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lammps/tools/moltemplate/src/moltemplate.sh
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moltemplate.sh
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#!/bin/bash
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2012, Regents of the University of California
# All rights reserved.
G_PROGRAM_NAME="moltemplate.sh"
G_VERSION="1.1"
G_DATE="2013-7-15"
echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2
echo "" >&2
# Check for python:
# I prefer python over python3 because python3 requires
# more memory. Just use regular python when available.
if which python > /dev/null; then
PYTHON_COMMAND='python'
elif which python3 > /dev/null; then
PYTHON_COMMAND='python3'
else
echo "Error: $G_PROGRAM_NAME requires python or python3" >&2
exit 1
fi
# First, determine the directory in which this shell script is located.
# (The python script files should also be located here as well.)
#SCRIPT_DIR=$(dirname $0)
SCRIPT_DIR=`dirname "$0"`
MSG_BAD_INSTALL=$(cat <<EOF
INSTALLATION ERROR:
Follow the instructions in the "Installation" chapter of the moltemplate manual.
(Note: You may need to log out and log in again before the changes take effect.)
EOF
)
ERR_BAD_INSTALL()
{
echo "$MSG_BAD_INSTALL" >&2
exit 1
}
ERR_INTERNAL()
{
echo " --- Possible internal error. ---" >&2
echo "This could be a bug in moltemplate." >&2
echo "Please report this error." >&2
echo "(And please include the last few lines of moltemplate output preceeding this.)" >&2
echo " Thank you." >&2
exit 100
}
MOLTEMPLATE_FILES_NEEDED=$(cat <<EOF
ttree.py
lttree.py
lttree_check.py
lttree_postprocess.py
nbody_by_type.py
nbody_fix_ttree_assignments.py
nbody_reorder_atoms.py
pdbsort.py
postprocess_input_script.py
remove_duplicate_atoms.py
remove_duplicates_nbody.py
renumber_DATA_first_column.py
ttree_render.py
EOF
)
OIFS=$IFS
#IFS=$'\n'
IFS="
"
for f in $MOLTEMPLATE_FILES_NEEDED; do
if [ ! -s "${SCRIPT_DIR}/$f" ]; then
echo "Error: Missing file \"${SCRIPT_DIR}/$f\"" >&2
ERR_BAD_INSTALL
fi
done
IFS=$OIFS
IMOLPATH=""
if [ -n "${MOLTEMPLATE_PATH}" ]; then
IMOLPATH="-importpath \"${MOLTEMPLATE_PATH}\""
fi
# command that invokes lttree.py
LTTREE_COMMAND="$PYTHON_COMMAND \"${SCRIPT_DIR}/lttree.py\" ${IMOLPATH}"
# command that invokes lttree_check.py
LTTREE_CHECK_COMMAND="$PYTHON_COMMAND \"${SCRIPT_DIR}/lttree_check.py\" ${IMOLPATH}"
# command that invokes lttree_postprocess.py
LTTREE_POSTPROCESS_COMMAND="$PYTHON_COMMAND \"${SCRIPT_DIR}/lttree_postprocess.py\" ${IMOLPATH}"
# What is the name of the .LT file we are reading?
for LAST_ARG; do true; done
# (I copied this code from a web page:
# http://stackoverflow.com/questions/1853946/getting-the-last-argument-passed-to-a-shell-script)
# Check to see if this string ends in .lt or .LT
# If so, then set the base name of the output files
# to equal the base name of the .LT file being read.
# (Being careful here.
# Sometimes the last argument is not the .lt or .LT file.
# Sometimes that file appears earlier in the argument list.
# I want to supply a default value.)
#
# Note, in bash you can use:
# if [ "${LAST_ARG/%.lt/}" -neq "$LAST_ARG" ]; then
# OUT_FILE_BASE="${LAST_ARG/%.lt/}"
# But in the original bourn shell (sh), this does not work.
# Instead we use a hack involving basename and dirname:
LTFILE="$LAST_ARG"
LTFILE_DIR=`dirname "$LTFILE"`
LTFILE_BASE=`basename "$LTFILE" .lt`
LTFILE_NO_EXT="${LTFILE_DIR}/${LTFILE_BASE}"
OUT_FILE_BASE="system"
if [ "$LTFILE_NO_EXT" != "$LTFILE" ]; then
OUT_FILE_BASE="$LTFILE_BASE"
else
LTFILE_BASE=`basename "$LAST_ARG" .LT`
LTFILE_NO_EXT="${LTFILE_DIR}/${LTFILE_BASE}"
if [ "$LTFILE_NO_EXT" != "$LTFILE" ]; then
OUT_FILE_BASE="$LTFILE_BASE"
fi
fi
OUT_FILE_INPUT_SCRIPT="${OUT_FILE_BASE}.in"
OUT_FILE_INIT="${OUT_FILE_BASE}.in.init"
OUT_FILE_SETTINGS="${OUT_FILE_BASE}.in.settings"
OUT_FILE_DATA="${OUT_FILE_BASE}.data"
OUT_FILE_COORDS="${OUT_FILE_BASE}.in.coords"
rm -f "$OUT_FILE_INPUT_SCRIPT" "$OUT_FILE_INIT" "$OUT_FILE_SETTINGS" "$OUT_FILE_DATA" "$OUT_FILE_COORDS"
# -----------------------------------------------------------
# If everything worked, then running ttree usually
# generates the following files:
#
# Users of lttree typically generate the following files:
# The variable below refer to file names generated by
# write() and write_once() commands in a lttree-file.
# (I keep changing my mind what I want these names to be.)
data_prefix="Data "
data_prefix_no_space="Data"
data_header="Data Header"
data_atoms="Data Atoms"
data_masses="Data Masses"
data_velocities="Data Velocities"
data_bonds="Data Bonds"
data_angles="Data Angles"
data_dihedrals="Data Dihedrals"
data_impropers="Data Impropers"
data_bond_coeffs="Data Bond Coeffs"
data_angle_coeffs="Data Angle Coeffs"
data_dihedral_coeffs="Data Dihedral Coeffs"
data_improper_coeffs="Data Improper Coeffs"
data_pair_coeffs="Data Pair Coeffs"
# interactions-by-type (not id. This is not part of the LAMMPS standard.)
data_angles_by_type="Data Angles By Type"
data_dihedrals_by_type="Data Dihedrals By Type"
data_impropers_by_type="Data Impropers By Type"
# class2 data sections
data_bondbond_coeffs="Data BondBond Coeffs"
data_bondangle_coeffs="Data BondAngle Coeffs"
data_middlebondtorsion_coeffs="Data MiddleBondTorsion Coeffs"
data_endbondtorsion_coeffs="Data EndBondTorsion Coeffs"
data_angletorsion_coeffs="Data AngleTorsion Coeffs"
data_angleangletorsion_coeffs="Data AngleAngleTorsion Coeffs"
data_bondbond13_coeffs="Data BondBond13 Coeffs"
data_angleangle_coeffs="Data AngleAngle Coeffs"
# sections for non-point-like particles:
data_ellipsoids="Data Ellipsoids"
data_lines="Data Lines"
data_triangles="Data Triangles"
# periodic boundary conditions
data_boundary="Data Boundary"
# (for backward compatibility), an older version of this file was named:
data_pbc="Data PBC"
