Dear LAMMPS developers and users:
I am trying to product the LAMMPS data file using msi2lmp file. First, I
created my data (PDB) using nanoengineer-1 software, then I used material
studio to obtain the .car and .mdf files after calculating the energy of
cvff in material studio (Modulus/Discover/Stepup, Energy and cvff then
calculate). My mistake showed up when I used msi2lmp.exe. In this step, I
copied the msi2lmp.ese file into my directory (windows environment), then I
used the following command to export the data file:
msi2lmp.exe PVDF -class I -frc cvff > data.PVDF
Again, the two car and mdf files are in the same directory. The error is
$ msi2lmp.exe PVDF -class I -frc cvff > data.PVDF
Warning: type name overflow for 'hspc
'. Truncating to 4 characters.
Warning: type name overflow for 'htip
'. Truncating to 4 characters.
------------------------------------------------------------
-----------------------------------------------------------------
And the output file (data.PVDF) consists this error as well
Running msi2lmp v3.9.7 / 24 Oct 2015
Forcefield: Class I
Forcefield file name: C:\Program Files\LAMMPS 64-bit
20160902\frc_files\cvff.frc
Output is recentered around geometrical center
Output contains style flag hints
System translated by: 0 0 0
Reading car file: PVDF.car
Reading mdf file: PVDF.mdf
Building internal coordinate lists
Reading forcefield file
Get force field parameters for this system
Unable to find oop data for h c c1 f
If you can, please let me know what is my mistake(s) in these steps.
please check the msi2lmp documentation. the data file will *not* be
written to standard out, but to a file <ROOTNAME>.data, i.e. PVDF.data in
your case. so you are just redirecting what would be screen output to a
file of the same name. while this has nothing to do with your immediate
problem, it is wrong.
while executing, apparently msi2lmp seems to determine that you need to
have improper dihedrals for certain groups of atoms, but there are no
parameters for them in the cvff force field file. that can mean one of two
things: a) msi2lmp is wrong and you can just ignore those or b) you need a
more complete force field file and add those parameters manually.
since you have built the structure, you are in the best position to judge
what is the right way to proceed. you can tell msi2lmp to ignore missing
parameters by adding the -ignore flag, e.g. like this.
msi2lmp.exe PVDF -frc cvff -ignore
and then, edit the resulting data file by removing the parts pertinent to
impropers.
axel.