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falonne.nkou@uni-due.de — Tue, 01 Apr 2025 11:57:43 -0000

Dear All,

I am writing to seek your guidance regarding an issue I am encountering with DDEC6 charge calculation using Chargemol. I performed a spin-polarized SCF calculations using the last trajectory of my AIMD data, obtained with CP2K version 2024.1. I noticed that a similar issue was reported on the group list on 2018-08-13 08:47:46, but it appears to remain unaddressed.

In my case, I successfully generated valence_density.cube and spin_density.cube files and places them in the same directory as the Chargemol input file (attached to this email). While Chargemol reads the valence_density.cube file without issues, it fails to read the spin_density.cube file, stopping abruptly without providing an error message. The Slurm output file reports a "Segmentation fault" error (also attached), which offers little insight into the problem.

I have attempt to tighten the grid spacing when generating the .cube files, but this did not resolve the issue.

I would greatly appreciate any advice or suggestions you may have on how to resolve this error.

Thank you in advance for your time and assistance.

Best Regards

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Barsha Bhattacharjee — Fri, 20 Dec 2024 14:55:13 -0000

I am trying to calculate the DDEC6 charges for my system for which I use VASP (version 6.4) as my electronic structure code but seem to fail due to the following errors:
1. If I use the older 2017 version, I get the following error " Atomic symbol not properly identified. Program will terminate." The examples work well (tried with precompiled Windows-64bit-parallel GUI).
2. If I try the new version I am unsure where to obtain the smooth_atomic_densities from. Apologies for my oversight if it is already available with the downloaded folder, where can I find it? Is it possible to use the atomic densities from the 2017 version?

Thank you for your time and help!
Happy Holidays!

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Thomas Manz — Fri, 02 Aug 2024 04:32:13 -0000

Hello All,
Please I am experiencing this error when running chargemol:
" Atomic symbol not properly identified. Program will terminate."

What seems to be wrong with the setup?

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Subrata Kundu — Wed, 13 May 2020 04:16:29 -0000

Dear All,

For one of my projects, I am thinking to perform atomic charge calculation with DDEC6. In that regards, I have some questions regarding available CHARGEMOL version.

Following is the link of available version posted by Dr. Manz.
https://sourceforge.net/projects/ddec/

The latest version is about 3 year old (September 2017 version). I am asking this question because he released this version (SEP 2017) after publishing a PART-3 paper on DDEC-6.(https://pubs.rsc.org/en/content/articlelanding/2017/RA/C7RA07400J#!divAbstract)

After releasing this 2017 CHARGEMOL version, he released other papers on DDEC-6 Part 4, Part-5 in 2018, 2019 considering efficient parallel computation of net atomic charges, atomic spin moments, bond order, polarizability and dispersion coefficients

https://pubs.rsc.org/en/content/articlelanding/2018/RA/C7RA11829E#!divAbstract
https://pubs.rsc.org/en/content/articlehtml/2019/ra/c9ra01983a
https://pubs.rsc.org/en/content/articlehtml/2019/ra/c9ra03003d
That's why I am concerning about availability of any updated version after 2017. Please let me know which version you are using. As far I saw somewhere, there are other version 3.95 (2019 Nov) version is also available.

more VASP_DDEC_analysis.output

**** TIME CONTROL ***
Starting Chargemol version 3.95 revised November 2019.
*********

Starting DDEC program
Copyright (c) 2014, 2015, 2016, 2017, 2018, 2019 by Thomas A. Manz and Nidia Gabaldon Limas. Rights reserved.

Thanks
Subrata

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Thomas Manz — Tue, 23 Apr 2013 14:07:43 -0000

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