Frequently asked questions
- How do I create G03 input files displaced along normal modes?
- How do I extract constants from a G03 file and convert them to Gvib format?
- How can I find out which modes contribute to a given peak in the Harm+VCI spectra?
- How to perform a calculation with isotopic substitutions?
- How to transfer molecular properties between two molecules?
- Why Gvib skips an action which I want it to run?
- Some of the gvib programs ends abruptly.
- The VCI and VSCF methods do not converge.
Gvib does not compile.
How do I create G03 input files displaced along normal modes?
- Create project directory containing the optimized molecular geometry, e.g. project/project.x.
- Create config file gvib -h > project/jobrc. Do not forget to edit the gcmd_harmonic and gcmd_displaced options to meet your requirements.
- Check that the default pbs-job.template suits you, including the type of the PBS job (short,normal,long). Otherwise make a copy in the project directory and edit as necessary.
- Run gvib -a ff2,harmonic-freqs,create-nm-inputs project/. This command will run Gaussian on the displaced geometry, create harmonic force-field and finally create the displaced G03 inputs and PBS scripts.
- After all the G03 jobs are done, put the outputs in the project/gauss-disps
directory and run gvib -a nm,all to create cubic and quartic constants and
to run all implemented anharmonic methods.
How do I extract constants from a G03 file and convert them to Gvib format?
However, more convenient way is to set up a new Gvib project and let the gvib script do the job, as in the following example:
mkdir project cd project cp ../somewhere/my-gaussian.inp project.x ln -s ../somewhere/my-gaussian.out.gz gauss.out.gz gvib -h > jobrc gvib -a harmonic-constants .And you are done.
How can I find out which modes contribute to a given peak in the Harm+VCI spectra?
How to perform a calculation with isotopic substitutions?
How to transfer molecular properties between two molecules?
For instance, assume that ROA tensors were calculated at low electronic level and low-ROA.out is the Gaussian output, and high electronic level was used only for evaluating of Raman tensors high-Raman.out.
- First, find out the atom indexing in the two files. In the simplest case, when the molecules
are the same and differ only in atom ordering, bond-lengths etc., the utility
reorder may be used:
reorder --cctn -s low-ROA.inp 1,2,3 -d high-Raman.inp 5,6,7 > conf
- Extract polarizability tensor from the higher precision output
get-gauss-field --gvib -f polard high-Raman.out > tgt-polard
- Now transfer the tensors:
transfer-all-props -c conf -g low-ROA.out -m high-Raman.inp -p tgt-polard -o outdir
- Run gvib:
cp ../high-Raman.inp outdir.x
ln -s ../high-Raman.out gauss.out
gvib -h > jobrc
gvib -r -a harmonic-constants,harmonic-freqs,harmonic-intensities .
TroubleshootingWhy Gvib skips an actions which I want it to run?
Alternatively, when gvib is run with the -d switch, it will tell you why a particular action is skipped. For example, the following lines may appear in the output:
run_gaussian_ff34: the file test2/disp_cff2 done. run_gaussian_ff34: the file test2/disp_dipd done. All files of run_gaussian_ff34 already done. Note: Skipping the action run_gaussian_ff34
Identify the offending files, move them to some other location or rename and run gvib again.
Some of the gvib programs ends abruptly
Running program: run_project_cff2 run_project_cff2 ... Thu Aug 17 10:07:47 2006 list in: end of file apparent state: unit 11 named /scratch/anonym/etc/etc/etc... last format: list io lately reading sequential formatted external IOThis happens to programs written in Fortran, when a string exceeds the length of an internal buffer holding a file name. Currently the limit is 500 characters and it can be raised by editing parameters.h and recompiling.
The VCI and VSCF methods do not converge.
ERROR: VCI divergence detected!and the VSCF method may end with the message
Sorry, the VSCF did not converge in 50 iterations, diff still too large: 1.796930e+16.Usually the cause of the problem is some low-lying vibrational mode. Run gmm ./project.nmodes to visualize the normal modes as calculated by default by the nm_anim action. Rotational movements of CH3 but also other vibrational modes with frequency less than 200 1/cm are often the cause of the problem. Edit the jobrc file and set the option ignore_modes appropriately. Then run gvib gvib -r -a cc to recalculate the constants and proceed as usually.