#!/usr/bin/env bash
# (note: Classic Bourne shell (#!/bin/sh) also worked at some point.)
#
# Author: Andrew Jewett (jewett.aij at g mail)
#         http://www.moltemplate.org
#         http://jensenlab.caltech.edu
#         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="2.3.7"
G_DATE="2017-8-22"

echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2
echo "" >&2

# Check for python:
# I prefer python over python3 because python3 requires slightly
# more memory.  Use regular python (ie 2.7) 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 the python scripts are located.
# (such as ttree.py).  It could either be the directory where the script
# file is located, OR it could be the parent of this directory.
PY_SCR_DIR=`dirname "$0"`
if [ ! -s "${PY_SCR_DIR}/ttree.py" ]; then
    PY_SCR_DIR="$PY_SCR_DIR/.."
fi


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
dump2data.py
raw2data.py
EOF
)



OIFS=$IFS
#IFS=$'\n'
IFS="
"

for f in $MOLTEMPLATE_FILES_NEEDED; do
    if [ ! -s "${PY_SCR_DIR}/$f" ]; then
        echo "Error: Missing file \"${PY_SCR_DIR}/$f\"" >&2
        ERR_BAD_INSTALL
    fi
done
IFS=$OIFS

# command that invokes lttree.py
LTTREE_COMMAND="$PYTHON_COMMAND \"${PY_SCR_DIR}/lttree.py\""

# command that invokes lttree_check.py
LTTREE_CHECK_COMMAND="$PYTHON_COMMAND \"${PY_SCR_DIR}/lttree_check.py\""

# command that invokes lttree_postprocess.py
LTTREE_POSTPROCESS_COMMAND="$PYTHON_COMMAND \"${PY_SCR_DIR}/lttree_postprocess.py\""


# -----------------------------------------------------------
# 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_bond_list="Data Bond List"
data_bonds_atomid_atomid="Data Bonds AtomId AtomId"
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"
data_pairij_coeffs="Data PairIJ Coeffs"

# interactions-by-type (not id. This is not part of the LAMMPS standard.)
data_charge_by_bond="Data Charge By Bond"
data_bonds_by_type="Data Bonds By Type"
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"
in_charges="In Charges"

#     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_pairij_coeffs
$data_bond_coeffs
$data_angle_coeffs
$data_dihedral_coeffs
$data_improper_coeffs
$data_atoms
$data_velocities
$data_bonds
$data_bond_list
$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_header
$data_bonds_by_type*
${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.

-checkff       This cause moltemplate.sh to check to make sure that there
               are valid angle and dihedral interactions defined for every
               3 or 4 consecutively bonded atoms in the system
               (defined in "Angles/Dihedrals By Type").

-overlay-angles     Normally, moltemplate.sh checks to see if multiple angle
-overlay-dihedrals  interactions are defined for the same triplet of atoms.
-overlay-impropers  If so, it deletes the redundant ones (keeping the last one).
-overlay-bonds     (It does the same thing for bonds, dihedrals, and impropers.)
                    Use these options to prevent that behavoir.

-angle-symmetry file.py     Normally moltemplate.sh reorders the atoms in each
-dihedral-symmetry file.py  angle, dihedral, improper, and bond interaction.
-improper-symmetry file.py  TO TURN OFF ATOM REORDERING, SET file.py to "NONE"
-bond-symmetry file.py      You can override the rules that moltemplate.sh uses
                            by supplying a file (file.py) with symmetry rules.
                            See nbody_Dihedrals.py, nbody_Impropers.py (in the
                            moltemplate directory) to learn the file format.

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=""
LT_FILE=""
OUT_FILE_BASE="system"
# 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"
CHECKFF=""
RUN_VMD_AT_END=""


ARGC=0
for A in "$@"; do
    A_FIRSTCHAR="$(echo $A| cut -c 1)"
    # (Note to self: this next line only works in bash, not classic sh.)
    if [ "$A_FIRSTCHAR" = "\$" ]; then
        A="\\$A" # put an extra slash in front to prevent expansion later
    fi

    ARGC=$((ARGC+1))
    eval ARGV${ARGC}=\"$A\"
done

TTREE_ARGS=""
ATOM_STYLE="full"
ATOM_STYLE_ARG="-atomstyle \"$ATOM_STYLE\""

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" = "-checkff" ]; then
        # Disable syntax checking by undefining LTTREE_CHECK_COMMAND
        CHECKFF="$A"
    elif [ "$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-dihedrals" ]; 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" = "-vmd" ]; then
        RUN_VMD_AT_END="true"
    elif [ "$A" = "-raw" ]; then
        if [ "$i" -eq "$ARGC" ]; then
            echo "$SYNTAX_MSG" >&2
            exit 7
        fi
        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 [ "$A" = "-bond-symmetry" ]; then
        # Change the atom ordering rules in a 2-body bonded interaction:
        if [ "$i" -eq "$ARGC" ]; then
            echo "$SYNTAX_MSG" >&2
            exit 7
        fi
        i=$((i+1))
        eval A=\${ARGV${i}}
	if [ "$A" = "NONE" ]; then
            SUBGRAPH_SCRIPT_BONDS="bonds_nosym.py"
	else
            SUBGRAPH_SCRIPT_BONDS=$A
	fi

