missing forcefield parameters for PCFF using msi2lmp tool

LAMMPS LAMMPS Mailing List Mirror
1

Hello Everyone,

I have to switch to LAMMPS for simulation due to its flexibility. But while using msi2lmp tool, I found that some parameters were missing, msi2lmp tool failed to bond coefficient data between carbon and nitrogen and more. Any Idea about this missing parameters. I have observed
C:\one\msdata\compass>“C:\Program Files\LAMMPS 64-bit 19Mar2020-MPI\bin\msi2lmp.exe” C:\one\msdata\pcff\OCOOHTENXLINKNPTMS -p 2 -c 2 -frc “C:\Program Files\LAMMPS 64-bit 19Mar2020-MPI\frc_files\pcff.frc” -i

Running msi2lmp v3.9.9 / 05 Nov 2018

Forcefield: Class II
Forcefield file name: C:\Program Files\LAMMPS 64-bit 19Mar2020-MPI\frc_files\pcff.frc
Output is recentered around geometrical center
Output contains style flag hints
System translated by: 0 0 0
Reading car file: C:\one\msdata\pcff\OCOOHTENXLINKNPTMS.car
There are 20833 atoms in 1 molecules in this file
The total charge in the system is -0.318.
7441 of 20833 atoms with nonzero image flags

Reading mdf file: C:\one\msdata\pcff\OCOOHTENXLINKNPTMS.mdf

Building internal coordinate lists

Number of bonds, types = 22936 20
Number of angles, types = 41438 40
Number of dihedrals, types = 63120 52
Number of out-of-planes, types = 7372 9
Number of Angle Angle Terms, types = 12036 23

Reading forcefield file
Using higher version of parameters for #equivalence Na Na Na Na Na Na version 2.10
Using higher version of parameters for #nonbond c= version 2.10
Using higher version of parameters for #nonbond ho2 version 2.10
Using higher version of parameters for #nonbond n= version 3.10
Using higher version of parameters for #nonbond nz version 2.10
Using higher version of parameters for #nonbond o_1 version 2.10
Using higher version of parameters for #nonbond s’ version 2.10
Using higher version of parameters for #nonbond si version 2.20
Using higher version of parameters for #quartic_bond c c version 2.10
Using higher version of parameters for #quartic_bond c h version 2.10
Using higher version of parameters for #quartic_bond c o_2 version 2.20
Using higher version of parameters for #quartic_bond c= c=1 version 3.10
Using higher version of parameters for #quartic_bond c_1 o_1 version 2.10
Using higher version of parameters for #quartic_bond cp cp version 2.10
Using higher version of parameters for #quartic_bond cp cp version 2.10
Using higher version of parameters for #quartic_bond cp h version 2.10
Using higher version of parameters for #torsion_3 c c c c version 2.10
Using higher version of parameters for #torsion_3 c c c h version 2.10
Using higher version of parameters for #torsion_3 h c c h version 2.10
Using higher version of parameters for #torsion_3 h c cp cp version 2.00
Using higher version of parameters for #wilson_out_of_plane c cp cp cp version 2.00
Using higher version of parameters for #wilson_out_of_plane cp cp cp h version 3.10
Using higher version of parameters for #middle_bond-torsion_3 o_1 c_1 o_2 c version 2.10
Using higher version of parameters for #bond-bond_1_3 cp cp cp cp version 2.10

Item #atom_types has 133 entries
Item #equivalence has 133 entries
Item #nonbond has 87 entries
Item #quartic_bond has 119 entries
Item #quartic_angle has 303 entries
Item #bond-bond has 245 entries
Item #bond-angle has 234 entries
Item #torsion_3 has 488 entries
Item #angle-torsion_3 has 303 entries
Item #angle-angle-torsion_1 has 328 entries
Item #end_bond-torsion_3 has 291 entries
Item #middle_bond-torsion_3 has 350 entries
Item #bond-bond_1_3 has 63 entries
Item #wilson_out_of_plane has 69 entries
Item #angle-angle has 270 entries

Get force field parameters for this system
Trying Atom Equivalences if needed
Unable to find bond data for c2 nb
Unable to find bondbond data for cp c2 cp
Unable to find bondangle data for cp c2 cp
Unable to find bondbond data for cp oc c2
Unable to find bondangle data for cp oc c2
Unable to find angle data for c1 c2 nb
Unable to find bondbond data for c1 c2 nb
Unable to find bondangle data for c1 c2 nb
Unable to find angle data for hc c2 nb
Unable to find bondbond data for hc c2 nb
…

I have no idea about how atom equivalencies are performed. Currently, I am looking at how to do it. I have seen authors have use PCFF for crosslinked structure. Any idea about how to do it or update regarding another tool that I can use.

Thanks,
Ankit

2

there are several issues without a clean solution for msi2lmp:

  • most forcefield data/parameters for materials studio are licensed and thus cannot be made available in open source packages
  • the .frc force field files bundled with LAMMPS have not been updated in many years
  • the msi2lmp code implements only a subset of the functionality in the force field files (e.g. support for different bond styles or auto-equivalences is missing).
  • for the class2 force field, some interactions have no parameters, so those are supposed to be zero and can be ignored (check out the -i flag). but in your case a bond term is missing. that is something else that may not be ignored.
  • you may be able to use your own force field files from a licensed materials studio implementation, but nobody has checked, whether the file formats are still the same. the core of the msi2lmp implementation goes back nearly 20 years and no significant updates with respect to the processing of force field files have been added since

axel.