| 1 | #!@SHELL@
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| 2 | #
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| 3 | # Performs an molecular dynamics simulation with the BOSSANOVA method
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| 4 |
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| 5 | #MPIRUN="/opt/packages/mpichgm-1.2.7..15/bin/mpirun.ch_gm"
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| 6 | MPIRUN="/usr/bin/mpirun.mpich"
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| 7 | exec_prefix="@prefix@"
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| 8 | database="@bindir@"
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| 9 | MOLECUILDER="@bindir@/molecuilder"
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| 10 | JOINER="@bindir@/joiner"
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| 11 | CRUNCHER="/mount/bespin/heber/build/mpqc-2.3.0/bin/mpqc"
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| 12 | CONVERTER="/mount/bespin/heber/tmp/mpqc/espack2mpqc.sh"
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| 13 | PREPARER="/mount/bespin/heber/tmp/mpqc/convertresults.sh"
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| 14 |
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| 15 | . /mount/bespin/heber/scripts/check
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| 16 |
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| 17 | function RunSim {
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| 18 | # 1 is the config file
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| 19 | # 2 is the number of nodes
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| 20 | # 3 further command line option
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| 21 | # 4 and argument
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| 22 | # set the maximum number of nodes
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| 23 | MaxNodes=`cat $2 | awk 'END{print NR}'`
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| 24 | gamma=`grep ProcPEGamma $1 | awk -F"\t" {'print $2'}`
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| 25 | psi=`grep ProcPEPsi $1 | awk -F"\t" {'print $2'}`
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| 26 | let nodes=$gamma*$psi
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| 27 | if [ $nodes -gt $MaxNodes ]; then
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| 28 | echo "Process $1 needs too many nodes! Breaking." | tee -a dynamic.log
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| 29 | exit 1
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| 30 | fi
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| 31 | ${MPIRUN} -machinefile $2 -np $nodes ${CRUNCHER} $3 $4 $1 2>/dev/stdout 1>${1/in/out}
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| 32 | check | tee -a dynamic.log
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| 33 | }
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| 34 |
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| 35 | function MultiRunSim {
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| 36 | # 1 is config file
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| 37 | # 2 is the number of groups
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| 38 |
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| 39 | # find the next free proc group
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| 40 | DIR=`dirname $1`
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| 41 | started=0
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| 42 | while [ $started -eq 0 ]; do
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| 43 | groupnr=1
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| 44 | while [ $groupnr -le $2 ]; do
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| 45 | if [ ! -e "${DIR}/ProcRuns${groupnr}" ]; then
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| 46 | MaxNodes=`cat ${DIR}/ProcGroup${groupnr} | awk 'END{print NR}'`
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| 47 | gamma=`grep ProcPEGamma $1 | awk -F"\t" {'print $2'}`
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| 48 | psi=`grep ProcPEPsi $1 | awk -F"\t" {'print $2'}`
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| 49 | let nodes=$gamma*$psi
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| 50 | if [ $nodes -gt $MaxNodes ]; then
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| 51 | echo "Process $1 needs too many nodes! Breaking." | tee -a dynamic.log
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| 52 | exit 1
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| 53 | fi
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| 54 | echo "touch ${DIR}/ProcRuns${groupnr}" >"${DIR}/ProcBatch${groupnr}"
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| 55 | echo "#${MPIRUN} -machinefile ${DIR}/ProcGroup${groupnr} -np $nodes" >>"${DIR}/ProcBatch${groupnr}"
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| 56 | echo "${CRUNCHER} ${1/conf/in} 2>/dev/stdout 1>${1/conf/out}" >>"${DIR}/ProcBatch${groupnr}"
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| 57 | echo "rm -f ${DIR}/ProcRuns${groupnr}" >>"${DIR}/ProcBatch${groupnr}"
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| 58 | /bin/sh "${DIR}/ProcBatch${groupnr}" &
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| 59 | started=1
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| 60 | let groupnr=${2}+1
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| 61 | else
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| 62 | let groupnr=$groupnr+1
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| 63 | fi
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| 64 | done
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| 65 | # wait a few seconds
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| 66 | if [ $2 -gt 1 ]; then
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| 67 | sleep 2
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| 68 | fi
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| 69 | done
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| 70 | }
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| 71 |
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| 72 | # get command line options
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| 73 | if [ -z $4 ]; then
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| 74 | echo "Usage: $0 <config file> <Order> <max. bond distance> <MaxNodes> [MaxMDsteps]"
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| 75 | echo -e "\t<config file> the pcp config file of the total molecule"
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| 76 | echo -e "\t<Order> the highest bond order (i.e. the cutoff number in ANOVA series expansion)"
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| 77 | echo -e "\t<max. bond distance> maximum distance to look for bonds (bonds are associated by element covalent radii criterion)"
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| 78 | echo -e "\t<MaxNodes> number of nodes to use"
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| 79 | echo -e "\t[MaxMDSteps] overrides given MaxOuterStep in config file"
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| 80 | exit 1;
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| 81 | else
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| 82 | arg=$1
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| 83 | mainname=`grep mainname $arg | awk -F"\t" {'print $2'}`
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| 84 | order=$2
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| 85 | distance=$3
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| 86 | MaxNodes=$4
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| 87 | if [ -z $5 ]; then
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| 88 | MaxSteps=`grep MaxOuterStep $arg | awk -F"\t" {'print $2'}`