    elif [ "$A" = "-angle-symmetry" ]; then
        # Change the atom ordering rules in a 3-body "angle" interaction:
        if [ "$i" -eq "$ARGC" ]; then
            echo "$SYNTAX_MSG" >&2
            exit 7
        fi
        i=$((i+1))
        eval A=\${ARGV${i}}
	if [ "$A" = "NONE" ]; then
            SUBGRAPH_SCRIPT_ANGLES="angles_nosym.py"
	else
            SUBGRAPH_SCRIPT_ANGLES=$A
	fi

    elif [ "$A" = "-dihedral-symmetry" ]; then
        # Change the atom ordering rules in a 4-body "dihedral" interaction:
        if [ "$i" -eq "$ARGC" ]; then
            echo "$SYNTAX_MSG" >&2
            exit 7
        fi
        i=$((i+1))
        eval A=\${ARGV${i}}
	if [ "$A" = "NONE" ]; then
            SUBGRAPH_SCRIPT_DIHEDRALS="dihedrals_nosym.py"
	else
            SUBGRAPH_SCRIPT_DIHEDRALS=$A
	fi

    elif [ "$A" = "-improper-symmetry" ]; then
        # Change the atom ordering rules in a 4-body "improper" interaction:
        if [ "$i" -eq "$ARGC" ]; then
            echo "$SYNTAX_MSG" >&2
            exit 7
        fi
        i=$((i+1))
        eval A=\${ARGV${i}}
	if [ "$A" = "NONE" ]; then
            SUBGRAPH_SCRIPT_IMPROPERS="impropers_nosym.py"
	else
            SUBGRAPH_SCRIPT_IMPROPERS=$A
	fi

    elif [ "$A" = "-xyz" ]; then
        if [ "$i" -eq "$ARGC" ]; then
            echo "$SYNTAX_MSG" >&2
            exit 7
        fi
        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

        # "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

        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 ! $PYTHON_COMMAND "${PY_SCR_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

    elif [ "$A" = "-atomstyle" ] || [ "$A" = "-atom-style" ] || [ "$A" = "-atom_style" ]; then
        if [ "$i" -eq "$ARGC" ]; then
            echo "$SYNTAX_MSG" >&2
            exit 7
        fi
        i=$((i+1))
        eval A=\${ARGV${i}}
        if [ -z "$A" ]; then
            echo "$SYNTAX_MSG" >&2
            echo "-----------------------" >&2
            echo "" >&2
            echo "Error: The \"-atomstyle\" argument should be followed by an atom style." >&2
            echo "       (See the \"atom_style\" command in the LAMMPS documentation." >&2
            echo "        Note: hybrid atom styles are allowed but should be enclosed in quotes.)" >&2
            exit 8
        fi

        #echo "  (atom_style=\"$A\")" >&2
        #echo "" >&2

        ATOM_STYLE="$A"
        ATOM_STYLE_ARG="-atomstyle \"$A\""

        # (minor detail: $ATOM_STYLE_ARG should also be appended to TTREE_ARGS)
        if [ -z "$TTREE_ARGS" ]; then
            TTREE_ARGS="$ATOM_STYLE_ARG"
        else
            TTREE_ARGS="${TTREE_ARGS} $ATOM_STYLE_ARG"
        fi


    #else:  If the arguments are not understood in this script, then
    #       pass them on to "lttree.py"
    else
        A_FIRSTCHAR="$(echo $A| cut -c 1)"

        if [ "$A_FIRSTCHAR" = "\$" ]; then
            A="\\$A" # put an extra slash in front to prevent expansion later
        fi

        if [ -z "$TTREE_ARGS" ]; then
            TTREE_ARGS="\"$A\""
        else
            TTREE_ARGS="${TTREE_ARGS} \"$A\""
        fi
        # Check to see if this string ($A) ends in .lt or .LT
        # If so, then set the base name of the output files
        # to equal the base name of the .LT file being read.
        # (Being careful here.
        #  Sometimes the last argument is not the .lt or .LT file.
        #  Sometimes that file appears earlier in the argument list.
        #  I want to supply a default value.)
        #
        #   Note, in bash you can use:
        # if [ "${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:

        if [ "$A_FIRSTCHAR" != "-" ]; then
            DN=`dirname "$A"`
            if [ "$DN" = "." ]; then
                DN=""
            else
                DN="${DN}/"
            fi

            BN=`basename "$A" .lt`
            if [ "${DN}${BN}" != "$A" ]; then
                OUT_FILE_BASE="$BN"
            else
                BN=`basename "$A" .LT`
                if [ "${DN}${BN}" != "$A" ]; then
                    OUT_FILE_BASE="$BN"
                fi
            fi
        fi
    fi
done


if [ -z "$ATOM_STYLE" ]; then
  #echo '########################################################' >&2
  #echo '##            WARNING: atom_style unspecified         ##' >&2
  #echo '##              Assuming atom_style = \"full\"          ##' >&2
  #echo '########################################################' >&2
  ATOM_STYLE="full"
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"





# --------------------------------------------------------------------
# --- 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





# Now count the number of atom-types, bond-types, angle-types, etc...

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`

if [ -z "$NATOMTYPES" ]; then
    # Moltemplate can be used as a simple hierarchical template renderer
    # that knows nothing about LAMMPS.  In that case NATOMTYPES is undefined.
    # In that case, terminate now and do not try to interpret the files.
    exit 0
fi





