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--- exercises:2018_uzh_acpc2:l-j_flu [2018/04/25 09:00] – mpauletti
+++ exercises:2018_uzh_acpc2:l-j_flu [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 62: / Line 62: @@
   &MM
     &FORCEFIELD
+    &SPLINE
+     EMAX_SPLINE 100000
+    &END
       &CHARGE             #charge of the MM atoms
         ATOM Ar           #Defines the atomic kind of the charge
@@ Line 84: / Line 87: @@
       &SUBSYS                 ! system description
        &CELL
-         ABC [angstrom] 10 10 10
+         ABC [angstrom] 40 40 40
          PERIODIC NONE
        &END CELL
@@ Line 105: / Line 108: @@
 <code>
-for d in $(seq 2 0.1 4); do
+for d in $(seq 3.0 0.1 9); do
   sed -e "s|4 0 0|${d} 0 0|" argon.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
+  awk '/Total FORCE_EVAL/ { print "'"${d}"'", $9; }' energy_${d}A.out >> Pot_En_vs_distance.dat
 done
 </code>
-  * The command ''seq 2 0.1 4'' generates the numbers ''2.0'', ''2.1'', ''2.2'', ... , ''4.0'' (try it out!)
+  * The command ''seq 3 0.1 9.0'' generates the numbers ''3.0'', ''3.1'', ''3.2'', ... , ''9.0'' (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'')
+  * With ''for d in $(seq 3 0.1 9.0); do'' we use the shell to run all commands which follow once for every number (stored in ''$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'', ...)
+  * ''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: ''3.0'', ''3.1'', ''3.2'', ...)
-  * ... and using ''> energy_${d}A.out'' we redirect the output of the ''sed'' command to new files ''energy_2.0A.out'', ''energy_2.1A.out'', etc.
+  * ... and using ''> energy_${d}A.out'' we redirect the output of the ''sed'' command to new files ''energy_3.0A.out'', ''energy_3.1A.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
+  * The energy as a function of distance for all the single point calculations is then printed to the file ''Pot_En_vs_distance.dat''
 Plot distance vs. potential energy and find the minimum in energy, which corresponds to the equilibrium distance. After having done it, you can calculate the minimum analytically as well.