1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
|
# -*- coding: utf-8 -*-
#***********************************************************************
# This file is part of OpenMolcas. *
# *
# OpenMolcas is free software; you can redistribute it and/or modify *
# it under the terms of the GNU Lesser General Public License, v. 2.1. *
# OpenMolcas is distributed in the hope that it will be useful, but it *
# is provided "as is" and without any express or implied warranties. *
# For more details see the full text of the license in the file *
# LICENSE or in <http://www.gnu.org/licenses/>. *
# *
# Copyright (C) 2020-2022, Bruno Tenorio *
#***********************************************************************
import subprocess, time, re, fnmatch, sys, os, importlib.util, h5py
from os import listdir
from os.path import isfile, join
# auger_main.py needs python3
# USE "pip install auger-oca" TO INSTALL the auger_oca package.
# This file can be copied around and executed anywhere as long as you (installed auger-oca with pip)
# and have Project.rassi.h5 in the same directory.
ocaimport = importlib.util.find_spec('auger_oca') # First, Let me check if I have auger_oca packages
if ocaimport is None:
print("auger_oca package is not installed. USE: pip install auger-oca ")
sys.exit()
from auger_oca import *
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# ----------------------------------------------------------------------------------------------
# See README file
# It reads a file (or directory) containing 2-e rTDM files and rassi.h5 generated by OpenMolcas.
# A rassi.h5 file is used to get information on the basis set.
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#
def main():
args = parseCL()
if args.inp:
input_file = args.inp
file_based,folder_based,RAES,NAES,NAES_T,NAES_S,\
OCA_atom,OCA_center,OCA_line,benergy,totalSymmetry,symmetry,nbasf,nash,nmo,cmotab,tdmtab,ncmo,nbasft,\
nasht,nosht,comtaboff,comtbasoff,comtbasoff2,comtcmoff,comtnashoff,cmob,cmoa,tdmab,dyson,\
hd5_file,basis_id_hd5,element = my_variables(input_file)
#
driver_auger(input_file,RAES,NAES,NAES_T,NAES_S,\
OCA_atom,OCA_line,benergy,totalSymmetry,symmetry,nbasf,cmotab,nbasft,comtaboff,comtbasoff,comtbasoff2,\
comtcmoff,cmob,cmoa,nmo,tdmab,dyson,hd5_file,element,basis_id_hd5) #
if args.directory:
n_files = 0
myfiles = []
pwd = os.getcwd() #to get the current working directory
folder_exists = os.path.exists('auger_outputs')
if folder_exists:
subprocess.Popen('rm -r auger_outputs', stdout=subprocess.PIPE, shell=True)
time.sleep(2)
subprocess.Popen('mkdir auger_outputs', stdout=subprocess.PIPE, shell=True)
myfiles0 = [f for f in listdir(args.directory) if isfile(join(args.directory, f))]
myfiles = [n for n in myfiles0 if fnmatch.fnmatch(n, 'r2TM_*')]
n_files = len(myfiles)
for j in range(n_files):
i=myfiles[j]
rscr=args.directory
r2TDM=re.sub(r'/$','', rscr) # a simple trick to deal with inputs '-d folder' or '-d folder/' without crashing
input_file = r2TDM+"/"+i # After removing '/' if given, then I add it back.
file_based,folder_based,RAES,NAES,NAES_T,NAES_S,\
OCA_atom,OCA_center,OCA_line,benergy,totalSymmetry,symmetry,nbasf,nash,nmo,cmotab,tdmtab,ncmo,nbasft,\
nasht,nosht,comtaboff,comtbasoff,comtbasoff2,comtcmoff,comtnashoff,cmob,cmoa,tdmab,dyson,\
hd5_file,basis_id_hd5,element = my_variables(input_file)
driver_auger(i,RAES,NAES,NAES_T,NAES_S,\
OCA_atom,OCA_line,benergy,totalSymmetry,symmetry,nbasf,cmotab,nbasft,comtaboff,comtbasoff,comtbasoff2,\
comtcmoff,cmob,cmoa,nmo,tdmab,dyson,hd5_file,element,basis_id_hd5) #
if args.parse_oca:
subprocess.Popen('mv Auger_OCA.* auger_outputs', stdout=subprocess.PIPE, shell=True)
time.sleep(3)
if args.parse_spec:
subprocess.Popen('for f in $(ls auger_outputs/Auger_OCA.*); do grep "Spectrum: BE(eV) and Intensity" $f \
>> tmp.spectrum.out; done ; cat tmp.spectrum.out | cut -b 1-42 --complement >> auger.spectrum.out; rm -f tmp.spectrum.out',\
stdout=subprocess.PIPE, shell=True) # another option is $bash oca.spectrum.sh auger_outputs
# The End!
if __name__ == "__main__":
main()
|
