#!/usr/bin/python
#import argparse - only available in version 2.7
import sys
import theo_header, lib_struc
theo_header.print_header('Openbabel wrapper - conversion of coordinate files')
print("""\
Usage: molecular structure conversion based on the openbabel package
- increased support for Columbus (col) and Tinker (txyz2) formats
- velocity conversion Newton-X (vnx) and Tinker (vtxyz)
Syntax: babel.py <intype> <infile> <outtype> <outfile>
e.g. babel.py tmol coord xyz coord.xyz
""")
if len(sys.argv) < 4+1:
print(""" Supported file types:
col -- Columbus and Newton-X format
colr -- Columbus format, atoms reordered
txyz2 -- Tinker format with reading possibility (verify the atom types in the output)
vnx -- veloctiy (Newton-X format)
ntxyz -- velocity (Tinker format)
additionally all formats from openbabel are included
type 'babel -H' for a complete list""")
print('\nFour arguments required.')
sys.exit()
(intype,infile,outtype,outfile) = sys.argv[1:]
#!/usr/bin/python
"""
Driver script for analyzing a set of NO files.
"""
import theo_header, lib_sden, input_options
import sys
theo_header.print_header('NO file analysis')
def ihelp():
print(" analyze_NOs.py <MO_file> [<NO_file_ref> <NO_file2> ...]\n")
print(" Command line options:")
print(" -h, -H, -help: print this help")
print(" -ifile [dens_ana.in]: name of the input file")
exit(0)
#--------------------------------------------------------------------------#
# Input options
#--------------------------------------------------------------------------#
tmp = sys.argv.pop(0)
no_files = []
ifile = 'dens_ana.in'
while len(sys.argv) > 0:
arg = sys.argv.pop(0)
if arg in ["-h", "-H", "-help"]:
ihelp()
if xunit.lower() == 'ev':
xlist = self.en
pylab.xlabel('Energy (eV)')
xfac = 0.
elif xunit.lower() == 'nm':
xlist = self.lam
#pylab.xlabel(r'$\lambda$') not working ...
pylab.xlabel('Wavelength (nm)')
xfac = units.energy['nm'] * units.energy['eV']
else:
raise error_handler.ElseError(xunit, 'xunit')
pylab.ylabel('Absorption (norm.)')
pylab.plot(xlist, self.spec, 'k-')
for A, x0 in self.sticks:
pylab.plot([xfac / x0, xfac / x0], [0., A], 'r-')
pylab.savefig(pname)
if lvprt >= 1:
print("Spectrum file %s created." % pname)
if __name__ == '__main__':
theo_header.print_header('Create a convoluted spectrum')
sopt = spec_options('spectrum.in')
sopt.spec_input()
sopt.make_spec()
elif jopt['spec'] == 'frontier':
moc = mocollf(jopt['en_ind'], mldfile)
elif jopt['spec'] == 'occ':
moc = mocoll_occ(jopt['occmin'], jopt['occmax'], mldfile)
else:
raise error_handler.ElseError(self['spec'], 'spec')
moout = mo_output_jmol(moc, jopt)
moout.output(jo)
moh = mo_output_html(moc, jopt)
moh.output(ho)
mol = mo_output_tex(moc, jopt)
mol.output(lo)
jo.post(lvprt=1)
if mldfiles == [""]:
print(" -> Open the Molden-file in jmol and execute the commands contained in this file.")
else:
print(" -> Now simply run \"jmol -n %s\" to plot all the orbitals.\n"%jo.name)
ho.post(lvprt=1)
print(" -> View in browser.")
lo.post(lvprt=1)
print(" -> Compile with pdflatex (or adjust first).")
if __name__=='__main__':
import sys
theo_header.print_header('Orbital plotting in Jmol')
run()
pylab.colorbar()
pylab.axis('off')
pylab.savefig('axes.%s' % self['output_format'], dpi=self['plot_dpi'])
tel = '<img src="axes.%s", border="1" width="200">\n' % self[
'output_format']
tel += '<br>Axes / Scale'
htable.add_el(tel)
hfile.write(htable.ret_table())
hfile.post()
print(
" HTML file %s containing the electron-hole correlation plots written."