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| 89 | else
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| 90 | MaxSteps=$5
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| 91 | fi
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| 92 | echo "Going to run for a total of $MaxSteps steps, bond order $order and maximum distance $distance of config file $arg with a total of $MaxNodes nodes." | tee -a dynamic.log
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| 93 | fi
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| 94 |
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| 95 |
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| 96 | # get the directory
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| 97 | DIR=`dirname $arg`
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| 98 | if [ -z "`grep $DIR $arg`" ]; then
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| 99 | echo "Cannot find the directory $DIR in the config file." | tee -a dynamic.log
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| 100 | exit 1;
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| 101 | else
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| 102 | echo "Using $DIR as directory." | tee -a dynamic.log
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| 103 | fi
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| 104 |
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| 105 | PBS_NODEFILE="${DIR}/machines"
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| 106 | if [ ! -e $PBS_NODEFILE ]; then
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| 107 | echo "localhost" >$PBS_NODEFILE
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| 108 | fi
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| 109 |
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| 110 | # delete old processor group files
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| 111 | rm ${DIR}/ProcGroup* -f
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| 112 | rm ${DIR}/ProcRuns* -f
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| 113 | rm ${DIR}/ProcBatch* -f
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| 114 |
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| 115 | # put nodes into groups
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| 116 | gamma=`grep ProcPEGamma $arg | awk -F"\t" {'print $2'}`
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| 117 | psi=`grep ProcPEPsi $arg | awk -F"\t" {'print $2'}`
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| 118 | let nodes=$gamma*$psi
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| 119 | let divisor=$MaxNodes/$nodes
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| 120 | echo "Using $divisor processor groups." | tee -a dynamic.log
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| 121 | nodenr=0
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| 122 | groupnr=1
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| 123 | for node in `cat <$PBS_NODEFILE`; do
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| 124 | let nodenr=$nodenr+1
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| 125 | #echo "Current node $nodenr is $node." | tee -a dynamic.log
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| 126 | let currentgrouplimit=$groupnr*$nodes
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| 127 | if [ $currentgrouplimit -lt $nodenr ]; then
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| 128 | let groupnr=$groupnr+1
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| 129 | fi
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| 130 | #echo "Putting into group $groupnr." | tee -a dynamic.log
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| 131 | echo "$node" >>"${DIR}/ProcGroup${groupnr}"
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| 132 | done
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| 133 | i=0
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| 134 | while [ $i -lt $groupnr ]; do
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| 135 | let i=$i+1
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| 136 | echo "Group nr. $i" | tee -a dynamic.log
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| 137 | echo "===========" | tee -a dynamic.log
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| 138 | cat <"${DIR}/ProcGroup${i}"
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| 139 | cat <"${DIR}/ProcGroup${i}" >>dynamic.log
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| 140 | echo -e "\n" | tee -a dynamic.log
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| 141 | done
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| 142 |
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| 143 | # copy first conf
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| 144 | cp $arg ${arg}.MD
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| 145 |
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| 146 |
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| 147 | i=1;
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| 148 | while [ $i -le $MaxSteps ]; do
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| 149 | # break down the molecule with molecuilder
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| 150 | echo -n "Fragmenting ... " | tee -a dynamic.log
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| 151 | ${MOLECUILDER} ${arg}.MD -e ${database} -f $distance $order 2>/dev/null >/dev/null
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| 152 | check | tee -a dynamic.log
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| 153 | echo "done." | tee -a dynamic.log
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| 154 |
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| 155 | # get the number of digits of the fragment count
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| 156 | digits=1
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| 157 | while [ ! -e ${DIR}/BondFragment`printf "%0${digits}d" 0`.conf ]; do
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| 158 | let digits=$digits+1
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| 159 | done
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| 160 | echo "Found $digits digits for the fragment number." | tee -a dynamic.log
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| 161 |
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| 162 | # get the fragment count
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| 163 | frag=0
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| 164 | while [ -e ${DIR}/BondFragment`printf "%0${digits}d" $frag`.conf ]; do
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| 165 | # unset MaxOuterStep in config file
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| 166 | sed -i -e "s#MaxOuterStep.*\##MaxOuterStep\t0\t\##" ${DIR}/BondFragment`printf "%0${digits}d" $frag`.conf
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| 167 | rm -rf ${DIR}/BondFragment`printf "%0${digits}d" $frag`
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| 168 | let frag=$frag+1
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| 169 | done
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| 170 | echo "There are $frag fragments." | tee -a dynamic.log
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| 171 |
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| 172 | # evaluate each fragment
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| 173 | j=0;
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| 174 | while [ $j -lt $frag ]; do
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| 175 | number=`printf "%0${digits}d" $j`
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| 176 | # convert all configs
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| 177 | echo -n "Converting ${DIR}/BondFragment${number}.conf ..."
