Usage
Below an autogenerated documentation of all of the functionality in TheoDORE is given.
usage: theodore [-h] options ...
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
Subparser argument: options
---------------------------------------------------
theoinp Input generation for TheoDORE
analyze_tden Transition density matrix analysis
analyze_tden_unr Transition density matrix analysis (UHF/UKS)
analyze_tden_es2es Transition density matrix ana. (state-to-state)
analyze_tden_soc 1TDM analysis for spin-orbit coupled states
analyze_sden State density matrix analysis
analyze_nos Analysis of natural orbital (NO) files
parse_libwfa Parse libwfa output from Q-Chem or OpenMolcas
plot_vist Read NICS values and prepare VIST plot
plot_omfrag Plot Omega matrices as pseudocolor matrix plot
plot_om_bars Plot Omega matrices as bar graphs
plot_frag_decomp Plot fragment decomposition of Omega matrix
plot_graph Graph plotting for potential curves etc.
plot_graph_nx Graph plotting (Newton-X)
jmol_mos Orbital/density plotting in Jmol
jmol_vibs Plotting of vibrations in Jmol
vmd_plots Automatic plotting of cube files in VMD
draw_moments Plotting of dipole and quadrupole moments
babel Openbabel wrapper - conversion of coordinate files
cc_opt Analysis of geom. opt. or relaxed scan
cc_check Check if a logfile can be parsed with cclib
extract_molden Extract hole/particle parts from Molden file
spectrum Convoluted spectrum from analyze_tden output
tden_ov Transition density matrix overlap
convert_table Convert the output to latex/html table
dgrid_prep Prepare input for DGrid
fcd Fragment charge difference analysis
theoinp
Input generation for TheoDORE
usage: theodore ... theoinp [-h]
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
analyze_tden
Transition density matrix analysis
usage: theodore ... analyze_tden [-h] [-f ifile] [-k]
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
-f/--ifile Main input file
-k/--keywords Print all keywords and their current values; Default=False,
if set value=True
analyze_tden_unr
Transition density matrix analysis (UHF/UKS)
usage: theodore ... analyze_tden_unr [-h] [-f ifile]
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
-f/--ifile
analyze_tden_es2es
Transition density matrix ana. (state-to-state)
usage: theodore ... analyze_tden_es2es [-h] [-f ifile] [-r iref]
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
-f/--ifile Main input file
-r/--iref Reference state
analyze_tden_soc
1TDM analysis for spin-orbit coupled states
usage: theodore ... analyze_tden_soc [-h] [-f ifile] [-s]
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
-f/--ifile
-s/--spin_comp Default=False, if set value=True
analyze_sden
State density matrix analysis
usage: theodore ... analyze_sden [-h] [-f ifile] [-k]
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
-f/--ifile Main input file
-k/--keywords Print all keywords and their current values; Default=False,
if set value=True
analyze_nos
Analysis of natural orbital (NO) files
usage: theodore ... analyze_nos [-h] [-f ifile] [-r ref] [-o occ_fac] [-u] [-e] no_files [no_files ...]
positional arguments:
---------------------------------------------------
no_files List of NO files in Molden format
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
-f/--ifile Input file (optional)
-r/--ref Reference MO file for computing AO overlap matrix
-o/--occ_fac Multiply occupations with this factor
-u/--unrestricted Use if unrestricted orbitals are present; Default=False, if
set value=True
-e/--rd_ene Interpret energies as occupations; Default=False, if set val
ue=True
parse_libwfa
Parse libwfa output from Q-Chem or OpenMolcas
usage: theodore ... parse_libwfa [-h] [-f ifile] logfile typ
positional arguments:
---------------------------------------------------
logfile Logfile from Q-Chem or OpenMolcas
typ Type of calculation (qcadc, qctddft, qctda, rassi)
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
-f/--ifile Input file
plot_vist
Read NICS values and prepare VIST plot
usage: theodore ... plot_vist [-h] [-v vist] [-o ofile] [-s scale] [-c] [-p] [-l lab_min] logfiles [logfiles ...]