% hfname)
def run_plot():
Oopt = OmFrag_options('plot.in')
Oopt.read_OmFrag()
Oopt.OmFrag_input()
Oopt.plot()
if __name__ == '__main__':
theo_header.print_header('Plot Omega matrices')
run_plot()
#!/usr/bin/python
"""
Check if a file can be read by cclib and if all the required information is available.
"""
import theo_header, cclib_interface, input_options, error_handler
import sys
theo_header.print_header('Check cclib')
print("cc_check.py <logfile>")
print("Check if a logfile can be parsed with cclib")
try:
logfile = sys.argv[1]
except IndexError:
raise error_handler.MsgError("Please enter the name of the logfile!")
ioptions = input_options.dens_ana_options(ifile=None, check_init=False)
ioptions['rtype'] = 'cclib'
ioptions['rfile'] = logfile
ccparser = cclib_interface.file_parser_cclib(ioptions)
errcode = ccparser.check()
if errcode <= 1:
print("\n %s can be parsed by using rtype='cclib' in dens_ana.in." %
logfile)
if errcode == 0:
print(" Conversion to Molden format also possible")
else:
#!/usr/bin/python
"""
Driver script for transition density matrix analysis.
"""
import theo_header, lib_tden, lib_exciton, input_options, error_handler
import os, sys, time
theo_header.print_header('Transition density matrix analysis')
(tc, tt) = (time.clock(), time.time())
def ihelp():
print(" analyze_tden.py")
print(" Command line options:")
print(" -h, -H, -help: print this help")
print(" -ifile, -f [dens_ana.in]: name of the input file")
exit(0)
#--------------------------------------------------------------------------#
# Parsing and computations
#--------------------------------------------------------------------------#
ifile = 'dens_ana.in'
arg=sys.argv.pop(0)
while len(sys.argv)>0:
arg = sys.argv.pop(0)
if arg in ["-h", "-H", "-help"]:
ihelp()
elif arg == '-ifile' or arg == '-f':
ifile = sys.argv.pop(0)
#!/usr/bin/python
import os, sys
import numpy
import theo_header, lib_mo, error_handler
theo_header.print_header('Extract molden files')
print("""\
usage: Extract the hole/particle components out of a molden file
syntax: extract_molden.py <mo_file1> [<mo_file2> ...]
options: -ene - interpret energies as occupations
-thresh=0.001 - threshold for print-out
""")
class extract_mld:
def __init__(self, thresh=0.001, rd_ene=False, decompose=True):
self.thresh = thresh # threshold for print-out into output file
self.rd_ene = rd_ene # interpret energies as occupations
self.decompose = decompose # decompose (for NDOs or NTOs)
self.stdir = os.getcwd()
def extract(self, mo_file):
print("Extracting %s ..."%mo_file)
os.chdir(self.stdir)
mos = lib_mo.MO_set_molden(file=mo_file)
mos.read()
orb_dir = "%s.dir"%mo_file
#!/usr/bin/python
"""
Driver script for transition density matrix analysis.