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| 178 | sh $CONVERTER ${DIR}/BondFragment${number}.conf
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| 179 | check | tee -a dynamic.log
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| 180 | # and evaluate
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| 181 | echo -n "Starting calculation of Fragment $number at step $i ... " | tee -a dynamic.log
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| 182 | MultiRunSim ${DIR}/BondFragment${number}.conf $divisor
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| 183 | echo "done." | tee -a dynamic.log
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| 184 | let j=$j+1
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| 185 | done
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| 186 |
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| 187 | # wait till all ProcRuns files are gone
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| 188 | if [ $divisor -gt 1 ]; then
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| 189 | echo "Waiting for all running jobs at step $i to end ... " | tee -a dynamic.log
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| 190 | while [ ! -z "${DIR}/ProcRuns*" ]; do
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| 191 | sleep 3
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| 192 | done
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| 193 | echo "done." | tee -a dynamic.log
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| 194 | fi
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| 195 |
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| 196 | # convert results
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| 197 | sleep 1 # necessary for result files to close
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| 198 | echo -n "Converting all results ... "
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| 199 | sh $PREPARER $DIR
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| 200 | check | tee -a dynamic.log
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| 201 |
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| 202 | # join the resulting forces into a single file
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| 203 | # cp ${DIR}/pcp.full.energy.all ${DIR}/pcp.energy.all
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| 204 | # cp ${DIR}/pcp.full.forces.all ${DIR}/pcp.forces.all
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| 205 | echo -n "Joining fragment energies ... " | tee -a dynamic.log
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| 206 | ${JOINER} ${DIR}/ $mainname >/dev/null 2>/dev/null
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| 207 | check | tee -a dynamic.log
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| 208 | echo "done." | tee -a dynamic.log
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| 209 |
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| 210 | # move the ions by calling pcp with this force file
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| 211 | sed -i -e "s#MaxOuterStep.*\##MaxOuterStep\t$i\t\##" ${arg}.MD
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| 212 | echo -n "Moving ions with obtained forces at step $i ... " | tee -a dynamic.log
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| 213 | $MOLECUILDER ${arg}.MD -e ${database} -P "${DIR}/pcp.Order${order}.forces.all" 2>/dev/null >/dev/null
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| 214 | echo "done" | tee -a dynamic.log
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| 215 |
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| 216 | # last of all, put "joined" energy and forces under this step
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| 217 | cp ${DIR}/pcp.Order${order}.energy.all ${DIR}/pcp.step${i}.energy.all
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| 218 | cp ${DIR}/pcp.Order${order}.forces.all ${DIR}/pcp.step${i}.forces.all
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| 219 |
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| 220 | # next step
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| 221 | let i=$i+1
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| 222 | done
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| 223 |
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| 224 | # draw densities of each step
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| 225 | #sed -e "s#DoOutVis.*\##DoOutVis\t2\t\##" ${arg}.MD.MD >${arg}.MD
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| 226 | #echo -n "Calling simulation to draw final densities of all steps ... " | tee -a dynamic.log
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| 227 | #RunSim ${arg}.MD $PBS_NODEFILE
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| 228 | #echo "done." | tee -a dynamic.log
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| 229 |
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| 230 | exit 0
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