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Visualization of the trajectories of the particles of highest MSD

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The R.I.N.G.S. code allows the user to visualize the "trajectories" of the Nth particles of highest Mean Square Displacement.

  1. Activate the calculation of the mean square displacement, the mean square displacement for each single atom, as well as the ouputting of the trajectories in the "options" file
  2. Run the R.I.N.G.S. code
  3. Download the "PathDX" OpenDX module
  4. Using OpenDX open the "PathDX" module
  5. Browse and open the file named "MY_WORKING_DIRECTORY/dx/SYSTEM-path.dx"

Visualizing the trajectories of the atoms along the simulation

The procedure is illustrated in details in the following example.

  1. Activate the calculation of the mean square displacement, the mean square displacement for each single atom, as well as the ouputting of the trajectories in the "options" file
    ]$ cd MY_WORKING_DIRECTORY
    ]$ ls -l
    drwxrwxr-x 2 user user-group 4,0K janv. 31 00:33 data
    -rw-r--r-- 1 user user-group 2,0K janv. 31 00:33 my-input
    -rw-r--r-- 1 user user-group 3,1K janv. 31 00:33 options
    ]$ vi options
    ...
    MSD              .false.               #
    atMSD            .false.               #
    ...
    TrajOut          .false.               #
    ...
    =>
    ...
    MSD              .true.                #
    atMSD            .true.                #
     ...
    TrajOut          .true.                #
    ...
    Notice that activating the outputting option is enough since in this case the MSD and the MSD for single atoms will also be activated.
  2. Run the R.I.N.G.S. code ex:
    ]$ rings my-input
  3. Download the "PathDX" OpenDX module
  4. Using OpenDX open the "PathDX" module
    Please follow the procedure as describe in details for the visualization of the strong ring algorithm
  5. Using the "Main Interface" of the "PathDX" module open the file named "MY_WORKING_DIRECTORY/dx/SYSTEM-path.dx"
    Open file containing barycenter positions
  6. Visualize
    Trajectories and positions of barycenters
    The default option of the R.I.N.G.S. code is to allow to visualize the trajectories of the 5 particles of highest MSD for each chemical species. Nevertheless it is possible to modify this value by changing an options before the compilation of the R.I.N.G.S. code.
    To modify this option:
    1. Edit and modify the "extra.f90" file located in the "rings-code/src" directory:
      • This file contains miscellaneous variables used to prepare the OpenDX input files.
      • Locate and modify the following lines:
        60 ! Print the trajectories for the NVALT"th" particles
        61 ! of highest Mean Square Displacement for each chemical species
        62 INTEGER :: NVALT=5
        63 ! Note that if for one chemical species the number of particles
        64 ! by species NBSPBS for one or more chemical species (i) is < NVALT then 
        65 ! for this chemical species NVALT for this species will be NBSPBS(i)
        in
        60 ! Print the trajectories for the NVALT"th" particles
        61 ! of highest Mean Square Displacement for each chemical species
        62 INTEGER :: NVALT=NEW_VALUE
        63 ! Note that if for one chemical species the number of particles
        64 ! by species NBSPBS for one or more chemical species (i) is < NVALT then 
        65 ! for this chemical species NVALT for this species will be NBSPBS(i)
    2. Build and install a version (serial or MPI) of the so-modified R.I.N.G.S. code ex:
      ]$ ./configure FC=ifort FCFLAGS="-O3 -mtune=core2"
      ]$ make
      ]$ make install
    3. Run the modified R.I.N.G.S. code:
      ]$ cd MY_WORKING_DIRECTORY
      ]$
      rings my-input
    4. Using the "Main Interface" of the "PathDX" module open the new "SYSTEM-path.dx" file located in the "MY_WORKING_DIRECTORY/dx" directory
    5. Visualize

 

Last Updated on Sunday, 15 November 2009 13:44  

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