adding in placentia files

clean.sh

@@ -0,0 +1,8 @@
+#!/bin/tcsh
+
+foreach machine (cl001 cl002 cl003 cl004 cl005 cl006)
+
+  echo $machine
+  ssh $machine /usr/local/bin/qclean-mx.sh
+
+end

convert_coor_TRAJEC.lithium-no_com.pwscf

@@ -0,0 +1,8 @@
+#!/bin/csh
+
+set acell=`grep celldm lithium.pw.inp | awk '{print $3}' | sed s/,//g`
+set natoms=`grep nat lithium.pw.inp | tail -1 | awk '{print $3}' | sed s/,//g`
+
+touch output/fake.out
+
+grep -A $natoms ATOMIC_POSITIONS output/*.out | awk '/Li/{print $2," ",$3," ",$4}' | sed s/"\-"/" \-"/g | awk -f ~/scripts/utils/convert_coor_TRAJEC.awk acell=$acell natoms=$natoms > TRAJEC.xyz

extract.sh

@@ -0,0 +1,3 @@
+#!/bin/csh
+
+grep -A 28 Summary output.log | grep "\." | awk '{print $2,$3 }' > energy.dat

form.ch

@@ -0,0 +1,8 @@
+#!/bin/tcsh
+
+set file=$1
+
+setenv g09root /usr/local/gaussian
+setenv GAUSS_SCRDIR /globalscratch/$USER/
+source /usr/local/gaussian/g09/bsd/g09.login
+formchk $file

gPressure.cpmd

@@ -0,0 +1,39 @@
+#!/bin/tcsh
+
+set timeStep = $1
+
+awk '/STRESS/{n+=1;a=0;getline;a=$1/10;getline;a+=$2/10;getline;a+=$3/10;print n "   "  a/3}'  STRESS > outPressure_GPa
+
+ln -s outPressure_GPa outPressure_GPa.250
+ln -s outPressure_GPa outPressure_GPa.500
+ln -s outPressure_GPa outPressure_GPa.1000
+
+~/scripts/utils/running-average.py outPressure_GPa.250 2 250 &
+~/scripts/utils/running-average.py outPressure_GPa.500 2 500 &
+~/scripts/utils/running-average.py outPressure_GPa.1000 2 1000 &
+
+wait
+
+set cmd="gnuplot.scr"
+cat > $cmd << END
+set data style linespoints
+set xlabel "Time (ps)"
+set ylabel "Pressure (GPa)"
+set yrange [*:*]
+set terminal png
+set output 'pressure.png'
+#plot "outPressure_GPa" u (\$1*$timeStep*2.4188E-17/1.0E-12):2 t "pressure (GPa)" with linespoints, "outPressure_GPa.250.running" u (\$1*$timeStep*2.4188E-17/1.0E-12):2 t "running pressure (GPa), 250 steps", "outPressure_GPa.500.running" u (\$1*$timeStep*2.4188E-17/1.0E-12):2 t "running pressure (GPa), 500 steps", "outPressure_GPa.1000.running" u (\$1*$timeStep*2.4188E-17/1.0E-12):2 t "running pressure (GPa), 1000 steps"
+set terminal x11
+#plot "outPressure_GPa" u (\$1*$timeStep*2.4188E-17/1.0E-12):2 t "pressure (GPa)" with linespoints, "outPressure_GPa.250.running" u (\$1*$timeStep*2.4188E-17/1.0E-12):2 t "running pressure (GPa), 250 steps", "outPressure_GPa.500.running" u (\$1*$timeStep*2.4188E-17/1.0E-12):2 t "running pressure (GPa), 500 steps", "outPressure_GPa.1000.running" u (\$1*$timeStep*2.4188E-17/1.0E-12):2 t "running pressure (GPa), 1000 steps"
+plot "outPressure_GPa" u (\$1*$timeStep*2.4188E-17/1.0E-12):2 t "pressure (GPa)" with linespoints, "outPressure_GPa.250.running" u (\$1*$timeStep*2.4188E-17/1.0E-12):2 t "running pressure (GPa), 250 steps"
+pause -1 "Showing pressure.\nPress enter to quit"
+quit
+END
+
+gnuplot $cmd
+
+\rm $cmd
+
+~/bin/blocker outPressure_GPa 2 | grep Final
+
+rm outPressure_GPa.*

getEnergy.py

@@ -0,0 +1,24 @@
+#!/usr/bin/python
+
+import sys, commands
+
+combined_energy = float(commands.getoutput('grep "Convergence criterion met" ../output.out | tail -1 ').split()[1])
+iso_counter = int(commands.getoutput('grep "Convergence criterion met" output.out | wc -l '))
+
+iso_energy_line = commands.getoutput('grep "Convergence criterion met" output.out').split()
+
+total = combined_energy
+
+
+
+iso_energy = []
+
+for i in range(iso_counter):
+
+    iso_energy.append(float(iso_energy_line[1 + i*6]))
+    total -= iso_energy[-1]
+
+print combined_energy, iso_energy
+print -total*627.509469
+
+

