Dear:
I use the PCFF potential to create polymer molecules. Polymers contain Si, O, C, H. The molecules generated in the new version don’t include # Improper Coeffs and # AngleAngle Coeffs. The old version does not have this issue.
Dear user,
I am not aware of this problem and have no example for which this occurs. Regrettably, debugging will not be possible without you providing an explicit example.
This is my input and my output. Sorry, new users can not upload attachments.
ITEM OPTIONS
replace true
field pcff
number false
ntotal 5200
density 1
ITEM END
# Groups
ITEM GROUPS
SiCCO *[Si]()(C)(C)O*,1,SiCCO:2 #left and right stars are hidend,I don't know why the star on the left is hidden when displayed. I hope you understand.
SiCCC *[Si]()(C)(C)(C),1,SiCCO:2 #left star is hidend
CSiCCO C[Si]()(C)(C)O*,1,SiCCO:1#right star is hidend
ITEM END
# Clusters
ITEM CLUSTERS
polymer alternate,1
ITEM END
# Polymers
ITEM POLYMERS
polymer
10 SiCCO,49,SiCCC,1,CSiCCO,1
ITEM END
Difference:
New version output in params file: only the title
# Improper Coeffs
# AngleAngle Coeffs
Old version ouput in params file:
# AngleAngle Coeffs
improper_coeff 1 aa -0.31570 -0.31570 -0.31570 107.66000 107.66000 107.66000 # c,hc,hc,hc
Dear user,
Thank you for your input. I actually went ahead and used insight2lammps.pl
as provided by EMC in the ${EMC_ROOT}/scripts
directory. This script converts InsightII input in the form of .car
and .mdf
– in combination with a ClassII force field such as PCFF – to produce a valid LAMMPS .data
coordinate file, which includes the force field parameters.
I used the following setup.esh
to create one toluene molecule with the PCFF force field, which serves a as a good proxy for your observed issue:
# Options section
ITEM OPTIONS
replace true
field pcff
density 0.1
number true
focus true
insight true
emc_execute true
ITEM END # OPTIONS
# Shorthand section
ITEM SHORTHAND
molecule Cc1ccccc1,1
ITEM END # SHORTHAND
The insight true
option creates setup.car
and setup.mdf
which is needed by insight2lammps.pl
. The latter was called with
insight2lammps.pl -forcefield=pcff -base=tmp setup
to create tmp.data
, which now serves as a difference source for obtaining ClassII force field constants and can be used to compare to setup.params
. I noticed that not only the above mentioned line was missing, but also a second line:
# AngleAngle Coeffs
improper_coeff 1 aa 2.37940 3.01180 2.37940 111.00000 111.00000 107.66000 # c,cp,hc,hc
improper_coeff 2 aa -0.31570 -0.31570 -0.31570 107.66000 107.66000 107.66000 # c,hc,hc,hc
EMC was adapted to include dummy entries for improper contributions:
# Improper Coeffs
improper_coeff 1 0.00000 0.00000 # c,cp,hc,hc
improper_coeff 2 0.00000 0.00000 # c,hc,hc,hc
I recompiled EMC for all targets and uploaded these corrected versions to https://sourceforge.net/projects/montecarlo/files/.