positional arguments:
---------------------------------------------------
logfiles Log files to be parsed
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
-v/--vist VIST for only these dummy atoms, e.g. -v '0 3 5'
-o/--ofile Name of output file (for VMD)
-s/--scale Scale factor for VIST dumb-bells
-c/--coor Create coordinate files (using cclib); Default=False, if set
value=True
-p/--plot_all Render and plot all tensors separately; Default=False, if se
t value=True
-l/--lab_min Add labels for eigenvalues above this value (in ppm), e.g. -
l 10
plot_omfrag
Plot Omega matrices as pseudocolor matrix plot
usage: theodore ... plot_omfrag [-h] [--use_new]
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
--use_new Use new colt interface; Default=False, if set value=True
plot_om_bars
Plot Omega matrices as bar graphs
usage: theodore ... plot_om_bars [-h]
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
plot_frag_decomp
Plot fragment decomposition of Omega matrix
usage: theodore ... plot_frag_decomp [-h]
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
plot_graph
Graph plotting for potential curves etc.
usage: theodore ... plot_graph [-h]
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
plot_graph_nx
Graph plotting (Newton-X)
usage: theodore ... plot_graph_nx [-h]
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
jmol_mos
Orbital/density plotting in Jmol
usage: theodore ... jmol_mos [-h] [-f mldfiles [mldfiles ...]]
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
-f/--mldfiles List of Molden files with orbitals
jmol_vibs
Plotting of vibrations in Jmol
usage: theodore ... jmol_vibs [-h] vibfile
positional arguments:
---------------------------------------------------
vibfile Molden file with info about vibrations
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
vmd_plots
Automatic plotting of cube files in VMD
usage: theodore ... vmd_plots [-h] pltfiles [pltfiles ...]
positional arguments:
---------------------------------------------------
pltfiles List of cube files (or other format VMD can read)
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
draw_moments
Plotting of dipole and quadrupole moments
usage: theodore ... draw_moments [-h] ana_file
positional arguments:
---------------------------------------------------
ana_file File produced by analyze_tden
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
babel
Openbabel wrapper - conversion of coordinate files
usage: theodore ... babel [-h] [-i intype] [-o outtype] infile outfile
positional arguments:
---------------------------------------------------
infile Input molecular structure file
outfile Output molecular structure file
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
-i/--intype File type for input file
-o/--outtype File type for output file
cc_opt
Analysis of geom. opt. or relaxed scan
usage: theodore ... cc_opt [-h] [-s] [-t thresh] [-o output] logfile
positional arguments:
---------------------------------------------------
logfile Logfile of quant. chemistry program
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
-s/--scan Analyse a relaxed scan; Default=False, if set value=True
-t/--thresh Threshold for energy change (for scan)
-o/--output Name of output xyz file
cc_check
Check if a logfile can be parsed with cclib
usage: theodore ... cc_check [-h] [-p printlevel] logfile
positional arguments:
---------------------------------------------------
logfile
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
-p/--printlevel
extract_molden
Extract hole/particle parts from Molden file
usage: theodore ... extract_molden [-h] [-e] [-t thresh] [-ab] mo_files [mo_files ...]
positional arguments:
---------------------------------------------------
mo_files List of MO files to analyse
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
-e/--ene Interpret energies as occupations; Default=False, if set val
ue=True
-t/--thresh Threshold for print-out
-ab/--alphabeta Use alpha/beta labels for hole/electron; Default=False, if s
et value=True
spectrum
Convoluted spectrum from analyze_tden output
usage: theodore ... spectrum [-h] tden_summs [tden_summs ...]
positional arguments:
---------------------------------------------------
tden_summs Files produced by analyze_tden.py
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
tden_ov
Transition density matrix overlap
usage: theodore ... tden_ov [-h] [--ao_ov ao_ov] [-f ifile] [-f2 ifile2] dir1 dir2
positional arguments:
---------------------------------------------------
dir1
dir2
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
--ao_ov
-f/--ifile name of the input file
-f2/--ifile2 name of input file for the second computation
convert_table
Convert the output to latex/html table
usage: theodore ... convert_table [-h]
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
dgrid_prep
Prepare input for DGrid
usage: theodore ... dgrid_prep [-h] mldfiles [mldfiles ...]
positional arguments:
---------------------------------------------------
mldfiles Molden files
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
fcd
Fragment charge difference analysis
usage: theodore ... fcd [-h] [-f ifile]
optional arguments:
---------------------------------------------------
-h/--help show this help message and exit
-f/--ifile name of the input file