# ---------------------------------------------------------------
# Note: The files above are fragments of a LAMMPS data file.
# In addition, moltemplate will probably also generate the following files:
# (These files represent different sections of the LAMMPS input script.)
# ---------------------------------------------------------------
in_prefix="In "
in_prefix_no_space="In"
in_init="In Init"
in_settings="In Settings"
in_coords="In Coords"
# If present, the various "In " files contain commands which should be
# included by the user in their LAMMPS input script. (This task is left
# to the user.) However, the "Data " files are processed and pasted together
# automatically in order to build a LAMMPS data file.
# ---------------------------------------------------------------
tmp_atom_coords="tmp_atom_coords.dat" #<-temporary file for storing coordinates
MOLTEMPLATE_TEMP_FILES=$(cat <<EOF
*.template
ttree_assignments.txt
$tmp_atom_coords
$data_masses
$data_pair_coeffs
$data_bond_coeffs
$data_angle_coeffs
$data_dihedral_coeffs
$data_improper_coeffs
$data_atoms
$data_velocities
$data_bonds
$data_angles
$data_dihedrals
$data_impropers
$data_bondbond_coeffs
$data_bondangle_coeffs
$data_middlebondtorsion_coeffs
$data_endbondtorsion_coeffs
$data_angletorsion_coeffs
$data_angleangletorsion_coeffs
$data_bondbond13_coeffs
$data_angleangle_coeffs
$data_ellipsoids
$data_lines
$data_triangles
$data_boundary
$data_angles_by_type
$data_dihedrals_by_type
$data_impropers_by_type
$in_init
$in_settings
EOF
)
OIFS=$IFS
#IFS=$'\n'
IFS="
"
for f in $MOLTEMPLATE_TEMP_FILES; do
#echo "removing [$f]"
rm -f "$f"
done
IFS=$OIFS
rm -rf output_ttree
SYNTAX_MSG=$(cat <<EOF
Syntax example:
Usage:
moltemplate.sh [-atomstyle style] \
[-pdb/-xyz coord_file] \
[-a assignments.txt] file.lt
Optional arguments:
-atomstyle style By default, moltemplate.sh assumes you are using the "full"
atom style in LAMMPS. You can change the atom style to "dipole"
using -atomstyle dipole. If you are using a hybrid style,
you must enclose the list of styles in quotes. For example:
-atomstyle "hybrid full dipole"
For custom atom styles, you can also specify the
list of column names manually (enclosed in quotes):
-atomstyle "molid x y z atomid atomtype mux muy muz"
-xyz xyz_file An optional xyz_file argument can be supplied as an argument
following "-xyz".
This file should contain the atomic coordinates in xyz format.
(The atoms must appear in the same order in the data file.)
-pdb pdb_file An optional pdb_file argument can be supplied as an argument
following "-pdb".
This should be a PDB file (with ATOM or HETATM records) with
the coordinates you wish to appear in the LAMMPS data file.
(The atoms must appear in the same order in the data file.)
If the PDB file contains periodic boundary box information
(ie., a "CRYST1" record), this information is also copied
to the LAMMPS data file.
(Support for triclinic cells is experimental as of 2012-2-13.
Other molecular structure formats may be supported later.)
-a "@atom:x 1"
-a assignments.txt
The user can customize the numbers assigned to atom, bond,
angle, dihedral, and improper types or id numbers by using
-a "VARIABLE_NAME VALUE"
for each variable you want to modify. If there are many
variables you want to modify, you can save them in a file
(one variable per line). For an example of the file format
run moltemplat.sh once and search for a file named
"ttree_assignments.txt". (This file is often located in
the "output_ttree/" directory.) Once assigned, the remaining
variables in the same category will be automatically assigned
to values which do not overlap with your chosen values.
-b assignments.txt
"-b" is similar to "-a". However, in this case, no attempt
is made to assign exclusive (unique) values to each variable.
-nocheck
Normally moltemplate.sh checks for common errors and typos and
halts if it thinks it has found one. This forces the variables
and categories as well as write(file) and write_once(file)
commands to obey standard naming conventions. The "-nocheck"
argument bypasses these checks and eliminates these restrictions.
EOF
)
# --- Periodic boundary box information (default) ---
# We will determine these numbers later.
TRICLINIC=""
BOXSIZE_MINX=0.0
BOXSIZE_MINY=0.0
BOXSIZE_MINZ=0.0
BOXSIZE_MAXX=""
BOXSIZE_MAXY=""
BOXSIZE_MAXZ=""
BOXSIZE_XY=0.0
BOXSIZE_XZ=0.0
BOXSIZE_YZ=0.0
if [ "$1" = "--help" ]; then
echo "$SYNTAX_MSG" >&2
exit 0
fi
# --- Did the user specify a file containing atomic coordinates?
rm -f "$tmp_atom_coords"
# Optional files containing atom coordinates:
PDB_FILE=""
XYZ_FILE=""
RAW_FILE=""
# REMOVE_DUPLICATE variables:
# ...If true (default), then any duplicate entries in the lists of bonds
# bonds, angles, dihedrals, or impropers in the LAMMPS DATA file
# are removed, giving priority to the most recent entry in the list.
# (This might not be necessary, but I want to be careful.)
REMOVE_DUPLICATE_BONDS="true"
REMOVE_DUPLICATE_ANGLES="true"
REMOVE_DUPLICATE_DIHEDRALS="true"
REMOVE_DUPLICATE_IMPROPERS="true"
ARGC=0
for A in "$@"; do
ARGC=$((ARGC+1))
eval ARGV${ARGC}=\"$A\"
done
TTREE_ARGS=""
i=0
while [ "$i" -lt "$ARGC" ]; do
i=$((i+1))
eval A=\${ARGV${i}}
if [ "$A" = "-nocheck" ]; then
# Disable syntax checking by undefining LTTREE_CHECK_COMMAND
unset LTTREE_CHECK_COMMAND
unset LTTREE_POSTPROCESS_COMMAND
elif [ "$A" = "-overlay-bonds" ]; then
# In that case, do not remove duplicate bond interactions
unset REMOVE_DUPLICATE_BONDS
elif [ "$A" = "-overlay-angles" ]; then
# In that case, do not remove duplicate angle interactions
unset REMOVE_DUPLICATE_ANGLES
elif [ "$A" = "-overlay-dihdedrals" ]; then
# In that case, do not remove duplicate dihedral interactions
unset REMOVE_DUPLICATE_DIHEDRALS
elif [ "$A" = "-overlay-impropers" ]; then
# In that case, do not remove duplicate improper interactions
unset REMOVE_DUPLICATE_IMPROPERS
elif [ "$A" = "-raw" ]; then
if [ "$i" -eq "$ARGC" ]; then
echo "$SYNTAX_MSG" >&2
exit 7
fi
# "isnum(x)" returns 1 or 0 depending upon whether or not
# a string is numeric.
#http://rosettacode.org/wiki/Determine_if_a_string_is_numeric#AWK
i=$((i+1))
eval A=\${ARGV${i}}
RAW_FILE=$A
if [ ! -s "$RAW_FILE" ]; then
echo "$SYNTAX_MSG" >&2
echo "-----------------------" >&2
echo "" >&2
echo "Error: Unable to open RAW-file \"$RAW_FILE\"." >&2
echo " (File is empty or does not exist.)" >&2
exit 8
fi
#echo " (extracting coordinates from \"$RAW_FILE\")" >&2
awk '{if (NF==3) {print $0}}' < "$RAW_FILE" > "$tmp_atom_coords"
