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[lammps-users] ERROR: Molecule topology/atom exceeds system topology/atom (../molecule.cpp:1398)
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[lammps-users] ERROR: Molecule topology/atom exceeds system topology/atom (../molecule.cpp:1398)


From: "sunny" <254958987@...1204...>
Date: Fri, 29 Sep 2017 14:40:04 +0800


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