"""
import theo_header, lib_tden, lib_exciton, input_options, error_handler
import os, sys, time
theo_header.print_header('Transition density matrix analysis')
(tc, tt) = (time.clock(), time.time())
def ihelp():
print(" analyze_tden.py")
print(" Command line options:")
print(" -h, -H, -help: print this help")
print(" -ifile, -f [dens_ana.in]: name of the input file")
exit(0)
#--------------------------------------------------------------------------#
# Parsing and computations
#--------------------------------------------------------------------------#
ifile = 'dens_ana.in'
arg = sys.argv.pop(0)
while len(sys.argv) > 0:
arg = sys.argv.pop(0)
if arg in ["-h", "-H", "-help"]:
ihelp()
# pylab.figure(figsize=(2,2))
pylab.pcolor(numpy.zeros([1, 1]), cmap=pylab.get_cmap(name=self['cmap']), vmin=0., vmax=self.maxOm)
pylab.colorbar()
pylab.axis('off')
pylab.savefig('axes.%s'%self['output_format'], dpi=self['plot_dpi'])
tel = '<img src="axes.%s", border="1" width="200">\n'%self['output_format']
tel += '<br>Axes / Scale'
htable.add_el(tel)
hfile.write(htable.ret_table())
hfile.post()
print(" HTML file %s containing the electron-hole correlation plots written."%hfname)
def run_plot():
Oopt = OmFrag_options('plot.in')
Oopt.read_OmFrag()
Oopt.OmFrag_input()
Oopt.plot()
if __name__ == '__main__':
theo_header.print_header('Plot Omega matrices')
run_plot()
if xunit.lower() == 'ev':
xlist = self.en
pylab.xlabel('Energy (eV)')
xfac = 0.
elif xunit.lower() == 'nm':
xlist = self.lam
#pylab.xlabel(r'$\lambda$') not working ...
pylab.xlabel('Wavelength (nm)')
xfac = units.energy['nm'] * units.energy['eV']
else:
raise error_handler.ElseError(xunit, 'xunit')
pylab.ylabel('Absorption (norm.)')
pylab.plot(xlist, self.spec, 'k-')
for A,x0 in self.sticks:
pylab.plot([xfac/x0, xfac/x0], [0., A], 'r-')
pylab.savefig(pname)
if lvprt >= 1:
print("Spectrum file %s created."%pname)
if __name__ == '__main__':
theo_header.print_header('Create a convoluted spectrum')
sopt = spec_options('spectrum.in')
sopt.spec_input()
sopt.make_spec()
#!/usr/bin/python
#import argparse - only available in version 2.7
import sys
import theo_header, lib_struc
theo_header.print_header('Openbabel wrapper - conversion of coordinate files')
print("""\
Usage: molecular structure conversion based on the openbabel package
- increased support for Columbus (col) and Tinker (txyz2) formats
- velocity conversion Newton-X (vnx) and Tinker (vtxyz)
Syntax: babel.py <intype> <infile> <outtype> <outfile>
e.g. babel.py tmol coord xyz coord.xyz
""")
if len(sys.argv) < 4 + 1:
print(""" Supported file types:
col -- Columbus and Newton-X format
colr -- Columbus format, atoms reordered
txyz2 -- Tinker format with reading possibility (verify the atom types in the output)
vnx -- veloctiy (Newton-X format)
ntxyz -- velocity (Tinker format)
additionally all formats from openbabel are included
type 'babel -H' for a complete list""")
print('\nFour arguments required.')
sys.exit()
(intype, infile, outtype, outfile) = sys.argv[1:]
if (not dotden) and (wopt['rtype'] in ['nos', 'colmcscf', 'rassi']):
if wopt.ret_yn('Analysis of state density matrices?', True):
wopt.read_yn('Print out Mulliken populations?', 'pop_ana', True)
if wopt['rtype'] in ['nos']:
if wopt.read_yn('Compute number of unpaired electrons?', 'unpaired_ana', True):
wopt['prop_list'] += ['nu', 'nunl']
wopt.AD_ana()
wopt.BO_ana()
wopt.ddm_parse()
wopt.write_prop_list()
# Program specific input
if wopt['rtype'] in ['colmrci']:
wopt.get_ncore()
elif wopt['rtype'] in ['rassi']:
wopt.get_rassi_list()
wopt.output_options()
wopt.flush(lvprt=1, choose_file=True)
if wopt['rtype'] == 'colmcscf':
print("\nNow, please run write_den.bash to prepare the MCSCF density matrices!")
if __name__ == '__main__':
theo_header.print_header('Input generation')
run_theoinp()
self['fformat'] = '%.2f'
def run_table():
infilen = 'table.in'
topt = write_table_options(infilen)
ropt = read_table_options(infilen, False)
if ropt.init == 0:
copy = topt.ret_yn(
'Found %s. Use this file directly rather than performing an interactive input?'
