Module Document - Load_Simulation

<table cellspacing="0" cellpadding="0"> <tr height="150"> <td align="left"><img src="../../../../img/logo.gif" alt="IAC logo"></img></td> <td width="100%" rowspan="2" align="left" valign="center"> <table cellspacing="0" cellpadding="0"> <tr> <td> <a name="Load_Simulation"> <table width="84%" border="0" align="center"> <tr bgcolor="FFFFAA" align="center"> <td nowrap width="15%" height="32"> <tt class="label">1729</tt></td> <td nowrap width="100%"> <tt class="label">Load_Simulation</tt></td> <td nowrap width="150"><tt class="label">12/14/93</tt></td> </tr> <tr><td align="left" colspan="3"><p>The Loadsim module will create a ball and stick geometry representation of molecular dynamics or Monte Carlo data. The ability to interactively select positions in the data file as well as individual chains is advantageous for visualizing chain motions. Although written for visualizing simple chain-like molecules it can be extended to other systems.</p></td></tr> <tr><td align="left" colspan="3"><table class="avs5_repository"> <tr valign="top"><td><b>Author:</b></td><td>Prashant Gupta & Steven Smith, North Carolina State University</td></tr> <tr><td><b>Version:</b></td><td>1.000</td></tr> <tr><td><b>Language:</b></td><td>C</td></tr> <tr> <td><b>Path:</b></td><td>source/data_input/Load_Simulation/</td></tr> </table></td></tr> <tr><td align="left" colspan="3"><p> <a href="Load_Simulat.shtml" target="_top"> <img src="../../../../../img/doc_mod.gif" border="0" width="30" height="30" alt="Module Document - Load_Simulation"></a> <a href="source/data_input/Load_Simulation/Load_Simulation.tar.gz"> <img src="../../../../../img/targz.gif" border="0" width="52" height="30" alt="Archive - Load_Simulation.tar.gz"></a> <a href="source/data_input/Load_Simulation/Load_Simulation.tar.Z"> <img src="../../../../../img/tarz.gif" border="0" width="52" height="30" alt="Archive - Load_Simulation.tar.Z"></a> <a href="source/data_input/Load_Simulation/Load_Simulation.zip"> <img src="../../../../../img/zip.gif" border="0" width="52" height="30" alt="Archive - Load_Simulation.zip"></a> </p></td> </tr> </table> <br> </td> </tr> <tr> <td>  <html> <head> <title> Load_sim - a module to present molecular dynamics data of chain-like molecules. </title> </head> <body bgcolor=#FFFFCC> <h2> Load_sim - a module to present molecular dynamics data of chain-like molecules. </h2> <h3>Name</h3> <blockquote> <pre> Load_sim - a module to present molecular dynamics data of chain-like molecules. </pre> </blockquote> <h3>Summary</h3> <blockquote> <pre> Name Loadsim </pre> </blockquote> <h3>Type</h3> <blockquote> <pre> data </pre> </blockquote> <h3>Inputs</h3> <blockquote> <pre> x-y-z coordinate data in binary form </pre> </blockquote> <h3>Outputs</h3> <blockquote> <pre> geometry </pre> </blockquote> <h3>Parameters</h3> <blockquote> <pre> Name Type Default Config File File Browser Sleep Toggle On Apply PBC/Unfold Traj. Choice Off Bounding Box Toggle Off Sticks Only Toggle Off New Colors One Shot Show All One Shot Square Wells Toggle Off Snapshot Oneshot Radius Float 2.00 Kill Module Oneshot Rewind/Fast Forward Panels </pre> </blockquote> <h3>Description</h3> <blockquote> <pre> The Loadsim module will create a ball and stick geometry representation of molecular dynamics or Monte Carlo data. The ability to interactively select positions in the data file as well as individual chains is advantageous for visualizing chain motions. Although written for visualizing simple chain-like molecules it can be extended to other systems. INPUTS The input data is a binary file generated from your Fortran or C simulation program and consists of header information followed by x,y,z coordinates. The source(read_conf.c) for data input expects binary data, but can be modified to read ascii files. The reason for this is to minimize storage space for very large coordinate data files. The data file should be structured as follows: Header: Number of Chains, Chain Length, Simulation