Hello all,
I am using msi2lmp tool to convert .mdf and .car files to lammps files. I tested the files already present in the msi2lmp test folder, so assuming the msi2lmp is compiled well, I tried converting my .mdf and .car files. But the issue is, although my system has 3001 molecules, the converted data file gives only 5 molecule ID. I know someone who uses msi2lmp.exe. When he used, he got right data file.
I am not able to figure out the where am I going wrong as the test files ran correctly and same Material Studio file work with him. I am attaching the .mdf, .car file, data file. one is with 3001 molecules(data.solar_salts(50%)) and other with 5(solar_salts(50%).lammps05).
Also I get errors like:
…
… WARNING inconsistent # of connects on atom 392 type cp
WARNING inconsistent # of connects on atom 395 type cp
WARNING inconsistent # of connects on atom 397 type cp
Reading forcefield file
Get parameters for this molecular system
Unable to find bond data for o- np
Unable to find angle data for o- np o-
Unable to find oop data for o- np o- o-
…
If i am not wrong, these errors make the mol ID wrong. But I am not able to get solution on it.
data.solar_salts(50%) (1.03 MB)
solar_salts(50%).mdf (752 KB)
solar_salts(50%).car (642 KB)
solar_salts(50%).lammps05 (1.03 MB)
Hello all,
I am using msi2lmp tool to convert .mdf and .car files to lammps files. I
tested the files already present in the msi2lmp test folder, so assuming the
msi2lmp is compiled well, I tried converting my .mdf and .car files. But the
issue is, although my system has 3001 molecules, the converted data file
gives only 5 molecule ID. I know someone who uses msi2lmp.exe. When he used,
he got right data file.
which version of msi2lmp was that? ...and more importantly, which frc
file did he use?
I am not able to figure out the where am I going wrong as the test files
ran correctly and same Material Studio file work with him. I am attaching
the .mdf, .car file, data file. one is with 3001
molecules(data.solar_salts(50%)) and other with
5(solar_salts(50%).lammps05).
it looks to me that you are using a very old version of msi2lmp.
quite a few bugs have been fixed since.
Also I get errors like:
..........................................................................................
...... WARNING inconsistent # of connects on atom 392 type cp
WARNING inconsistent # of connects on atom 395 type cp
WARNING inconsistent # of connects on atom 397 type cp
Reading forcefield file
Get parameters for this molecular system
Unable to find bond data for o- np
Unable to find angle data for o- np o-
Unable to find oop data for o- np o- o-
this means, that the frc file you are using is missing crucial
parameters. please note that the files shipped with msi2lmp can only
contain published and thus publicly available parameters. most
parameters, however, are proprietary and thus only available when
using the .frc files from materials studio.
one more comment.
Hello all,
I am using msi2lmp tool to convert .mdf and .car files to lammps files. I
tested the files already present in the msi2lmp test folder, so assuming the
msi2lmp is compiled well, I tried converting my .mdf and .car files. But the
issue is, although my system has 3001 molecules, the converted data file
gives only 5 molecule ID. I know someone who uses msi2lmp.exe. When he used,
he got right data file.
which version of msi2lmp was that? ...and more importantly, which frc
file did he use?
I am not able to figure out the where am I going wrong as the test files
ran correctly and same Material Studio file work with him. I am attaching
the .mdf, .car file, data file. one is with 3001
molecules(data.solar_salts(50%)) and other with
5(solar_salts(50%).lammps05).
it looks to me that you are using a very old version of msi2lmp.
quite a few bugs have been fixed since.
Also I get errors like:
..........................................................................................
...... WARNING inconsistent # of connects on atom 392 type cp
WARNING inconsistent # of connects on atom 395 type cp
WARNING inconsistent # of connects on atom 397 type cp
this warning indicates that you have a different number of bonds for
atoms of the same type. after looking at your example file, this
happens, because you have a CNT which seems to be meant to be
continued across periodic boundary conditions, so you have some "cp"
type atoms with only 2 bonds, while others have 3 bonds. depending on
what you intend to simulate and what level of detail and accuracy you
desire, you need to add the missing bonds, or saturate the vacant
valences with hydrogens, or ignore the warnings.
axel.