#!/usr/bin/env python # -*- coding: utf-8 -*- """ Create the pseudo potential for a given atom Usage: put_pseudo_in_ezfio.py --ezfio= --atom=... --zeff=... """ import os import sys from docopt import docopt from subprocess import Popen, PIPE qpackage_root = os.environ['QPACKAGE_ROOT'] EZFIO = "{0}/EZFIO".format(qpackage_root) sys.path = [EZFIO + "/Python"] + sys.path from ezfio import ezfio import re p = re.compile(ur'\|(\d+)><\d+\|') def get_pseudo_str(l_atom): """ Run EMSL_local for geting the str of the speudo potential """ EMSL_root = "{0}/EMSL_Basis/".format(qpackage_root) EMSL_path = "{0}/EMSL_api.py".format(EMSL_root) db_path = "{0}/db/Pseudo.db".format(EMSL_root) l_cmd_atom = [] for a in l_atom: l_cmd_atom += ["--atom", a] l_cmd_head = [EMSL_path, "get_basis_data", "--db_path", db_path, "--basis", "BFD-Pseudo"] process = Popen(l_cmd_head + l_cmd_atom, stdout=PIPE, stderr=PIPE) stdout, _ = process.communicate() return stdout.strip() def get_v_n_dz_local(str_ele): """ From a str_ele of the pseudo (aka only one ele in the str) get the list ussefull for the Local potential : v_k n_k and dz_k """ l_v_k = [] l_n_k = [] l_dz_k = [] for l in str_ele.splitlines(): try: v, n, dz = l.split() v = float(v) n = int(n) dz = float(dz) except ValueError: pass else: l_v_k.append(v) l_n_k.append(n) l_dz_k.append(dz) return l_v_k, l_n_k, l_dz_k def get_v_n_dz_l_nonlocal(str_ele): """ From a str_ele of the pseudo (aka only one ele in the str) get the list ussefull for the non Local potential v_kl (v, l) n_k (v, l) dz_k (dz ,l) """ l_v_kl = [] l_n_kl = [] l_dz_kl = [] for l in str_ele.splitlines(): try: v, n, dz, proj = l.split() v = float(v) n = int(n) dz = float(dz) l = int(p.match(proj).group(1)) except ValueError: pass else: l_v_kl.append([v]) l_n_kl.append([n]) l_dz_kl.append([dz]) if not l_v_kl: l_v_kl.append([0.]) l_n_kl.append([0]) l_dz_kl.append([0.]) return l_v_kl, l_n_kl, l_dz_kl if __name__ == "__main__": arguments = docopt(__doc__) # ___ # | ._ o _|_ # _|_ | | | |_ # # ~#~#~#~#~ # # E Z F I O # # ~#~#~#~#~ # ezfio_path = arguments["--ezfio"] ezfio_path = os.path.expanduser(ezfio_path) ezfio_path = os.path.expandvars(ezfio_path) ezfio_path = os.path.abspath(ezfio_path) ezfio.set_file("{0}".format(ezfio_path)) # ~#~#~#~#~#~#~#~#~#~#~ # # P s e u d o _ d a t a # # ~#~#~#~#~#~#~#~#~#~#~ # l_ele = arguments["--atom"] str_ = get_pseudo_str(l_ele) # _ # |_) _. ._ _ _ # | (_| | _> (/_ # l_str_ele = [str_ele for str_ele in str_.split("Element Symbol: ") if str_ele] for str_ele in l_str_ele: # ~#~#~#~#~ # # S p l i t # # ~#~#~#~#~ # l = str_ele.find("Local component:") nl = str_ele.find("Non-local component") # ~#~#~#~#~ # # L o c a l # # ~#~#~#~#~ # print "local" l_v, l_n, l_dz = get_v_n_dz_local(str_ele[l:nl]) print l_v print l_n print l_dz ezfio.pseudo_klocmax = len(l_v) ezfio.pseudo_v_k = l_v ezfio.pseudo_n_k = l_n ezfio.pseudo_dz_k = l_dz # ~#~#~#~#~#~#~#~#~ # # N o n _ L o c a l # # ~#~#~#~#~#~#~#~#~ # print "non local" l_v_kl, l_n_kl, l_dz_kl = get_v_n_dz_l_nonlocal(str_ele[nl:]) print l_v_kl print l_n_kl print l_dz_kl ezfio.pseudo_lmaxpo = len(l_v_kl) ezfio.pseudo_kmax = len(l_v_kl[0]) ezfio.pseudo_v_kl = l_v_kl ezfio.pseudo_n_kl = l_n_kl ezfio.pseudo_dz_kl = l_dz_kl if arguments["--zeff"]: ezfio.nuclei_nucl_charge = map(int, arguments["--zeff"])