elif [ "$A" = "-xyz" ]; then
if [ "$i" -eq "$ARGC" ]; then
echo "$SYNTAX_MSG" >&2
exit 7
fi
# "isnum(x)" returns 1 or 0 depending upon whether or not
# a string is numeric.
#http://rosettacode.org/wiki/Determine_if_a_string_is_numeric#AWK
i=$((i+1))
eval A=\${ARGV${i}}
XYZ_FILE=$A
if [ ! -s "$XYZ_FILE" ]; then
echo "$SYNTAX_MSG" >&2
echo "-----------------------" >&2
echo "" >&2
echo "Error: Unable to open XYZ-file \"$XYZ_FILE\"." >&2
echo " (File is empty or does not exist.)" >&2
exit 8
fi
#echo " (extracting coordinates from \"$XYZ_FILE\")" >&2
awk 'function isnum(x){return(x==x+0)} BEGIN{targetframe=1;framecount=0} {if (isnum($0)) {framecount++} else{if (framecount==targetframe){ if (NF>0) { if ((NF==3) && isnum($1)) {print $1" "$2" "$3} else if ((NF==4) && isnum($2)) {print $2" "$3" "$4} }}}}' < "$XYZ_FILE" > "$tmp_atom_coords"
elif [ "$A" = "-pdb" ]; then
if [ "$i" -eq "$ARGC" ]; then
echo "$SYNTAX_MSG" >&2
exit 9
fi
i=$((i+1))
eval A=\${ARGV${i}}
PDB_FILE=$A
if [ ! -s "$PDB_FILE" ]; then
echo "$SYNTAX_MSG" >&2
echo "-----------------------" >&2
echo "" >&2
echo "Error: Unable to open PDB-file \"$PDB_FILE\"." >&2
echo " (File is empty or does not exist.)" >&2
exit 10
fi
#echo " (extracting coordinates from \"$PDB_FILE\")" >&2
if grep -q '^ATOM \|^HETATM' "$PDB_FILE"; then
# Extract the coords from the "ATOM" records in the PDB file
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/pdbsort.py" < "$PDB_FILE" \
| awk '/^ATOM |^HETATM/{print substr($0,31,8)" "substr($0,39,8)" "substr($0,47,8)}' > "$tmp_atom_coords"; then
ERR_INTERNAL
fi
else
echo "$SYNTAX_MSG" >&2
echo "-----------------------" >&2
echo "" >&2
echo "Error: File \"$PDB_FILE\" is not a valid PDB file." >&2
exit 11
fi
# Now extract the periodic bounding-box informatio from the PDB file
# The CRYST1 records are described at:
# http://deposit.rcsb.org/adit/docs/pdb_atom_format.html
BOXSIZE_A=-1.0
BOXSIZE_B=-1.0
BOXSIZE_C=-1.0
ALPHA=" 90.00" #Note: The space before the number in " 90.00" is intentional.
BETA=" 90.00" # Later we will check to see if the system is triclinic
GAMMA=" 90.00" # by comparing these strings for equality with " 90.00"
if grep -qF "CRYST1" "$PDB_FILE"; then
BOXSIZE_A=`awk '/CRYST1/{print substr($0,8,8)}' < "$PDB_FILE"`
BOXSIZE_B=`awk '/CRYST1/{print substr($0,17,8)}' < "$PDB_FILE"`
BOXSIZE_C=`awk '/CRYST1/{print substr($0,26,8)}' < "$PDB_FILE"`
ALPHA=`awk '/CRYST1/{print substr($0,35,6)}' < "$PDB_FILE"`
BETA=`awk '/CRYST1/{print substr($0,42,6)}' < "$PDB_FILE"`
GAMMA=`awk '/CRYST1/{print substr($0,49,6)}' < "$PDB_FILE"`
fi
if [ `echo "$ALPHA!=90.0"|bc` -eq 1 ] || [ `echo "$BETA!=90.0"|bc` -eq 1 ] || [ `echo "$GAMMA!=90.0"|bc` -eq 1 ]; then
# I transform the parameters from one format to the other by inverting
# the transformation formula from the LAMMPS documentation (which matches
# http://www.ccl.net/cca/documents/molecular-modeling/node4.html)
# Disclaimer:
# As of September 2012, I have not tested the code below. I think the
# equations are correct, but I don't know if their are special cases
# that require the coordinates to be rotated or processed beforehand.
# This is an experimental feature.
TRICLINIC="True"
PI=3.1415926535897931
BOXSIZE_X=$BOXSIZE_A
BOXSIZE_Y=`awk "BEGIN{print $BOXSIZE_B*sin($GAMMA*$PI/180.0)}"`
BOXSIZE_XY=`awk "BEGIN{print $BOXSIZE_B*cos($GAMMA*$PI/180.0)}"`
BOXSIZE_XZ=`awk "BEGIN{print $BOXSIZE_C*cos($BETA*$PI/180.0)}"`
BOXSIZE_YZ=`awk "BEGIN{ca=cos($ALPHA*$PI/180.0); cb=cos($BETA*$PI/180.0); cg=cos($GAMMA*$PI/180.0); sg=sin($GAMMA*$PI/180.0); c=$BOXSIZE_C; print c*(ca-(cg*cb))/sg}"`
BOXSIZE_Z=`awk "BEGIN{print sqrt(($BOXSIZE_C**2)-(($BOXSIZE_XZ**2)+($BOXSIZE_YZ**2)))}"`
else
BOXSIZE_X=$BOXSIZE_A
BOXSIZE_Y=$BOXSIZE_B
BOXSIZE_Z=$BOXSIZE_C
BOXSIZE_XY=0.0
BOXSIZE_XZ=0.0
BOXSIZE_YZ=0.0
fi
BOXSIZE_MINX=0.0
BOXSIZE_MINY=0.0
BOXSIZE_MINZ=0.0
BOXSIZE_MAXX=$BOXSIZE_X
BOXSIZE_MAXY=$BOXSIZE_Y
BOXSIZE_MAXZ=$BOXSIZE_Z
#else: If the arguments are not understood in this script, then
# pass them on to "lttree.py"
else
if [ -z "$TTREE_ARGS" ]; then
TTREE_ARGS="\"$A\""
else
TTREE_ARGS="${TTREE_ARGS} \"$A\""
