The file params obtained from the two versions is different

EMC
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1

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.

2

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.

3

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
4

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 only 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/.