| 1 | #!/bin/sh
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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 | MOLECUILDER="@bindir@/molecuilder"
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| 9 | JOINER="@bindir@/joiner"
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| 10 | PCP="@bindir@/pcp"
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| 11 |
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| 12 | function check {
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| 13 | if [ ! $? -eq 0 ]; then
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| 14 | echo "An error occured." | tee -a dynamic.log
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| 15 | exit 1;
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| 16 | fi
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| 17 | }
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| 18 |
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| 19 | function RunSim {
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| 20 | # 1 is the config file
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| 21 | # 2 is the number of nodes
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| 22 | # 3 further command line option
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| 23 | # 4 and argument
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| 24 | # set the maximum number of nodes
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| 25 | MaxNodes=`cat $2 | awk 'END{print NR}'`
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| 26 | gamma=`grep ProcPEGamma $1 | awk -F"\t" {'print $2'}`
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| 27 | psi=`grep ProcPEPsi $1 | awk -F"\t" {'print $2'}`
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| 28 | let nodes=$gamma*$psi
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| 29 | if [ $nodes -gt $MaxNodes ]; then
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| 30 | echo "Process $1 needs too many nodes! Breaking." | tee -a dynamic.log
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| 31 | exit 1
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| 32 | fi
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| 33 | ${MPIRUN} -machinefile $2 -np $nodes ${PCP} -a 86000 $3 $4 $1 2>/dev/null >/dev/null
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| 34 | check
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| 35 | }
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| 36 |
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| 37 | function MultiRunSim {
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| 38 | # 1 is config file
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| 39 | # 2 is the number of groups
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| 40 |
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| 41 | # find the next free proc group
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| 42 | DIR=`dirname $1`
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| 43 | started=0
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| 44 | while [ $started -eq 0 ]; do
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| 45 | groupnr=1
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| 46 | while [ $groupnr -le $2 ]; do
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| 47 | if [ ! -e "${DIR}/ProcRuns${groupnr}" ]; then
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| 48 | MaxNodes=`cat ${DIR}/ProcGroup${groupnr} | awk 'END{print NR}'`
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| 49 | gamma=`grep ProcPEGamma $1 | awk -F"\t" {'print $2'}`
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| 50 | psi=`grep ProcPEPsi $1 | awk -F"\t" {'print $2'}`
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| 51 | let nodes=$gamma*$psi
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| 52 | if [ $nodes -gt $MaxNodes ]; then
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| 53 | echo "Process $1 needs too many nodes! Breaking." | tee -a dynamic.log
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| 54 | exit 1
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| 55 | fi
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| 56 | echo "touch ${DIR}/ProcRuns${groupnr}" >"${DIR}/ProcBatch${groupnr}"
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| 57 | echo "${MPIRUN} -machinefile ${DIR}/ProcGroup${groupnr} -np $nodes ${PCP} -a 86000 $1 2>/dev/null >/dev/null" >>"${DIR}/ProcBatch${groupnr}"
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| 58 | echo "rm -f ${DIR}/ProcRuns${groupnr}" >>"${DIR}/ProcBatch${groupnr}"
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| 59 | /bin/sh "${DIR}/ProcBatch${groupnr}" &
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| 60 | started=1
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| 61 | let groupnr=${2}+1
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| 62 | else
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| 63 | let groupnr=$groupnr+1
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| 64 | fi
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| 65 | done
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| 66 | # wait a few seconds
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| 67 | sleep 5
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| 68 | done
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| 69 | }
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| 70 |
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| 71 | #PBS_NODEFILE="${DIR}/machines"
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| 72 |
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| 73 | # get command line options
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| 74 | if [ -z $4 ]; then
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| 75 | echo "Usage: $0 <config file> <Order> <max. bond distance> <MaxNodes> [MaxMDsteps]"
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| 76 | echo -e "\t<config file> the pcp config file of the total molecule"
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| 77 | echo -e "\t<Order> the highest bond order (i.e. the cutoff number in ANOVA series expansion)"
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| 78 | echo -e "\t<max. bond distance> maximum distance to look for bonds (bonds are associated by element covalent radii criterion)"
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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 |
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| 106 | # delete old processor group files
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| 107 | rm ${DIR}/ProcGroup* -f
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| 108 | rm ${DIR}/ProcRuns* -f