machinesfilescript/hostlist.out

@@ -0,0 +1,33 @@
+Warning: no access to tty; thus no job control in this shell...
+Sun Microsystems Inc.	SunOS 5.10	Generic	January 2005
+Thu Aug  9 20:49:27 NDT 2007
+PE_HOSTFILE is /var/spool/sge/cl012/active_jobs/88217.1/pe_hostfile and contains:
+-----------------------------
+cl012 16 all.q@cl012 <NULL>
+-----------------------------
+HOSTNAME is cl012
+NHOSTS is 1
+NSLOTS is 16
+TMPDIR is /tmp/88217.1.all.q
+JOB_ID is 88217
+SGE_O_WORKDIR is /home/itamblyn/machinesfilescript
+/tmp/88217.1.all.q/machines contains:
+-----------------------------
+cl012
+cl012
+cl012
+cl012
+cl012
+cl012
+cl012
+cl012
+cl012
+cl012
+cl012
+cl012
+cl012
+cl012
+cl012
+cl012
+-----------------------------
+logout

machinesfilescript/hostlist.sh

@@ -0,0 +1,25 @@
+#!/bin/sh
+#$ -S /bin/csh
+#$ -cwd
+#$ -N hostlist
+#$ -j y
+#$ -o hostlist.out
+#$ -pe openmp 16 
+#$ -l h_vmem=250M,h_rt=00:01:00
+date
+echo PE_HOSTFILE is $PE_HOSTFILE and contains:
+echo -----------------------------
+cat $PE_HOSTFILE
+echo -----------------------------
+echo HOSTNAME is $HOSTNAME
+echo NHOSTS   is $NHOSTS
+echo NSLOTS   is $NSLOTS
+echo TMPDIR   is $TMPDIR
+echo JOB_ID   is $JOB_ID
+echo SGE_O_WORKDIR is $SGE_O_WORKDIR
+# You might want to adjust this next path to your liking...
+$SGE_O_WORKDIR/startmpi.sh $PE_HOSTFILE
+echo $TMPDIR/machines contains:
+echo -----------------------------
+cat $TMPDIR/machines
+echo -----------------------------

machinesfilescript/startmpi.sh

@@ -0,0 +1,46 @@
+#!/bin/sh
+#
+# preparation of the mpi machine file
+#
+# usage: startmpi.sh <pe_hostfile>
+#
+
+PeHostfile2MachineFile()
+{
+   cat $1 | while read line; do
+      host=`echo $line|cut -f1 -d" "|cut -f1 -d"."`
+      nslots=`echo $line|cut -f2 -d" "`
+      i=1
+      while [ $i -le $nslots ]; do
+         echo $host
+         i=`expr $i + 1`
+      done
+   done
+}
+
+#
+# on success the job will find a machine-file in $TMPDIR/machines
+# 
+
+me=`basename $0`
+
+# test number of args
+if [ $# -ne 1 ]; then
+   echo "$me: got wrong number of arguments" >&2
+   exit 1
+fi
+
+# get arguments
+pe_hostfile=$1
+
+# ensure pe_hostfile is readable
+if [ ! -r $pe_hostfile ]; then
+   echo "$me: can't read $pe_hostfile" >&2
+   exit 1
+fi
+
+machines="$TMPDIR/machines"
+PeHostfile2MachineFile $pe_hostfile >> $machines
+
+# signal success to caller
+exit 0

monitor.sh

@@ -1,9 +1,8 @@
 #!/bin/tcsh
 
-foreach machine ( selenium tellurium beryllium carbon neon nitrogen fluorine oxygen )
+foreach machine (cl001 cl002 cl003 cl004 cl005 cl006)
 
-  echo -n $machine " "
-
-  ssh ${machine} top -b -n1 | awk '/load/{print $10, $11, $12, "(5 min)", $14, "(15 min)"}' | sed s/,//g 
+  echo $machine
+  ssh $machine /usr/local/bin/qclean-mx.sh
 
 end

myrinet

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+qstat -u \* -f  | awk '/cl00/{print $0} /cl010/{print $0} /cl011/{print $0} /cl012/{print $0}' | awk '/short/{print $1, $3, $4}' > out.tmp
+cat out.tmp
+echo
+echo -n "Total slots in use: "
+sed s/@/" "/g out.tmp | sed s/"\/"/" "/g | awk '{nslots+=$3; print nslots}' | tail -1
+echo -n "Open slots: "
+sed s/@/" "/g out.tmp | sed s/"\/"/" "/g | awk '{nslots+=$3; print 192 - nslots}' | tail -1
+rm out.tmp

