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--- exercises:2017_ethz_mmm:replica_2017 [2017/05/11 07:37] – dpasserone
+++ exercises:2017_ethz_mmm:replica_2017 [2017/05/11 08:05] – dpasserone
@@ Line 169: / Line 169: @@
   - For all the ''log.lammps.*'' files from each replica take only the lines for which we also have a dump of the atomic coordinates. These lines are put in a file *.nxyz, one for each replica. Each line contains temperatures, potential energies, etc.
   - Compute the **q4** order parameter for all structure files and create ''*.q4'' files, one for each replica.
-  - now paste the ''*.nxyz'' and the ''*.q4'' files into a file ''t_ene_q4.*.out'' containing the dump of temperature, energy, q4 every 10000 steps.
+  - now paste the ''*.nxyz'' and the ''*.q4'' files into a file ''t_epot_q4_etot.*.out'' containing the dump of temperature, energy, q4 every 10000 steps.
 </note>
@@ Line 175: / Line 175: @@
 ===== Reordering the replica: one temperature, one files =====
-At this point, we have a set of ''t_ene_q4.*.out'', one for each replica (processor). But along each of these
+At this point, we have a set of ''t_ene_q4_etot.*.out'', one for each replica (processor). But along each of these files, the temperatures change a lot due to the exchanges. So, we use the file ''exchanges_nxyz.log'' that keeps track of the exchanges, and tells us at a given timestep which replica has which temperature: we scramble the ''t_ene_q4_etot.*.out'' files, and at the end we will have one file for each temperature. This is accomplished by the script ''02_reorder''.
+<note tip>
+  * Consider each file t_epot_q4_etot.*.out (processor by processor). Say you consider the number 5 (6th replica): ''t_epot_q4_etot.5.out''.
+  * At the step 50000, the file shows the following line:
+''50000 6.7133746 -1.7636174 0.189 -1.7315099''
+indicating a temperature of 6.7133746.
+  * The file ''exchanges_nxyz.log'', at the step 50000, gives us the following line:
+''50000 7 0 3 2 1 6 10 5 12 8 11 4 9 13 15 14''
+indicating that at the 6th replica (column **7**), we have the temperature **6**, which is (see input file) T=6.63 K. Meaning that at step 50000, the thermostat is keeping replica 5 around the temperature T=6.63 K.
+  * This means that this line has to be stored in the temperature file number **6**.
+</note>
+At the end of the procedure performed by the small script section:
+<code bash>
+NP=16
+NP1=$[NP-1]
+rm torder*
+for repl in `seq 0 $NP1`
+do
+   echo $repl
+   awk -v rep=$repl '{r2=rep+2;print $r2}'  < exchanges_nxyz.log  > rep_$repl
+   i=0
+   for a in `cat rep_$repl`
+   do
+        i=$[i+1]
+        head -$i t_epot_q4_etot.$repl.out | tail -1  >> torder.$a
+   done
+done
+</code>