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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14057 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-09-24 20:16:09 +00:00
parent ea547aaf79
commit 2ed7d366a6
4 changed files with 16 additions and 11 deletions
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6
tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step2_run_moltemplate.sh
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@ -7,7 +7,11 @@
moltemplate.sh system.lt moltemplate.sh system.lt
# This will generate various files with names ending in *.in* and *.data. # (Note: If you have VMD installed, try this instead:)
# moltemplate.sh system.lt -vmd
# Moltemplate will generate various files with names ending in *.in* and *.data.
# These files are the input files directly read by LAMMPS. # These files are the input files directly read by LAMMPS.
# Optional: # Optional:

2
tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.in
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@ -33,7 +33,7 @@ pair_coeff 15 15 0.02 3.0
pair_coeff 16 16 0.02 3.0 pair_coeff 16 16 0.02 3.0
group cnt type 1 group cnt type 1
group cnad type 2-16 group cnad type 2:16
displace_atoms cnad move 0 -7 0 units box displace_atoms cnad move 0 -7 0 units box
special_bonds charmm special_bonds charmm

15
tools/moltemplate/src/ltemplify.py
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@ -670,9 +670,10 @@ try:
# avec, bvec, cvec are the axis of the parallelepiped which # avec, bvec, cvec are the axis of the parallelepiped which
# define the simulation's boundary. They are described here: # define the simulation's boundary. They are described here:
#http://lammps.sandia.gov/doc/Section_howto.html#howto-12 #http://lammps.sandia.gov/doc/Section_howto.html#howto-12
if ((not boundary_xlo) or (not boundary_xhi) or if ((boundary_xlo==None) or (boundary_xhi==None) or
(not boundary_ylo) or (not boundary_yhi) or (boundary_ylo==None) or (boundary_yhi==None) or
(not boundary_zlo) or (not boundary_zhi)): (boundary_zlo==None) or (boundary_zhi==None)):
raise InputError('Error: The DATA file lacks a boundary-box header. You must specify:\n' raise InputError('Error: The DATA file lacks a boundary-box header. You must specify:\n'
' xlo xhi ylo yhi zlo zhi (and xy xz yz if triclinic)\n' ' xlo xhi ylo yhi zlo zhi (and xy xz yz if triclinic)\n'
' These numbers should appear before the \"Atoms\" section.\n' ' These numbers should appear before the \"Atoms\" section.\n'
@ -823,14 +824,14 @@ try:
# Read the next line of text but don't skip comments # Read the next line of text but don't skip comments
comment_char_backup = lex.commenters comment_char_backup = lex.commenters
lex.commenters = '' lex.commenters = ''
line_orig = lex.ReadLine() line = lex.ReadLine()
lex.commenters = comment_char_backup lex.commenters = comment_char_backup
comment_text = '' comment_text = ''
ic = line_orig.find('#') ic = line.find('#')
if ic != -1: if ic != -1:
line = line_orig[:ic] line = line[:ic]
comment_text = line_orig[ic+1:].strip() comment_text = line[ic+1:].strip()
line = line.rstrip() line = line.rstrip()
if line.strip() in data_file_header_names: if line.strip() in data_file_header_names:

4
tools/moltemplate/src/moltemplate.sh
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@ -9,8 +9,8 @@
# All rights reserved. # All rights reserved.
G_PROGRAM_NAME="moltemplate.sh" G_PROGRAM_NAME="moltemplate.sh"
G_VERSION="1.32" G_VERSION="1.33"
G_DATE="2015-8-17" G_DATE="2015-9-22"
echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2 echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2
echo "" >&2 echo "" >&2