% infilen, True)
else:
copy = False
if copy:
topt.copy(ropt)
else:
topt.table_input()
topt.write_table()
if not copy:
topt.flush()
if __name__ == '__main__':
theo_header.print_header('Table conversion')
run_table()
self['doplots']=True
self['dotxt']=True
def run_plot():
infilen = 'graph.in'
popt = write_plot_options(infilen)
ropt = read_plot_options(infilen, False)
if ropt.init == 0:
copy = popt.ret_yn('Found %s. Use this file directly rather than performing an interactive input?'%infilen, True)
else:
copy = False
if copy:
popt.copy(ropt)
else:
popt.plot_input()
popt.read_data()
if popt['doplots']: popt.plot()
if popt['dotxt']: popt.txt_files()
if not copy:
popt.flush()
if __name__ == '__main__':
theo_header.print_header('Graph plotting')
run_plot()
def run_plot():
infilen = 'graph.in'
popt = write_plot_options(infilen)
ropt = read_plot_options(infilen, False)
if ropt.init == 0:
copy = popt.ret_yn(
'Found %s. Use this file directly rather than performing an interactive input?'
% infilen, True)
else:
copy = False
if copy:
popt.copy(ropt)
else:
popt.plot_input()
popt.read_data()
if popt['doplots']: popt.plot()
if popt['dotxt']: popt.txt_files()
if not copy:
popt.flush()
if __name__ == '__main__':
theo_header.print_header('Graph plotting')
run_plot()
self['output_format'] = 'latex'
self['lformula'] = False
self['prop_list'] = []
self['fname'] = None
self['fformat'] = '%.2f'
def run_table():
infilen = 'table.in'
topt = write_table_options(infilen)
ropt = read_table_options(infilen, False)
if ropt.init == 0:
copy = topt.ret_yn('Found %s. Use this file directly rather than performing an interactive input?'%infilen, True)
else:
copy = False
if copy:
topt.copy(ropt)
else:
topt.table_input()
topt.write_table()
if not copy:
topt.flush()
if __name__ == '__main__':
theo_header.print_header('Table conversion')
run_table()
#!/usr/bin/python
"""
Driver script for analyzing a set of NO files.
"""
import theo_header, lib_sden, input_options
import os, sys
theo_header.print_header('State density matrix analysis')
def ihelp():
print(" analyze_sden.py\n")
print(" Command line options:")
print(" -h, -H, -help: print this help")
print(" -ifile, -f [dens_ana.in]: name of the input file")
exit(0)
#--------------------------------------------------------------------------#
# Input options
#--------------------------------------------------------------------------#
tmp = sys.argv.pop(0)
ifile = 'dens_ana.in'
while len(sys.argv) > 0:
arg = sys.argv.pop(0)
if arg in ["-h", "-H", "-help"]:
ihelp()
elif arg == '-ifile' or arg == '-f':
#!/usr/bin/python
"""
Driver script for analyzing a set of NO files.
"""
import theo_header, lib_sden, input_options
import os, sys
theo_header.print_header('State density matrix analysis')
def ihelp():
print(" analyze_sden.py\n")
print(" Command line options:")
print(" -h, -H, -help: print this help")
print(" -ifile, -f [dens_ana.in]: name of the input file")
exit(0)
#--------------------------------------------------------------------------#
# Input options
#--------------------------------------------------------------------------#
tmp = sys.argv.pop(0)
ifile = 'dens_ana.in'
while len(sys.argv)>0:
arg = sys.argv.pop(0)
if arg in ["-h", "-H", "-help"]:
ihelp()
elif arg == '-ifile' or arg == '-f':
ifile = sys.argv.pop(0)
#!/usr/bin/python
"""
Convert a log-file to Molden format with the help of cclib.
