This document is based on the Cheat-Sheet for tools-for-g16.bash
and was last updated with version 0.3.1, 2019-09-11.
This accompanies the repository polyluxus/tools-for-g16.bash.
Various bash scripts to aid the use of the quantum chemistry software package Gaussian 16.
The notation in brackets [ ] indicate optional arguments/inputs;
arguments in angles < > require human input; a slash / indicates
alternatives.
The following abbreviations will be used:
| abbreviation | description |
|---|---|
opt |
Short for option(s) |
ARG |
String type argument |
INT |
Positive integer (including zero) |
NUM |
Whole number (including zero) |
FLT |
Floating point number |
DUR |
Duration in format [[HH:]MM:]SS or INT[D/H/M] |
General settings for the scripts can be found in the file
g16.tools.rc. Alternatively, settings can be stored in .g16.toolsrc,
which always has precedence. Every script will check four different
directories in the order (1.) installation directory, (2.) user's home,
(3.) .config in user's home, (4.) parent working directory.
It will load the last configuration file it finds.
Setting files can be generated with the configure/configure.sh script,
see the manual for more detailed information.
This tool reads in a file containing a set of cartesian coordinates and
writes a Gaussian inputfile with predefined keywords. The script
interfaces to Xmol format, Turbomole/ GFN-xTB coord format, too.
Usage: g16.prepare.sh [opt] <file>
| option | description |
|---|---|
-T <FLT> |
Temperature (kelvin) |
-P <FLT> |
Pressure (atmosphere) |
-r <ARG> |
Add ARG to route section |
-R <ARG> |
Specific route section ARG
|
-l <INT> |
Load predefined route section |
-l list |
Show all predefined route sections |
-t <ARG> |
Adds ARG to end of file |
-C <ARG> |
Specify caption/title of job Replacements: %F : input filename, %f: input filename without .xyz, %s: like %f, also filtering start, %j: jobname, %c: charge (with indicator chrg), %M: multiplicity (with indicator mult), %U: unpaired electrons (with indicator uhf) |
-j <ARG> |
Jobname (derives filename of generated input; default: <file>) |
-j %f |
Jobname is <file> filtering .xyz
|
-j %s |
Jobname is <file> filtering start.xyz
|
-f <ARG> |
Filename of generated input |
-c <NUM> |
Charge |
-M <INT> |
Multiplicity ( |
-U <INT> |
Unpaired electrons ( |
-m <INT> |
Memory (megabyte) |
-p <INT> |
Processors |
-d <INT> |
disksize via MaxDisk (megabyte) |
-- |
Close reading options |
-s |
Silence script (incremental) |
-h |
Help file |
This tool reads in a Gaussian 16 inputfile (of a preferably completed calculation)
and adds relevant keywords for solvent corrections.
(Utilises the %OldChk directive and the geom/guess keywords.)
Usage: g16.dissolve.sh [opt] <file>
| option | description |
|---|---|
-o <ARG> |
Adds option ARG to the scrf keyword. |
-S <ARG> |
Adds option solvent=ARG to the scrf option list. |
-O |
Runs an optimisation (preserves or adds OPT) |
-r <ARG> |
Add ARG to route section |
-t <ARG> |
Adds ARG to end of file |
-f <ARG> |
Filename of generated input |
-m <INT> |
Memory (megabyte) |
-p <INT> |
Processors |
-d <INT> |
disksize via MaxDisk (megabyte) |
-- |
Close reading options |
-s |
Silence script (incremental) |
-h |
Help file |
This tool reads in a Gaussian 16 inputfile (of a preferably completed calculation)
and adds relevant keywords for a frequency calculation.
(Utilises the %OldChk directive and the geom/guess keywords.)
Usage: g16.freqinput.sh [opt] <file>
| option | description |
|---|---|
-o <ARG> |
Adds option ARG to the freq keyword. |
-R |
Adds option ReadFC to the freq option list. |
-T <FLT> |
Temperature (kelvin) |
-P <FLT> |
Pressure (atmosphere) |
-r <ARG> |
Add ARG to route section |
-t <ARG> |
Adds ARG to end of file |
-f <ARG> |
Filename of generated input |
-m <INT> |
Memory (megabyte) |
-p <INT> |
Processors |
-d <INT> |
disksize via MaxDisk (megabyte) |
-- |
Close reading options |
-s |
silence script (incremental) |
-h |
Help file |
This tool reads in a Gaussian 16 inputfile from a (previously completed) frequency run
and adds relevant keywords for two separate irc calculations.
(Utilises the %OldChk directive and the geom/guess keywords.)
Usage: g16.ircinput.sh [opt] <file>
| option | description |
|---|---|
-o <ARG> |
Adds option ARG to the irc keyword. |
-r <ARG> |
Add ARG to route section |
-t <ARG> |
Adds ARG to end of file |
-f <ARG> |
Filenametemplate of generated input files; format jobname.suffix to produce jobname.fwd.suffix and jobname.rev.suffix |
-m <INT> |
Memory (megabyte) |
-p <INT> |
Processors |
-d <INT> |
disksize via MaxDisk (megabyte) |
-- |
Close reading options |
-s |
silence script (incremental) |
-h |
Help file |
This tool reads in a Gaussian 16 inputfile preferably from a (previously completed) IRC run
and writes and inputfile for a subsequent structure optimisation.
(Utilises the %OldChk directive and the geom/guess keywords.)