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| 109 | rm ${DIR}/ProcBatch* -f
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| 110 |
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| 111 | # put nodes into groups
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| 112 | gamma=`grep ProcPEGamma $arg | awk -F"\t" {'print $2'}`
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| 113 | psi=`grep ProcPEPsi $arg | awk -F"\t" {'print $2'}`
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| 114 | let nodes=$gamma*$psi
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| 115 | let divisor=$MaxNodes/$nodes
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| 116 | echo "Using $divisor processor groups." | tee -a dynamic.log
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| 117 | nodenr=0
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| 118 | groupnr=1
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| 119 | for node in `cat <$PBS_NODEFILE`; do
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| 120 | let nodenr=$nodenr+1
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| 121 | #echo "Current node $nodenr is $node." | tee -a dynamic.log
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| 122 | let currentgrouplimit=$groupnr*$nodes
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| 123 | if [ $currentgrouplimit -lt $nodenr ]; then
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| 124 | let groupnr=$groupnr+1
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| 125 | fi
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| 126 | #echo "Putting into group $groupnr." | tee -a dynamic.log
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| 127 | echo "$node" >>"${DIR}/ProcGroup${groupnr}"
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| 128 | done
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| 129 | i=0
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| 130 | while [ $i -lt $groupnr ]; do
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| 131 | let i=$i+1
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| 132 | echo "Group nr. $i" | tee -a dynamic.log
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| 133 | echo "===========" | tee -a dynamic.log
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| 134 | cat <"${DIR}/ProcGroup${i}"
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| 135 | cat <"${DIR}/ProcGroup${i}" >>dynamic.log
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| 136 | echo -e "\n" | tee -a dynamic.log
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| 137 | done
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| 138 |
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| 139 | # copy first conf
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| 140 | cp $arg ${arg}.MD
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| 141 | cp $arg ${arg}.MD.MD
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| 142 |
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| 143 | # create fake pcp.energy.all by parsing a bit of the config file
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| 144 | MaxLevel=`grep MaxLevel $arg | awk -F"\t" '{print $2'}`
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| 145 | echo -e "Time\tTotal\tKinetic\tNonLocal\tCorrelation\tExchange\tPseudo\tHartree\t-Gauss\tEwald\tIonKin\tETotal\t" >${DIR}/pcp.full.energy.all
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| 146 | j=0
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| 147 | while [ $j -lt $MaxLevel ]; do
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| 148 | let j=$j+1
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| 149 | i=0
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| 150 | while [ $i -lt 12 ]; do
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| 151 | let i=$i+1
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| 152 | printf "%e\t" 0 >>${DIR}/pcp.full.energy.all
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| 153 | done
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| 154 | echo -n -e "\n" >>${DIR}/pcp.full.energy.all
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| 155 | done
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| 156 | echo "$MaxLevel lines created in ${DIR}/pcp.full.energy.all."
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| 157 |
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| 158 | # create fake pcp.forces.all by parsing a bit of the config file
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| 159 | MaxTypes=`grep MaxTypes $arg | awk -F"\t" '{print $2'}`
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| 160 | MaxIons=0
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| 161 | i=0
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| 162 | echo -e "Type\tNo\tPos0\tPos1\tPos2\tTotal0\tTotal1\tTotal2\tLocal0\tLocal1\tLocal2\tNLocal0\tNLocal1\tNLocal2\tMagnetic0\tMagnetic1\tMagnetic2\tEwald0\tEwald1\tEwald2" >${DIR}/pcp.full.forces.all
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| 163 | while [ $i -lt $MaxTypes ]; do
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| 164 | let type=$i+1
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| 165 | j=`grep -E "^Ion_Type${type}[^_]+" $arg | awk -F"\t" '{print $2'}`
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| 166 | echo "Ion type ${type} has $j ions."
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| 167 | ionnr=0
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| 168 | while [ $ionnr -lt $j ]; do
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| 169 | echo -n -e "$i\t$ionnr\t" >>${DIR}/pcp.full.forces.all
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| 170 | k=0
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| 171 | while [ $k -lt 18 ]; do
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| 172 | printf "%e\t" 0 >>${DIR}/pcp.full.forces.all
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| 173 | let k=$k+1
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| 174 | done
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| 175 | echo -n -e "\n" >>${DIR}/pcp.full.forces.all
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| 176 | let ionnr=$ionnr+1
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| 177 | done
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| 178 | let MaxIons=$MaxIons+$j
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| 179 | let i=$i+1
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| 180 | done
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| 181 | echo -e "MeanForce:\t0." >>${DIR}/pcp.full.forces.all
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| 182 | echo "$MaxIons lines created in ${DIR}/pcp.full.forces.all."
