Symmetry change from Monoclinic to Orthorhombic in Moltemplate or LAMMPS

Hello everyone,

I have a monoclinic system I want to make orthogonal in LAMMPS. The lattice params are: a=6.735, b=7.425, c=27.987, alpha=beta=90 and gamma=123.25. I built the unit cell and replicated 4x3x1 times in Moltemplate. When I observed the system in VMD, it looked like a monoclinic system which is good so far. But when I am running the system in LAMMPS, I need to make it orthorhombic because I am doing tension testing on it. I used change_box command, but the system is still monoclinic. I also tried to follow the methods suggested in the examples of Moltemplate manual, but somehow I can’t make the system orthorhombic. Probably, I am missing something. I send the email in LAMMPS mailing list because I am using LAMMPS as the MD tool. Also, I hope I will catch the attention of Andrew Jewett. I followed the previous suggestions by him but somehow I am not able to produce the correct result.

Here’s part of my code in moltemplate and LAMMPS:

T14unitcell {

write_once(“In Init”){

LAMMPS input file

units real
newton on
boundary p p p

atom_style full
pair_style lj/cut/coul/long 12.0 10.0
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
kspace_style pppm 1e-6
pair_modify mix arithmetic
run_style verlet

neighbor 3
neigh_modify delay 0 every 1 check yes

}

write (“Data Atoms”){
coords

}
write(“Data Bonds”) {

bonds
}

write(“Data Angles”) {

masses

write_once(“Data Masses”) {
masses
}

write_once(“In Settings”) {

potential
}

} # T14 unit cell

T14supercell = new T14unitcell [4].move(6.735,0,0)
[3].move(-4.071,6.2094,0)
[1].move(0,0,27.987)

write_once(“Data Boundary”){

-3.35 27 xlo xhi
0.07 24 ylo yhi
0.053 27.987 zlo zhi
0.0 0.0 0.0 xy xz yz

}

LAMMPS input file

Tobermorite-14A

XY-shearing Equilibration

Declare variable

variable t equal 300
echo screen
log t14x3.log

units real
newton on
processors * * *
boundary p p p

atom_style full
pair_style lj/cut/coul/long 12.0 10.0
bond_style harmonic
angle_style harmonic

read_data t14test5.data

bond_coeff 1 554.1349 1.0
bond_coeff 2 554.1349 1.0
angle_coeff 1 45.7696 109.47

pair_coeff 1 1 5.03e-6 6.2484
pair_coeff 2 2 1.8405e-6 3.7064
pair_coeff 3 3 0.1554 3.5532
pair_coeff 4 4 0.1554 3.5532
pair_coeff 5 5 0.1554 3.5532
pair_coeff 6 6 0.1554 3.5532
pair_coeff 7 7 0.0 0.0
pair_coeff 8 8 0.0 0.0
pair_coeff 9 9 0.1 3.2237
pair_coeff 10 10 0.1001 4.9388

kspace_style pppm 1e-6
pair_modify mix arithmetic tail no
run_style verlet

neighbor 3 bin
neigh_modify delay 0 every 1 one 10000 check yes

group cao type 1
group st type 2
group ob type 3
group obts type 4
group oh type 5
group o* type 6
group h* type 7
group ho type 8
group Ca type 9
group cl type 10

group water type 6 7
group solid subtract all water
group rest subtract all cl
neigh_modify exclude group cl cl
neigh_modify exclude group cl rest

set type 1 charge 1.36
set type 2 charge 2.1
set type 3 charge -1.050166667
set type 4 charge -1.1689
set type 5 charge -0.95
set type 6 charge -0.82
set type 7 charge 0.41
set type 8 charge 0.425
set type 9 charge 2.0
set type 10 charge -1.0

replicate 1 1 1
change_box all ortho
write_data t14xbig4.data

region leftbdy block INF -2 INF INF INF INF units box
group leftbdy region leftbdy
region rightbdy block 7 INF INF INF INF INF units box
group rightbdy region rightbdy
group mobile subtract all leftbdy rightbdy

compute newtemp all temp
velocity all create ${t} 12345 temp newtemp dist gaussian mom yes rot no

minimize 1.0e-20 1.0e-20 500000 1000000
min_style cg
min_modify dmax 0.1

#fix 1 all nve
fix 2 water shake 1e-4 20 0 b 1 a 1
#fix 3 all temp/berendsen {t} {t} 100
#thermo 100

#run 10000
#unfix 1
fix 4 all npt temp {t} {t} 100 iso 1 1 1000 pchain 1
thermo_style custom step temp epair etotal press vol density
#dump d_movie all movie 10000 t14x.equil3.movie.mpeg type type
dump 5 all xyz 10 t14.xyz
thermo 100
run 10000

pict14.docx (176 KB)