How to generate the output viewable using rasmol?
aji wibowo
Gavin Abo
Hello Aji,
Perhaps, the following can help as I'm also new to using Vampire. My operating system is Ubuntu 20.04.2.0 LTS [1].
As as described at [2], I installed Vampire under Ubuntu using:
username@computername:~$ git clone git://github.com/richard-evans/vampire.git
username@computername:~$ cd vampire
username@computername:~/vampire$ make
As described on slide 60 of [3], I followed the instructions
there to build the vdc executable:
username@computername:~/vampire/util/vdc$ make
I copied and pasted from the bilayer tutorial [4] to create a input and bilayer.mat file.
I followed Richard's instructions at [5] for running the calculation:
username@computername:~/bilayer$ ls
bilayer.mat input
username@computername:~/bilayer$
/home/username/vampire/vampire-serial
_
(_)
__ ____ _ _ __ ___ _ __ _ _ __ ___
\ \ / / _` | '_ ` _ \| '_ \| | '__/ _ \
\ V / (_| | | | | | | |_) | | | | __/
\_/ \__,_|_| |_| |_| .__/|_|_| \___|
| |
|_|
Version 5.0.1 Jul 19 2021 05:54:31
Git commit:
c0cb858d7dcdcdfc6474938324e363599e728b30
Licensed under the GNU Public License(v2). See licence file
for details.
Lead Developer: Richard F L Evans
<richar...@york.ac.uk>
Contributors: Andrea Meo, Rory Pond, Weijia Fan,
Phanwadee Chureemart, Sarah Jenkins, Joe Barker,
Thomas Ostler, Andreas Biternas, Roy W
Chantrell,
Wu Hong-Ye, Matthew Ellis, Razvan Ababei,
Sam Westmoreland, Oscar Arbelaez, Sam Morris
Compiled with: GNU C++ Compiler
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.
================================================================================
Mon Jul 19 22:22:38 2021
================================================================================
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: 4176
Starting Simulation with Program Time-Series...
Simulation run time [s]: 29.68
Monte Carlo statistics:
Total moves: 45936000
3.60398% Accepted
96.396% Rejected
Simulation ended gracefully.
As described on slide 60 of [3], I followed the instructions there to run vdc and rasmol:
username@computername:~/bilayer$
/home/username/vampire/util/vdc/vdc
|------------------------------------------------------------|
| Vampire Data Converter for v5+ |
|------------------------------------------------------------|
Reading meta-data
Data format: text
Setting data format to text mode
Number of atoms: 4176
Number of materials: 2
Material 0 2 Ag FM
Material 1 2 Fe FM
Number of files: 1
atoms-coords.data
Reading coordinate data... done!
Reading non-magnetic meta-data
Reading non-magnetic data... done!
Writing xyz file... done!
--------------------------------------------------------------------
Processing snapshot 00000000
Reading spin meta-data file spins-00000000.meta
Number of data files: 1
spins-00000000.data
Reading spin data... done!
Writing povray file spins-00000000.inc...done!
--------------------------------------------------------------------
Processing snapshot 00000001
Reading spin meta-data file spins-00000001.meta
Number of data files: 1
spins-00000001.data
Reading spin data... done!
Writing povray file spins-00000001.inc...done!
username@computername:~/bilayer$ rasmol -xyz crystal.xyz
In rasmol, I clicked Display -> Molecular Surface, then the
mouse was used to rotate the view. I got an image similar to, but
perhaps unfortunately different from that seen on the bilayer
tutorial page [4].
Kind Regards,
Gavin
[2] https://vampire.york.ac.uk/download/
[3] https://vampire.york.ac.uk/resources/workshop2017_day1.pdf
[4] https://vampire.york.ac.uk/tutorials/bilayer-system-generation
[5] https://groups.google.com/g/vampire-users/c/LS51ZlvZeyw/m/F7gfJCBLAgAJ