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exercises:2017_ethz_mmm:replica_2017

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exercises:2017_ethz_mmm:replica_2017 [2017/05/11 07:37] – dpasseroneexercises:2017_ethz_mmm:replica_2017 [2017/05/11 08:03] – dpasserone
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   - 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.   - 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.   - 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> </note>
  
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 ===== Reordering the replica: one temperature, one files ===== ===== 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 put in the temperature file number **6**.  
 +</note>
  
exercises/2017_ethz_mmm/replica_2017.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1