Hello,
I try to use moltemplate to build complex periodic structures from a single molecule.
I first use ltemplify.py to convert LAMMPS input/data files for a single molecule into a .LT file. No error reports.
processing "Pair Coeffs"
processing "Bond Coeffs"
processing "Angle Coeffs"
processing "Dihedral Coeffs"
processing "Masses"
processing "Atoms"
processing "Bonds"
processing "Angles"
processing "Dihedrals"
But the final .LT file does not have the information about "Pair Coeffs". And in the "In Init" section, it misses one command "pair_modify shift yes mix geometric
" which I already set in the LAMMPS input file.
I am using lj/cut/coul/long, the "Pair Coeffs" section in LAMMPS data file is:
Pair Coeffs
1 0.0700287 3.550 # CA
2 0.0700287 3.550 # CA1
3 0.0700287 3.550 # CA2
4 0.0659656 3.500 # CN2
5 0.0659656 3.500 # CN3
6 0.0700287 3.550 # CP
7 0.150096 3.650 # CZ
8 0.0301147 2.420 # HA
9 0.0301147 2.500 # HC
10 0.169933 3.200 # NZ
And the LAMMPS input file is :
#Basic parameters
newton on
units real
atom_style full
dimension 3
boundary p p p
read_data LC.data
timestep 2.0
thermo 2000
#Non-banded energy
pair_style lj/cut/coul/long 10.0
kspace_style ewald 0.00001
pair_modify shift yes mix geometric
special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.125
#Bond stretching force constants
bond_style harmonic
#Bond angle bending force constants
angle_style harmonic
#Torsional Rotation
dihedral_style opls
Thanks
Best wishes,
Wei
Dear Wei
All of these problems sound like bugs in "ltempllify.py". I don't use
this script much, so it does not get as much testing. But I consider
it important. I am grateful for your bug reports.
But the final .LT file does not have the information about "Pair Coeffs".
There were no "Pair Coeffs" sections in the data files I used to test
ltemplify.py. (Instead they were stored as "pair_coeff" commands in
the input script. That might explain why I missed this bug. Who
knows.)
I'll fix it within 24 hours.
And in the "In Init" section, it misses one command
"pair_modify shift yes mix geometric"
I will make sure that "ltemplify.py" copies the "pair_modify"
command to "In Init", where it belongs. I worry there are probably
other relevant input script commands that ltemplify.py is ignoring.
I'll check the input script you included.
I suspect ltemplify.py was buggy, so but I did not realize how buggy it was.
Thank you for reporting these!
Andrew
There is a big update coming for both ltemplify.py and moltemplate in
the next day or two.
Hello,
I try to use moltemplate to build complex periodic structures from a single molecule.
I first use ltemplify.py to convert LAMMPS input/data files for a single molecule into a .LT file. No error reports.
processing "Pair Coeffs"
processing "Bond Coeffs"
processing "Angle Coeffs"
processing "Dihedral Coeffs"
processing "Masses"
processing "Atoms"
processing "Bonds"
processing "Angles"
processing "Dihedrals"
And in the "In Init" section, it misses one command "pair_modify
shift yes mix geometric
Dear Chen
This issue has finally been patched and the documentation for
ltemplify.py (moltemplate_manual.pdf) has been updated. There is a
new (and much-improved) version of moltemplate as well. I updated the
software links at www.moltemplate.org and will email them to Steve for
inclusion in the next LAMMPS release. Please let me know if you
discover more bugs with ltemplify.py or moltemplate. Again, thanks
for the post.
Andrew