pdos.py

@@ -0,0 +1,120 @@
+#!/usr/bin/env python
+
+import sys
+sys.path.append("/usr/local/numpy.1.0.4/lib64/python2.3/site-packages/")
+import numpy
+import commands
+
+try:
+    input_filename = sys.argv[1]
+except IndexError:
+    print '\nusage: ' + sys.argv[0] + ' input_filename'
+    print '\nexiting...\n'
+    sys.exit(0)
+
+core_valence_divide = 401 # <- this corresponds to -20 eV 
+
+command_line_counter = commands.getoutput('wc -l ' + input_filename).split()
+
+if len(command_line_counter) != 2:
+    print 'Error determining file size'
+else:
+    number_of_lines = int(command_line_counter[0])
+
+outputFile_dos = open('dos.dat', 'w')
+outputFile_pdos = open('pdos.dat', 'w')
+
+inputFile = open(input_filename, 'r')
+
+for i in range(5):
+    inputFile.readline()
+
+inline_total = inputFile.readline()
+
+emin_total = float(inline_total.split()[1])
+emax_total = float(inline_total.split()[0])
+enum_total = int(inline_total.split()[2])
+efermi_total = float(inline_total.split()[3])
+
+dos = numpy.zeros((enum_total, 3), dtype = numpy.float) # E, dos, idos
+
+for i in range(enum_total):
+    inline_total = inputFile.readline().split()
+    dos[i][0] = float(inline_total[0])  #- efermi_total 
+#    dos[i][0] = float(inline_total[0]) - efermi_total 
+    dos[i][1], dos[i][2] = float(inline_total[1]), float(inline_total[2])
+
+for row in dos:
+    for element in row:
+        outputFile_dos.write(str(element) + ' ')
+    outputFile_dos.write('\n')
+
+############
+
+inline_project = inputFile.readline()
+
+emin_project = float(inline_project.split()[1])
+enum_project = int(inline_project.split()[2])
+efermi_project = float(inline_project.split()[3])
+
+spacing = (emax_total - emin_total)/enum_total
+efermi_bin = int((efermi_total - emin_total)/spacing)
+
+pdos = numpy.zeros((enum_project, 1 + 3*2), dtype = numpy.float) # E, s, p, d
+
+for i in range(len(pdos)):
+
+   pdos[i][0] = dos[i][0]  # fills in the E column of pdos
+
+for i in range(enum_project):
+    inline_project = inputFile.readline().split()
+    pdos[i][1] += float(inline_project[1])
+    pdos[i][2] += float(inline_project[2])
+    pdos[i][3] += float(inline_project[3])
+
+for i in numpy.arange(1,enum_project):
+    pdos[i][4] = pdos[i - 1][4] + pdos[i][1]
+    pdos[i][5] = pdos[i - 1][5] + pdos[i][2]
+    pdos[i][6] = pdos[i - 1][6] + pdos[i][3]
+
+
+energies  = numpy.transpose(pdos)[0]
+s_project = numpy.transpose(pdos)[1]
+p_project = numpy.transpose(pdos)[2]
+d_project = numpy.transpose(pdos)[3]
+
+energies_core  =  energies[0:core_valence_divide]
+s_project_core = s_project[0:core_valence_divide]
+p_project_core = p_project[0:core_valence_divide]
+d_project_core = d_project[0:core_valence_divide]
+
+
+energies_valence  =  energies[core_valence_divide:efermi_bin]
+s_project_valence = s_project[core_valence_divide:efermi_bin]
+p_project_valence = p_project[core_valence_divide:efermi_bin]
+d_project_valence = d_project[core_valence_divide:efermi_bin]
+
+spd_sum_core    = sum(s_project_core)    + sum(p_project_core)    + sum(d_project_core)
+spd_sum_valence = sum(s_project_valence) + sum(p_project_valence) + sum(d_project_valence)
+
+s_fraction_core = sum(s_project_core)/spd_sum_core
+p_fraction_core = sum(p_project_core)/spd_sum_core
+
+s_fraction_valence = sum(s_project_valence)/spd_sum_valence
+p_fraction_valence = sum(p_project_valence)/spd_sum_valence
+
+print
+print "%s core", s_fraction_core*100
+print "%p core", p_fraction_core*100
+print
+print "%s valence", s_fraction_valence*100
+print "%p valence", p_fraction_valence*100
+print
+print "efermi_total = ", efermi_total
+print "spacing = ", spacing
+print
+
+for row in pdos:
+    for element in row:
+        outputFile_pdos.write(str(element) + ' ')
+    outputFile_pdos.write('\n')