Zero-distance atoms when structure in Xcrysden is fine

Hi everyone,

I’m modeling the adsorption of organic molecule on disordered SiO2 surface with exciting-oxygen. The initial structure (513 atoms) was obtained from previous AIMD. Exciting reported zero-distance atoms and muffin-tin overlap although the structure visualized in Xcrysden looked fine. The input file, Xcrysden file, and a screenshot are attached. Any suggestions would be greatly appreciated.

Best,
Kewei Zhao

Input.xml

<input>
 
   <title>SiO2</title>
 
   <structure speciespath="/home/kewei/Software/exciting/species">
      <crystal scale="1.88973">
         <basevect>13.5500 0.0000 0.0000</basevect>
         <basevect>0.0000 13.9700 0.0000</basevect>
         <basevect>0.0000 0.0000 29.8200</basevect>
      </crystal>
      <species speciesfile="Si.xml" rmt="1.0">
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   </structure>
 
   <groundstate
      rgkmax="12"
      ngridk="1 1 1"
      xctype="GGA_PBE"
      >
   </groundstate>
 
</input>

xcrysden_file.xcrysden
https://drive.google.com/file/d/11DjVUb5vljk6SgGpAqPyREANBUZg-87-/view?usp=sharing

Screenshot of visualization, input file, and error report

Dear Kewei Zhao,

The reason for the apparent muffin-tin overlap for your system is that in exciting the maximum number of atoms (fixed by the parameter maxatoms inside the module $EXCITINGROOT/src/constants/constants.f90) is set to the value of 200. Your system has much more than 200 atoms. First, you should change the value of the parameter maxatoms inside the module $EXCITINGROOT/src/constants/constants.f90 accordingly. Then, you should recompile exciting before running it again. By the way, the number of atoms in your system is very large: Be aware that even a single ground-state calculation could be very expensive in terms of both memory and CPU time…

Your sincerely,
Pasquale Pavone
(exciting team)

Dear Pasquale,

Thanks for your prompt reply. The issue was resolved after modifying constants.f90.

Best,
Kewei