# Attempt to remove any the DOS return-cairrage characters
# from inside the standard LAMMPS files generated by the user:
# (Users are free to put whatever weird characters they want in other
#  (custom) auxilliary files.  But not in the standard LAMMPS files.)
OIFS=$IFS
#IFS=$'\n'
IFS="
"
for file in $MOLTEMPLATE_TEMP_FILES; do
    if [ -e "$file" ]; then
        #dos2unix < "$file" > "$file.dos2unix"
        tr -d '\r' < "$file" > "$file.dos2unix"
        rm -f "$file" >/dev/null 2>&1 || true
	mv -f "$file.dos2unix" "$file"
    fi
done
IFS=$OIFS


if [ -s "${data_atoms}" ]; then
    if ! $PYTHON_COMMAND "${PY_SCR_DIR}/remove_duplicate_atoms.py" \
                                   < "${data_atoms}" \
                                   > "${data_atoms}.tmp"; then
        ERR_INTERNAL
    fi
    mv -f "${data_atoms}.tmp" "${data_atoms}"
    if ! $PYTHON_COMMAND "${PY_SCR_DIR}/remove_duplicate_atoms.py" \
                                   < "${data_atoms}.template" \
                                   > "${data_atoms}.tmp"; then
        ERR_INTERNAL
    fi
    mv -f "${data_atoms}.tmp" "${data_atoms}.template"

    if ! $PYTHON_COMMAND "${PY_SCR_DIR}/renumber_DATA_first_column.py" \
                                       < "${data_atoms}" \
                                       > "${data_atoms}.tmp"; then
        ERR_INTERNAL
    fi
    mv -f "${data_atoms}.tmp" "${data_atoms}"
else
    if [ -n "$NATOMTYPES" ]; then
	echo "Error: There are no atoms in your system. Suggestions:" >&2
	echo "" >&2
	echo "       Make sure that you have the correct number of curly parenthesis {}." >&2
	echo "       (Extra \"}\" parenthesis can cause this error.)" >&2
	echo "" >&2
	echo "       Your files must contain at least one" >&2
	echo "           write(\"${data_atoms}\")" >&2
	echo "       command.  These commands are typically located somewhere in" >&2
	echo "       one of the molecule object(s) you have defined." >&2
	echo "" >&2
	echo "       This error often occurs if your input files lack \"new\" commands." >&2
	echo "       Once you have defined a type of molecule, you must create a copy" >&2
	echo "       of it using \"new\", if you want it to appear in your simulation." >&2
	echo "       See the moltemplate manual or online tutorials for examples." >&2
	echo "" >&2
	echo "       (This error also occurs if you instantiated an object using \"new\"" >&2
	echo "       which you thought was a molecule, but it is actually only a" >&2
	echo "       namespace, a force-field name or category containing only the" >&2
	echo "       definitions of other molecules, lacking any atoms of its own.)" >&2
	echo "" >&2
	exit 200
    fi
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_bond_list}.template" ]; then

    if [ ! -s "$data_bonds_by_type" ]; then
        echo "Error: You have a \"Data Bond List\", section somewhere"
        echo "       without a \"Data Bonds By Type\" section to support it."
        echo "       (Did you mean to use \"Data Bonds\" instead?)"
        echo "Details:"
        echo "       Unlike the \"Data Bonds\" section, the \"Data Bond List\" section"
        echo "       allows the user to omit the bond types.  Instead moltemplate attempts"
        echo "       to infer the type of bond by considering the pair of atom types."
        echo "       However you must define a \"Data Bonds By Type\" section"
        echo "       to make this feature work (or use \"Data Bonds\" instead)."

        exit 15
    fi
    echo "Looking up bond types according to atom type" >&2
    #-- Generate a file containing bondid bondtype atomid1 atomid2 --
    if ! $PYTHON_COMMAND "${PY_SCR_DIR}/bonds_by_type.py" \
            -atom-style "$ATOM_STYLE" \
            -atoms "${data_atoms}.template" \
            -bond-list "${data_bond_list}.template" \
            -bondsbytype "${data_bonds_by_type}.template" \
            -prefix '$/bond:bytype' > gen_bonds.template.tmp; then
        exit 4
    fi

    # ---- cleanup: ----
    # ---- Create or re-build the "${data_bonds}.template" file ----
    # Instert these lines into the "${data_bonds}.template" file which includes
    # the newly generated interactions. (Note: these are in .template format)

    cp gen_bonds.template.tmp new_bonds.template.tmp
    if [ -s "${data_bonds}.template" ]; then
        # Then append existing "Bonds" to the end of the generated interactions
        # (Hopefully this way they will override those interactions.)
        cat "${data_bonds}.template" >> new_bonds.template.tmp
    fi
    mv -f new_bonds.template.tmp "${data_bonds}.template"



    #  ------  THE NEXT STEP IS NOT CURRENTLY NEEDED ------
    # All of the $bond variables have already been created, they just lack types
    # However we will need to do this if the user wants to omits the bond-ids.
    # In case I plan to allow the user to omit bond-ids, I leave this code here.
    #
    #echo "(Repairing ttree_assignments.txt file after bonds 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 ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_fix_ttree_assignments.py" \
    #      '/bond' gen_bonds.template.tmp \
    #      < ttree_assignments.txt \
    #      > ttree_assignments.tmp; then
    #    exit 5
    #fi
    #
    #echo "(Rendering ttree_assignments.tmp file after bonds added.)" >&2
    #mv -f ttree_assignments.tmp ttree_assignments.txt
    #  ----------------------------------------------------



