def test_header(self):
# TODO: use local path rather than THEODIR
theo_header.print_header('TheoDORE tests')
warnings.warn("THEODIR: " + os.environ["THEODIR"])
sys.path.append(os.environ["THEODIR"] + "/bin")
#!/usr/bin/env python3
from __future__ import print_function, division
"""
Driver script for analyzing a set of NO files.
"""
import os, sys
from theodore import theo_header, lib_sden, input_options
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"]:
vopt.write_lfile(pltfiles, auxfiles)
vopt.write_pfile(pltfiles, auxfiles)
vopt.write_cfile(pltfiles)
vopt.write_hfile(pltfiles)
print("Converting coordinate file ...")
struc = lib_struc.structure()
try:
struc.read_file(file_path=pltfiles[0], file_type=None)
struc.make_coord_file(file_path='coord.xyz',file_type='xyz',lvprt=1)
except:
print("*** WARNING: The coordinate file coord.xyz could not be created. ***")
print(" Please create this file yourself.\n\n")
print("""
Files created. Now do the following:
1. vmd coord.xyz
2. File - Load Visualization State - %s
3. Adjust the perspective
4. File - Load Visualization State - %s
5. bash %s
6. Open in browser: %s
"""%(vopt['lfile'], vopt['pfile'], vopt['cfile'], vopt['hfile']))
if __name__=='__main__':
import sys
theo_header.print_header('Automatic plotting in VMD')
run()
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()
from __future__ import print_function, division
from theodore import theo_header, input_options, error_handler, lib_diab
import sys, os, numpy
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)
if __name__ == '__main__':
theo_header.print_header('Fragment charge difference analysis')
ifile = 'fcd.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)
else:
raise error_handler.ElseError(arg, 'command line option')
if not os.path.exists(ifile):
print('Input file %s not found!' % ifile)
ifile = sys.argv.pop(0)
else:
args2.append(arg)
ioptions = input_options.libwfa_parse_options(ifile, check_init=False)
if len(args2) >= 1:
ioptions['rfile'] = args2[0]
if len(args2) >= 2:
ioptions['rtype'] = args2[1]
if ioptions['rtype'] == 'qctda':
ioptions['TDA'] = True
ioptions['rtype'] = 'qctddft'
if (not 'rfile' in ioptions) or (not 'rtype' in ioptions):
ihelp()
theo_header.print_header('Parse libwfa output', ioptions=ioptions)
#--------------------------------------------------------------------------#
# Parsing and computations
#--------------------------------------------------------------------------#
dena = dens_ana_base.dens_ana_base(ioptions)
#sdena.read_mos()
dena.read_dens()
dena.print_summary()
value=(value+1.)*10./2.
big=int(value)
small=value-big
string='%s!%i!%s' % (colors_all[big+1],int(small*100),colors_all[big])
return string
# =======================================================================
# =======================================================================
# =======================================================================
def run_plot():
anOm = AnCorr_options('ancorr.in')
anOm.read_OmFrag()
anOm.AnCorr_input()
anOm.compute()
anOm.print_results(anOm.output_h,'Hole')
anOm.print_results(anOm.output_e,'Electron')
anOm.print_results(anOm.output_m,'Mixed')
if anOm.opt_dict['dolatex']:
anOm.create_latex(anOm.output_h, anOm.output_e, anOm.output_m)
if __name__ == '__main__':
theo_header.print_header('Correlation analysis and clustering of Omega matrices ')
run_plot()
#!/usr/bin/env python3
from __future__ import print_function, division
import os, sys
import numpy
from theodore 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
-alphabeta - use alpha/beta labels for hole/electron
""")
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)
if weight == 1:
pylab.plot(xlist, self.spec / max(self.spec), 'k-')
for A, x0 in plot_sticks:
pylab.plot([x0, x0], [-1., A], 'rx-')
elif weight == 2:
pylab.plot(xlist, self.dos / max(self.dos), 'k-')
else:
raise error_handler.ElseError('weight', weight)
pylab.axis(xmin=xmin, xmax=xmax, ymin=0., ymax=1.)
pylab.savefig(pname)
if lvprt >= 1:
print("Spectrum file %s created." % pname)
if __name__ == '__main__':
import sys
theo_header.print_header('Create a convoluted spectrum')
print('spectrum.py <tden_summ1> [<tden_summ2> ...]')