fi
fi
done
# --------------------------------------------------------------------
# --- Now run ttree/lttree to generate the file fragments we need. ---
# ------ (Afterwards, we will paste these fragments together.) -----
# --------------------------------------------------------------------
# If checking is not disabled, then first check for common spelling errors.
if [ -n "$LTTREE_CHECK_COMMAND" ]; then
if ! eval $LTTREE_CHECK_COMMAND $TTREE_ARGS; then
exit 1
fi
fi
# --- Run ttree. ---
#
# 3, 2, 1, ...
if ! eval $LTTREE_COMMAND $TTREE_ARGS; then
exit 2
fi
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
# > Traceback (most recent call last):
# > File "./lttree.py", line...
# .-.
# (0.0)
# '=.|m|.='
# .='`"``=.
#
# Hopefully this does not happen.
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
echo "" >&2
if [ -s "${data_atoms}" ]; then
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicate_atoms.py" \
< "${data_atoms}" \
> "${data_atoms}.tmp"; then
ERR_INTERNAL
fi
mv -f "${data_atoms}.tmp" "${data_atoms}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicate_atoms.py" \
< "${data_atoms}.template" \
> "${data_atoms}.tmp"; then
ERR_INTERNAL
fi
mv -f "${data_atoms}.tmp" "${data_atoms}.template"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/renumber_DATA_first_column.py" \
< "${data_atoms}" \
> "${data_atoms}.tmp"; then
ERR_INTERNAL
fi
mv -f "${data_atoms}.tmp" "${data_atoms}"
else
echo "Error: There are no atoms in your system." >&2
echo "" >&2
echo " Make sure that the object(s) you created are indeed molecules." >&2
echo " (Molecule objects must contain at least one" >&2
echo " write(\"${data_atoms}\") command.)" >&2
echo "" >&2
echo " (This error often occurs if you instantiated an object" >&2
echo " which you thought was a molecule, but it is actually" >&2
echo " only a namespace, a force-field name or category" >&2
echo " containing the definitions of other molecules.)" >&2
echo "" >&2
exit 200
fi
# ---------------- Interactions By Type -----------------
# At the time of writing, bonded-interactions-by-atom-type were not
# understood by LAMMPS. These features require auxilliary python scripts.
# These data sections must be processed before everything else (because
# they effect the other data sections, and the ttree_assignments.txt file.)
# -------------------------------------------------------
if [ -s "$data_angles_by_type" ]; then
echo "Generating 3-body angle interactions by atom/bond type" >&2
#-- Generate a file containing the list of interactions on separate lines --
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_by_type.py" \
Angles \
-atoms "${data_atoms}.template" \
-bonds "${data_bonds}.template" \
-nbodybytype "${data_angles_by_type}.template" \
-prefix '$/angle:bytype' > gen_Angles.template.tmp; then
exit 4
#WARNING: DO NOT REPLACE THIS WITH
#if ! $NBODY_COMMAND ...<-this sometimes causes a shell quotes-related error
fi
# ---- cleanup: ----
# ---- Re-build the "${data_angles}.template" file ----
# Instert these lines into the "${data_angles}.template" file which includes
# the newly generated interactions. (Note: these are in .template format)
cp gen_Angles.template.tmp new_Angles.template.tmp
if [ -s "${data_angles}.template" ]; then
# Then append existing "Angles" to the end of the generated interactions
# (Hopefully this way they will override those interactions.)
cat "${data_angles}.template" >> new_Angles.template.tmp
fi
mv -f new_Angles.template.tmp "${data_angles}.template"
echo "(Repairing ttree_assignments.txt file after angles added.)" >&2
# ---- Repair the ttree_assignments.txt file ----
# The next 2 lines extract the variable names from data_new.template.tmp
# and instert them into the appropriate place in ttree_assignments.txt
# (renumbering the relevant variable-assignments to avoid clashes).
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \
'/angle' gen_Angles.template.tmp \
< ttree_assignments.txt \
> ttree_assignments.tmp; then
exit 5
fi
echo "(Rendering ttree_assignments.tmp file after angles added.)" >&2
# ---- Re-build (render) the "$data_angles" file ----
# Now substitute these variable values (assignments) into the variable
# names present in the .template file. (We want to convert the file from
# a .template format into an ordinary (numeric) LAMMPS data-section format.)
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/ttree_render.py" \
ttree_assignments.tmp \
< "${data_angles}.template" \
> "$data_angles"; then
exit 6
fi
mv -f ttree_assignments.tmp ttree_assignments.txt
rm -f gen_Angles.template.tmp new_Angles.template.tmp
fi
if [ -s "$data_dihedrals_by_type" ]; then
echo "Generating 4-body dihedral interactions by atom/bond type" >&2
#-- Generate a file containing the list of interactions on separate lines --
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_by_type.py" \
Dihedrals \
-atoms "${data_atoms}.template" \
-bonds "${data_bonds}.template" \
-nbodybytype "${data_dihedrals_by_type}.template" \
-prefix '$/dihedral:bytype' > gen_Dihedrals.template.tmp; then
exit 4
#WARNING: DO NOT REPLACE THIS WITH
#if ! $NBODY_COMMAND ...<-this sometimes causes a shell quotes-related error
fi
# ---- cleanup: ----
# ---- Re-build the "${data_dihedrals}.template" file ----
# Instert these lines into the "${data_dihedrals}.template" file which includes
# the newly generated interactions. (Note: these are in .template format)
cp gen_Dihedrals.template.tmp new_Dihedrals.template.tmp
if [ -s "${data_dihedrals}.template" ]; then
# Then append existing "Dihedrals" to the end of the generated interactions
# (Hopefully this way they will override those interactions.)
cat "${data_dihedrals}.template" >> new_Dihedrals.template.tmp
fi
mv -f new_Dihedrals.template.tmp "${data_dihedrals}.template"
echo "(Repairing ttree_assignments.txt file after dihedrals added.)" >&2
# ---- Repair the ttree_assignments.txt file ----
# The next 2 lines extract the variable names from data_new.template.tmp
# and instert them into the appropriate place in ttree_assignments.txt
# (renumbering the relevant variable-assignments to avoid clashes).
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \
'/dihedral' gen_Dihedrals.template.tmp \
< ttree_assignments.txt \
> ttree_assignments.tmp; then
exit 5
fi
echo "(Rendering ttree_assignments.tmp file after dihedrals added.)" >&2
# ---- Re-build (render) the "$data_dihedrals" file ----
# Now substitute these variable values (assignments) into the variable
# names present in the .template file. (We want to convert the file from
# a .template format into an ordinary (numeric) LAMMPS data-section format.)
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/ttree_render.py" \
ttree_assignments.tmp \
< "${data_dihedrals}.template" \
> "$data_dihedrals"; then
exit 6
fi
mv -f ttree_assignments.tmp ttree_assignments.txt
rm -f gen_Dihedrals.template.tmp new_Dihedrals.template.tmp
fi
if [ -s "$data_impropers_by_type" ]; then
echo "Generating 4-body improper interactions by atom/bond type" >&2
#-- Generate a file containing the list of interactions on separate lines --
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_by_type.py" \
Impropers \
-atoms "${data_atoms}.template" \
-bonds "${data_bonds}.template" \
-nbodybytype "${data_impropers_by_type}.template" \
-prefix '$/improper:bytype' > gen_Impropers.template.tmp; then
exit 4
#WARNING: DO NOT REPLACE THIS WITH
#if ! $NBODY_COMMAND ...<-this sometimes causes a shell quotes-related error
fi
# ---- cleanup: ----
# ---- Re-build the "${data_impropers}.template" file ----
# Instert these lines into the "${data_impropers}.template" file which includes
# the newly generated interactions. (Note: these are in .template format)
cp gen_Impropers.template.tmp new_Impropers.template.tmp
if [ -s "${data_impropers}.template" ]; then
# Then append existing "Impropers" to the end of the generated interactions
# (Hopefully this way they will override those interactions.)
cat "${data_impropers}.template" >> new_Impropers.template.tmp
fi
mv -f new_Impropers.template.tmp "${data_impropers}.template"
