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

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).""")
+

src/utils_complex/Gen_Ezfio_from_pyscf_mol.sh

@@ -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 
+

src/utils_complex/MolPyscfToQPkpts.py

@@ -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=norm)
-        #c2s = mol.cart2sph_coeff(normalized='sp')
+        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                   #

src/utils_complex/create_ezfio_pyscf_mol.py

@@ -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)