Differences

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--- exercises:2016_summer_school:gga [2016/08/23 06:46] – created ibethune
+++ exercises:2016_summer_school:gga [2016/08/23 06:51] – ibethune
@@ Line 28: / Line 28: @@
 <code - job>
 #PBS -N mode1
+#PBS -l select=2
+#PBS -l walltime=0:20:0
+#PBS -A y14
 #PBS -j oe
-#PBS -q dist_small
-#PBS -l nodes=4:ppn=16
-#PBS -l walltime=10:00
-#PBS -A cp2k2015
 cd $PBS_O_WORKDIR
+module load cp2k
-module purge
+aprun -n 48 cp2k.popt -i mode1.inp -o mode1.out
-module load cp2k/2.6
-prun cp2k.popt -i mode1.inp -o mode1.out
 </code>
@@ Line 83: / Line 80: @@
 Create the .xyz files (check with vmd that they contain the right subsystems), and create mode1_dye.inp, mode1_slab.inp by changing both ''COORD_FILE_NAME'' and ''PROJECT'' accordingly.
-After computing these input files, we analyze the results using a tool provided with cp2k ''cubecruncher.x'' that manipulates cube files (e.g. can compute difference).
+After computing these input files, we analyze the results using a tool provided with cp2k ''cubecruncher.x'' that manipulates cube files (e.g. can compute difference).  To build cubecruncher, make a copy of the code in your own directory and compile it:
+<code>
+~$ module load cp2k
+~$ cp -r $CP2K/../../tools/cubecruncher .
+~$ cd cubecruncher
+~$ module swap PrgEnv-cray PrgEnv-gnu
+~$ make
+</code>
+Then run it as follows:
 <code>
 ~$ cubecruncher.x -i MODE1-ELECTRON_DENSITY-1_0.cube -subtract MODE1_dye-ELECTRON_DENSITY-1_0.cube -o tmp.cube