if len(sys.argv) < 2:
raise error_handler.MsgError('Enter at least one argument')
sopt = spec_options('spectrum.in')
sopt['ana_files'] = sys.argv[1:]
sopt.spec_input()
sopt.make_spec()
from theodore import theo_header, lib_NICS, error_handler, cclib_interface, input_options
def ihelp():
print(" plot_VIST.py [options] <logfile1> <logfile2>")
print(" Command line options:")
print(" -h, -H, --help: print this help")
print(" -v, --vist : VIST for only these dummy atoms, e.g. -v '0 3 5'")
print(" -o : Name of output file (for VMD)")
print(" -s, --scale : Scale factor for VIST dumb-bells")
print(" -c, --coor : Create coordinate files (using cclib)")
print(" -p : Render and plot all tensors separately")
exit(0)
theo_header.print_header('Read NICS values and prepare VIST plot')
vlist = None
logfiles = []
do_coor = False
ofile = 'VIST.vmd'
scale = 1.
plot_all = False
arg = sys.argv.pop(0)
while len(sys.argv) > 0:
arg = sys.argv.pop(0)
if arg in ["-h", "-H", "--help"]:
ihelp()
elif arg in ["-v", "--vist"]:
arg = sys.argv.pop(0)
#!/usr/bin/env python3
"""
Convert a log-file to Molden format with the help of cclib.
"""
from __future__ import print_function, division
import sys
from theodore import theo_header, cclib_interface, input_options, error_handler, lib_mo
theo_header.print_header('cc2molden')
print("cc2molden.py <logfile>")
print("Convert a log-file to Molden format with the help of cclib.")
print(
" WARNING: This script is not well-tested and might fail for some of the quantum chemistry codes."
)
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:
mos = ccparser.read_mos()
"""
def __init__(self, st_ind, en_ind, mldfile):
self.mldfile = mldfile
self.viblist = list(range(st_ind, en_ind+1))
def vibname(self, ivib):
return str(ivib)
def vibpath(self, ivib, of='png'):
if of == 'pngt': of = 'png'
return "vib_%i.%s"%(ivib,of)
if __name__=='__main__':
import sys
theo_header.print_header('Plotting of vibrations in Jmol')
print('jmol_MOs.py <mldfile>\n')
vibfile = sys.argv[1]
jopt = jmol_vib_opts('jmol.in')
jopt.input()
jo = lib_file.wfile('jmol_vibs.spt')
ho = lib_file.htmlfile('vibs.html')
ho.pre('Vibrations')
vibc = vibcoll(jopt['st_ind'], jopt['en_ind'], vibfile)
vibout = vib_output_jmol(vibc, jopt)
/pgf/number format/precision=1},
legend style={at={(1.01,0.00)}, anchor=south west, draw=none, fill=black!5, inner sep=0.5pt, outer sep=0.5pt},
legend columns=1, legend cell align=left},
}
\pgfplotsset{colormap={CI}{color=(white); color=(blue!50); color=(O!70);}}
% ===========================================================================
\\tikzstyle{orb} = [ellipse, draw, color=black, fill=black!5, inner sep=-1pt, align=center]
\\tikzstyle{arrow} = [-open triangle 45, black, thick]
\\newcommand{\\incMO}[1]{\\includegraphics[width=4.5cm, trim=1cm 1cm 1cm 1cm, clip=true]{#1}}
\\begin{document}
\\begin{tikzpicture}
"""
return str
def run_plot():
opt = Om_bar_options('plot.in')
opt.read_str("Name of the file with the Omega matrix entries", "OmFfile", "OmFrag.txt", autocomp=True)
opt.read_OmFrag(opt['OmFfile'])
opt.Om_bar_input()
opt.Om_bar_data()
opt.make_tex()
if __name__ == '__main__':
theo_header.print_header('Plot Omega matrices as bar graphs')
run_plot()
# self.vmd_coors(-.4 * fac, -.6 * fac, coor[0, mu], coor[1, mu], coor[2, mu])
# self.af.write('radius % .3f\n'%(2*self['2P_rad']))
def vmd_coors(self, fac1, fac2, x, y, z):
self.af.write('{% .3f % .3f % .3f} ' % (fac1 * x, fac1 * y, fac1 * z))
self.af.write('{% .3f % .3f % .3f} ' % (fac2 * x, fac2 * y, fac2 * z))
def vmd_color(self, val, eps=1.e-3):
if abs(val) < eps:
return False
elif val > 0.0:
self.af.write('draw color blue\n')
return True
else:
self.af.write('draw color red\n')
return True
if __name__ == '__main__':
import sys
theo_header.print_header('Plotting of dipole and quadrupole moments')
print('draw_moments.py <tden_summ>')
if len(sys.argv) < 2:
raise error_handler.MsgError('Enter one argument')
opt = mom_options('mom.in')
opt['ana_file'] = sys.argv[1]
opt.input()
opt.write_afile()
#!/usr/bin/env python3
"""
Driver script for analyzing a set of NO files.
