Dear lammps users,
I am using Lammps March 3, 2020 version. I am running the GCMC simulation of CO2 in zeolite NaY. But after running, I am getting the following error.
ERROR on proc 0: Shake determinant = 0.0 (src/RIGID/fix_shake.cpp:2315)
I input file as follows. I also attached the data file and CO2_zeo.txt file. Kindly help me to rectify this problem. Thank you well in advance.
#LAMMPS Input file for GCMC CO2 adsorbed on zeolite NaY
zeo 2.43
#variable available on command line
variable mu index -8.1
variable disp index 0.1
variable temp index 300.0
variable lbox index 24.8536
variable spacing index 1.0
Intialization
units real
dimension 3
boundary p p p
atom_style full
atom_modify map array sort 500 2.0
Atom Definition
#read_restart restart.500000.equil
read_data data.zeoco2
replicate 1 1 1
box, start molecules on simple cubic lattice
lattice sc {spacing}
region box block 0 {lbox} 0 {lbox} 0 {lbox} units box
#create_box 2 box &
bond/types 1 &
angle/types 1 &
extra/bond/per/atom 2 &
extra/angle/per/atom 1 &
extra/special/per/atom 2
molecule co2mol CO2_zeo.txt
#create_atoms 0 box mol co2mol 464563 units box
bond_style harmonic
bond_coeff 1 300.290000000000 1.600000000000000 #Si-O
bond_coeff 2 222.200000000000 1.70000000000000 #Al-O
bond_coeff 3 30.0200000000000 3.12000000000000 #Si-O-Si
bond_coeff 4 30.0200000000000 3.18000000000000 #Al-O-Si
bond_coeff 5 1000.0000000000000 1.16100000000000 #C-O dummy K
angle_style harmonic
angle_coeff 1 7.01000000000000 149.500000000000 #Si-O-Si
angle_coeff 2 5.00000000000000 149.500000000000 #Al-O-Si
angle_coeff 3 75.0700000000000 109.500000000000 #O-Si-O
angle_coeff 4 65.0500000000000 109.500000000000 #O-Al-O
angle_coeff 5 100.0000000000000 109.490000000000 # O-C-O dummy K
#pair_style lj/long/coul/long long long 12.0
pair_style lj/cut/coul/long 12.0
kspace_style pppm 1.0e-4
#kspace_style ewald/disp 1.0e-4
pair_coeff 1 1 0.6004 3.9200
pair_coeff 1 2 0.6250 3.9200
pair_coeff 1 3 0.3032 3.5350
pair_coeff 1 4 0.3032 3.5350
pair_coeff 1 5 0.3101 3.1750
pair_coeff 1 6 0.1860 3.3525
pair_coeff 1 7 0.3142 3.4920
pair_coeff 2 2 0.6507 3.9200
pair_coeff 2 3 0.3156 3.5350
pair_coeff 2 4 0.3156 3.5350
pair_coeff 2 5 0.3229 3.1750
pair_coeff 2 6 0.1936 3.3525
pair_coeff 2 7 0.3271 3.4920
pair_coeff 3 3 0.1531 3.1500
pair_coeff 3 4 0.1531 3.1500
pair_coeff 3 5 0.1566 2.7900
pair_coeff 3 6 0.0939 2.9675
pair_coeff 3 7 0.1586 3.1070
pair_coeff 4 4 0.1531 3.1500
pair_coeff 4 5 0.1566 2.7900
pair_coeff 4 6 0.0939 2.9675
pair_coeff 4 7 0.1586 3.1070
pair_coeff 5 5 0.1602 2.4300
pair_coeff 5 6 0.0961 2.6075
pair_coeff 5 7 0.1623 2.7470
pair_coeff 6 6 0.0576 2.7850
pair_coeff 6 7 0.0973 2.9245
pair_coeff 7 7 0.1644 3.0640
group zeolite type 1:5
group co2 type 6:7
group freeze id 577:632
mass of atoms of co2
mass 6 12.0111
mass 7 15.9994
MD Settings
#velocity uranyl create 300.0 4928459 rot yes dist gaussian
#velocity nitrate create 300.0 4928458 rot yes dist gaussian
#velocity water create 300.0 4928457 rot yes dist gaussian
#velocity guest scale 200.0
velocity freeze set 0.0 0.0 0.0 units box
velocity co2 create ${temp} 54654
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.01
minimize 0.0 0.0 100 100 #1.0e-6 1.0e-6 1000 1000
reset_timestep 0
run 0
Rigid constraints with thermostst
fix mynvt all nvt temp {temp} {temp} 100
fix cshake co2 shake 0.0001 10 0 b 5 a 5 mol co2mol
#fix 3 water shake 0.0001 10 0 b 7 a 7
fix 4 freeze setforce 0.0 0.0 0.0
#unfix 3
important to make tempreture dofs dynamic
compute_modify thermo_temp dynamic/dof yes
compute_modify mynvt_temp dynamic/dof yes
run 1000
reset_timestep 0
gcmc
#unfix cshake
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc co2 gcmc 1 100 0 0 99 {temp} {mu} {disp} mol co2mol maxangle 180 full_energy &
tfac_insert {tfac} group co2 shake cshake
#maxangle 180 full_energy
#fix cshake
atom counts
variable carbon atom “type==6”
variable oxygen atom “type==7”
group carbon dynamic all var carbon
group oxygen dynamic all var oxygen
variable nC equal count(carbon)
variable nO equal count(oxygen)
Output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
thermo 1000
run 20000
With regards
Shamimul Ahsan
CO2_zeo.txt (591 Bytes)
data.zeoco2 (181 KB)
in.zeoco2_gcmc (5.23 KB)