circle geometry

[Vinod Naik Bhukya]

Hi,

I have created a structure and using a geometry file called circle.geom and using create:select-material-by-geometry, but in the visualization the non-magnetic material is not showing up as circular. 

I am using material[#]:geometry-file=circle.geom

for all the materials. 

[gabo...@gmail.com]

I was able to reproduce the same issue:

Calculation without Patch File

username@computername:~/stack$ ls -l
total 12
-rw-r--r-- 1 username username  813 Dec 25 16:38 circle.geo
-rw-r--r-- 1 username username  585 Dec 26 19:31 input
-rw-r--r-- 1 username username 1063 Dec 27 17:16 stack.mat
username@computername:~/stack$ vampire-serial
                                                _          
                                               (_)        
                    __   ____ _ _ __ ___  _ __  _ _ __ ___
                    \ \ / / _` | '_ ` _ \| '_ \| | '__/ _ \
                     \ V / (_| | | | | | | |_) | | | |  __/
                      \_/ \__,_|_| |_| |_| .__/|_|_|  \___|
                                         | |              
                                         |_|              

                      Version 7.0.0 Dec 27 2025 17:26:35

             Git commit: fed31aa8d06f278d43089352e126350bfdca26f2

  Licensed under the GNU Public License(v2). See licence file for details.

  Developers:   Richard F L Evans, Sarah Jenkins, Andrea Meo,
                Daniel Meilak, Andrew Naden, Matthew Ellis,
                Oscar Arbelaez, Sam Morris, Rory Pond, Weijia Fan,
                Phanwadee Chureemart, Pawel Sobieszczyk, Joe Barker,
                Thomas Ostler, Andreas Biternas, Roy W Chantrell,
                Wu Hong-Ye, Razvan Ababei, Sam Westmoreland,
                Milton Persson
 
                Compiler Flags:

  Vampire includes a copy of the qhull library from C.B. Barber and The
  Geometry Center and may be obtained via http from www.qhull.org.

================================================================================
Sat Dec 27 18:34:47 2025
================================================================================
Initialising system variables
Creating system
Generating neighbour list..........done!
Copying system data to optimised data structures.
Using generic/normalised form of exchange interaction with 6 total interactions.
Number of atoms generated: 29240
Starting Simulation with Program Hysteresis-Loop...
Simulation run time [s]: 101.766
Simulation ended gracefully.
username@computername:~/stack$ ~/vampire/util/vdc/vdc --xyz
|------------------------------------------------------------|
|              Vampire Data Converter for v5+                |
|------------------------------------------------------------|
Processing snapshot 00000000
...
Processing snapshot 00000029
username@computername:~/stack$ rasmol -xyz crystal.xyz 

I may have found a way to improve the code to have it work.  I have attached a patch file for it (filename: system_type.patch).  Of note, use it at your own risk as more testing or verification may be needed.  

Applying the Patch File

username@computername:~/stack$ cd ~/vampire/src/create/
username@computername:~/vampire/src/create$ patch -b system_type.cpp system_type.patch
patching file system_type.cpp
username@computername:~/vampire/src/create$ cd ~/vampire
username@computername:~/vampire$ make serial GCC=g++-10
...

Rerunning the calculation after applying the patch file

username@computername:~/vampire$ cd ~/stack
username@computername:~/stack$ rm *.xyz *.data *.meta
username@computername:~/stack$ vampire-serial
...
Simulation ended gracefully.
username@computername:~/stack$ ~/vampire/util/vdc/vdc --xyz
...
Processing snapshot 00000029
username@computername:~/stack$ rasmol -xyz crystal.xyz

The rasmol visualization after the patch file was applied:

Kind Regards,

Gavin

VAMPIRE user

[Vinod Naik Bhukya]

I will try the patch. Thank you so much for the reply.

gabo...@gmail.com 在 2025年12月28日 星期日上午10:14:08 [UTC+8] 的信中寫道：