Merge pull request #214 from mariavd/scripts-update

Scripts bug fixes
qmcurrents · Feb 13, 2019 · 554d8e6 · 554d8e6
2 parents 5b59069 + 4c59e96
commit 554d8e6
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Showing 4 changed files with 44 additions and 30 deletions.
diff --git a/jobscripts/src/crit_pts.sh.in b/jobscripts/src/crit_pts.sh.in
@@ -161,7 +161,7 @@ x0z=$(A2bohr ${crd0[2]})
 x1z=$(A2bohr ${crd1[2]})
 dz=$(awk -v z0=$x0z -v z1=$x1z 'BEGIN{dz = z0-z1; print dz;}')
 
-echo dz = $dz
+#echo dz = $dz
 
 length=$( echo $x0A $x1A | point_dist )
 length=$(A2bohr $length)

diff --git a/jobscripts/src/current-profile-header b/jobscripts/src/current-profile-header
@@ -30,6 +30,35 @@ function createInpTemplate()
     fi
 }
 
+function printSummary() {
+cat /dev/null > ./$dirname/calculation.dat
+echo atom1=$atom1  >> ./$dirname/calculation.dat
+echo atom2=$atom2 >> ./$dirname/calculation.dat
+echo distance=$distance >> ./$dirname/calculation.dat
+echo in=$start out=$out up=$up down=$down  >> ./$dirname/calculation.dat
+echo fixed point: Fx=$Fx Fy=$Fy Fz=$Fz  >> ./$dirname/calculation.dat
+echo delta=$delta nsteps=$nsteps >> ./$dirname/calculation.dat
+#echo spacing: spacingX=$spacingX spacingY=$spacingY spacingZ=$spacingZ  >> ./$dirname/calculation.dat
+echo spacing: spacingX=$spacingX spacingY=$spacingY  >> ./$dirname/calculation.dat
+echo magnetic field: MFx=$MFx MFy=$MFy MFz=$MFz  >> ./$dirname/calculation.dat
+echo rotation angles: rotX=$rotX rotY=$rotY rotZ=$rotZ >> ./$dirname/calculation.dat
+
+################################################################################
+
+printf "\n\n*****************************************************************************\n\nSUMMARY\n\n"
+printf "Bond: ["$bond"], distance = $distance\n\n"
+echo "Integration plane coordinates"
+printf "in = $start  out = $out  up = $up  down = $down \n"
+printf "Split into $nsteps slices with width $delta and grid spacing [$spacingX; $spacingY] \n"
+printf "Fixed coordinate: ( $Fx; $Fy; $Fz )\n"
+printf "Magnetic field direction: ( $MFx; $MFy; $MFz ) \n"
+printf "Rotation angles: ( $rotX; $rotY; $rotZ ) \n\n"
+
+printf "\n*****************************************************************************\n\n"
+}
+
+checkGimic 
+
 checkIfInputExists
 
 printf "\nSTARTING CURRENT PROFILE ANALYSIS\n"
@@ -312,31 +341,7 @@ then
     fi
 fi
 
