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] [-a afile]  



  optional arguments:
  ---------------------------------------------------
    -h/--help            show this help message and exit                             
    -a/--afile           Fragment def (at_lists) using coords from afile             
 

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] [-q qccode] 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                                                        
    -q/--qccode          Quantum chemistry code (g09, qchem, turbomole)              
 

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] [-f dlist [dlist ...]]  



  optional arguments:
  ---------------------------------------------------
    -h/--help            show this help message and exit                             
    -f/--dlist           List of directories to analyze                              
 

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