echo "(Repairing ttree_assignments.txt file after impropers added.)" >&2
# ---- Repair the ttree_assignments.txt file ----
# The next 2 lines extract the variable names from data_new.template.tmp
# and instert them into the appropriate place in ttree_assignments.txt
# (renumbering the relevant variable-assignments to avoid clashes).
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \
'/improper' gen_Impropers.template.tmp \
< ttree_assignments.txt \
> ttree_assignments.tmp; then
exit 5
fi
echo "(Rendering ttree_assignments.tmp file after impropers added.)" >&2
# ---- Re-build (render) the "$data_impropers" file ----
# Now substitute these variable values (assignments) into the variable
# names present in the .template file. (We want to convert the file from
# a .template format into an ordinary (numeric) LAMMPS data-section format.)
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/ttree_render.py" \
ttree_assignments.tmp \
< "${data_impropers}.template" \
> "$data_impropers"; then
exit 6
fi
mv -f ttree_assignments.tmp ttree_assignments.txt
rm -f gen_Impropers.template.tmp new_Impropers.template.tmp
fi
if [ -n "$LTTREE_POSTPROCESS_COMMAND" ]; then
echo "" >&2
if ! eval $LTTREE_POSTPROCESS_COMMAND $TTREE_ARGS; then
exit 3
fi
echo "" >&2
fi
# -------------------------------------------------------
# If present, then remove duplicate bonds, angles, dihedrals, and impropers
# (unless overridden by the user).
# -------------------------------------------------------
if [ -s "${data_masses}" ]; then
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicate_atoms.py" \
< "${data_masses}" \
> "${data_masses}.tmp"; then
ERR_INTERNAL
fi
mv -f "${data_masses}.tmp" "${data_masses}"
fi
if [ -s "${data_bonds}" ]; then
if [ ! -z $REMOVE_DUPLICATE_BONDS ]; then
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_reorder_atoms.py" \
Bonds \
< "${data_bonds}" \
> "${data_bonds}.tmp"; then
ERR_INTERNAL
fi
cp -f "${data_bonds}.tmp" "${data_bonds}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 2 \
< "${data_bonds}" \
> "${data_bonds}.tmp"; then
ERR_INTERNAL
fi
mv "${data_bonds}.tmp" "${data_bonds}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 2 \
< "${data_bonds}.template" \
> "${data_bonds}.tmp"; then
ERR_INTERNAL
fi
mv "${data_bonds}.tmp" "${data_bonds}.template"
fi
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/renumber_DATA_first_column.py" \
< "${data_bonds}" \
> "${data_bonds}.tmp"; then
ERR_INTERNAL
fi
mv -f "${data_bonds}.tmp" "${data_bonds}"
fi
if [ -s "${data_angles}" ]; then
if [ ! -z $REMOVE_DUPLICATE_ANGLES ]; then
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_reorder_atoms.py" \
Angles \
< "${data_angles}" \
> "${data_angles}.tmp"; then
ERR_INTERNAL
fi
cp -f "${data_angles}.tmp" "${data_angles}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 3 \
< "${data_angles}" \
> "${data_angles}.tmp"; then
ERR_INTERNAL
fi
mv "${data_angles}.tmp" "${data_angles}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 3 \
< "${data_angles}.template" \
> "${data_angles}.tmp"; then
ERR_INTERNAL
fi
mv "${data_angles}.tmp" "${data_angles}".template
fi
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/renumber_DATA_first_column.py" \
< "${data_angles}" \
> "${data_angles}.tmp"; then
ERR_INTERNAL
fi
mv -f "${data_angles}.tmp" "${data_angles}"
fi
if [ -s "${data_dihedrals}" ]; then
if [ ! -z $REMOVE_DUPLICATE_DIHEDRALS ]; then
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_reorder_atoms.py" \
Dihedrals \
< "${data_dihedrals}" \
> "${data_dihedrals}.tmp"; then
ERR_INTERNAL
fi
cp -f "${data_dihedrals}.tmp" "${data_dihedrals}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 4 \
< "${data_dihedrals}" \
> "${data_dihedrals}.tmp"; then
ERR_INTERNAL
fi
mv "${data_dihedrals}.tmp" "${data_dihedrals}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 4 \
< "${data_dihedrals}.template" \
> "${data_dihedrals}.tmp"; then
ERR_INTERNAL
fi
mv "${data_dihedrals}.tmp" "${data_dihedrals}.template"
fi
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/renumber_DATA_first_column.py" \
< "${data_dihedrals}" \
> "${data_dihedrals}.tmp"; then
ERR_INTERNAL
fi
mv -f "${data_dihedrals}.tmp" "${data_dihedrals}"
fi
if [ -s "${data_impropers}" ]; then
if [ ! -z $REMOVE_DUPLICATE_IMPROPERS ]; then
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_reorder_atoms.py" \
Impropers \
< "${data_impropers}" \
> "${data_impropers}.tmp"; then
ERR_INTERNAL
fi
cp -f "${data_impropers}.tmp" "${data_impropers}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 4 \
< "${data_impropers}" \
> "${data_impropers}.tmp"; then
ERR_INTERNAL
fi
mv "${data_impropers}.tmp" "${data_impropers}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 4 \
< "${data_impropers}.template" \
> "${data_impropers}.tmp"; then
ERR_INTERNAL
fi
mv "${data_impropers}.tmp" "${data_impropers}.template"
fi
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/renumber_DATA_first_column.py" \
< "${data_impropers}" \
> "${data_impropers}.tmp"; then
ERR_INTERNAL
fi
mv -f "${data_impropers}.tmp" "${data_impropers}"
fi
# -------------------------------------------------------
NATOMTYPES=`awk '/^@\/atom:/{n++}END{print n}' < ttree_assignments.txt`
NBONDTYPES=`awk '/^@\/bond:/{n++}END{print n}' < ttree_assignments.txt`
NANGLETYPES=`awk '/^@\/angle:/{n++}END{print n}' < ttree_assignments.txt`
NDIHEDRALTYPES=`awk '/^@\/dihedral:/{n++}END{print n}' < ttree_assignments.txt`
NIMPROPERTYPES=`awk '/^@\/improper:/{n++}END{print n}' < ttree_assignments.txt`
#NATOMS=`awk '/^\$\/atom:/{n++}END{print n}' < ttree_assignments.txt`
#NBONDS=`awk '/^\$\/bond:/{n++}END{print n}' < ttree_assignments.txt`
#NANGLES=`awk '/^\$\/angle:/{n++}END{print n}' < ttree_assignments.txt`
#NDIHEDRALS=`awk '/^\$\/dihedral:/{n++}END{print n}' < ttree_assignments.txt`
#NIMPROPERS=`awk '/^\$\/improper:/{n++}END{print n}' < ttree_assignments.txt`
NATOMS="0"
NBONDS="0"
NANGLES="0"
NDIHEDRALS="0"
NIMPROPERS="0"
if [ -s "${data_atoms}" ]; then
NATOMS=`awk 'END{print NR}' < "${data_atoms}"`
fi
if [ -s "${data_bonds}" ]; then
NBONDS=`awk 'END{print NR}' < "${data_bonds}"`
fi
if [ -s "${data_angles}" ]; then
NANGLES=`awk 'END{print NR}' < "${data_angles}"`
fi
if [ -s "${data_dihedrals}" ]; then
NDIHEDRALS=`awk 'END{print NR}' < "${data_dihedrals}"`
fi
if [ -s "${data_impropers}" ]; then
NIMPROPERS=`awk 'END{print NR}' < "${data_impropers}"`
fi
rm -f "$OUT_FILE_DATA"
echo "LAMMPS Description" > "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
echo " $NATOMS atoms" >> "$OUT_FILE_DATA"
if [ -n "$NBONDS" ]; then
echo " $NBONDS bonds" >> "$OUT_FILE_DATA"
fi
if [ -n "$NANGLES" ]; then
echo " $NANGLES angles" >> "$OUT_FILE_DATA"
fi
if [ -n "$NDIHEDRALS" ]; then
echo " $NDIHEDRALS dihedrals" >> "$OUT_FILE_DATA"
fi
if [ -n "$NIMPROPERS" ]; then
echo " $NIMPROPERS impropers" >> "$OUT_FILE_DATA"
fi
echo "" >> "$OUT_FILE_DATA"
echo " $NATOMTYPES atom types" >> "$OUT_FILE_DATA"
if [ -n "$NBONDTYPES" ]; then
echo " $NBONDTYPES bond types" >> "$OUT_FILE_DATA"
fi
if [ -n "$NANGLETYPES" ]; then
echo " $NANGLETYPES angle types" >> "$OUT_FILE_DATA"
fi
if [ -n "$NDIHEDRALTYPES" ]; then
echo " $NDIHEDRALTYPES dihedral types" >> "$OUT_FILE_DATA"
fi
if [ -n "$NIMPROPERTYPES" ]; then
echo " $NIMPROPERTYPES improper types" >> "$OUT_FILE_DATA"
fi
echo "" >> "$OUT_FILE_DATA"
