Respected Scientific Community,
I am facing an issue with reading data in .chk file that I have just transferred (using win-SCP) from Gaussian installed on supercomputer.
I have tried the tutorial available on Gaussian website (from Gaussian step > Utilities > Fchk using my window-based laptop (Gaussian 09)
It generated the .fchk file with 0 kb.
I would be highly obliged If any lead assist me in this regard?
Dear Hira, why not to convert chk into fchk directly in your working directory of the supercomputer? It is similar as you submit Gaussian jobs.
Besides, once Gaussian Team told me not to transfer the binary file chk, it should be converted first before transfering it to another system.
Best, Pablo
Thank you, Sir, for your prompt response.
I am operating supercomputer using Putty (for running files) and Win-SCP for transferring the input and output files from my laptop to supercomputer and vice versa.
I do not know how to directly convert .chk to fchk in putty or winscp. So, I transferred the .chk file in binary form to my laptop.
I would be highly obliged if you could please share any source/link/ or anything regarding direct conversion of files in putty or winscp.
previously, I have used Gaussian on linux based system (PC). And I used to directly convert .chk to .fchk in job TERMINAL by using command formchk filename.chk filename.fchk.
however, for supercomputer I can't find any command or tutorial.
Dear Hira Karim yes I also use Putty and WinSCP in the same way as you mention. These programs cannot convert chk into fchk, this is only made by Gaussian itself.
"And I used to directly convert .chk to .fchk in job TERMINAL by using command formchk filename.chk filename.fchk"
That's exactly the way to do. Now, how do you run Gaussian? command line? or sbatch/slurm? or...?
For example, I run something like this in my working directory:
/DIR/g16/formchk my_input my_output
Here DIR is from g16 is run.
Pablo
Respected sir, Thank you for the nice explanation.
Now what I have do is to write the command in putty (where I run the job)
I usually use the command "nohup g09 filename.gjf &" (Gaussian 9 is installed)
So, after the job completion I would have to write in putty the following command for conversion:
/DIR/g09/formchk filename.chk filename.fchk ? (is it right?)
or this formchk filename.chk filename.fchk?
Your kind guidance is highly appreciated sir !
Dear Hira Karim
/DIR/g09/formchk is my example, DIR is a DIRectory in which I have installed my Gaussian.
This one looks fine,
formchk filename.chk filename.fchk
if don't, I'd try
nohup formchk filename.chk filename.fchk &
or
nohup g09/formchk filename.chk filename.fchk &
Hope it works
Dear Hira Karim , as Pablo Mtz mentioned, try to find out the formchk executable.
It is located along with g09 executable.
Follow these steps
1. Find the executable using the command locate formchk.
2. path/to/formchk filename.chk filename.fchk& to convert chk to fchk.
Hope it helps.
Hi,
In this video, explained how to convert .chk to .fchk using Gaussian 09W
please make use of it. this is simple.
https://youtu.be/2w-Baau9ipc?si=92rSCsnpMAdw6Kgm
Dear Pablo Mtz,
I am facing a similar problem as Hira Karim. However, I run Gaussian with sbatch/slurm. I would highly appreciate it if you can provide some guidance into how to run the formchk filename.chk filename.fchk command using Putty or WinSCP.
Best,
Héctor
Dear Hector Pascual
For Windows users, Putty is useful to connect to the clusters via ssh (among other capabilities), and WinSCP is useful to transfer files from and to the clusters.
In your cluster/system, check your slurm script to run gaussian, you should be able to find something like
export GAUSS_EXEDIR="path-to-gaussian"
path-to-gaussian/g16 my_input > my_output
the program g16 is located at some path in your cluster, then just replace "g16" with "formchk":
path-to-gaussian/formchk filename.chk filename.fchk
In summary, it is like running gaussian g16 (or g09), just replace that with "formchk".
Hope this helps.
Best, Pablo
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