"""
from __future__ import print_function, division
import sys
from theodore import theo_header, lib_sden, input_options
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)
if len(sys.argv) == 0: ihelp()
no_files = []
ifile = 'dens_ana.in'
while len(sys.argv) > 0:
#!/usr/bin/env python3
"""
Check if a file can be read by cclib and if all the required information is available.
"""
from __future__ import print_function, division
import sys
from theodore import theo_header, cclib_interface, input_options, error_handler
theo_header.print_header('Check cclib')
print("cc_check.py <logfile> [<printlevel=1>]")
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!")
if len(sys.argv) >= 3:
lvprt = int(sys.argv[2])
else:
lvprt = 1
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(lvprt=lvprt)
if errcode <= 1:
elif arg == '-ifile' or arg == '-f':
ifile = sys.argv.pop(0)
elif arg == '-s':
spin_comp = True
else:
raise error_handler.ElseError(arg, 'command line option')
if not os.path.exists(ifile):
print('Input file %s not found!' % ifile)
print(
'Please create this file using theoinp or specify its location using -ifile\n'
)
ihelp()
ioptions = input_options.tden_ana_options(ifile)
theo_header.print_header('1TDM analysis for spin-orbit coupled states',
ioptions=ioptions)
tdena = lib_soc.tden_ana_soc(ioptions)
if 'mo_file' in ioptions: tdena.read_mos()
tdena.read_dens()
tdena.compute_all_OmAt(fullmat=True)
tdena.soc_transform()
tdena.print_info('mch')
if spin_comp:
tdena.print_info('aa')
tdena.print_info('bb')
tdena.print_info('ab')
tdena.print_info('ba')
tdena.print_info('soc')
pylab.colorbar()
pylab.savefig('axes.%s' % self.settings['output_format'],
dpi=self.settings['plot_dpi'])
tel = '<img src="axes.%s", border="1" width="200">\n' % self.settings[
'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():
# read data from commandline
state_list, maxOm = read_om_frag()
Oopt = OmFrag_options.from_questions(state_list,
maxOm,
config='plot_OmFrag.in')
Oopt.plot()
if __name__ == '__main__':
theo_header.print_header('Plot Omega matrices')
run_plot()
bfilen = basen + '.md'
ifilen = basen + '.inp'
print('\nAnalyzing %s -> %s ...'%(mldfile, bfilen))
iproc += 1
if iproc%dopt['nproc'] == 0:
lend = '|| exit 1'
else:
lend = '&'
wfile.write('echo " *** Running %s ..."\n'%mldfile)
wfile.write('$DGRID %s && $DGRID %s %s\n'%(mldfile, ifilen, lend))
wfile.write('ln -s %s.md.rho_r %s.cube\n\n'%(basen, basen2))
with open(ifilen, 'w') as ifile:
ifile.write(""":: dgrid_prep.py
basis=%s
output=.
