Hi,
I am using lammps and I have a question about the setting of groups. According to the tutorial, there is only one defalt group, “all”.
But in my system, some groups not defined by me have been found. E.g.:
0 atoms in group FixGCMC:gcmc_exclusion_group:fixgcmc
3 atoms in group FixGCMC:rotation_gas_atoms:fixgcmc
But I never defined such a group (and it looks wield that 0 atoms or 3 atoms are included in these groups). Also, it seems, in my system of water and NaCl, the water and nacl are also default groups, no matter I defined them or not. I am very confused with this. Could anybody help me to give any detailed explanations? The compete information are as follows (there are water moecules and salt ions):
#!/bin/bash
# -V #Inherit the submission environment
# -cwd # Start job in submission directory
# -N H2OzSalt # Job Name
# -j y # Combine stderr and stdout
#$ -o $JOB_NAME.o$JOB_ID # Name of the output file (eg. myMPI.oJobID)
# -pe 1way 12 # Requests 12 tasks/node, 24 cores total
### -q development # Queue name “normal”
# -q normal
# -l h_rt=02:59:59 # Run time (hh:mm:ss) - 11.59 hrs
# -m be # Email at Begin and End of job
# -A A-ch6
set -x
Echo commands, use “set echo” with csh
ibrun lmp_mpi -in in.parameter -e screen
Hi,
I am using lammps and I have a question about the setting of groups.
According to the tutorial, there is only one defalt group, "all".
But in my system, some groups not defined by me have been found. E.g.:
0 atoms in group FixGCMC:gcmc_exclusion_group:fixgcmc
3 atoms in group FixGCMC:rotation_gas_atoms:fixgcmc
But I never defined such a group (and it looks wield that 0 atoms or 3
atoms are included in these groups).
you *did* define those groups, they get defined through fix gcmc. they
are needed internally. there is only one group defined by default (all) and
that is it.
Also, it seems, in my system of water and NaCl, the water and nacl are
also default groups, no matter I defined them or not. I am very confused
with this. Could anybody help me to give any detailed explanations? The
compete information are as follows (there are water moecules and salt ions):
again, there is only one default group. everything else will be defined
implicitly. in your case that seems to be exclusively due to fix gcmc. if
the LAMMPS version you are using is new enough, you can print out a list of
defined groups at any point of your script using the "info groups" command.
axel.
Thanks for your answers.
I test the “info command” and got the following information (actually I defined no groupt in my input script).
Group information:
Group[ 0]: all (static)
Group[ 1]: H2O (static)
Group[ 2]: FixGCMC:gcmc_exclusion_group:fixgcmc (static)
Group[ 3]: FixGCMC:rotation_gas_atoms:fixgcmc (static)
Group[ 4]: water (static)
Group[ 5]: nacl (static)
So, it seems the group “all” is default, and the rest groups are implicity defined.
I am very stranged that “nacl” is also defined as a group.
(for the implicitly defined groups, which cpp files are they due to? Where and how to modify the code?)
Does this means that I can delete or insert a pair of Na+ and Cl- ions, as I did for water molecules?
Actually, my aim is to do gcmc simulations on these ions. I think two possibilities can be attempted:
-
deal with Na+ and Cl- ion pair as a molecule, i.e. do gcmc in molecule mode
-
insert/delete simultaneously a Na+ ion and a Cl- ion, i.e. do gcmc in atom mode but twice
In any case, I am afraid, I have to modify the code. Can you give me some tips which .cpp file and what part to start with?
Best,
Yongbiao