Dear Lammps User,
So the thing is, In my input deck I have initialized some groups with some number of atoms in it. After just running the the that part in LAMMPS, just to see whether the number of atoms in the groups are same or not, I saw some anomaly between what I executed and what I expected. I am not able to figure out why this is happening.
Below is the snippet of input deck:
#************************************************
# SETTING UP BOUNDARY CONDITIONS
#****************************************************
units lj
atom_style full
dimension 3
boundary p p p
#****************************************************
#SETTING UP POTENTIALS
#****************************************************
pair_style lj/cut/coul/cut 2.5 9.0
angle_style harmonic
bond_style harmonic
neigh_modify every 1 delay 5 check yes
special_bonds coul 0.0 0.0 0.5
dielectric 1.0
#****************************************************
#DEFINING REGION &&&& READING DATA FILE
#****************************************************
read_data data3.txt extra/atom/types 1 extra/bond/types 1 extra/angle/types 1
region reg1 cylinder z 25.0 25.0 7.0 -0.5 0.5
delete_atoms region reg1 bond yes
read_data polymer.txt add append offset 1 1 1 0 0
region myreg1 block 0 50 0 50 -100 -10.0 #This region is defined to use for create_atoms
region myreg2 block 0 50 0 50 10.0 100 #This region is defined to use for create_atoms
create_atoms 2 random 200 341341 myreg1
create_atoms 3 random 200 127569 myreg1
create_atoms 2 random 200 341341 myreg2
create_atoms 3 random 200 127569 myreg2
set type 2 charge 0.5
set type 3 charge -0.5
include wallparam.lammps
include ionsparam.lammps
include polyparam.lammps
pair_modify shift yes mix geometric
reset_ids
#****************************************************
#DEFINING GROUPS
#****************************************************
group gcar type 1 #This is group for graphene sheet which contains 1008 atoms but since
#I used delete_atoms command so there must atoms less than 1008 atoms
group gpot type 2 #This group for monovalent +ve atoms, say, Potassium. There are 400 atoms here.
group gchl type 3 #This group for monovalent -ve atoms, say, Chloride. There are 400 atoms here
group gpoly type 4 #This group is for polymer chain. There are 20 atoms in here.
#Since I have to fix the graphene sheet in such a manner that it should stay exactly in the middle of the simulation box with
#its dimension being equal to that of x,y dimensions of the box.
variable xmax equal bound(gcar,xmax)+1.0
variable xmin equal bound(gcar,xmin)-1.0
variable ymax equal bound(gcar,ymax)+1.0
variable ymin equal bound(gcar,ymin)-1.0
variable xmax1 equal bound(gcar,xmax)-0.5
variable xmin1 equal bound(gcar,xmin)+0.5
variable ymax1 equal bound(gcar,ymax)-0.5
variable ymin1 equal bound(gcar,ymin)+0.5
#This part of the code disects the graphene sheet in 4 parts. I'll explain one and the reasoning for the other 3 is similar.
# say rright, a region which is formed on the right of graphene sheet, it includes only the edge atoms on that side of the graphene
# sheet. The idea is that the 4 edges will have setforce 0 only the mid section will be equilibrated.
region rright block ${xmax1} INF INF INF -0.5 0.5
region rleft block INF ${xmin1} INF INF -0.5 0.5
region rmid block ${xmin1} ${xmax1} ${ymin1} ${ymax1} -0.5 0.5
region rtop block INF INF ${ymin1} INF -0.5 0.5
region rbot block INF INF INF ${ymin1} -0.5 0.5
group gright region rright
group gleft region rleft
group gmid region rmid
group gions union gpot gchl
group gtop region rtop
group gbot region rbot
group gall union gions gpoly
change_box all x final ${xmin} ${xmax}
change_box all y final ${ymin} ${ymax}
the data3.txt is
LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.8 on Wed Sep 28 11:43:09 IST 2022
1008 atoms
1467 bonds
2846 angles
3 atom types
1 bond types
1 angle types
-6.04 53.94 xlo xhi
-4.86 54.44 ylo yhi
-50.000000 50.000000 zlo zhi
# Pair Coeffs
#
# 1 CA
# Bond Coeffs
#
# 1 CA-CA
# Angle Coeffs
#
# 1 CA-CA-CA
Atoms # full
1 1 1 0.000000 0.000000 0.000000 0.000000 # CA GRA
2 2 1 0.000000 -1.228024 0.709000 0.000000 # CA GRA
3 3 1 0.000000 -1.228024 2.127000 0.000000 # CA GRA
4 4 1 0.000000 0.000000 2.836000 0.000000 # CA GRA
5 5 1 0.000000 2.456048 0.000000 0.000000 # CA GRA
.
.
.
Bonds
1 1 1 2
2 1 1 6
3 1 2 3
4 1 3 4
5 1 4 7
.
.
.
Angles
1 1 2 1 6
2 1 1 2 3
3 1 2 3 4
4 1 3 4 7
5 1 3 4 85
and polymer.txt is:
# LAMMPS data file
20 atoms
19 bonds
18 angles
1 atom types
1 bond types
1 angle types
Atoms
1 1 1 -7.00000 25.00000 25 19.000000
2 1 1 -7.00000 25.00000 25 18.035000
3 1 1 -7.00000 25.00000 25 17.070000
4 1 1 -7.00000 25.00000 25 16.105000
5 1 1 -7.00000 25.00000 25 15.140000
.
.
.
Bonds
1 1 1 2
2 1 2 3
3 1 3 4
.
.
.
Angles
1 1 1 2 3
2 1 2 3 4
3 1 3 4 5
What i’m getting after running is this:
when the delete_atom command is commented out
1008 atoms in group gcar
400 atoms in group gpot
400 atoms in group gchl
0 atoms in group gpoly
when the delete_atom command is not commented out, I’m getting this
948 atoms in group gcar
396 atoms in group gpot
393 atoms in group gchl
0 atoms in group gpoly
The group gpoly shouldn’t have 0 atoms. I’m not able to figure out why this is happening. Please help me out.
Thanks