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| 183 |
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| 184 | i=1;
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| 185 | while [ $i -le $MaxSteps ]; do
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| 186 | # break down the molecule with molecuilder
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| 187 | sed -i -e "s#MaxOuterStep.*\##MaxOuterStep\t0\t\##" $arg.MD.MD
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| 188 | echo -n "Fragmenting ... " | tee -a dynamic.log
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| 189 | PWD=`pwd`
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| 190 | cd `dirname ${MOLECUILDER}`
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| 191 | ./`basename ${MOLECUILDER}` ${arg}.MD.MD -f $distance $order A
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| 192 | check
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| 193 | cd $PWD
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| 194 | echo "done." | tee -a dynamic.log
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| 195 |
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| 196 | # get the number of digits of the fragment count
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| 197 | digits=1
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| 198 | while [ ! -e ${DIR}/BondFragment`printf "%0${digits}d" 0`.conf ]; do
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| 199 | let digits=$digits+1
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| 200 | done
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| 201 | echo "Found $digits digits for the fragment number." | tee -a dynamic.log
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| 202 |
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| 203 | # get the fragment count
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| 204 | frag=0
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| 205 | while [ -e ${DIR}/BondFragment`printf "%0${digits}d" $frag`.conf ]; do
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| 206 | # unset MaxOuterStep in config file
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| 207 | sed -i -e "s#MaxOuterStep.*\##MaxOuterStep\t0\t\##" ${DIR}/BondFragment`printf "%0${digits}d" $frag`.conf
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| 208 | mkdir -p ${DIR}/BondFragment`printf "%0${digits}d" $frag`
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| 209 | let frag=$frag+1
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| 210 | done
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| 211 | echo "There are $frag fragments." | tee -a dynamic.log
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| 212 |
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| 213 | # evaluate each fragment
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| 214 | j=0;
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| 215 | while [ $j -lt $frag ]; do
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| 216 | number=`printf "%0${digits}d" $j`
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| 217 | echo -n "Starting calculation of Fragment $number at step $i ... " | tee -a dynamic.log
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| 218 | MultiRunSim ${DIR}/BondFragment${number}.conf $divisor
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| 219 | echo "done." | tee -a dynamic.log
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| 220 | let j=$j+1
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| 221 | done
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| 222 |
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| 223 | # wait till all ProcRuns files are gone
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| 224 | echo "Waiting for all running jobs at step $i to end ... " | tee -a dynamic.log
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| 225 | while [ ! -z "`ls ${DIR}/ProcRuns*`" ]; do
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| 226 | sleep 15
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| 227 | done
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| 228 | echo "done." | tee -a dynamic.log
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| 229 |
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| 230 | # join the resulting forces into a single file
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| 231 | cp ${DIR}/pcp.full.energy.all ${DIR}/pcp.energy.all
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| 232 | cp ${DIR}/pcp.full.forces.all ${DIR}/pcp.forces.all
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| 233 | echo -n "Joining fragment energies ... " | tee -a dynamic.log
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| 234 | ${JOINER} ${DIR}/ $mainname >/dev/null 2>/dev/null
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| 235 | check
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| 236 | echo "done." | tee -a dynamic.log
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| 237 |
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| 238 | # move the ions by calling pcp with this force file
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| 239 | sed -e "s#MaxOuterStep.*\##MaxOuterStep\t$i\t\##" ${arg}.MD.MD >${arg}.MD
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| 240 | echo -n "Moving ions with obtained forces at step $i ... " | tee -a dynamic.log
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| 241 | RunSim ${arg}.MD $PBS_NODEFILE -F "${DIR}/pcp.Order${order}.forces.all"
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| 242 | echo "done" | tee -a dynamic.log
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| 243 |
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| 244 | # last of all, put "joined" energy and forces under this step
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| 245 | cp ${DIR}/pcp.Order${order}.energy.all ${DIR}/pcp.step${i}.energy.all
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| 246 | cp ${DIR}/pcp.Order${order}.forces.all ${DIR}/pcp.step${i}.forces.all
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| 247 |
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| 248 | # next step
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| 249 | let i=$i+1
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| 250 | done
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| 251 |
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| 252 | # draw densities of each step
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| 253 | sed -e "s#DoOutVis.*\##DoOutVis\t2\t\##" ${arg}.MD.MD >${arg}.MD
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| 254 | echo -n "Calling simulation to draw final densities of all steps ... " | tee -a dynamic.log
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| 255 | RunSim ${arg}.MD $PBS_NODEFILE
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| 256 | echo "done." | tee -a dynamic.log
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| 257 |
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| 258 | exit 0
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