From 7be215fb439606ee098ac9684ac5e108b8b36728 Mon Sep 17 00:00:00 2001 From: TApplencourt Date: Fri, 15 Jan 2016 15:19:40 +0100 Subject: [PATCH] Add qmcpack pack converter --- scripts/qp_convert_qmcpack_from_ezfio.py | 194 ++++++++++++++++++++++- 1 file changed, 193 insertions(+), 1 deletion(-) diff --git a/scripts/qp_convert_qmcpack_from_ezfio.py b/scripts/qp_convert_qmcpack_from_ezfio.py index 693737ff..7387cb13 100755 --- a/scripts/qp_convert_qmcpack_from_ezfio.py +++ b/scripts/qp_convert_qmcpack_from_ezfio.py @@ -1 +1,193 @@ -#!/usr/bin/python \ No newline at end of file +#!/usr/bin/python + +print "#QP -> QMCPACK" + +from ezfio import ezfio + +import sys +ezfio_path = sys.argv[1] + +ezfio.set_file(ezfio_path) + +ao_num = ezfio.get_ao_basis_ao_num() +print ao_num + +mo_num = ezfio.get_mo_basis_mo_tot_num() +print mo_num + + +alpha = ezfio.get_electrons_elec_alpha_num() +beta = ezfio.get_electrons_elec_beta_num() +print "elec_alpha_num", alpha +print "elec_beta_num", beta +print "elec_tot_num", alpha + beta +print "spin_multiplicity", 2*(alpha-beta)+1 + +print "Atomic coord in Bohr" +l_label = ezfio.get_nuclei_nucl_label() +l_charge = ezfio.get_nuclei_nucl_charge() +l_coord = ezfio.get_nuclei_nucl_coord() + +l_coord_str = [" ".join(map(str,i)) for i in l_coord] + +for i in zip(l_label,l_charge,l_coord_str): + print " ".join(map(str,i)) + + +import subprocess +process = subprocess.Popen(['qp_print_basis', ezfio_path], stdout=subprocess.PIPE) +out, err = process.communicate() + +basis_raw, sym_raw, mo_raw = out.split("\n\n\n") + +basis_without_header = "\n".join(basis_raw.split("\n")[7:]) +for i,l in enumerate(l_label): + basis_without_header=basis_without_header.replace('Atom {0}'.format(i+1),l) + +print "BEGIN_BASIS_SET" +print basis_without_header +print "END_BASIS_SET" + +# _ +# |\/| / \ _ +# | | \_/ _> +# +def same_character(item1): + return item1==item1[0]* len(item1) + +def compare_gamess_style(item1, item2): + if len(item1) < len(item2): + return -1 + elif len(item1) > len(item2): + return 1 + elif same_character(item1) and same_character(item2): + if item1 < item2: + return -1 + else: + return 1 + elif same_character(item1) and not same_character(item2): + return -1 + elif not same_character(item1) and same_character(item2): + return 1 + else: + return compare_gamess_style(item1[:-1],item2[:-1]) + +def expend_and_order_sym(str_): + #Expend + for i,c in enumerate(str_): + try: + n = int(c) + except ValueError: + pass + else: + str_ = str_[:i-1] + str_[i-1]*n + str_[i+1:] + + #Order by frequency + return "".join(sorted(str_,key=str_.count,reverse=True)) + +def get_nb_permutation(str_): + + l = len(str_)-1 + if l==0: + return 1 + else: + return 2*(2*l + 1) + +## We will order the symetry +l_sym_without_header = sym_raw.split("\n")[3:-2] + +l_l_sym = [i.split() for i in l_sym_without_header] + +for l in l_l_sym: + l[2] = expend_and_order_sym(l[2]) + + +print l_l_sym + +l_l_sym_iter = iter(l_l_sym) +for i,l in enumerate(l_l_sym_iter): + n = get_nb_permutation(l[2]) + if n !=1: + l_l_sym[i:i+n] = sorted(l_l_sym[i:i+n],key=lambda x : x[2], cmp=compare_gamess_style) + for next_ in range(n-1): + next(l_l_sym_iter) + +#Is orderd now + +l_block = mo_raw.split("\n\n")[5:-1] + + +l_block_format=[] + +print "" +print "BEGIN_MO" +for block in l_block: + print "" + l_ligne = block.split("\n") + print l_ligne.pop(0) + + for l in l_l_sym: + i = int(l[0]) - 1 + i_a = int(l[1]) - 1 + sym = l[2] + + print l_label[i_a],sym,l_ligne[i] + +print "END_MO" + + +print "BEGIN_PSEUDO" +do_pseudo = ezfio.get_pseudo_do_pseudo() + +zcore = ezfio.get_pseudo_nucl_charge_remove() +klocmax = ezfio.get_pseudo_pseudo_klocmax() +kmax = ezfio.get_pseudo_pseudo_kmax() +lmax = ezfio.get_pseudo_pseudo_lmax() + + +n_k = ezfio.get_pseudo_pseudo_n_k() +v_k = ezfio.get_pseudo_pseudo_v_k() +dz_k = ezfio.get_pseudo_pseudo_dz_k() + +n_kl = ezfio.get_pseudo_pseudo_n_kl() +v_kl = ezfio.get_pseudo_pseudo_v_kl() +dz_kl = ezfio.get_pseudo_pseudo_dz_kl() + +def list_to_string(l): + return " ".join(map(str,l)) + +for i,a in enumerate(l_label): + + l_str = [] + + l_dump = [] + for k in range(klocmax): + if v_k[k][i]: + l_ = list_to_string([v_k[k][i], n_k[k][i]+2, dz_k[k][i]]) + l_dump.append(l_) + + l_str.append(l_dump) + print "non loc" + for l in range(lmax+1): + l_dump = [] + for k in range(kmax): + if v_kl[l][k][i]: + l_ = list_to_string([v_kl[l][k][i], n_kl[l][k][i]+2, dz_kl[l][k][i]]) + l_dump.append(l_) + if l_dump: + l_str.append(l_dump) + + str_ = "PARAMETERS FOR {0} ON ATOM {1} WITH ZCORE {2} AND LMAX {3} ARE" + print str_.format(a,i+1,zcore[i],len(l_str)) + + for i, l in enumerate(l_str): + str_ = "FOR L= {0} COEFF N ZETA" + print str_.format(len(l_str)-i-1) + for ii, ll in enumerate(l): + print " ",ii+1, ll + +str_ = "THE ECP RUN REMOVES {0} CORE ELECTRONS, AND THE SAME NUMBER OF PROTONS." +print str_.format(sum(zcore)) +print "END_PSEUDO" + +print "BEGIN_DET" \ No newline at end of file