Random Sequential Adsorption of simple models for tilted molecules
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README

README

Tilted RSA is a code which can perform Random Sequential Adsorption (RSA)
simulations on extremely simple models for molecules which land on Gold 
surfaces.

A good place to read about this program is the following article: 
Matthew A. Meineke and J. Daniel Gezelter, "A Random Sequential Adsorption 
model for the differential coverage of Gold (111) surfaces by two related 
Silicon phthalocyanines," J. Phys. Chem. B 105, 6515-6519 (2001).
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  This is the documentation for the tilted_RSA package of
simulations. The simulations themselves are fairly
straightforward. The size of the system to simulate is controlled in
the parameters.h file. Also other important variables such as the
default file names and the quitting threshold can be changed within
this header file.

  One should be careful however, that there is enough available memory
to run these simulations. We have found that a lattice size of 4000 x
4000 will require around 140 MB of RAM. Also, having the bent_umbrella
simulation do the surface scan to calculate the surface coverage, can
add anywhere from 5 - 24 hrs to a simulation depending on computer
speed and system size.

  One bug (feature) you should be aware of is that both classes of
simulations use a lot of memory off of the stack. When running the
simulation be sure to unlimit the stacksize if some memory limiting
software is used.

  As for the visualization program. This is there to generate a PovRay
script from the output locations of either simulation. PovRay can be
obtained for a variety of platforms at:

http://www.povray.org

 The visualization program will simply take the locations written from
the original simulation, and write them as disk objects. Camera
locations and light sources are specified in the "pov_header.pov"
file. Use the -g option to generate this file. 

If you have any questions or comments regarding the simulations,
please email me at: mmeineke@nd.edu


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INSTALL:

change to the src directory, and 'make all'

-------------------------------------------------------------------------

USAGE:

-note: Only the correlate program needs filenames given to it. All the
       other programs have default names specified in the parameters.h file.

-=bent_umbrella=-

  bent_umbrella [options]

  Options:
     -D         turn on the debugging output
     -o <name>  the name of the orientation output file
     -c <name>  the name of the coverage output file
     -L         turns on the lattice constraint
     -V         generate output locations and orientations
                for visualization
     -v <name>  the name for the visualization file
     -S         turn on the surface probe scan for coverage


-=octopus=-

  octopus [options]

  Options:
     -D         turn on the debugging output
     -o <name>  the name of the orientation output file
     -c <name>  the name of the coverage output file
     -L         turns on the lattice constraint
     -V         generate output locations and orientations
               for visualization
     -v <name>  the name for the visualization file
     -S         turn on the surface probe scan for coverage

-=correlate=-

  correlate filename1 filename2 ...


-=visualize=-

  visualize [options]

  Options:
     -I <input name>   the name of input locations file
     -O <output name>  the name of the output script
     -g                generate the pov_header.pov file
                         -contains info on lighting and
                          camera locations
     -c                Turns on the color gradient.
                         -note: will work only for the
                                tilted umbrellas.