
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EZFIO_FILE = get_full_path(ARGUMENTS["--output"])
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else:
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EZFIO_FILE = "{0}.ezfio".format(FILE)
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if ARGUMENTS["--qmc"]:
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qmcpack = True
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with h5py.File(FILE,'r') as qph5:
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do_kpts = ('kconserv' in qph5['nuclei'].keys())
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if (do_kpts):
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print("converting HDF5 to EZFIO for periodic system")
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convert_kpts(EZFIO_FILE,FILE)
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convert_kpts(EZFIO_FILE,FILE,qmcpack)
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else:
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print("converting HDF5 to EZFIO for molecular system")
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convert_mol(EZFIO_FILE,FILE)
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@ -892,9 +892,9 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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with h5py.File(qph5path,'a') as qph5:
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qph5.create_dataset('qmcpack/PBE',(1,),dtype="b1",data=True)
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qph5['qmcpack'].attrs['PBC']=True
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qph5.create_dataset('qmcpack/Super_Twist',(1,3),dtype="f8",data=sp_twist)
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qph5.create_dataset('qmcpack/LatticeVectors',(3,3),dtype="f8",data=cell.lattice_vectors())
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qph5.create_dataset('qmcpack/LatticeVectors',(3,3),dtype="f8",data=cell.lattice_vectors().T)
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qph5.create_dataset('qmcpack/eigenval',(1,Nk*nmo),dtype="f8",data=mf.mo_energy)
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