    # ---- Re-build (render) the "$data_bonds" 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 ! $PYTHON_COMMAND "${PY_SCR_DIR}/ttree_render.py" \
           ttree_assignments.txt \
           < "${data_bonds}.template" \
           > "$data_bonds"; then
        exit 6
    fi

    echo "" >&2

    rm -f gen_bonds.template.tmp new_bonds.template.tmp

    echo "" >&2

fi











#for FILE in "$data_angles_by_type"*.template; do
IFS_BACKUP="$IFS"
IFS=$(echo -en "\n\b")
for FILE in `ls -v "$data_angles_by_type"*.template`; do

    if [ ! -s "$FILE" ] || [ ! -s "$data_bonds" ]; then
        break;  # This handles with the special cases that occur when
                # 1) There are no bonds in your system
                # 2) "$data_angles_by_type"*.template matches nothing
    fi

    echo "Generating 3-body angle interactions by atom/bond type" >&2

    # Extract the text between parenthesis (if present, empty-str otherwise)
    # Example: FILE="Data Angles By Type (gaff_angle.py)"
    SUBGRAPH_SCRIPT=`echo "$FILE" | awk '/\(.*\)/ {print $0}' | cut -d'(' -f2-| cut -d')' -f 1`
    # Example: (continued) SUBGRAPH_SCRIPT should equal "gaff_angle.py"

    # The user can also override this choice:
    if [ -n "$SUBGRAPH_SCRIPT_ANGLES" ]; then
        SUBGRAPH_SCRIPT="$SUBGRAPH_SCRIPT_ANGLES"
    elif [ -n "$SUBGRAPH_SCRIPT" ]; then
        SUBGRAPH_SCRIPT_ANGLES="$SUBGRAPH_SCRIPT"
    fi

    if [ -z "$SUBGRAPH_SCRIPT" ]; then
        SUBGRAPH_SCRIPT="nbody_Angles.py"
    else
        echo "(using the rules in \"$SUBGRAPH_SCRIPT\")" >&2
        # if [ ! -s "${PY_SCR_DIR}/nbody_alt_symmetry/$SUBGRAPH_SCRIPT" ]; then
        #     echo "Error: File \"$SUBGRAPH_SCRIPT\" not found." >&2
	    #     echo "       It should be located in this directory:" >&2
        #     echo "       ${PY_SCR_DIR}/nbody_alt_symmetry/" >&2
        #     exit 4
        # fi
    fi

    #-- Generate a file containing the list of interactions on separate lines --
    if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_by_type.py" \
            -subgraph "${SUBGRAPH_SCRIPT}" \
            -section "Angles" \
            -sectionbytype "Angles By Type" \
            -atom-style "$ATOM_STYLE" \
            -atoms "${data_atoms}.template" \
            -bonds "${data_bonds}.template" \
            -nbodybytype "${FILE}" \
	    $CHECKFF \
            -prefix '$/angle:bytype' > gen_angles.template.tmp; then
        exit 4
    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 ! $PYTHON_COMMAND "${PY_SCR_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 ! $PYTHON_COMMAND "${PY_SCR_DIR}/ttree_render.py" \
           ttree_assignments.tmp \
           < "${data_angles}.template" \
           > "$data_angles"; then
        exit 6
    fi
    echo "" >&2

    mv -f ttree_assignments.tmp ttree_assignments.txt
    rm -f gen_angles.template.tmp new_angles.template.tmp
done
IFS="$IFS_BACKUP"






FILE_dihedrals_by_type1=""
FILE_dihedrals_by_type2=""
#for FILE in "$data_dihedrals_by_type"*.template; do
IFS_BACKUP="$IFS"
IFS=$(echo -en "\n\b")
for FILE in `ls -v "$data_dihedrals_by_type"*.template`; do

    if [ ! -s "$FILE" ] || [ ! -s "$data_bonds" ]; then
        break;  # This handles with the special cases that occur when
                # 1) There are no bonds in your system
                # 2) "$data_dihedrals_by_type"*.template matches nothing
    fi

    echo "Generating 4-body dihedral interactions by atom/bond type" >&2

    # Extract the text between parenthesis (if present, empty-str otherwise)
    # Example: FILE="Data Dihedrals By Type (gaff_dih.py)"
    SUBGRAPH_SCRIPT=`echo "$FILE" | awk '/\(.*\)/ {print $0}' | cut -d'(' -f2-| cut -d')' -f 1`
    # Example: (continued) SUBGRAPH_SCRIPT should equal "gaff_dih.py"

    # The user can also override this choice:
    if [ -n "$SUBGRAPH_SCRIPT_DIHEDRALS" ]; then
        SUBGRAPH_SCRIPT="$SUBGRAPH_SCRIPT_DIHEDRALS"
    elif [ -n "$SUBGRAPH_SCRIPT" ]; then
        SUBGRAPH_SCRIPT_DIHEDRALS="$SUBGRAPH_SCRIPT"
    fi

    if [ -z "$SUBGRAPH_SCRIPT" ]; then
        SUBGRAPH_SCRIPT="nbody_Dihedrals.py"
    else
        echo "(using the rules in \"$SUBGRAPH_SCRIPT\")" >&2
        # if [ ! -s "${PY_SCR_DIR}/nbody_alt_symmetry/$SUBGRAPH_SCRIPT" ]; then
        #     echo "Error: File \"$SUBGRAPH_SCRIPT\" not found." >&2
	    # echo "       It should be located in this directory:" >&2
        #     echo "       ${PY_SCR_DIR}/nbody_alt_symmetry/" >&2
        #     exit 4
        # fi
    fi

