COLUMBUS is organized as a set of individual programs which communicate via files. For each program an input file is required. These input files can be set up by using the interactive input facility colinp. Most standard calculations are covered in this way. After having generated the input files, the Perl script runc is used to carry out the calculation.
The main input generation facility $COLUMBUS/colinp is divided into several sections taking care of
For more information on colinp features see:
After having set up all required input files, the Perl script runc is used to start the calculation in your job directory. The GEOMS, LISTINGS, MOCOEFS, RESTART, MOLDEN and WORK subdirectories are created. The WORK directory is used to perform the calculation. The remaining subdirectories contain the various output files.
The Perl script runc takes care of most standard calculations available with COLUMBUS. Geometry optimizations are carried out fully automatically. Analytical gradients are available with the Dalton package only. The maximum number of geometry optimization cycles is determined by the niter keyword in the job control file control.run. If the file curr_iter exists, numbering starts with the value stored there, otherwise counting starts with one. Unconverged geometry optimizations may be restarted by simply re-invoking runc.
The runc script hs the following form:
$COLUMBUS/runc -m core >& logfile &
where core indicates the amount of core memory available (real*8).
runc writes short summary information on the progress of the calculation to stdout and additionally writes status messages of the individual programs to runc.error which is helpful for trouble shooting.
Important: In all calculations the geom (Cartesian geometry) and mocoef (MO coefficients) files from the main directory are used. The only exception is for the mocoef file in case SCF method is specified. In this case MOs are generated by the SCF program.
For more (technical) details on runc see the run script documentation.
The results are stored in the directories LISTINGS (listing files), WORK (actual working directory), MOCOEFS (MO coefficients), RESTART ( MCSCF restart files), GEOMS (geometries) and MOLDEN (MO and NO coefficients, basis set and geometry optimization information in the MOLDEN proprietary format).
The output of the runc script provides a compact summary of the results and the status of the calculation. In order to monitor the progress of a running calculation redirect the output of runc to some file and invoke tail -f myfilename. Additionally, a file runc.error contains some error logging (i.e. the name of the last successfully executed program plus the error message of the program that failed).
The following table contains the directory and file names of the various result files. Single point calculations produce filenames with the suffix '.sp', in geometry optimizations output files corresponding to a specific cycle have the suffix '.iter' (the current iteration number). Additionally filenames with the suffix '.all' contain the concatenated listing files of the individual optimization cycles with the beginning of each iteration marked by a header.
MOs and the course of geometry optimizations can be viewed via MOLDEN (see the MOLDEN directory for appropriate files).
|
directory |
file name |
file description |
|
LISTINGS |
hermitls |
DALTON standard AO integral output |
| argosls |
Argos AO integral output |
|
| scfls |
SCF output |
|
| mcscfls |
MCSCF output (possibly state-averaged) |
|
| mcscfls.drt.state |
state-specific MCSCF output based upon the MOs obtained through a state-averaged MCSCF calculation |
|
| mcpcls.drt.state |
MCSCF wavefunction analysis for for DRT drt and state state |
|
| ciudgls.drt.state |
state-specific CI output (root following active) |
|
| ciudgls.drt |
CI output for all states of DRT drt |
|
| cipcls.drt.state |
CI wavefunction analysis for DRT drt and state state (root following active) |
|
| cipcls.drt |
CI wavefunction analysis for all states of DRT drt |
|
| propls.scf |
SCF properties |
|
| propls.mcscf.drt.state |
MCSCF properties for drt and state state |
|
| propls.ci.drt.state |
CI properties for drt and state state |
|
| trncils.FROM.drt1.state1TO .drt2.state2 |
CI transition properties for the transition from drt drt1 state state1 to drt drt2 state state2 |
|
| transls.FROM.drt1.state1TO .drt2.state2 |
MCSCF transition properties for the transition from drt drt1 state state1 to drt drt2 state state2 |
|
| transftls.FROM.drt1.state1TO .drt2.state2 |
Formula tape output for the MCSCF transition from drt drt1 state state1 to drt drt2 state state2 |
|
| abacusls |
DALTON derivative integral and gradient output |
|
| cartgrd |
cartesian gradients |
|
| cidenls.cigrd |
CI density calculation output |
|
| cigrdls |
CI gradient output |
|
| gdiisfl |
summary information from gdiis |
|
| gdiisls |
gdiis output |
|
| gdiisls.min |
gdiis output for optimized geometry |
|
| tranls.den |
output from the density transformation from AO to MO basis |
|
| GEOMS | geom |
Cartesian geometry (of cycle iter) |
| geom.min |
optimized geometry |
|
| GRADIENTS | cartgrd.drtI.stateJ |
Cartesian gradient (of cycle iter) |
| intgrd.drtI.stateJ |
Gradient in internal coordinates (of cycle iter) |
|
| cartgrd.nad.drt1.stateI.drt1.stateJ |
Cartesian non adiabatic coupling between states I and J (of cycle iter) |
|
| intgrd.nad.drt1.stateI.drt1.stateJ |
Non adiabatic coupling between states I and J in int. coord. (of cycle iter) |
|
| RESTART | restart |
MCSCF restart file (of cycle iter) |
| MOCOEFS | mocoef_scf |
SCF MO coefficients (of cycle iter) |
| mocoef_mc |
(state-averaged) MCSCF MO coefficients (of cyle iter) |
|
| nocoef_mc |
(state-averaged) MCSCF NO coefficients (of cyle iter) |
|
| nocoef_ci.drt.state |
CI NO coefficients for drt drt and state state . |
|
| nocoef_mc.drt.state |
specific MCSCF NO coefficients for drt drt and state state . |
|
| MOLDEN | molden_mo* |
the various MO coefficient files in Molden format |
| molden_no* |
the various NO coefficient files in Molden format |
|
| molden.all |
convergence informations in case of RGF-search and GDIIS-geometry optimnization in Molden format |
|
| molden.freq |
harmonic frequencies in Molden format |