Dear All,
I want to simulate the adsorption of ethene in zeolites by using fix gcmc. Now I met the error
“ERROR: Molecule topology/atom exceeds system topology/atom (…/molecule.cpp:1398)
Last command: fix mygcmc ethene gcmc 25 1000 1000 0 54341 {temp} {mu} {disp} mol ethenemol maxangle 180 pressure {pres} group ethene rigid myrigidnvt full_energy”.
However, it worked well when I replace ethene with carbon dioxide (the molecule file of carbon dioxide used is from the the example in the lammps-31Mar17 softe package).
The in.file data.file ethenemol.txt are below.
run.in
variables available on command line
variable temp index 673.0
variable mu index 2.0
variable disp index 0.4
variable pres index 0.001 #atmos 0.1Kpa
global model settings
units real
boundary p p p
atom_style full
pair_style lj/class2/coul/long 12.8
pair_modify mix arithmetic tail yes
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2
kspace_style ewald 0.0001
box
read_data CHA444.data &
extra/atom/types 2 &
extra/bond/types 2 &
extra/angle/types 2 &
extra/dihedral/types 1 &
extra/improper/types 1
molecule ethenemol ethene.txt
mass 3 12.011150 # c=
mass 4 1.007970 # hc
pcff model
pair_coeff 1 1 0.1622000000 3.4506000000 # oss
pair_coeff 2 2 0.0000000000 0.0001000000 # sz
pair_coeff 3 3 0.0640000000 3.9000000000 # c=
pair_coeff 4 4 0.0200000000 2.9950000000 # hc
bond_coeff 1 1.6155 325.4430 -943.3640 1454.6700 # oss-sz
bond_coeff 2 1.3521 545.2663 -1005.6330 1225.7415 # c=-c=
bond_coeff 3 1.0883 365.7679 -725.5404 781.6621 # c=-hc
angle_coeff 1 176.2650 18.8146 37.9749 42.8222 # sz-oss-sz
angle_coeff 2 110.6120 154.1860 -68.6595 23.6292 # oss-sz-oss
angle_coeff 3 124.8800 35.2766 -17.7740 -1.6215 # c=-c=-hc
angle_coeff 4 115.4900 29.6363 -12.4853 -6.2218 # hc-c=-hc
dihedral_coeff 1 -0.3417 0.0000 0.0961 0.0000 0.1683 0.0000# sz-oss-sz-oss
dihedral_coeff 2 0.0000 0.0000 4.8974 0.0000 0.0000 0.0000# hc-c=-c=-hc
improper_coeff 1 0.0000 0.0000
improper_coeff 2 2.8561 0.0000 # c=-c=-hc-hc
MD settings
group zeo type 1 2
group ethene type 3 4
neighbor 2.0 bin
neigh_modify delay 5 every 1 check yes
velocity all create ${temp} 54654
timestep 1.0
rigid constraints with thermostat
fix myrigidnvt ethene rigid/nvt/small molecule temp {temp} {temp} 100 mol ethenemol
fix_modify myrigidnvt dynamic/dof no
fix 1 zeo setforce 0.0 0.0 0.0
gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) #fix tfac_insert ${tfac}
fix mygcmc ethene gcmc 25 1000 1000 0 54341 {temp} {mu} {disp} mol ethenemol & maxangle 180 pressure {pres} group ethene rigid myrigidnvt full_energy
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)
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density etotal atoms v_iacc v_dacc v_tacc v_racc
thermo 1000
dump 1 all atom 1000 ethene.lammpstrj
dump_modify 1 sort id
dump 2 all cfg 1000 dump.sorption.*.cfg mass type xs ys zs vx vy vz
dump_modify 2 element O Si C H
run
run 6000000
CHA444.data
LAMMPS data file. msi2lmp v3.9.8 / 06 Oct 2016 / CGCMM for /home/yangg/data/Sorption/ethane/CHA444/pcff/CHA444
6912 atoms
9216 bonds
18432 angles
27648 dihedrals
9216 impropers
2 atom types
1 bond types
2 angle types
1 dihedral types
1 improper types
extra bond per atom 3
extra angle per atom 3
extra dihedral per atom 4
extra improper per atom 1
extra special per atom 14
-13.818299785 41.047600215 xlo xhi
0.114553150 47.635663364 ylo yhi
0.309259304 59.761671330 zlo zhi
-27.421619721 0.002905392 -0.001438278 xy xz yz
Masses
1 15.994910 # oss
2 28.086000 # sz
Atoms # full
1 1 1 -0.261800 8.005972073 3.350172726 11.658608383 0 0 0 # oss
2 1 1 -0.261800 1.148170989 7.310552784 1.749931363 0 0 0 # oss
3 1 1 -0.261800 -5.708916495 11.270545392 6.704115031 0 0 0 # oss
4 1 1 -0.261800 3.323391126 11.464182903 11.658461207 0 0 0 # oss
5 1 1 -0.261800 3.321059925 3.544362789 1.749879569 0 0 0 # oss
…
ethene.txt
#LAMMPS data file. msi2lmp v3.9.8 / 06 Oct 2016 / CGCMM for /home/yangg/data/Diffuse/ethene/one-molecular/pcff/ethene
6 atoms
5 bonds
6 angles
4 dihedrals
2 impropers
Coords
1 0.32202227 0.42654041 0.33323114 # c=
2 0.30127603 0.43263046 0.33304085 # c=
3 0.32061220 0.40884550 0.32379967 # hc
4 0.34127845 0.43901622 0.34283738 # hc
5 0.28200853 0.42019943 0.32343633 # hc
6 0.30270993 0.45031817 0.34249773 # hc
Types
1 1
2 1
3 2
4 2
5 2
6 2
Charges
1 -0.253600 # c=
2 -0.253600 # c=
3 0.126800 # hc
4 0.126800 # hc
5 0.126800 # hc
6 0.126800 # hc
Bonds
1 1 1 2
2 2 1 3
3 2 1 4
4 2 2 5
5 2 2 6
Angles
1 1 2 1 3
2 1 2 1 4
3 2 3 1 4
4 1 1 2 5
5 1 1 2 6
6 2 5 2 6
Dihedrals
1 1 3 1 2 5
2 1 3 1 2 6
3 1 4 1 2 5
4 1 4 1 2 6
Impropers
1 1 2 1 3 4
2 1 1 2 5 6
Special Bond Counts
1 3 2 0
2 3 2 0
3 1 2 2
4 1 2 2
5 1 2 2
6 1 2 2
Special Bonds
1 2 3 4 5 6
2 1 5 6 3 4
3 1 2 4 5 6
4 1 2 3 5 6
5 2 1 6 3 4
6 2 1 5 3 4
I definitely need help on this from lammps users. Thanks very much!
Guang Yang
Sinopec,China