Box Length, Segment or Bead Radius, Number of H type beads(under development) Coordinates: Move Number, Array of x coord., Array of y coord. Array of z coord. Move Number, Array of x coord., Array of y coord. Array of z coord. ...... Your favorite data type for each of these variables may be specified in the header file(mytypes.h). The default is to read data generated from a FORTRAN program with the following output statements: REAL BOXL,RAD,X(N),Y(N),Z(N) INTEGER NCHN,ICHNLEN,MOVNUM OPEN(UNIT=60,FORM='UNFORMATTED') WRITE(60)NCHN,ICHNLEN,BOXL,RAD,INT(0) WRITE(60)MOVNUM,X,Y,Z PARAMETERS Config File Use this file browser to select the input file. Sleep Use this toggle to start/stop the program. Apply PBC/Unfold Traj It is assumed that the coordinate data is the actual position rather the the periodic one. This switch applies periodic boundary conditions from the box length information contained in the header portion of the input data. Bounding Box Turn on/off the bounding box for the simulation. Sticks Only Represent the chain as a series of sticks rather than a ball and stick model. New Colors Randomly generate new colors. Attempts to generate saturated colors. Show all Chains Redraws all chains. Selected after picking one or more chains from the system in order to restore the view of all chains. The module uses upstream geometry to allow the visualization of one or more chains by simply selecting a chain. Square Wells Draws a semi-transparent sphere 1.5*(ball radius) around each bead. Snapshot Draws a tube of size Radius around a given chain. Radius Adjust the radius of the tube from snapshot. Must be applied before the tube is constructed. Rewind/Forward Presents a control panel to allow selection of particular frames from the data file. OUTPUTS Geometry data suitable for geometry viewer </pre> </blockquote> <h3>Example</h3> <blockquote> <pre> Load Simulation | Geometry Viewer </pre> </blockquote> <h3>Limitations</h3> <blockquote> <pre> NOTES AVS Module Prashant Gupta Steven Smith North Carolina State University </pre> </blockquote> </body> </html>  </td> </tr> </table> </td> </tr> <tr height="100%"> <td class="sideLink" width="25%" align="left" valign="top" nowrap="nowrap"> <p><a href="../../../../../general/index.shtml" target="_top">General Information</a></p> <p><a href="../../../../../repository/index.shtml" target="_top">Repositories</a></p> <p class="sideLinkLevel2"><a href="../../../../new/index.shtml" target="_top">  New Releases</a></p> <p class="sideLinkLevel2"><a href="../../../../download/index.shtml" target="_top">  Download</a></p> <p class="sideLinkLevel2"><a href="../../../../submit/index.shtml" target="_top">  Submit</a></p> <p class="sideLinkLevel2"><a href="../../../../pfiles/index.shtml" target="_top">  Project Files</a></p> <p class="sideLinkLevel2"><a href="../../../../avs5/index.shtml" target="_top">  AVS5</a></p> <p class="sideLinkLevel3"><a href="../../../input.shtml" target="_top">    Data Input</a></p> <p class="sideLinkLevel3"><a href="../../../filters.shtml" target="_top">    Filters</a></p> <p class="sideLinkLevel3"><a href="../../../mappers.shtml" target="_top">    Mappers</a></p> <p class="sideLinkLevel3"><a href="../../../output.shtml" target="_top">    Data Output</a></p> <p class="sideLinkLevel3"><a href="../../../misc.shtml" target="_top">    Miscellaneous</a></p> <p class="sideLinkLevel2"><a href="../../../../express/index.shtml" target="_top">  AVS/Express</a></p> <p class="sideLinkLevel2"><a href="../../../../pog/index.shtml" target="_top">  Project Guidelines</a></p> <p><a href="../../../../../usergroup/index.shtml" target="_top">User Group</a></p> <p><a href="../../../../../training/index.shtml" target="_top">Training Materials</a></p> </td> </tr> </table> <table width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="c6c6e0"> <tr> <td><img src="../../../../../img/foot1.gif" alt="IAC" width="155" height="25"></td> <td width="100%"> Last Updated:  26th November 2002 </td> </tr> </table>