gmxcpi

#!/bin/bash

idx=""
jobid="${JOB_ID}"
jobidin=""
while getopts "i:j:k:h" opt; do
    case ${opt} in
        h)
            echo "Usage: $(basename $0) [-h] [-i index] [-j jobid] [-k jobid_in]"
            exit 0
            ;;
        i)
            idx="${OPTARG}"
            ;;
        j)
            jobid="${OPTARG}"
            ;;
        k)
            jobidin="${OPTARG}"
            ;;
        ?|*)
            echo "No such option available."
            ;;
    esac
done
echo "Idx = ${idx}"
pref="${idx:+${idx}_}"
suff="${jobid:+_${jobid}}"
suffin="${jobidin:+_${jobidin}}"

if [ -z "${pref}" ]; then
    echo "Must specify a step index"
    exit 127
fi

# Check for presence of all required files
if [ ! -f ${pref}topol.top ]; then
    echo "Missing ${pref}topol.top" >&2
    exit 126 # Unsigned byte => -1
else
    echo "Using topology file ${pref}topol.top" >&2
    file_top="${pref}topol.top"
fi
if [ ! -f ${pref}step.mdp ]; then
    echo "Missing ${pref}step.mdp" >&2
    exit 125 # Unsigned byte => -2
else
    echo "Using MD parameters in ${pref}step.mdp" >&2
    file_mdp="${pref}step.mdp"
fi
if [ ! -f ${pref}confout${suffin}.gro ]; then
    echo "Missing ${pref}confout${suffin}.gro" >&2
    echo "Checking to see if similar exist" >&2
    read -a files <<<$(ls -rt1 ./${pref}confout*.gro | xargs)
    if [ ${#files[@]} -gt 0 ]; then
        echo "Checking files found:" >&2
        for ((i=0;i<${#files[@]};i++))
        do
            echo "(${i}) ${files[i]}" >&2
        done
        echo "Using most recent: ${files[0]}" >&2
        echo -n "Okay? (y/N): "
        read ans
        if [ "${ans}" = "y" ] || [ "${ans}" = "Y" ]; then
            echo "Okay. Using GRO file ${files[0]}" >&2
            file_gro="${files[0]}"
        else
            if [[ ${ans} =~ ^[0-9]+$ ]]; then
                if [ ${ans} -ge ${#files[@]} ]; then
                    echo "Bad file index. Bye." >&2
                    exit 125
                else
                    echo "Using file ${ans}, ${files[${ans}]}"
                    file_gro="${files[${ans}]}"
                fi
            else
                echo "Cannot resolve which confin.gro to use" >&2
                exit 124 # Unsigned byte => -3
            fi
        fi
    else
        echo "Could not find any alternative matching files"
        exit 123 # Unsigned byte => -4
    fi
else
    file_gro="${pref}confout${suffin}.gro"
fi

if [ ! -f ${pref}traj${suffin}.trr ]; then
    echo "Missing ${pref}traj${suffin}.trr" >&2
    echo "Checking to see if similar exist" >&2
    read -a files <<<$(ls -rt1 ./${pref}traj*.trr | xargs)
    if [ ${#files[@]} -gt 0 ]; then
        echo "Checking files found:" >&2
        for ((i=0;i<${#files[@]};i++))
        do
            echo "(${i}) ${files[i]}" >&2
        done
        echo "Using most recent: ${files[0]}" >&2
        echo -n "Okay? (y/N): "
        read ans
        if [ "${ans}" = "y" ] || [ "${ans}" = "Y" ]; then
            echo "Okay. Using TRR file ${files[0]}" >&2
            file_trr="${files[0]}"
        else
            if [[ ${ans} =~ ^[0-9]+$ ]]; then
                if [ ${ans} -ge ${#files[@]} ]; then
                    echo "Bad file index. Bye." >&2
                    exit 125
                else
                    echo "Using file ${ans}, ${files[${ans}]}"
                    file_trr="${files[${ans}]}"
                fi
            else
                echo "Cannot resolve which traj.trr to use" >&2
                exit 124 # Unsigned byte => -3
            fi
        fi
    else
        echo "Could not find any alternative matching files"
        exit 123 # Unsigned byte => -4
    fi
else
    file_trr="${pref}traj${suffin}.trr"
fi