    FILE_dihedrals_by_type2="$FILE_impropers_by_type1"
    FILE_dihedrals_by_type1="$FILE"

    #-- Generate a file containing the list of interactions on separate lines --
    if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_by_type.py" \
            -subgraph "${SUBGRAPH_SCRIPT}" \
            -section "Dihedrals" \
            -sectionbytype "Dihedrals By Type" \
            -atom-style "$ATOM_STYLE" \
            -atoms "${data_atoms}.template" \
            -bonds "${data_bonds}.template" \
            -nbodybytype "${FILE}" \
	    $CHECKFF \
            -prefix '$/dihedral:bytype' > gen_dihedrals.template.tmp; then
        exit 4
    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 ! $PYTHON_COMMAND "${PY_SCR_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 ! $PYTHON_COMMAND "${PY_SCR_DIR}/ttree_render.py" \
           ttree_assignments.tmp \
           < "${data_dihedrals}.template" \
           > "$data_dihedrals"; then
        exit 6
    fi
    echo "" >&2

    mv -f ttree_assignments.tmp ttree_assignments.txt
    rm -f gen_dihedrals.template.tmp new_dihedrals.template.tmp
done
IFS="$IFS_BACKUP"





FILE_impropers_by_type1=""
FILE_impropers_by_type2=""
#for FILE in "$data_impropers_by_type"*.template; do
IFS_BACKUP="$IFS"
IFS=$(echo -en "\n\b")
for FILE in `ls -v "$data_impropers_by_type"*.template`; do

    if [ ! -s "$FILE" ] || [ ! -s "$data_bonds" ]; then
        break;  # This handles with the special cases that occur when
                # 1) There are no bonds in your system
                # 2) "$data_impropers_by_type"*.template matches nothing
    fi

    echo "Generating 4-body improper interactions by atom/bond type" >&2

    # Extract the text between parenthesis (if present, empty-str otherwise)
    # Example: FILE="Data Impropers By Type (gaff_impr.py)"
    SUBGRAPH_SCRIPT=`echo "$FILE" | awk '/\(.*\)/ {print $0}' | cut -d'(' -f2-| cut -d')' -f 1`
    # Example: (continued) SUBGRAPH_SCRIPT should equal "gaff_impr.py"

    # The user can also override this choice:
    if [ -n "$SUBGRAPH_SCRIPT_IMPROPERS" ]; then
        SUBGRAPH_SCRIPT="$SUBGRAPH_SCRIPT_IMPROPERS"
    elif [ -n "$SUBGRAPH_SCRIPT" ]; then
        SUBGRAPH_SCRIPT_IMPROPERS="$SUBGRAPH_SCRIPT"
    fi

    if [ -z "$SUBGRAPH_SCRIPT" ]; then
        SUBGRAPH_SCRIPT="nbody_Impropers.py"
    else
        echo "(using the rules in \"$SUBGRAPH_SCRIPT\")" >&2
        # if [ ! -s "${PY_SCR_DIR}/nbody_alt_symmetry/$SUBGRAPH_SCRIPT" ]; then
        #     echo "Error: File \"$SUBGRAPH_SCRIPT\" not found." >&2
	    # echo "       It should be located in this directory:" >&2
        #     echo "       ${PY_SCR_DIR}/nbody_alt_symmetry/" >&2
        #     exit 4
        # fi
    fi

    FILE_impropers_by_type2="$FILE_impropers_by_type1"
    FILE_impropers_by_type1="$FILE"

    #-- Generate a file containing the list of interactions on separate lines --
    if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_by_type.py" \
            -subgraph "${SUBGRAPH_SCRIPT}" \
            -section "Impropers" \
            -sectionbytype "Impropers By Type" \
            -atom-style "$ATOM_STYLE" \
            -atoms "${data_atoms}.template" \
            -bonds "${data_bonds}.template" \
            -nbodybytype "${FILE}" \
            -prefix '$/improper:bytype' > gen_impropers.template.tmp; then
        exit 4
    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 ! $PYTHON_COMMAND "${PY_SCR_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 ! $PYTHON_COMMAND "${PY_SCR_DIR}/ttree_render.py" \
           ttree_assignments.tmp \
           < "${data_impropers}.template" \
           > "$data_impropers"; then
        exit 6
    fi
    echo "" >&2

    mv -f ttree_assignments.tmp ttree_assignments.txt
    rm -f gen_impropers.template.tmp new_impropers.template.tmp
done
IFS="$IFS_BACKUP"







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 ! $PYTHON_COMMAND "${PY_SCR_DIR}/remove_duplicate_atoms.py" \
                                   < "${data_masses}" \
                                   > "${data_masses}.tmp"; then
        ERR_INTERNAL
    fi
    mv -f "${data_masses}.tmp" "${data_masses}"
fi


