Tina Düren

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Department of Chemical Engineering, University of Bath

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Post Processing

When you ran your gcmc simulation, a lot of useful information about the simulation set-up plus statistics about the number of molecules in your simulated systems was written to the screen (or the logfile). Music has also written the restart files which you can use as initial configuration if you want to restart a simulation or create a snapshot and the config files. The config files contain all the important information collected during the simulation such as number of molecules, energies, positions, etc in binary format. The aim of the post processing step is to read the binary file and summarise the information in a way that you can read.

Compile the program "music_post" as described before, creating a link in your gcmc folder.

Copy the "post.ctr" file into your gcmc folder.


The control file looks like this:

# this section is required for working with any post code
#
#
------------------------------------------------------------
   ### Required section ######
-- Post Processor Information ------------
GCMC                      # Type of simulation GCMC, NVTMC , MD .... 
methane.con               # basename for config files what your .con files are called in your gcmc folder   
1, 15                          # The first and last numbers of the .con files that were created in the gcmc folder 
new.met                     # name for new ctrlfile that will be regenerated 
met.post                    # Base name for output files 
40, 0                         # Percentages of data to skipped at start and end 
			        # In this case 40% of the data at the beginning of the simulation
                                # is skipped to allow the system to equilibrate

# The sections below are necessary only if you want the corresponding 
# analysis performed
# ---------------- ALL OF THEM ARE OPTIONAL ------------------------

####    This section is reqd for energy averages in your post code output files
####    as of now only total enrgies vs sim. step
------ Post : Energy Average Info -----------------------------------
20       # Number of blocks into which data should be divided for stats

####    This section is reqd for Loading averages in your post code outputfiles
####    as of now only species loading vs sim. step (for all species)
------ Post : Loading Average Info -----------------------------------
20       # Number of blocks into which data should be divided for stats

From the original post.ctr file, delete all the rest of the lines as it is not needed here.

Run the post processing program

>music_post post_ctr

After the post processing is done, the following files will be created in your gcmc directory:

• Isotherm.IRMOF1 - This file will not contain anything useful as the adsorbent does not change
  
  
• Isotherm.Methane
  
  
• met.post - This file displays the information from the .con files in the number of blocks that you specified in the post.ctr file.
  
  
• finalconfig.xyz - File to see what the final configuration looked like

Have a look at the *.post file, to see how the number of molecules plus the energy varied in the different blocks. The Methane.isotherm files contains the absolute number adsorbed as function of the fugacity. In order to compare your simulated absolute amount adsorbed to experimental data, you need to convert it to excess data. The program that does this is not part of music but is a service program that further analyses the *.post file.