if [ ! -e "$((idx+1))_topol.top" ]; then
    echo "Copying ${file_top} => $((idx+1))_topol.top" >&2
    cp ${file_top} $((idx+1))_topol.top
else
    echo "File $((idx+1))_topol.top already exists" >&2
    echo -n "Overwrite? (y/N): " >&2
    read ans
    if [ "${ans}" = "y" ] || [ "${ans}" = "Y" ]; then
        cp ${file_top} $((idx+1))_topol.top
    else
        echo "Continuing with file already present" >&2
    fi
fi

if [ ! -e "$((idx+1))_step.mdp" ]; then
    echo "Copying ${file_mdp} => $((idx+1))_step.mdp" >&2
    cp ${file_mdp} $((idx+1))_step.mdp
else
    echo "File $((idx+1))_step.mdp already exists" >&2
    echo -n "Overwrite? (y/N): " >&2
    read ans
    if [ "${ans}" = "y" ] || [ "${ans}" = "Y" ]; then
        cp ${file_mdp} $((idx+1))_step.mdp
    else
        echo "Continuing with file already present" >&2
    fi
fi
cp ${file_mdp} $((idx+1))_step.mdp

if [ ! -e "$((idx+1))_confin.gro" ]; then
    echo "Linked ${file_gro} => $((idx+1))_confin.gro" >&2
    ln -s ${file_gro} $((idx+1))_confin.gro
else
    echo "Link already exists" >&2
    echo -n "Remove and relink? (y/N): "
    read ans
    if [ "${ans}" = "y" ] || [ "${ans}" = "Y" ]; then
        rm $((idx+1))_confin.gro
        ln -s ${file_gro} $((idx+1))_confin.gro
    else
        echo "Cannot continue without this link as input" >&2
        exit 122
    fi
fi

if [ ! -e "$((idx+1))_trajin.trr" ]; then
    echo "Linked ${file_trr} => $((idx+1))_trajin.trr" >&2
    ln -s ${file_trr} $((idx+1))_trajin.trr
else
    echo "Link already exists" >&2
    echo -n "Remove and relink? (y/N): "
    read ans
    if [ "${ans}" = "y" ] || [ "${ans}" = "Y" ]; then
        rm $((idx+1))_trajin.trr
        ln -s ${file_trr} $((idx+1))_trajin.trr
    else
        echo "Cannot continue without this link as input" >&2
        exit 122
    fi
fi

fntmpin="${pref}sge-mdrun"
echo -n "Copy and update submit scripts? (y/N): " >&2
read ans
if [ "${ans}" = "y" ] || [ "${ans}" = "Y" ]; then
    sed -r -e '/^#\$ \-N /s/'${idx}'/'$((idx+1))'/g' -e '/^[ \t]*idx="[^"]".*/s/'${idx}'/'$((idx+1))'/g' ${pref}sge-mdrun > .$((idx+1))_sge-mdrun.tmp
    fntmpin=".$((idx+1))_sge-mdrun.tmp"
fi

echo -n "Update parallel methodology for this run? (y/N): " >&2
read ans
if [ "${ans}" = "y" ] || [ "${ans}" = "Y" ]; then
    echo -n "Enter number of threads for thread MPI (0 for no tMPI): " >&2
    read ans
    if [ "${ans}" -gt 0 ]; then
        echo "Adding -nt ${ans} switch to EXENAME_MDRUN" >&2
        sed -r -e '/^[ \t]*EXENAME_MDRUN="\$\{MDRUN\} (-nt [0-9]+)?"/s/\$\{MDRUN\} (-nt [0-9]+)?/${MDRUN} -nt '${ans}'/g' ${fntmpin} > $((idx+1))_sge-mdrun
    else
        echo "Removing -nt switch from arguments" >&2
        sed -r -e '/^[ \t]*EXENAME_MDRUN="\$\{MDRUN\} (-nt [0-9]+)?"/s/\$\{MDRUN\} (-nt [0-9]+)?/${MDRUN} /g' ${fntmpin} > $((idx+1))_sge-mdrun
    fi
fi

if [ -f ".$((idx+1))_sge-mdrun.tmp" ]; then
    echo -n "Cleaning up temporary files... " >&2
    rm -rf ".$((idx+1))_sge-mdrun.tmp"
    echo "Done." >&2
fi

echo "Finished" >&2

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