"""
import theo_header, cclib_interface, input_options, error_handler, lib_mo
import sys
theo_header.print_header('cc2molden')
print("cc2molden.py <logfile>")
print("Convert a log-file to Molden format with the help of cclib.")
try:
logfile = sys.argv[1]
except IndexError:
raise error_handler.MsgError("Please enter the name of the logfile!")
ioptions = input_options.dens_ana_options(ifile=None, check_init=False)
ioptions['rtype'] = 'cclib'
ioptions['rfile'] = logfile
ccparser = cclib_interface.file_parser_cclib(ioptions)
errcode = ccparser.check()
if errcode > 0:
print(" Conversion to Molden format not possible!")
print(" %s does not contain all required information"%logfile)
else:
mos = ccparser.read_mos()
mos.write_molden_file(fname="cc.mld")
#!/usr/bin/python
"""
Check if a file can be read by cclib and if all the required information is available.
"""
import theo_header, cclib_interface, input_options, error_handler
import sys
theo_header.print_header('Check cclib')
print("cc_check.py <logfile>")
print("Check if a logfile can be parsed with cclib")
try:
logfile = sys.argv[1]
except IndexError:
raise error_handler.MsgError("Please enter the name of the logfile!")
ioptions = input_options.dens_ana_options(ifile=None, check_init=False)
ioptions['rtype'] = 'cclib'
ioptions['rfile'] = logfile
ccparser = cclib_interface.file_parser_cclib(ioptions)
errcode = ccparser.check()
if errcode <= 1:
print("\n %s can be parsed by using rtype='cclib' in dens_ana.in."%logfile)
if errcode == 0:
print(" Conversion to Molden format also possible")
else:
print(" But conversion to Molden format is not possible")
#!/usr/bin/python
import os, sys
import numpy
import theo_header, lib_mo, error_handler
theo_header.print_header('Extract molden files')
print("""\
usage: Extract the hole/particle components out of a molden file
syntax: extract_molden.py <mo_file1> [<mo_file2> ...]
options: -ene - interpret energies as occupations
-thresh=0.001 - threshold for print-out
""")
class extract_mld:
def __init__(self, thresh=0.001, rd_ene=False, decompose=True):
self.thresh = thresh # threshold for print-out into output file
self.rd_ene = rd_ene # interpret energies as occupations
self.decompose = decompose # decompose (for NDOs or NTOs)
self.stdir = os.getcwd()
def extract(self, mo_file):
print("Extracting %s ..." % mo_file)
os.chdir(self.stdir)
mos = lib_mo.MO_set_molden(file=mo_file)
mos.read()
#!/usr/bin/python
"""
Driver script for analyzing a set of NO files.
"""
import theo_header, lib_sden, input_options
import sys
theo_header.print_header("NO file analysis")
def ihelp():
print(" analyze_NOs.py <MO_file> [<NO_file_ref> <NO_file2> ...]\n")
print(" Command line options:")
print(" -h, -H, -help: print this help")
print(" -ifile [dens_ana.in]: name of the input file")
exit(0)
# --------------------------------------------------------------------------#
# Input options
# --------------------------------------------------------------------------#
tmp = sys.argv.pop(0)
no_files = []
ifile = "dens_ana.in"
while len(sys.argv) > 0:
arg = sys.argv.pop(0)
if arg in ["-h", "-H", "-help"]:
ihelp()
if wopt['rtype'] in ['nos']:
if wopt.read_yn('Compute number of unpaired electrons?',
'unpaired_ana', True):
wopt['prop_list'] += ['nu', 'nunl']
wopt.AD_ana()
wopt.BO_ana()
wopt.ddm_parse()
wopt.write_prop_list()
# Program specific input
if wopt['rtype'] in ['colmrci']:
wopt.get_ncore()
elif wopt['rtype'] in ['rassi']:
wopt.get_rassi_list()
wopt.output_options()
wopt.flush(lvprt=1, choose_file=True)
if wopt['rtype'] == 'colmcscf':
print(
"\nNow, please run write_den.bash to prepare the MCSCF density matrices!"
)
if __name__ == '__main__':
theo_header.print_header('Input generation')
run_theoinp()