if [ -s "${data_bonds}" ]; then
    SUBGRAPH_SCRIPT="nbody_Bonds.py"
    if [ -n "$SUBGRAPH_SCRIPT_BONDS" ]; then
	SUBGRAPH_SCRIPT="$SUBGRAPH_SCRIPT_BONDS"
    fi
    if [ ! -z $REMOVE_DUPLICATE_BONDS ]; then
        if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_reorder_atoms.py" \
                             Bonds \
	                     "$SUBGRAPH_SCRIPT" \
                             < "${data_bonds}" \
                             > "${data_bonds}.tmp"; then
            ERR_INTERNAL
        fi
        cp -f "${data_bonds}.tmp" "${data_bonds}"
        if ! $PYTHON_COMMAND "${PY_SCR_DIR}/remove_duplicates_nbody.py" 2 \
                             < "${data_bonds}" \
                             > "${data_bonds}.tmp"; then
            ERR_INTERNAL
        fi
        mv "${data_bonds}.tmp" "${data_bonds}"
        if ! $PYTHON_COMMAND "${PY_SCR_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 ! $PYTHON_COMMAND "${PY_SCR_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 "${data_angles}" ]; then
    SUBGRAPH_SCRIPT="nbody_Angles.py"
    if [ -n "$SUBGRAPH_SCRIPT_ANGLES" ]; then
	SUBGRAPH_SCRIPT="$SUBGRAPH_SCRIPT_ANGLES"
    fi
    if [ ! -z $REMOVE_DUPLICATE_ANGLES ]; then
        if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_reorder_atoms.py" \
                             Angles \
	                     "$SUBGRAPH_SCRIPT" \
                             < "${data_angles}" \
                             > "${data_angles}.tmp"; then
            ERR_INTERNAL
        fi
        cp -f "${data_angles}.tmp" "${data_angles}"
        if ! $PYTHON_COMMAND "${PY_SCR_DIR}/remove_duplicates_nbody.py" 3 \
                             < "${data_angles}" \
                             > "${data_angles}.tmp"; then
            ERR_INTERNAL
        fi
        mv "${data_angles}.tmp" "${data_angles}"
        if ! $PYTHON_COMMAND "${PY_SCR_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 ! $PYTHON_COMMAND "${PY_SCR_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 "${data_dihedrals}" ]; then
    SUBGRAPH_SCRIPT="nbody_Dihedrals.py"
    if [ -n "$SUBGRAPH_SCRIPT_DIHEDRALS" ]; then
	SUBGRAPH_SCRIPT="$SUBGRAPH_SCRIPT_DIHEDRALS"
    fi
    if [ ! -z $REMOVE_DUPLICATE_DIHEDRALS ]; then
        if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_reorder_atoms.py" \
                             Dihedrals \
	                     "$SUBGRAPH_SCRIPT" \
                             < "${data_dihedrals}" \
                             > "${data_dihedrals}.tmp"; then
            ERR_INTERNAL
        fi
        cp -f "${data_dihedrals}.tmp" "${data_dihedrals}"
        if ! $PYTHON_COMMAND "${PY_SCR_DIR}/remove_duplicates_nbody.py" 4 \
                             < "${data_dihedrals}" \
                             > "${data_dihedrals}.tmp"; then
            ERR_INTERNAL
        fi
        mv "${data_dihedrals}.tmp" "${data_dihedrals}"
        if ! $PYTHON_COMMAND "${PY_SCR_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 ! $PYTHON_COMMAND "${PY_SCR_DIR}/renumber_DATA_first_column.py" \
                         < "${data_dihedrals}" \
                         > "${data_dihedrals}.tmp"; then
        ERR_INTERNAL
    fi
    mv -f "${data_dihedrals}.tmp" "${data_dihedrals}"

    if  [ ! -z $FILE_dihedrals_by_type2 ]; then
	MSG_MULTIPLE_DIHEDRAL_RULES=$(cat <<EOF
#############################################################################
WARNING:
  It appears as though multiple conflicting rules were used to generate
DIHEDRAL interactions.  (This can occur when combining molecules built with
different force-field rules).  In your case, you are using rules defined here:
   "$FILE_dihedrals_by_type2"
   "$FILE_dihedrals_by_type1"
   (Files ending in .py are located here:
    $PY_SCR_DIR/nbody_alt_symmetry/)
If the molecules built using these two different force-field settings are not
connected, AND if you do NOT override force-field dihedrals with explicitly
defined dihedrals, then you can probably ignore this warning message.  Otherwise
please check the list of dihedral interactions to make sure they are correct!
(It might help to build a much smaller system using the same molecule types.)
#############################################################################

EOF
)
	echo "$MSG_MULTIPLE_DIHEDRAL_RULES" >&2
    fi
fi


if [ -s "${data_impropers}" ]; then
    SUBGRAPH_SCRIPT="nbody_Impropers.py"
    if [ -n "$SUBGRAPH_SCRIPT_IMPROPERS" ]; then
	SUBGRAPH_SCRIPT="$SUBGRAPH_SCRIPT_IMPROPERS"
    fi
    if [ ! -z $REMOVE_DUPLICATE_IMPROPERS ]; then
        if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_reorder_atoms.py" \
                             Impropers \
	                     "$SUBGRAPH_SCRIPT" \
                             < "${data_impropers}" \
                             > "${data_impropers}.tmp"; then
            ERR_INTERNAL
        fi
        cp -f "${data_impropers}.tmp" "${data_impropers}"
        if ! $PYTHON_COMMAND "${PY_SCR_DIR}/remove_duplicates_nbody.py" 4 \
                             < "${data_impropers}" \
                             > "${data_impropers}.tmp"; then
            ERR_INTERNAL
        fi
        mv "${data_impropers}.tmp" "${data_impropers}"
        if ! $PYTHON_COMMAND "${PY_SCR_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 ! $PYTHON_COMMAND "${PY_SCR_DIR}/renumber_DATA_first_column.py" \
                         < "${data_impropers}" \
                         > "${data_impropers}.tmp"; then
        ERR_INTERNAL
    fi
    mv -f "${data_impropers}.tmp" "${data_impropers}"

