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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN"><HTML><HEAD> <META NAME="GENERATOR" CONTENT="SGML-Tools 1.0.9"> <TITLE>XMD - Molecular Dynamics Program: Trouble Shooting a Molecular Dynamics Simulation</TITLE> <LINK HREF="xmd-14.html" REL=next> <LINK HREF="xmd-12.html" REL=previous> <LINK HREF="xmd.html#toc13" REL=contents></HEAD><BODY><A HREF="xmd-14.html">Next</A><A HREF="xmd-12.html">Previous</A><A HREF="xmd.html#toc13">Contents</A><HR><H2><A NAME="s13">13. Trouble Shooting a Molecular Dynamics Simulation</A></H2><P><P><DL><P><DT><B>Little or No Motion</B><DD><P>Either the temperature clamp near or at 0K, or system was started withno initial velocities (ITEMP command) when in a stable state.<P><DT><B> Potential and / or Kinetic Energy Increases Too Much</B><DD><P>This can be caused by a using a time step that is too large.If the energy increases at a physically unreasonable rate, thenthe cause is almost certainly a too large time step. Sometimethe energy can increase slowly enough so that it appears to bedue to physical causes. If unsure test the time step size(see the section<P><DT><B>Electron Density (xxx) out of range [xx, xx] for atom ? (type n).</B><DD><P>This message specifies a particle number in place of the"?"in the heading above.This is caused by two particles being too close togetherwhen using some EAM potential models.Sometimes this happens because a simulation is started witha faulty initial configuration. This is certainly the caseif this error occurs at the first time step. Sometimes a faulty initial configuration will not manifestuntil a few time steps, as when there is anunrealistic localized stress which forces two atoms closetogether after a few steps.<P>It is usefull to examine the nearest neighbors of the particlementioned in the error messages. This can be done withthe following code fragment in XMD,<BLOCKQUOTE><CODE><PRE>select near 1 index ?write sel particle</PRE></CODE></BLOCKQUOTE>where "?" is the number from the error message.This will write the type and position of the particle closestto the particle in the message, and may offer a clue asto the root problem.<P><P>The second way this might arise is if the time step is toolarge, which imparts too much energy to one or more particlesand sometimes results in two atoms approaching too closely.If this is the case, you can rerun the simulation with CLAMP OFFand see if the total energy rises, a sign that the time step is too large.<P></DL><P><P><HR><A HREF="xmd-14.html">Next</A><A HREF="xmd-12.html">Previous</A><A HREF="xmd.html#toc13">Contents</A></BODY></HTML>⌨️ 快捷键说明
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