# --- PERIODIC BOUNDARY CONDITIONS ---
# Note: If there is a "$data_boundary" file present, it overrides any settings
# which may have been stored in a pdb file or other external file.
if [ -s "$data_pbc" ] && [ ! -s "$data_boundary" ]; then
mv -f "$data_pbc" "$data_boundary"
echo "WARNING: write_once(\"$data_pbc\") is depreciated" >&2
echo " Use write_once(\"$data_boundary\") instead" >&2
fi
if [ -s "$data_boundary" ]; then
# Copy the boundary conditions from the "$data_boundary" file.
# Don't assume there is only one line containing "xlo xhi", for example.
# It's possible the user wrote the boundary conditions multiple times.
# As always, the most recent setting overrides the earlier settings.
BOXSIZE_MINX=`awk '{if ($3=="xlo") {xlo=$1}} END{print xlo}' < "$data_boundary"`
BOXSIZE_MAXX=`awk '{if ($4=="xhi") {xhi=$2}} END{print xhi}' < "$data_boundary"`
BOXSIZE_MINY=`awk '{if ($3=="ylo") {ylo=$1}} END{print ylo}' < "$data_boundary"`
BOXSIZE_MAXY=`awk '{if ($4=="yhi") {yhi=$2}} END{print yhi}' < "$data_boundary"`
BOXSIZE_MINZ=`awk '{if ($3=="zlo") {zlo=$1}} END{print zlo}' < "$data_boundary"`
BOXSIZE_MAXZ=`awk '{if ($4=="zhi") {zhi=$2}} END{print zhi}' < "$data_boundary"`
if [ -z "$BOXSIZE_MINX" ] || [ -z "$BOXSIZE_MAXX" ]; then
echo "Error: Problem with box boundary format (\"xlo xhi\") in \"$data_boundary\"" >&2
exit 12
fi
if [ -z "$BOXSIZE_MINY" ] || [ -z "$BOXSIZE_MAXY" ]; then
echo "Error: Problem with box boundary format (\"ylo yhi\") in \"$data_boundary\"" >&2
exit 12
fi
if [ -z "$BOXSIZE_MINZ" ] || [ -z "$BOXSIZE_MAXZ" ]; then
echo "Error: Problem with box boundary format (\"zlo zhi\") in \"$data_boundary\"" >&2
exit 12
fi
BOXSIZE_XY=`awk '{if ($4=="xy") {xy=$1}} END{print xy}' < "$data_boundary"`
BOXSIZE_XZ=`awk '{if ($5=="xz") {xz=$2}} END{print xz}' < "$data_boundary"`
BOXSIZE_YZ=`awk '{if ($6=="yz") {yz=$3}} END{print yz}' < "$data_boundary"`
if [ -n "$BOXSIZE_XY" ] || [ -n "$BOXSIZE_XZ" ] || [ -n "$BOXSIZE_YZ" ]; then
if [ -n "$BOXSIZE_XY" ] && [ -n "$BOXSIZE_XZ" ] && [ -n "$BOXSIZE_YZ" ]; then
#echo "triclinic_parameters: XY XZ YZ = $BOXSIZE_XY $BOXSIZE_XZ $BOXSIZE_YZ" >&2
TRICLINIC="True"
else
echo "Error: Problem with triclinic format (\"xy xz yz\") in \"$data_boundary\"" >&2
exit 13
fi
fi
fi
if [ -z "$BOXSIZE_MINX" ] || [ -z "$BOXSIZE_MAXX" ] || [ -z "$BOXSIZE_MINY" ] || [ -z "$BOXSIZE_MAXY" ] || [ -z "$BOXSIZE_MINZ" ] || [ -z "$BOXSIZE_MAXZ" ]; then
echo "Periodic boundary conditions unspecified. Attempting to generate automatically." >&2
# By default, disable triclinic
BOXSIZE_XY=""
BOXSIZE_XZ=""
BOXSIZE_YZ=""
TRICLINIC=""
if [ -s "$tmp_atom_coords" ]; then
# Estimate the minimimum, maximum x,y,z values
# from the coordinate data.
MINMAX_BOUNDS=`awk 'BEGIN{first=1}{if (NF>=3){x=$1; y=$2; z=$3; if (first) {first=0; xmin=x; xmax=x; ymin=y; ymax=y; zmin=z; zmax=z;} else {if (x<xmin) xmin=x; if (x>xmax) xmax=x; if (y<ymin) ymin=y; if (y>ymax) ymax=y; if (z<zmin) zmin=z; if (z>zmax) zmax=z;}}} END{print xmin" "xmax" "ymin" "ymax" "zmin" "zmax;}' < "$tmp_atom_coords"`
# ...and add a narrow margin (10%) around the boundaries:
BOXSIZE_MINX=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$2-$1; print $1-0.5*margin*width}"`
BOXSIZE_MAXX=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$2-$1; print $2+0.5*margin*width}"`
BOXSIZE_MINY=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$4-$3; print $3-0.5*margin*width}"`
BOXSIZE_MAXY=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$4-$3; print $4+0.5*margin*width}"`
BOXSIZE_MINZ=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$6-$5; print $5-0.5*margin*width}"`
BOXSIZE_MAXZ=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$6-$5; print $6+0.5*margin*width}"`
else
# By default, choose some reasonably large box:
BOXSIZE_MINX="-100.0"
BOXSIZE_MAXX="100.0"
BOXSIZE_MINY="-100.0"
BOXSIZE_MAXY="100.0"
BOXSIZE_MINZ="-100.0"
BOXSIZE_MAXZ="100.0"
# ...and print message scolding the user for being lazy
echo "----------------------------------------------------------------------" >&2
echo "---- WARNING: Unable to determine periodic boundary conditions. ----" >&2
echo "---- (A default cube of volume=(200.0)^3 was used. ----" >&2
echo "---- This is probably not what you want!) ----" >&2
echo "---- It is recommended that you specify your periodic boundary ----" >&2
echo "---- by adding a write_once(\"Boundary\") command to your .lt file. ----" >&2
echo "---- For example: ----" >&2
#echo "----------------------------------------------------------------------" >&2
echo "---- ----" >&2
echo "---- write_once(\"Boundary\") { ----" >&2
echo "---- 2.51 46.79 xlo xhi ----" >&2
echo "---- -4.38 35.824 ylo yhi ----" >&2
echo "---- 0.3601 42.95 zlo zhi ----" >&2
echo "---- } ----" >&2
echo "----------------------------------------------------------------------" >&2
fi
fi
if [ -z "$TRICLINIC" ]; then
echo " $BOXSIZE_MINX $BOXSIZE_MAXX xlo xhi" >> "$OUT_FILE_DATA"
echo " $BOXSIZE_MINY $BOXSIZE_MAXY ylo yhi" >> "$OUT_FILE_DATA"
echo " $BOXSIZE_MINZ $BOXSIZE_MAXZ zlo zhi" >> "$OUT_FILE_DATA"