    if  [ ! -z $FILE_impropers_by_type2 ]; then
	MSG_MULTIPLE_IMPROPER_RULES=$(cat <<EOF
#############################################################################
WARNING:
  It appears as though multiple conflicting rules were used to generate
IMPROPER interactions.  (This can occur when combining molecules built with
different force-field rules.)  In your case, you are using rules defined here:
   "$FILE_impropers_by_type2"
   "$FILE_impropers_by_type1"
   (Files ending in .py are located here:
    $PY_SCR_DIR/nbody_alt_symmetry/)
If the molecules built using these two different force-field settings are not
connected, AND if you do NOT override force-field imrpopers with explicitly
defined impropers, then you can probably ignore this warning message.  Otherwise
please check the list of improper interactions to make sure they are correct!
(It might help to build a much smaller system using the same molecule types.)
#############################################################################

EOF
)
	echo "$MSG_MULTIPLE_IMPROPER_RULES" >&2
    fi

fi






# ------------------ Charge By Bond ----------------------
# Assign atom partial charges according to who they are bonded to

if [ -s "$data_charge_by_bond" ]; then
    echo "Looking up partial charge contributions from bonds" >&2
    if ! $PYTHON_COMMAND "${PY_SCR_DIR}/charge_by_bond.py" \
         -atom-style "$ATOM_STYLE" \
         -atoms "${data_atoms}.template" \
         -bonds "${data_bonds}.template" \
         -bond-list "${data_bond_list}.template" \
         -chargebybond "${data_charge_by_bond}.template" \
         > gen_charges.template.tmp; then
        exit 4
    fi

    # ---- cleanup: ----
    # ---- Create or re-build the "${in_charges}.template" file ----
    # Instert these lines into the "${in_charges}.template" file which includes
    # the newly generated interactions. (Note: these are in .template format)

    cp gen_charges.template.tmp new_charges.template.tmp
    if [ -s "${in_charges}.template" ]; then
        # Then append existing "Bonds" to the end of the generated interactions
        # (Hopefully this way they will override those interactions.)
        cat "${in_charges}.template" >> new_charges.template.tmp
    fi
    mv -f new_charges.template.tmp "${in_charges}.template"

    # ---- Re-build (render) the "$in_charges" 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 ! $PYTHON_COMMAND "${PY_SCR_DIR}/ttree_render.py" \
         ttree_assignments.txt \
         < "${in_charges}.template" \
         >> "${in_charges}"; then
        exit 6
    fi
    echo "" >&2

    rm -f gen_charges.template.tmp new_charges.template.tmp

    echo "" >&2
fi




# -------------------------------------------------------

rm -f "$OUT_FILE_DATA"

#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


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"




if [ -s "$data_header" ]; then
  cat "$data_header" >> "$OUT_FILE_DATA"
  echo "" >> "$OUT_FILE_DATA"
fi




# --- 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=`tr -d '\015' < "$data_boundary" | awk '{if ($3=="xlo") {xlo=$1}} END{print xlo}'`
    BOXSIZE_MAXX=`tr -d '\015' < "$data_boundary" | awk '{if ($4=="xhi") {xhi=$2}} END{print xhi}'`

    BOXSIZE_MINY=`tr -d '\015' < "$data_boundary" | awk '{if ($3=="ylo") {ylo=$1}} END{print ylo}'`
    BOXSIZE_MAXY=`tr -d '\015' < "$data_boundary" | awk '{if ($4=="yhi") {yhi=$2}} END{print yhi}'`

    BOXSIZE_MINZ=`tr -d '\015' < "$data_boundary" | awk '{if ($3=="zlo") {zlo=$1}} END{print zlo}'`
    BOXSIZE_MAXZ=`tr -d '\015' < "$data_boundary" | awk '{if ($4=="zhi") {zhi=$2}} END{print zhi}'`

    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 "$data_masses" ]; then
    echo "Masses" >> "$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"
    PAIR_COEFFS_IN_DATA="true"
fi
if [ -s "$data_pairij_coeffs" ]; then
    echo "PairIJ Coeffs" >> "$OUT_FILE_DATA"
    echo "" >> "$OUT_FILE_DATA"
    cat "$data_pairij_coeffs" >> "$OUT_FILE_DATA"
    echo "" >> "$OUT_FILE_DATA"
    PAIR_COEFFS_IN_DATA="true"
fi
if [ -n "$PAIR_COEFFS_IN_DATA" ]; then
    if [ ! -s "$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 "$data_atoms" ]; then
    if [ -n "$ATOM_STYLE" ]; then
	echo "Atoms # $ATOM_STYLE" >> "$OUT_FILE_DATA"
    else
	echo "Atoms # full" >> "$OUT_FILE_DATA"
    fi
    #if [ -s "$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
    echo "" >> "$OUT_FILE_DATA"
    cat "$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

    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

    # Copy the coordinates in $tmp_atom_coords into $OUT_FILE_DATA
    rm -f "$OUT_FILE_COORDS"
    if ! eval $PYTHON_COMMAND "${PY_SCR_DIR}/raw2data.py" $ATOM_STYLE_ARG "$OUT_FILE_DATA" < "$tmp_atom_coords" > "$OUT_FILE_COORDS"; then
        ERR_INTERNAL
    fi
    mv -f "$OUT_FILE_COORDS" "$OUT_FILE_DATA"
    echo "copied atomic coordinates into $OUT_FILE_DATA"

