Some cube files are not generated with verbose 2

[Sahar Rabet]

Hi all, 
I am running a calculation using environ 3 and QE 7.1. But when I set the verbose to 2, I got the debug file and potential cube files (i.e. velectrostatic.cube, vreference.cube, vsoftcavity.cube, dvtot.cube). so there was no electron.cube neither charge.cube.
 Does anyone faced this problem before? what could be the reason behind that?

Many thanks,
Bests

Sahar Rabet (she/her)
TU Braunchsweig 

[andr...@gmail.com]

Hi Sahar,

You can increase the verbosity to 3 or 4 to get more files out of Environ. I admit that some of the 'usual' cube files have disappeared in the latest version of Environ and will be brought back as soon as we manage to release 3.1. In particular, currently there is no way to get the polarization_charge.cube or the dielectric.cube. However, electrons.cube and charge.cube should be printed with a higher verbosity (probably 3 is enough). 

We will try to make this more clear in the next release.

Thanks for reporting this.

Best,

Oliviero 

[Sahar Rabet]

Hi Oliviero,
Thanks for your response. I tried verbosity 3 and 4, for 4 and higher the electrons.cube was written but there is a problem in the cube file. I have 90 atoms in my system, but the cube file wrote them as 1 atom! I attached the header of the electrons.cube and the input files. Can I solve this problem?
I have another question also in this regard, is it possible to use pp.x  for electron density instead of environ. I think that it should be ok since pp.x generated the files using already generated "charge-density.dat" which should contain the environmental effect. please correct me if I am wrong.

Thanks in advance
Sahar 

[andr...@gmail.com]

Hi Sahar, 

Sorry for not replying earlier. You are right, the additional cube files are generated by more internal subroutines of Environ, which don't have access to the coordinates of the atoms. For this reason, they are only written with a single H atom at the origin. However, the header of the cubefiles generated by the main subroutines (e.g., velectrostatic.cube, vreference.cube, etc.) have all the atoms, you can just cut and past the initial part of those cubefiles into the electrons.cube file (or the one that you need). Also, if you are using a tool like VMD to visualize the cubefile, you could just load two cubefiles, one with the correct coordinates and one with the property that you need. 

If you want to plot the electron density you can definitely use PP, as this property does not need to have an environment correction added on top. 

Hope this helps,

Oliviero