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Visualization of the positions of the barycenters of the rings

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The R.I.N.G.S. code allows the user to visualize the "trajectories" of the barycenters of the rings:
ie. the position of the barycenters of the rings at each time step in the simulation box.

  1. Activate the outputting of the positions of the barycenters of the rings 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/rings-bc-SYSTEM-?-???.dx"

This visualization option is complementary to the visualization of the trajectories of the particles of highest mean square displacement.
Thus for both a single OpenDX module named "PathDX" is used.

Visualizing the positions of the barycenter of the rings along the simulation

It is clear that it is not possible to follow a ring along the simulation, since rings can be destroyed and re-build several times during the dynamics. Nevertheless it is possible to print for each step the positions of the barycenters of the rings as a function of their size and thus to follow the evolution of the position of the rings according to their size during the simulation.

The procedure is illustrated in details in the following example.

  1. Activate the outputting of the positions of the barycenters of the rings 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
    ...
    Rings            .false.              #
    ----- ! Ring statistics options ! -----
    Species             0                 #
    ABAB             .false.              #
    Rings0           .false.              #
    Rings1           .false.              #
    Rings2           .false.              #
    Rings3           .false.              #
    Rings4           .false.              #
    Prim_Rings       .false.              #
    Str_Rings        .false.              #
    BarycRings       .false.              #
    ...
    =>
    ....
    Rings           .true.                #
    ----- ! Ring statistics options ! -----
    Species             0                 #
    ABAB             .false.              #
    Rings0           .false.              #
    Rings1           .false.              #
    Rings2           .false.              #
    Rings3           .true.               #
    Rings4           .false.              #
    Prim_Rings       .false.              #
    Str_Rings        .false.              #
    BarycRings       .true.               #
    ...
    Notice that you have to activate the ring statistics as well as to chose one or more ring statistics analysis method to print the OpenDX file(s) containing the positions of the barycenters of the rings.
    A different file will be outputted for each analysis method therefore it will be possible to compare all results.
  2. Run the R.I.N.G.S. code
    ]$ 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/rings-bc-SYSTEM-?-???.dx"
    Open file containing barycenter positions
  6. Visualize
    Trajectories and positions of barycenters
    The Periodic Boundary Conditions do not modify the visualization of the trajectories of atoms since in they are reconstructed if PBC are applied. Nevertheless in such case the positions of the barycenters of the rings appears in the central cell (center of this cell has coordinates [0,0,0]). It is possible to visualize the positions of the barycenters of the rings in the 26 contiguous cells by activating an options before the compilation of the R.I.N.G.S. code.
    To activate 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:
        88 !******************* Barycenters ********************
        89 ! Visualize the positions of the barycenters of the
        90 ! rings also in the 26 contiguous cells
        92 ! Only applied if PBC are also applied
        93 DPBC=.false.
        in
        88 !******************* Barycenters ********************
        89 ! Visualize the positions of the barycenters of the
        90 ! rings also in the 26 contiguous cells
        92 ! Only applied if PBC are also applied
        93 DPBC=.true.
    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 "rings-bc-SYSTEM-?-???.dx" file located in the "MY_WORKING_DIRECTORY/dx" directory
    5. Visualize
    Trajectories and positions of barycenters in the 26 cells

 

Last Updated on Sunday, 15 November 2009 13:32  

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