mirror of
https://github.com/LCPQ/quantum_package
synced 2024-11-14 01:53:55 +01:00
184 lines
4.0 KiB
Python
Executable File
184 lines
4.0 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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"""
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Create the pseudo potential for a given atom
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Usage:
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put_pseudo_in_ezfio.py --ezfio=<path> --atom=<atom>...
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"""
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import os
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import sys
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from docopt import docopt
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from subprocess import Popen, PIPE
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qpackage_root = os.environ['QPACKAGE_ROOT']
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EZFIO = "{0}/EZFIO".format(qpackage_root)
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sys.path = [EZFIO + "/Python"] + sys.path
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from ezfio import ezfio
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import re
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p = re.compile(ur'\|(\d+)><\d+\|')
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def get_pseudo_str(l_atom):
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"""
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Run EMSL_local for geting the str of the speudo potential
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"""
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EMSL_root = "{0}/EMSL_Basis/".format(qpackage_root)
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EMSL_path = "{0}/EMSL_api.py".format(EMSL_root)
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db_path = "{0}/db/Pseudo.db".format(EMSL_root)
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l_cmd_atom = []
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for a in l_atom:
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l_cmd_atom += ["--atom", a]
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l_cmd_head = [EMSL_path, "get_basis_data",
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"--db_path", db_path,
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"--basis", "BFD-Pseudo"]
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process = Popen(l_cmd_head + l_cmd_atom, stdout=PIPE, stderr=PIPE)
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stdout, _ = process.communicate()
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return stdout.strip()
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def get_v_n_dz_local(str_ele):
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"""
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From a str_ele of the pseudo (aka only one ele in the str)
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get the list ussefull for the Local potential : v_k n_k and dz_k
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"""
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l_v_k = []
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l_n_k = []
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l_dz_k = []
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for l in str_ele.splitlines():
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try:
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v, n, dz = l.split()
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v = float(v)
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n = int(n)
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dz = float(dz)
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except ValueError:
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pass
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else:
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l_v_k.append(v)
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l_n_k.append(n)
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l_dz_k.append(dz)
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return l_v_k, l_n_k, l_dz_k
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def get_v_n_dz_l_nonlocal(str_ele):
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"""
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From a str_ele of the pseudo (aka only one ele in the str)
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get the list ussefull for the non Local potential
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v_kl (v, l)
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n_k (v, l)
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dz_k (dz ,l)
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"""
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l_v_kl = []
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l_n_kl = []
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l_dz_kl = []
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for l in str_ele.splitlines():
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try:
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v, n, dz, proj = l.split()
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v = float(v)
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n = int(n)
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dz = float(dz)
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l = int(p.match(proj).group(1))
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except ValueError:
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pass
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else:
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l_v_kl.append((v, l))
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l_n_kl.append((n, l))
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l_dz_kl.append((dz, l))
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return l_v_kl, l_n_kl, l_dz_kl
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if __name__ == "__main__":
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arguments = docopt(__doc__)
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# ___
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# | ._ o _|_
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# _|_ | | | |_
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#
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# ~#~#~#~#~ #
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# E Z F I O #
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# ~#~#~#~#~ #
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ezfio_path = arguments["--ezfio"]
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ezfio_path = os.path.expanduser(ezfio_path)
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ezfio_path = os.path.expandvars(ezfio_path)
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ezfio_path = os.path.abspath(ezfio_path)
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ezfio.set_file("{0}".format(ezfio_path))
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# ~#~#~#~#~#~#~#~#~#~#~ #
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# P s e u d o _ d a t a #
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# ~#~#~#~#~#~#~#~#~#~#~ #
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l_ele = arguments["--atom"]
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str_ = get_pseudo_str(l_ele)
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# _
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# |_) _. ._ _ _
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# | (_| | _> (/_
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#
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l_str_ele = [str_ele for str_ele in str_.split("Element Symbol: ")
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if str_ele]
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for str_ele in l_str_ele:
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# ~#~#~#~#~ #
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# S p l i t #
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# ~#~#~#~#~ #
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l = str_ele.find("Local component:")
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nl = str_ele.find("Non-local component")
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# ~#~#~#~#~ #
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# L o c a l #
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# ~#~#~#~#~ #
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print "local"
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l_v, l_n, l_dz = get_v_n_dz_local(str_ele[l:nl])
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print l_v
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print l_n
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print l_dz
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ezfio.pseudo_klocmax = len(l_v)
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ezfio.pseudo_v_k = l_v
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ezfio.pseudo_n_k = l_n
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ezfio.pseudo_dz_k = l_dz
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# ~#~#~#~#~#~#~#~#~ #
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# N o n _ L o c a l #
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# ~#~#~#~#~#~#~#~#~ #
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print "non local"
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l_v_kl, l_n_kl, l_dz_kl = get_v_n_dz_l_nonlocal(str_ele[nl:])
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print l_v_kl
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print l_n_kl
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print l_dz_kl
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if l_v_kl:
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ezfio.pseudo_lmax = max([i[1] for i in l_v_kl]) + 1
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ezfio.pseudo_kmax = len(l_v_kl)
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ezfio.pseudo_v_kl = l_v_kl
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ezfio.pseudo_n_kl = l_n_kl
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ezfio.pseudo_dz_kl = l_dz_kl
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