Dear Prof.Gale,
From which repository ,can the data for atomic positions be taken to specify in GULP ?
Thanks,
Supriya.
Hi Supriya,
I think that’s one for your supervisor to explain where crystal structures come from, since that’s a general science point and nothing to do with GULP.
Regards,
Julian
Yeah sir , I am aware of crystal structures but just wanted to know whether to specify atomic positions or Wyckoff positions. Now I have got hold for it as I run codes.
I have an other doubt wherein, when defect optimization happens the run terminates with a message killed. What can be done for this?
Regards,
Supriya
The input coordinate format is covered in the manual, help text (which documents all commands) and examples.
Without input, output, details of the version, system you are running on, how many cores, it’s hard to says what “killed” means. In general, “killed” means your machine stopped the job because you ran out of resource (queue limit, memory, etc) so you need to work out whether the job should fit your machine or request more resource from the queue manager.
Regards,
Julian
I have attached the input for your reference. Version is GULP 6.1.0. I run it through my aqua cluster account High Performance Computing Environment. I do not specify the number of cores to be used nor the time as I do not come across this problem very often.
opti defect regi conp
title
Example of defect impurity calc : D substituted into ABXY
end
4.113 4.113 4.113 90 90 90
fractional
A core 0.0 0.0 0.0 2.2 0.8
A shel 0.0 0.0 0.0 -0.2 0.8
D core 0.0 0.0 0.0 2.0 1.4
B core 0.5 0.5 0.5 5.2 0.8
B shel 0.5 0.5 0.5 -0.2 0.8
X core 0.5 0.0 0.5 0.04 1.0
X shel 0.5 0.0 0.5 -2.04 1.0
Y core 0.5 0.5 0.0 0.04 1.0
Y shel 0.5 0.5 0.0 -3.04 1.0
space
123
species
D 1.0
centre A
impurity D A
size 10.0 35.0
buck
A shel X shel 1150 0.38037 55 0.0 12.0 0 0 0
buck
B shel X shel 1315.572 0.36905 0.0 0.0 12.0 0 0 0
buck
A shel Y shel 10211.380 0.3205 0.0 0.0 12.0 0 0 0
buck
B shel Y shel 3510 0.3306 0.0 0.0 12.0 0 0 0
buck
X shel X shel 22764 0.149 43.0 0.0 12.0 0 0 0
buck
Y shel Y shel 5487.4667 0.3944 2033.636 0.0 12.0 0 0 0
buck
X shel Y shel 5050 0.1130 0.0 00 12.0 0 0 0
buck
D core X shel 5871.8968 0.2884 0.0 0.0 20.0 0 0 0
buck
D core Y shel 1217.6581 0.29 75.0 0.0 20.0 0 0 0
spri
X 74.92
spri
A 34.05
spri
B 9516.77
spri
Y 11.7092
spri
D 999999
The first thing to try fixing are the element names - there are no elements with symbols A or X & X in GULP is a wildcard (see the manual/help text). So it’s not surprising that this would fail unless you modify the code to add your new elements (or define them via input commands - e.g. mass, radii etc).
In my code A B C refer to alkali metals and X and Y refers to anions like Cl F Br.
You may know what A B C mean, but computer software takes user input “as is” and so needs to be told what the elements are explicitly, as computers are not so good at guessing.
This is for your kind information that I input the elements symbol while running the code. As it is a common platform I have not mentioned explicitly. For your reference I have told what does ABDXY belong to in my previous message. It will be great if you give some advice on the figures and numbers in the script.
THANKS.
I’m afraid your message doesn’t quite make sense to me. If you want help with scripting then you’ll need to post that to a different forum that deals with the scripting language (or talk to your supervisor).