compute=rho
format=cube
mesh=%.4f %.2f\n"""%(bfilen, dopt['msize'], dopt['mborder']))
wfile.close()
print("File run_dgrid.bash written.\n Run as:\n bash run_dgrid.bash")
if __name__=='__main__':
theo_header.print_header('Prepare input for DGrid')
run()
elif len(largs) == 3:
dir1 = largs[0]
dir2 = largs[1]
AO_OV = largs[2]
else:
ihelp()
if not os.path.exists(ifile):
print('Input file %s not found!' % ifile)
print(
'Please create this file using theoinp or specify its location using -ifile\n'
)
ihelp()
ioptions = input_options.tden_ana_options(ifile)
theo_header.print_header('Transition density matrix overlap',
ioptions=ioptions)
if ifile2 == '':
ioptions2 = ioptions
else:
ioptions2 = input_options.tden_ana_options(ifile2)
sdir = os.getcwd()
# Read info for the first job
os.chdir(dir1)
tdena1 = lib_tden.tden_ana(ioptions)
if 'mo_file' in ioptions:
tdena1.read_mos()
tdena1.read_dens()
os.chdir(sdir)
#!/usr/bin/env python3
"""
Use cclib and openbabel to analyze a geometry optimization.
"""
from __future__ import print_function, division
import sys
from theodore import theo_header, cclib_interface, input_options, error_handler, units
import openbabel
theo_header.print_header('Analysis of a geometry optimization or relaxed scan')
def ihelp():
print(" cc_opt.py <logfile>")
print(" Command line options:")
print(" -h, -H, --help: print this help")
print(" -s, --scan: Analyze a relaxed scan")
print(" -t, --thresh: Discontinuity threshold for scan")
print(" -o, --output: Name (and path) of output file")
exit(0)
logfile = None
scan = False
scan_thresh = 500
fname = "cc_opt.xyz"
arg = sys.argv.pop(0)
while len(sys.argv) > 0:
if arg in ["-h", "-H", "--help"]:
ihelp()
elif arg == '-ifile' or arg == '-f':
ifile = sys.argv.pop(0)
else:
raise error_handler.ElseError(arg, 'command line option')
if not os.path.exists(ifile):
print('Input file %s not found!' % ifile)
print(
'Please create this file using theoinp or specify its location using -ifile\n'
)
ihelp()
ioptions = input_options.tden_ana_options(ifile)
theo_header.print_header('Transition density matrix analysis',
ioptions=ioptions)
tdena = lib_tden.tden_ana(ioptions)
if 'mo_file' in ioptions: tdena.read_mos()
tdena.read_dens()
if 'at_lists' in ioptions or ioptions['eh_pop'] >= 1:
tdena.compute_all_OmAt()
if 'at_lists' in ioptions:
tdena.compute_all_OmFrag()
if ioptions['print_OmFrag']: tdena.fprint_OmFrag()
if ioptions['comp_ntos']: tdena.compute_all_NTO()
if ioptions['comp_dntos']: tdena.compute_all_DNTO()
color=self['colors'][iF],
**barkwargs)
hbottom += hpops[:, iF]
pylab.xlabel('Excited states')
pylab.ylabel(' Hole <---> Electron')
pylab.plot([ind[0] - 0.5, ind[-1] + 0.5 + self['barwidth']], [0., 0.],
'k-')
pylab.legend()
pylab.xticks([])
fname = 'frag_decomp.%s' % self['output_format']
pylab.savefig(fname, dpi=self['plot_dpi'])
print(("File %s written." % fname))
def run_plot():
opt = decomp_options('plot.in')
opt.read_OmFrag()
opt.decomp_input()
opt.plot()
if __name__ == '__main__':
theo_header.print_header('Plot fragment decomposition')
run_plot()
#!/usr/bin/env python3
#import argparse - only available in version 2.7
from __future__ import print_function, division
import sys
from theodore 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
or babel.py <infile> <outfile>
""")
if len(sys.argv) == 4 + 1:
(intype, infile, outtype, outfile) = sys.argv[1:]
elif len(sys.argv) == 2 + 1:
(infile, outfile) = sys.argv[1:]
intype = outtype = None
else:
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)
from __future__ import print_function, division
from theodore import theo_header, lib_plot
def run_plot():
infilen = 'graph.in'
popt = lib_plot.write_plot_options(infilen)
ropt = lib_plot.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.flush()
popt.read_data()
if popt['doplots']: popt.plot()
if popt['dotxt']: popt.txt_files()
if popt['dognu']: popt.gnu_inp()
if __name__ == '__main__':
theo_header.print_header('Graph plotting')
run_plot()
