added cleaner pyscf h5 converter

bin/qp_convert_h5_to_ezfio

@@ -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).""")
+