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--- exercises:2016_uzh_cmest:first_simulation_run [2016/09/22 14:43] – [Computation of the Lennard Jones curve] tmueller
+++ exercises:2016_uzh_cmest:first_simulation_run [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 7: / Line 7: @@
 To get you started, we will do a simple exercise using Molecular Mechanics (that is: a classical approach). The point is to get familiar with the options, organizing and editing the input file and analyze the output.
 ====== Computation of the Lennard Jones curve ======
@@ Line 103: / Line 104: @@
   **** **  *******  **  PROGRAM STARTED IN          /data/students/studentXX/ex1
 [...]
-  ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.):           0.003617048870059
+  ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.):          -0.000518941408898
 [...]
@@ Line 250: / Line 251: @@
 Plot again the energy curve.
+====== Tips & Tricks ======
+===== Parsing the output =====
+Many times you will have to get some value out of a simulation output, in this case, the energy.
+This can achieved in a number of ways:
+  * Using the ''grep'' command:<code>
+$ grep "Total FORCE_EVAL" energy.out
+</code>which gives you:<code>
+ ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.):             -0.000250281091139
+</code>
+  * Using the ''awk'' tool:<code>
+ $awk '/Total FORCE_EVAL/ { print$ 9; }' energy.out
+</code>which returns:<code>
+-0.000250281091139
+</code>''awk'' reads a given file line-by-line and splits a line into multiple fields (using whitespace as delimiter). The command above tells ''awk'' to look for the string ''Total FORCE_EVAL'' in a line and if found, print field number 9 of it, effectively returning the energy.
+===== Generating input files =====
+Many times you will have to run the same simulation with different parameters (here the distance).
+A simple way to generate the different input files is using shell scripting in combination with ''sed'' (the stream editor):
+<code>
+for d in $(seq 2 0.1 4); do
+  sed -e "s|4 0 0| ${d} 0 0|" energy.inp > energy_$ {d}A.inp
+  cp2k.sopt -i energy_ ${d}A.inp -o energy_$ {d}A.out
+  awk '/Total FORCE_EVAL/ { print  $9; }' energy_$ {d}A.out
+done
+</code>
+  * The command ''seq 2 0.1 4'' generates the numbers ''2.0'', ''2.1'', ''2.2'', ... , ''4.0'' (try it out!)
+  * With ''for d in  $(seq 2 0.1 4); do'' we use the shell to run all commands which follow once for every number (stored in ''$ d'')
+  * ''sed -e "s|4 0 0| $d 0 0|" energy.inp'' looks for ''4 0 0'' in the file ''energy.inp'' (the original file from above) and replaces ''4 0 0'' by ''$ d 0 0'' (that is: ''2.0'', ''2.1'', ''2.2'', ...)
+  * ... and using ''> energy_${d}A.out'' we redirect the output of the ''sed'' command to new files ''energy_2.0A.out'', ''energy_2.1A.out'', etc.
+  * Then we run ''cp2k.sopt'' as shown before on those new input files and write the output to new output files as well
+  * Using ''awk'' we extract the energy from the output file