else
echo "triclinic parameters: XY XZ YZ = $BOXSIZE_XY $BOXSIZE_XZ $BOXSIZE_YZ" >&2
echo "" >&2
# Otherwise, this is a triclinic (non orthoganal) crystal basis.
# LAMMPS represents triclinic symmetry using a different set of parameters
# (lx,ly,lz,xy,xz,yz) than the PDB file format (alpha,beta,gamma).
echo " $BOXSIZE_MINX $BOXSIZE_MAXX xlo xhi" >> "$OUT_FILE_DATA"
echo " $BOXSIZE_MINY $BOXSIZE_MAXY ylo yhi" >> "$OUT_FILE_DATA"
echo " $BOXSIZE_MINZ $BOXSIZE_MAXZ zlo zhi" >> "$OUT_FILE_DATA"
#echo " 0.000000 $BOXSIZE_X xlo xhi" >> "$OUT_FILE_DATA"
#echo " 0.000000 $BOXSIZE_Y ylo yhi" >> "$OUT_FILE_DATA"
#echo " 0.000000 $BOXSIZE_Z zlo zhi" >> "$OUT_FILE_DATA"
echo " $BOXSIZE_XY $BOXSIZE_XZ $BOXSIZE_YZ xy xz yz" >> "$OUT_FILE_DATA"
#echo "a,b,c,alpha,beta,gamma = $BOXSIZE_A,$BOXSIZE_B,$BOXSIZE_C,$ALPHA,$BETA,$GAMMA"
fi
echo "" >> "$OUT_FILE_DATA"
if [ -s "$data_header" ]; then
cat "$data_header" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_masses" ]; then
echo "Masses" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_masses" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
else
echo "WARNING: missing file \"$data_masses\"" >&2
fi
if [ -s "$data_pair_coeffs" ]; then
echo "Pair Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_pair_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
else
if [ ! -s "$in_settings" ] || (! grep -q pair_coeff "$in_settings"); then
echo "WARNING: no pair coeffs have been set!" >&2
fi
fi
if [ -s "$data_bond_coeffs" ]; then
echo "Bond Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_bond_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
else
if [ -n "$NBONDTYPES" ] && ( [ ! -s "$in_settings" ] || (! grep -q bond_coeff "$in_settings") ); then
echo "WARNING: no bond coeff have been set!" >&2
fi
fi
if [ -s "$data_angle_coeffs" ]; then
echo "Angle Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_angle_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
else
if [ -n "$NANGLETYPES" ] && ( [ ! -s "$in_settings" ] || (! grep -q angle_coeff "$in_settings") ); then
echo "WARNING: no angle coeffs have been set!" >&2
fi
fi
if [ -s "$data_dihedral_coeffs" ]; then
echo "Dihedral Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_dihedral_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
else
if [ -n "$NDIHEDRALTYPES" ] && ( [ ! -s "$in_settings" ] || (! grep -q dihedral_coeff "$in_settings") ); then
echo "WARNING: no dihedral coeffs have been set!" >&2
fi
fi
if [ -s "$data_improper_coeffs" ]; then
echo "Improper Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_improper_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
else
if [ -n "$NIMPROPERTYPES" ] && ( [ ! -s "$in_settings" ] || (! grep -q improper_coeff "$in_settings") ); then
echo "WARNING: no improper coeffs have been set!" >&2
fi
fi
# data file sections specific to class2 force-fields:
if [ -s "$data_bondbond_coeffs" ]; then
echo "BondBond Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_bondbond_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_bondangle_coeffs" ]; then
echo "BondAngle Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_bondangle_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_middlebondtorsion_coeffs" ]; then
echo "MiddleBondTorsion Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_middlebondtorsion_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_endbondtorsion_coeffs" ]; then
echo "EndBondTorsion Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_endbondtorsion_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_angletorsion_coeffs" ]; then
echo "AngleTorsion Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_angletorsion_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_angleangletorsion_coeffs" ]; then
echo "AngleAngleTorsion Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_angleangletorsion_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_bondbond13_coeffs" ]; then
echo "BondBond13 Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_bondbond13_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_angleangle_coeffs" ]; then
echo "AngleAngle Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_angleangle_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_atoms" ]; then
echo "Atoms" >> "$OUT_FILE_DATA"
if [ -s "$tmp_atom_coords" ]; then
echo "# (Note: x,y,z coordinates may overlap and can be modified later.)" >> "$OUT_FILE_DATA"
else
echo "" >> "$OUT_FILE_DATA"
fi
cat "$data_atoms" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
else
echo "WARNING: missing file \"$data_atoms\"" >&2
fi
if [ -s "$data_ellipsoids" ]; then
echo "Ellipsoids" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_ellipsoids" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_triangles" ]; then
echo "Triangles" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_triangles" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_lines" ]; then
echo "Lines" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_lines" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_velocities" ]; then
echo "Velocities" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_velocities" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
#else
# echo "Velocities" >> "$OUT_FILE_DATA"
# echo "" >> "$OUT_FILE_DATA"
# awk '{print $1 " 0.0 0.0 0.0"}' < "$data_atoms" >> "$OUT_FILE_DATA"
# echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_bonds" ]; then
echo "Bonds" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_bonds" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
#else
# echo "WARNING: missing file \"$data_bonds\"" >&2
fi
if [ -s "$data_angles" ]; then
echo "Angles" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_angles" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
#else
# echo "WARNING: missing file \"$data_angles\"" >&2
fi
if [ -s "$data_dihedrals" ]; then
echo "Dihedrals" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_dihedrals" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
#else
# echo "WARNING: missing file \"$data_dihedrals\"" >&2
fi
if [ -s "$data_impropers" ]; then
echo "Impropers" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_impropers" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
#else
# echo "WARNING: missing file \"$data_impropers\"" >&2
fi
rm -f $OUT_FILE_INPUT_SCRIPT
if [ -s "$in_init" ]; then
echo "" >> $OUT_FILE_INPUT_SCRIPT
cp -f "$in_init" $OUT_FILE_INIT
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "# ----------------- Init Section -----------------" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "include \"$OUT_FILE_INIT\"" >> $OUT_FILE_INPUT_SCRIPT
#echo "# \"$in_init\" typically contains various styles, dimensions, and units:" >> $OUT_FILE_INPUT_SCRIPT
#echo "include \"$in_init\"" >> $OUT_FILE_INPUT_SCRIPT
#cat "$in_init" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
fi
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "# ----------------- Atom Definition Section -----------------" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "read_data \"$OUT_FILE_DATA\"" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "# ----------------- Settings Section -----------------" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
if [ -s "$in_settings" ]; then
#echo "# \"$in_settings\" typically contains coeffs, fixes, groups & modify commands:" >> $OUT_FILE_INPUT_SCRIPT
#echo "include \"$in_settings\"" >> $OUT_FILE_INPUT_SCRIPT
#cat "$in_settings" >> $OUT_FILE_INPUT_SCRIPT
cp -f "$in_settings" $OUT_FILE_SETTINGS
echo "include \"$OUT_FILE_SETTINGS\"" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
fi
if [ -s "$tmp_atom_coords" ]; then
rm -f "$OUT_FILE_COORDS"
awk '{if (NF>=3) {natom++; print "set atom "natom" x "$1" y "$2" z "$3" image 0 0 0"}}' < "$tmp_atom_coords" >> "$OUT_FILE_COORDS"
echo "# Load the atom coordinates:" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "include \"$OUT_FILE_COORDS\"" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
NATOMS=`awk '/^\\\$\/atom:/{n++}END{print n}' < ttree_assignments.txt`
NATOMCRDS=`awk '{if (NF>=3) natom+=1} END{print(natom)}' < "$tmp_atom_coords"`
if [ $NATOMS -ne $NATOMCRDS ]; then
echo "Error: Number of atoms in coordinate file provided by user ($NATOMCRDS)" >&2
echo "does not match the number of atoms generated in ttree file ($NATOMS)" >&2
exit 14
fi
else
rm -f "$OUT_FILE_COORDS"
