coord.npy

[ayda1]

Into a frame, what exactly does the coordinates file (coord.npy ) represent and how do I get them?

[PabloPiaggi]

Hi @ayda1 , you can find a good description of the format of coord.npy here. The file contains the atomic coordinates of a system (number of frames * 3 * number of atoms). You can prepare this file in raw (plain text) format in any way you want to. I use ase to extract data from the output of electronic structure calculations, but you can also use dpdata. Once you have the data in raw format (coord.raw), you can convert it to numpy using the raw_to_set.sh script found in $deepmd_source_dir/data/raw/raw_to_set.sh

[ayda1]

I did not get my input.data neither from CP2K nor quantum espresso
I have a surface in the form of a fortran-code.
I generated this surface in cartesian coordinates and I obtained the attached data file.
my job is from my input.data to generate the files suitable for deep-md using the NumPy format
[(https://docs.deepmodeling.com/projects/deepmd/en/master/data/data-conv.html]
I generated the coord.raw, energy.raw files according to my input.dat and I could not generate the box.raw file.

[PabloPiaggi]

Is your system periodic? Do you have the lengths of each side of the simulation box?

[ayda1]

my system is water
what do you mean - lengths on each side of the simulation box

[PabloPiaggi]

If you are not familiar with the idea of a simulation box, please read a book on molecular simulation such as "Understanding Molecular Simulation" by Frenkel and Smit, or ask someone. These are basic concepts and it doesn't make sense to discuss them here.

[ayda1]

Thanks, I will check it out