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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</TITLE> <LINK HREF="xmd-1.html" REL=next></HEAD><BODY><A HREF="xmd-1.html">Next</A>PreviousContents<HR><H1>XMD - Molecular Dynamics Program</H1><H2>Jon Rifkin,<CODE>jon.rifkin@uconn.edu</CODE></H2>v2.5.30 20 Jan 2002<P><HR><EM>XMD is a program for performing molecular dynamics simulations.</EM><HR><P><H2><A NAME="toc1">1.</A> <A HREF="xmd-1.html">Features</A></H2><P><H2><A NAME="toc2">2.</A> <A HREF="xmd-2.html">Introduction</A></H2><P><H2><A NAME="toc3">3.</A> <A HREF="xmd-3.html">File Formats</A></H2><P><H2><A NAME="toc4">4.</A> <A HREF="xmd-4.html">Usage</A></H2><P><H2><A NAME="toc5">5.</A> <A HREF="xmd-5.html">Theory</A></H2><UL><LI><A HREF="xmd-5.html#ss5.1">5.1 Molecular Dynamics</A><LI><A HREF="xmd-5.html#ss5.2">5.2 Boundary Conditions</A><LI><A HREF="xmd-5.html#ss5.3">5.3 Adiabatic and Isothermal Simulations</A><LI><A HREF="xmd-5.html#ss5.4">5.4 Time Step Size</A><LI><A HREF="xmd-5.html#ss5.5">5.5 Metropolis Algorithm</A><LI><A HREF="xmd-5.html#ss5.6">5.6 Constant Pressure Algorithms </A></UL><P><H2><A NAME="toc6">6.</A> <A HREF="xmd-6.html">Implementation</A></H2><UL><LI><A HREF="xmd-6.html#ss6.1">6.1 Coordinates</A><LI><A HREF="xmd-6.html#ss6.2">6.2 Velocity, Force, and Higher Derivatives</A><LI><A HREF="xmd-6.html#ss6.3">6.3 Particle Selection</A><LI><A HREF="xmd-6.html#ss6.4">6.4 Neighbor List</A><LI><A HREF="xmd-6.html#ss6.5">6.5 External Forces</A><LI><A HREF="xmd-6.html#ss6.6">6.6 Velocity Damping</A><LI><A HREF="xmd-6.html#ss6.7">6.7 Temperature Control </A><LI><A HREF="xmd-6.html#ss6.8">6.8 Quenching </A><LI><A HREF="xmd-6.html#ss6.9">6.9 Fixing Particle Positions for Molecular Dynamics</A><LI><A HREF="xmd-6.html#ss6.10">6.10 Repeating Boundary Conditions</A><LI><A HREF="xmd-6.html#ss6.11">6.11 Constraints</A><LI><A HREF="xmd-6.html#ss6.12">6.12 Run Identification</A><LI><A HREF="xmd-6.html#ss6.13">6.13 RCV File Format</A><LI><A HREF="xmd-6.html#ss6.14">6.14 COR File Format</A><LI><A HREF="xmd-6.html#ss6.15">6.15 Atom Plots</A><LI><A HREF="xmd-6.html#ss6.16">6.16 REPEAT Command</A><LI><A HREF="xmd-6.html#ss6.17">6.17 Built-in Calculator </A><LI><A HREF="xmd-6.html#ss6.18">6.18 Macros </A><LI><A HREF="xmd-6.html#ss6.19">6.19 Using Color in Plots </A><LI><A HREF="xmd-6.html#ss6.20">6.20 Parallel Processing </A><LI><A HREF="xmd-6.html#ss6.21">6.21 Reproducibility </A></UL><P><H2><A NAME="toc7">7.</A> <A HREF="xmd-7.html">Command Summary</A></H2><P><H2><A NAME="toc8">8.</A> <A HREF="xmd-8.html">Commands</A></H2><P><H2><A NAME="toc9">9.</A> <A HREF="xmd-9.html">Fill Command </A></H2><UL><LI><A HREF="xmd-9.html#ss9.1">9.1 FILL Example 1: Filling a Sphere</A><LI><A HREF="xmd-9.html#ss9.2">9.2 FILL Example 2: Creating an Diamond Cubic Lattice</A><LI><A HREF="xmd-9.html#ss9.3">9.3 FILL Example 3: Twinning Plane</A><LI><A HREF="xmd-9.html#ss9.4">9.4 FILL commands</A></UL><P><H2><A NAME="toc10">10.</A> <A HREF="xmd-10.html">Write Command</A></H2><P><H2><A NAME="toc11">11.</A> <A HREF="xmd-11.html">Interatomic Potentials</A></H2><UL><LI><A HREF="xmd-11.html#ss11.1">11.1 Using Provided Potentials</A><LI><A HREF="xmd-11.html#ss11.2">11.2 Using Tersoff's Carbon-Silicon Potential</A><LI><A HREF="xmd-11.html#ss11.3">11.3 Using Stillinger-Webers Silicon Potential</A><LI><A HREF="xmd-11.html#ss11.4">11.4 Creating EAM Potentials</A></UL><P><H2><A NAME="toc12">12.</A> <A HREF="xmd-12.html">Techniques and Examples </A></H2><UL><LI><A HREF="xmd-12.html#ss12.1">12.1 Creating a B2 Lattice</A><LI><A HREF="xmd-12.html#ss12.2">12.2 Creating an L12 Lattice</A><LI><A HREF="xmd-12.html#ss12.3">12.3 Creating a B2 Lattice in <110> <1-10> <001> Orientation</A><LI><A HREF="xmd-12.html#ss12.4">12.4 Finding the Optimum Time Step</A><LI><A HREF="xmd-12.html#ss12.5">12.5 Initialize the Temperature</A><LI><A HREF="xmd-12.html#ss12.6">12.6 Finding the Equilbrium Lattice Constant</A><LI><A HREF="xmd-12.html#ss12.7">12.7 Calculating the Surface Energy</A><LI><A HREF="xmd-12.html#ss12.8">12.8 Simulating a Crack</A></UL><P><H2><A NAME="toc13">13.</A> <A HREF="xmd-13.html">Trouble Shooting a Molecular Dynamics Simulation</A></H2><P><H2><A NAME="toc14">14.</A> <A HREF="xmd-14.html">Companion Utilities</A></H2><P><H2><A NAME="toc15">15.</A> <A HREF="xmd-15.html">References</A></H2><P><H2><A NAME="toc16">16.</A> <A HREF="xmd-16.html">Acknowlegements</A></H2><HR><A HREF="xmd-1.html">Next</A>PreviousContents</BODY></HTML>⌨️ 快捷键说明
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