Usage: g16.optinput.sh [opt] <file>
| option | description |
|---|---|
-o <ARG> |
Adds option ARG to the opt keyword. |
-r <ARG> |
Add ARG to route section |
-t <ARG> |
Adds ARG to end of file |
-f <ARG> |
Filename of generated input |
-m <INT> |
Memory (megabyte) |
-p <INT> |
Processors |
-d <INT> |
disksize via MaxDisk (megabyte) |
-- |
Close reading options |
-s |
silence script (incremental) |
-h |
Help file |
This tool reads in a Gaussian 16 inputfile and writes and inputfile for
a subsequent calculation. It is possible to overwrite the existing route
section, but still add the geom/guess directives to base it on.
(Utilises the %OldChk directive.)
Usage: g16.spinput.sh [opt] <file>
| option | description |
|---|---|
-r <ARG> |
Add ARG to route section |
-R <ARG> |
Overwites route section with ARG |
-t <ARG> |
Adds ARG to end of file |
-f <ARG> |
Filename of generated input |
-m <INT> |
Memory (megabyte) |
-p <INT> |
Processors |
-d <INT> |
disksize via MaxDisk (megabyte) |
-- |
Close reading options |
-s |
silence script (incremental) |
-h |
Help file |
This tool reads in a Gaussian 16 inputfile and
writes a new inputfile for a subsequent NBO6 property calculation.
It is not recommended to amend or overwrite the existing route section.
This requires NBO6 to be installed additionally.
(Utilises the %OldChk directive and the geom/guess keywords.)
Usage: g16.nbo6prop.sh [opt] <file>
| option | description |
|---|---|
-o <ARG> |
Add ARG to the NBO6 input stack |
-r <ARG> |
Add ARG to route section |
-R <ARG> |
Overwites route section with ARG |
-t <ARG> |
Adds ARG to end of file (overwrites -o) |
-f <ARG> |
Filename of generated input |
-m <INT> |
Memory (megabyte) |
-p <INT> |
Processors |
-d <INT> |
disksize via MaxDisk (megabyte) |
-- |
Close reading options |
-s |
silence script (incremental) |
-h |
Help file |
This tool parses a Gaussian 16 inputfile and tests the route section for
syntax errors with the Gaussian 16 utility testrt.
Usage: g16.testroute.sh [opt] <file>
| option | description |
|---|---|
-- |
Close reading options |
-s |
Silence script (incremental) |
-h |
Help file |
This tool parses and then submits a Gaussian 16 inputfile to a queueing system.
Usage: g16.submit.sh [opt] <file>
| option | description |
|---|---|
-m <INT> |
Memory (megabyte) |
-p <INT> |
Processors |
-d <INT> |
disksize via MaxDisk (megabyte) |
-w <DUR> |
Walltime limit |
-e <ARG> |
Specify an environment variable ARG in format <VAR=value> |
-j <INT> |
Wait for job with ID INT |
-H |
Submit with status hold (PBS, SLURM) or PSUSP (BSUB) |
-k |
Only create (keep) the jobscript, do not submit it. |
-Q <ARG> |
Queue for which job script should be created <queue>-<special> (<queue>: pbs, slurm, bsub; <special>: gen [generic], rwth) |
-P <ARG> |
Account to project (BSUB) or account (SLURM); if ARG is default/0/'' presets are overwritten. |
-M <ARG> |
Specify a machine type (only bsub-rwth); if ARG is default/0/'' presets are overwritten. |
-u <ARG> |
set user email address (SLURM, BSUB); if ARG is default/0/'' presets are overwritten. |
-- |
Close reading options |
-s |
silence script (incremental) |
-h |
Help file |
This tool provides a Gaussian 16 environment to execute utilities interactively.
Usage: g16.wrapper.sh [opt] <utility (commandline)>
| option | description |
|---|---|
-m <INT> |
Memory (megabyte) |
-p <INT> |
Processors |
-- |
Close reading options |
-h |
Help file |
This tool finds energy statements from Gaussian 16 calculations.
Usage: g16.getenergy.sh [opt] [<file(s)>]
If no files given, it finds energy statements from all log files in the current directory.
| option | description |
|---|---|
-i <ARG> |
Specify input suffix if processing directory |
-o <ARG> |
Specify output suffix if processing directory |
-R |
Recurse into directories |
-L |
Print the full file and path name (seperated by newline) |
-1 |
Print only one line per file |
-- |
Close reading options |
-s |
silence script (incremental) |
-h |
Help file |
This tool summarises a frequency calculation and extracts the thermochemistry data.
Usage: g16.getfreq.sh [opt] <file(s)>
| option | description |
|---|---|
-v |
Incrementally increase verbosity |
-V <INT> |
Set level of verbosity directly, (0-4) |
-c |
Separate values by comma (-V0 or -V1) |
-C <ARG> |
Separate values with <ARG> (-V0 or -V1); arguments: space, comma, semicolon, colon, slash, pipe |
-f <ARG> |
Write summary to file instead of screen |
-- |
Close reading options |
-s |
silence script (incremental) |
-h |
Help file |
A tool to convert a checkpoint file to an xyz file. This formats the
chk first to a fchk.
Usage: g16.chk2xyz.sh [opt] [<chk-file(s)>]
| option | description |
|---|---|
-a |
Formats all checkpointfiles that are found in the current directory |
-A |
Formats almost all checkpointfiles that are found in the current directory (same as -aS) |
-B |
Create backup files in cases where it would overwrite them (default) |
-F |
Forces files to be overwritten |
-S |
Skips files in cases where it would overwrite them |
-R |
Recurse through directories |
-P |
Print; dry run |
-- |
Close reading options |
-s |
silence script (incremental) |
-h |
Help file |