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Study of a crystalline structure using the R.I.N.G.S. code

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Using the R.I.N.G.S. code it possible to study amorphous as well as crystalline structures.

Nevertheless the calculations for crystalline structures are slightly different and more CPU time consuming than the standard ones for amorphous structures.
Since calculations are simplified for amorphous structures we decided to use an option in order to activate or deactivate the computations for crystalline structures.

Note otherwise that crystalline groups as well as crystalline positions are not accepted by the R.I.N.G.S. code.
It is mandatory to provide a complete 3D model of the system to be studied.

In the R.I.N.G.S. code the default option for computations is to study amorphous cells and not crystalline cells !

Thus in order to study crystalline structures with the R.I.N.G.S. code a very simple procedure as to be followed:

  • Edit and modify the "parameters.F90" file located in the "rings-code/src" directory
  • Build and install a version (serial or MPI) of the so-modified R.I.N.G.S. code
  • Specify complete lattice parameters inlcuding lattice angles in the 'input' file.
  • Run the modified R.I.N.G.S. code on the crystalline structure

The detailed procedure is describe thereafter.

Last Updated on Tuesday, 05 October 2010 13:02 Read more...
 

The periodic boundary conditions

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The correct description of the finite size effects is a crucial point in numerical simulation methods. Thus it allows to evaluate macroscopic quantities using small size systems. 

Indeed even considering the calculation power of the actual computers it is not possible to run molecular dynamics simulations on systems with a number of atoms close to the Avogadro number ( $ \simeq$ 1023).

Last Updated on Friday, 27 February 2009 18:35 Read more...
 

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.

Last Updated on Sunday, 15 November 2009 13:32 Read more...
 

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"
Last Updated on Sunday, 15 November 2009 13:44 Read more...
 

Visualization of the strong rings analysis

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The R.I.N.G.S. code allows the user to visualize the strong ring analysis:
ie. the different steps of the algorithm implemented to look for strong rings in a material.

In order to visualize each step of the search of the strong rings in the network a simple procedure has to be followed:

  1. Edit and modify the "extra.f90" file located in the "rings-code/src" directory
  2. Build and install the serial version of the so-modified R.I.N.G.S. code
  3. Activate the primitive and the strong rings analysis in the "options" file and run the modified R.I.N.G.S. code
  4. Edit the file named "MY_ATOM_LABEL-MY_ATOM-s-MY_SIZE.dx" in the "dx/debug" directory
  5. Download the "StrongDX" OpenDX module
  6. Using OpenDX open the "StrongDX" module
  7. Browse and open the file named "MY_WORKING_DIRECTORY/dx/debug/MY_ATOM_LABEL-MY_ATOM-s-MY_SIZE.dx"
Last Updated on Monday, 16 November 2009 18:07 Read more...
 


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