    # Previously, in earlier versions of moltemplate, we used to
    # create a new input script containing "set" commands which the
    # user was supposed to tell LAMMPS to read using an "include" command.
    # If for some reason, you want to go back to doing it that way, then
    # uncomment the following 6 lines:
    #
    #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

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="
"
rm -f ttree_replacements.txt >/dev/null 2>&1 || true
for file in $MOLTEMPLATE_TEMP_FILES; do
    if [ -e "$file" ]; then
        rm -f "output_ttree/$file" >/dev/null 2>&1 || true
        #echo "file=\"$file\""
        mv "$file" output_ttree/ >/dev/null 2>&1 || true
    fi
done
IFS=$OIFS





# ############## DEAL WITH CUSTOM NON-STANDARD SECTIONS ################


# N_data_prefix=`expr length "$data_prefix"` <-- not posix compliant. AVOID
N_data_prefix=${#data_prefix}  #<-- works even if $data_prefix contains spaces
ls "${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` <-- not posix compliant. AVOID
    SECTION_NAME=`echo "" | awk "END{print 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



if [ -e "$OUT_FILE_DATA" ]; then
    mv -f "$OUT_FILE_DATA" "$OUT_FILE_DATA.tmp" >/dev/null 2>&1 || true
    #dos2unix < "$OUT_FILE_DATA.tmp" > "$OUT_FILE_DATA"
    tr -d '\r' < "$OUT_FILE_DATA.tmp" > "$OUT_FILE_DATA"
    rm -f "$OUT_FILE_DATA.tmp" >/dev/null 2>&1 || true
fi


#N_in_prefix=`expr length "$in_prefix"` <-- not posix compliant. AVOID.
N_in_prefix=${#in_prefix}  #<-- works even if $in_prefix contains spaces
ls "${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` <-- not posix compliant. AVOID
    SECTION_NAME=`echo "" | awk "END{print substr(\"$file_name\",$((N_in_prefix+1)),1000000)}"`
    FILE_SUFFIX=`echo "$SECTION_NAME" | awk '{print tolower($0)}'`
    # 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 -----------------" >> $OUT_FILE_INPUT_SCRIPT
    cp -f "$file_name" ${OUT_FILE_INPUT_SCRIPT}.${FILE_SUFFIX}

    echo "" >> $OUT_FILE_INPUT_SCRIPT
    echo "include \"${OUT_FILE_INPUT_SCRIPT}.${FILE_SUFFIX}\"" >> $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
        if ! $PYTHON_COMMAND "${PY_SCR_DIR}/postprocess_input_script.py" input_scripts_so_far.tmp < "$file_name" > "$file_name.tmp"; then
            ERR_INTERNAL
        fi
        echo "" >&2
        mv -f "$file_name.tmp" "$file_name"
        #cat "$file_name" >> input_scripts_so_far.tmp
        #dos2unix < "$file_name" >> input_scripts_so_far.tmp
        tr -d '\r' < "$file_name" >> input_scripts_so_far.tmp

        # Delete all "bond_style" statements when no bond types are defined
        if [ -z "$NBONDTYPES" ]; then
            awk '{if ($1!="bond_style") print $0}' < "$file_name" > "${file_name}.tmp"
            mv -f "$file_name.tmp" "$file_name"
        fi
        # Delete all "angle_style" statements when no angle types are defined
        if [ -z "$NANGLETYPES" ]; then
            awk '{if ($1!="angle_style") print $0}' < "$file_name" > "${file_name}.tmp"
            mv -f "$file_name.tmp" "$file_name"
        fi
        # Delete all "dihedral_style" statements when no dihedral types are defined
        if [ -z "$NDIHEDRALTYPES" ]; then
            awk '{if ($1!="dihedral_style") print $0}' < "$file_name" > "${file_name}.tmp"
            mv -f "$file_name.tmp" "$file_name"
        fi
        # Delete all "improper_style" statements when no improper types are defined
        if [ -z "$NIMPROPERTYPES" ]; then
            awk '{if ($1!="improper_style") print $0}' < "$file_name" > "${file_name}.tmp"
            mv -f "$file_name.tmp" "$file_name"
        fi
    fi
done


ls "${in_prefix}"* 2> /dev/null | while read file_name; do
    echo "postprocessing file \"$file_name\"" >&2
    if ! $PYTHON_COMMAND "${PY_SCR_DIR}/postprocess_input_script.py" input_scripts_so_far.tmp < "$file_name" > "$file_name".tmp; then
        ERR_INTERNAL
    fi
    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 "# fix fxNVE all nve  #(<--needed by fix langevin)" >> $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



# Finally, if the -vmd argument was included, start up VMD and
# view the system (using topotools to convert the

if [ ! -z $RUN_VMD_AT_END ]; then

    echo "topo readlammpsdata $OUT_FILE_DATA $ATOM_STYLE" > vmd_viz_moltemplate.tcl.tmp
    bn=`basename $OUT_FILE_DATA .data`
    echo "animate write psf $bn.psf" >> vmd_viz_moltemplate.tcl.tmp
    vmd -e vmd_viz_moltemplate.tcl.tmp
    rm -rf vmd_viz_moltemplate.tcl.tmp

fi
