GCMC + NVT simulations

Hi Lammps users,

I am trying to do GCMC simulations for water adsorption in silicate minerals with LAMMPS. My silicate surface consists of 688 atoms and 11 atom types. Therefore, in my lammps data file, i have used atomtypes 12 and 13 for water oxygen and hydrogen atoms respectively. i have mentioned the LJ parameters keeping the same atomtype order. Also, i have given the bond type (3) and angle type (1) number for water molecules. Below is the relevant section of my data file

688 atoms
64 bonds
0 angles
0 dihedrals
0 impropers

13 atom types
3 bond types
1 angle types

0.0 20.9603996 xlo xhi
0.0 18.1884003 ylo yhi
0.0 24. zlo zhi

Masses

1 24.305
2 28.086
3 15.999
4 15.999
5 15.999
6 15.999
7 15.999
8 1.0079
9 26.981
10 22.99
11 1.0079
12 15.999
13 1.0079

Pair Coeffs

1 9.0298E-07 5.26432051
2 1.8405E-06 3.302027
3 0.1554 3.16554131
4 0.1554 3.16554131
5 0.1554 3.16554131
6 0.1554 3.16554131
7 0.1554 3.16554131
8 0. 0.
9 9.0298E-06 4.21012006
10 0.1301 2.35001263
11 0. 0.
12 0.1554 3.16554131
13 0. 0.

Bond Coeffs

1 554.1349 1.
2 554.1349 1.
3 554.1349 1.

Angle Coeffs

1 45.7696 109.47

I am trying to use rigid SPC water model. So i prepared water molecule file “spc.txt” and is given as attachment for your reference. I am using special bonds and special bond count sections in the molecule file along with Shake section for keeping the water model rigid. However, when i run the simulations i get error message as “Molecule file special list does not match special count”. I did read the manual but could not understand the special bond section for the molecule file. Please help me figure it out and run GCMC simulations. I have also attached the lammps input file for your reference.

Thanks in advance,

Sincerely,

Naresh

spc.txt (687 Bytes)

in.lammps (1.12 KB)

Hi Lammps users,
                   I am trying to do GCMC simulations for water adsorption
in silicate minerals with LAMMPS. My silicate surface consists of 688 atoms
and 11 atom types. Therefore, in my lammps data file, i have used atomtypes
12 and 13 for water oxygen and hydrogen atoms respectively. i have mentioned
the LJ parameters keeping the same atomtype order. Also, i have given the
bond type (3) and angle type (1) number for water molecules. Below is the
relevant section of my data file

[...]

I am trying to use rigid SPC water model. So i prepared water molecule file
"spc.txt" and is given as attachment for your reference. I am using special
bonds and special bond count sections in the molecule file along with Shake
section for keeping the water model rigid. However, when i run the
simulations i get error message as "Molecule file special list does not
match special count". I did read the manual but could not understand the
special bond section for the molecule file. Please help me figure it out and

you forgot to mention the 1-3 pairs in your special bonds list. it should be:

Special Bonds

  1 2 3
  2 1 3
  3 1 2

BTW: you do not need a "masses" section, this is only needed for atom
types that have per-atom masses. however, in your case you have
per-type masses and thus the masses are already determined by the atom
type.

axel.

Hi,

Thanks for your reply. I corrected it. I ran it again to an other error “Molecule toplogy/atom exceeds system topology/atom”. I understand that i should leave space for any new bonds or angles added during the simulation.

So, i used “2 extra special per atom” to insert water molecules in to my silicate surface. But i am still having the same error message. Lammps input script, molecule file and read.datafile are attached for your reference. I should mention that i did not use neither “fix pour” or “fix deposit” command in my input script because both needs the number of molecules to be inserted explicitly. In my case, i dont know how much water would get into the silicate layers. Kindly help to get the simulations going.

Thanks in advance,

Sincerley,

Naresh

spc.txt (675 Bytes)

in.lammps (1.12 KB)

read.data (1.89 KB)

Hi,
Thanks for your reply. I corrected it. I ran it again to an other error “Molecule toplogy/atom exceeds system topology/atom”. I understand that i should leave space for any new bonds or angles added during the simulation.
So, i used “2 extra special per atom” to insert water molecules in to my silicate surface. But i am still having the same error message. Lammps input script, molecule file and read.datafile are attached for your reference. I should mention that i did not use neither “fix pour” or “fix deposit” command in my input script because both needs the number of molecules to be inserted explicitly. In my case, i dont know how much water would get into the silicate layers. Kindly help to get the simulations going.

Please search the mailing list archives. This kind of issue has come up before.
Axel

Hi,
           Thanks for your reply. I corrected it. I ran it again to an other
error "Molecule toplogy/atom exceeds system topology/atom". I understand
that i should leave space for any new bonds or angles added during the
simulation.
So, i used "2 extra special per atom" to insert water molecules in to my
silicate surface. But i am still having the same error message. Lammps input
script, molecule file and read.datafile are attached for your reference. I

the data file is bogus. you are wasting my time here.

axel.

Sorry. I didnt mean to do that. i thought to show the appropriate section since the Atoms section contains only the number.

I have put all information in that now.

Thanks,

Naresh

read.data (49.4 KB)

your molecule file is broken, too.

Sorry. I didnt mean to do that. i thought to show the appropriate section
since the Atoms section contains only the number.

it *does* matter. how else should i be able to run your input?

this is getting ridiculous. you have now officially exhausted my
amount of goodwill.

good luck,
     axel.

I dont know what happened to the molecule file. I sent it as such.

Anyway, thanks for your valuable time.

Thanks

Naresh