# echo "Warning: (moltemplate.sh)" >&2
# echo " Atomic coordinates were not supplied externally" >&2
# echo " (for example using the \"-pdb\" or \"-xyz\" arguments)." >&2
# echo " Hopefully you used rot(), trans() lttree commands to move" >&2
# echo " molecules to non-overlapping positions." >&2
fi
# ############## CLEAN UP ################
# A lot of files have been created along the way.
# However only a few of them are actually useful.
#
# Optional: clean up some non-essential temporary
# files created by running ttree
# We move the non-essential files into a different directory
# (but we don't delete them).
if [ ! -d output_ttree ]; then
mkdir output_ttree
fi
# Move temporary files into the "output_ttree/" directory:
OIFS=$IFS
#IFS=$'\n'
IFS="
"
for file in $MOLTEMPLATE_TEMP_FILES; do
#echo "file=\"$file\""
rm -f "output_ttree/$file" >/dev/null 2>&1 || true
mv "$file" output_ttree/ >/dev/null 2>&1 || true
done
IFS=$OIFS
# ############## DEAL WITH CUSTOM NON-STANDARD SECTIONS ################
N_data_prefix=`expr length "$data_prefix"`
ls "${data_prefix}"* 2> /dev/null | while read file_name; do
#If using bash:
#section_name="${file_name:$N_data_prefix}"
#If using sh:
section_name=`expr substr "$file_name" $(($N_data_prefix+1)) 1000000`
# Create a new section in the data file
# matching the portion of the name of
# the file after the data_prefix.
echo "" >> "$OUT_FILE_DATA"
echo "$section_name" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$file_name" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
mv -f "$file_name" output_ttree/
done
if [ -e "$data_prefix_no_space" ]; then
echo "" >> "$OUT_FILE_DATA"
cat "$data_prefix_no_space" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
mv -f "$data_prefix_no_space" output_ttree/
fi
N_in_prefix=`expr length "$in_prefix"`
ls "${in_prefix}"* 2> /dev/null | while read file_name; do
#If using bash:
#section_name="${file_name:$N_in_prefix}"
#If using sh:
section_name=`expr substr "$file_name" $(($N_in_prefix+1)) 1000000`
# Create a new section in the lammps input script
# matching the portion of the name of
# the file after the in_prefix.
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "# ----------------- $section_name Section -----------------" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
cat "$file_name" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
mv -f "$file_name" output_ttree/
done
if [ -e "$in_prefix_no_space" ]; then
echo "" >> $OUT_FILE_INPUT_SCRIPT
cat "$in_prefix_no_space" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
mv -f "$in_prefix_no_space" output_ttree/
fi
# Swap the order of atom types I, J in all "pair_coeff I J ..." commands
# whenever I > J. Do this for every input script file generated by moltemplate.
# (Perhaps later I'll check to make sure the user did not specify contradictory
# "pair_coeff I J ..." and "pair_coeff J I ..." commands, but I won't do it
# here, because at this point we've thrown away the original atom type names,
# so there's no easy way to explain the problem to the user if there is one.)
echo "" > input_scripts_so_far.tmp
for file_name in "$OUT_FILE_INIT" "$OUT_FILE_INPUT_SCRIPT" "$OUT_FILE_SETTINGS"; do
if [ -s "$file_name" ]; then
echo "postprocessing file \"$file_name\"" >&2
$PYTHON_COMMAND "${SCRIPT_DIR}/postprocess_input_script.py" input_scripts_so_far.tmp < "$file_name" > "$file_name".tmp
echo "" >&2
mv "$file_name".tmp "$file_name"
cat "$file_name" >> input_scripts_so_far.tmp
fi
done
ls "${in_prefix}"* 2> /dev/null | while read file_name; do
echo "postprocessing file \"$file_name\"" >&2
$PYTHON_COMMAND "${SCRIPT_DIR}/postprocess_input_script.py" input_scripts_so_far.tmp < "$file_name" > "$file_name".tmp
echo "" >&2
mv "$file_name".tmp "$file_name"
cat "$file_name" >> input_scripts_so_far.tmp
done
rm -f input_scripts_so_far.tmp
# ############ Optional: Add a fake run section as an example ############
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "# ----------------- Run Section -----------------" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "# The lines above define the system you want to simulate." >> $OUT_FILE_INPUT_SCRIPT
echo "# What you do next is up to you." >> $OUT_FILE_INPUT_SCRIPT
echo "# Typically a user would minimize and equilibrate" >> $OUT_FILE_INPUT_SCRIPT
echo "# the system using commands similar to the following:" >> $OUT_FILE_INPUT_SCRIPT
echo "# ---- examples ----" >> $OUT_FILE_INPUT_SCRIPT
echo "#" >> $OUT_FILE_INPUT_SCRIPT
echo "# -- minimize --" >> $OUT_FILE_INPUT_SCRIPT
echo "# minimize 1.0e-5 1.0e-7 1000 10000" >> $OUT_FILE_INPUT_SCRIPT
echo "# (Note: Some fixes, for example \"shake\", interfere with the minimize command," >> $OUT_FILE_INPUT_SCRIPT
echo "# You can use the \"unfix\" command to disable them before minimization.)" >> $OUT_FILE_INPUT_SCRIPT
echo "# -- declare time step for normal MD --" >> $OUT_FILE_INPUT_SCRIPT
echo "# timestep 1.0" >> $OUT_FILE_INPUT_SCRIPT
echo "# -- run at constant pressure (Nose-Hoover)--" >> $OUT_FILE_INPUT_SCRIPT
#echo "# timestep 1.0" >> $OUT_FILE_INPUT_SCRIPT
echo "# fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0">>$OUT_FILE_INPUT_SCRIPT
echo "# -- ALTERNATELY, run at constant volume (Nose-Hoover) --" >> $OUT_FILE_INPUT_SCRIPT
echo "# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1" >> $OUT_FILE_INPUT_SCRIPT
echo "# -- ALTERNATELY, run at constant volume using Langevin dynamics. --" >> $OUT_FILE_INPUT_SCRIPT
echo "# -- (This is good for sparse CG polymers in implicit solvent.) --" >> $OUT_FILE_INPUT_SCRIPT
echo "fix fxlan all langevin 300.0 300.0 5000 48279" >> $OUT_FILE_INPUT_SCRIPT
echo "# -- Now, finally run the simulation --" >> $OUT_FILE_INPUT_SCRIPT
echo "# run 50000" >> $OUT_FILE_INPUT_SCRIPT
#echo "# write_restart system_after_nvt.rst" >> $OUT_FILE_INPUT_SCRIPT
#echo "# run 50000" >> $OUT_FILE_INPUT_SCRIPT
#echo "# write_restart system_after_npt.rst" >> $OUT_FILE_INPUT_SCRIPT
echo "# ---- (end of examples) ----">> $OUT_FILE_INPUT_SCRIPT
#echo "# It is the responsibility of the user to learn LAMMPS and specify these">>$OUT_FILE_INPUT_SCRIPT
#echo "# these commands." >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
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