-
-cat /dev/null > ./$dirname/calculation.dat
-echo atom1=$atom1  >> ./$dirname/calculation.dat
-echo atom2=$atom2 >> ./$dirname/calculation.dat
-echo distance=$distance >> ./$dirname/calculation.dat
-echo in=$start out=$out up=$up down=$down  >> ./$dirname/calculation.dat
-echo fixed point: Fx=$Fx Fy=$Fy Fz=$Fz  >> ./$dirname/calculation.dat
-echo delta=$delta nsteps=$nsteps >> ./$dirname/calculation.dat
-#echo spacing: spacingX=$spacingX spacingY=$spacingY spacingZ=$spacingZ  >> ./$dirname/calculation.dat
-echo spacing: spacingX=$spacingX spacingY=$spacingY  >> ./$dirname/calculation.dat
-echo magnetic field: MFx=$MFx MFy=$MFy MFz=$MFz  >> ./$dirname/calculation.dat
-echo rotation angles: rotX=$rotX rotY=$rotY rotZ=$rotZ >> ./$dirname/calculation.dat
-
-################################################################################
-
-printf "\n\n*****************************************************************************\n\nSUMMARY\n\n"
-printf "Bond: ["$bond"], distance = $distance\n\n"
-echo "Integration plane coordinates"
-printf "in = $start  out = $out  up = $up  down = $down \n"
-printf "Split into $nsteps slices with width $delta and grid spacing [$spacingX; $spacingY] \n"
-printf "Fixed coordinate: ( $Fx; $Fy; $Fz )\n"
-printf "Magnetic field direction: ( $MFx; $MFy; $MFz ) \n"
-printf "Rotation angles: ( $rotX; $rotY; $rotZ ) \n\n"
-
-printf "\n*****************************************************************************\n\n"
+printSummary # print to stdout and to calculation.dat
 
 
 # Preparing the input files
@@ -379,11 +384,9 @@ do
     # gimic.0.inp already exists; create gimic.$last.inp
     start_last=$( awk -v xstart=$xstart -v delta=$delta -v nsteps=$nsteps 'BEGIN{ last = xstart + delta*nsteps; print last }')
     checkIfEmpty start_last $start_last
-    echo "start_last = " $start_last
 
     end_last=$( awk -v start_last=$start_last -v delta=$delta 'BEGIN{ end = start_last + delta; print end }')
     checkIfEmpty xend_last $end_last
-    echo "end_last = " $end_last
 
     lstring="s/@up@/$up/; s/@down@/$down/; s/@start@/$start_last/; s/@end@/$end_last/"
     sed -e "$lstring" ./$dirname/gimic.Inp > ./$dirname/gimic.last.inp
@@ -404,7 +407,8 @@ do
 
     if  [ -z $accept ]
     then
-	echo "skipping further plane checks and dry runs"
+	echo "Skipping further plane checks and dry runs"
+	printSummary 
 	checkPlane=""
 	doDryRun=""
     elif [ $accept == "y" ]

diff --git a/jobscripts/src/functions-def b/jobscripts/src/functions-def
@@ -206,6 +206,11 @@ function checkIfPreviousCalculationExists() {
     }
 
 
+function checkGimic() {
+    command -v gimic >/dev/null 2>&1 || { echo >&2 "GIMIC not found. Load the module or check your \$PATH."; exit 1; }
+    }
+
+
 function calculateFixedCoord() {
     # calculate the rotation matrix for 2D rotation with respect to the z axis such that the rotation will be counterclockwise
     # multiply the vector originating at (0;0;A2z) and ending at the second atom with coords (A2x; A2y; A2z).
@@ -284,7 +289,7 @@ function planeSanityCheck() {
     #$last=$(  (cd ./$dirname/ && find . -maxdepth 1 -type f -name '*.inp' | wc -l ) )
     #$last=$(( $last -1 ))
     #$checkIfEmpty last $last 
-    (cd ./$dirname/ && gimic --dryrun gimic.last.inp > /dev/null )
+    (cd ./$dirname/ && gimic --dryrun gimic.last.inp > /dev/null && rm -rf gimic.last.inp )
 
     # take the coords of the end of the int plane
     grep X ./$dirname/grid.xyz  | awk '{ if (NR <=2) {print $0} }' >> ./$dirname/grid.check.xyz

diff --git a/jobscripts/src/jobscript.IN b/jobscripts/src/jobscript.IN
@@ -26,6 +26,11 @@ echo "SLURM_JOB_ID is" $SLURM_JOB_ID
 echo 
 echo "Current profile calculation"
 
+# parallelization is ensured in a poor man's way
+export OMP_NUM_THREADS=1 
+
+module load gimic
+
 wrkdir=$( echo $1 )
 checkIfEmpty wrkdir $wrkdir