xmd.sgml

一个很好的分子动力学程序

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To Do
May 28, 1998
  (1) Write separate FILL section
  (2) Under THEORY, boundary conditions
  (3) Under COMMANDS, remove VOLUME, *add* PRESSURE
  (4) Under TECHNIQUES and EXAMPLES,
       - Creating lattice with non-cubic orietation
       - Finding equilibrium volume
       - Finding equilibrium HCP a, c values.
       - Calculating the surface energy
   (5) WRite INTERATOMIC potential section incorporating
       web page on potentials.

1 Jun 1998
  Finished Constant PRessure section.
  Finished Theory Boundary Conditions.
  Finished FILL command.
  Finished "Particle Too Close" message
  Finished B2 non-standard orientation example.

3 Jun 1998
  Completed task in NOTES

16 July 1998
  Update PRESSURE command syntax

25 Sep 1998
  Added PRESSURE EXTERNAL PressureX [ PressureY [ PressureZ] }

17 Mar 1999
  Updated WRITE RDF documentation to include [type1 type2] fields.

To Do
  (1)  Move some of the FILL examples to TECHNIQUES section
  (2)  Elaborate on Twinning Plane example
  (3)  Elaborate on INTERATOMIC potential section.

7 Dec 1999
   Added WRITE STRESS

15 Jun 2000
   Added STRESS THERMAL { ON | OFF } command

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<article>


<title>XMD  - Molecular Dynamics Program
<author>Jon Rifkin,
<tt>[e-mail]</tt>
<date>v2.5.30  20 Jan 2002
<abstract>
XMD is a program for performing molecular dynamics simulations.
</abstract>

<!-- Table of contents -->
<toc>


<!-- Begin the document -->

<!--
************************************************************************
Features
************************************************************************
-->

<sect> Features

<p>

XMD is a computer program for performing molecular dynamics simulations.
It is designed for the simulation of metals and ceramics.
It has the following features.

<descrip>

<tag> Computer System </tag>

<itemize>

<item>
C source code is availble for easy porting to a variety of computers.

<item>
Can be compiled using POSIX thread functions to take advantage
of multi-CPU computers
(see section on
<ref id="implementation-parallel" name="Parallel Processing">).

</itemize>

<tag> Molecular Dynamics </tag>

<itemize>

<item>
Constant temperature using velocity re-scaling algorithm
(CLAMP command).

<item>
Constant pressure using either Andersen's algorithm or
a simple volume "rescaling" algorithm suitable for
lattice constant versus temperature calculations.
(PRESSURE command).

<item>
Efficient system relaxation (local minima) algorithm (QUENCH command).

<item>
Constrain selected atoms to remain fixed in space (FIX command).

<item>
Constrain selected atoms to remain in a line or plane (CONSTRAIN command).

<item>
Apply an unique external force to individual atoms (EXTFORCE command).

<item>
Tether selected atoms to their initial positions with springs of
various spring constants (EXTSPRING command).

<item>
Apply velocity damping coefficients to selected atoms (DAMP command).

<item>
Uses pair potential, Embedded Atom Method potentials (EAM),
Tersoff's Silicon-Carbide potential or Stillinger-Weber Si potential.

</itemize>

<tag> Program Input </tag>

<itemize>

<item>
All program actions are controlled by commands read from one or more
text files.

<item>
A macro processor lets you enter strings from the command line
or define strings within the command file (MACRO command)
(see section on 
<ref id="implementation-macros" name="macros">).

<item>
A built-in calculator with variables that can be used with all number
input (CALC command)
(see section on the 
<ref id="implementation-calc" name="Built-in Calculator">).

<item>
Input file instruct the reading of another input file (READ command).

<item>
Flexible creation (FILL command) and editing of atomic structures.

<item>
Select subsets of atoms using a variety of patterns (SELECT, SET and TAG
commands).

<item>
Perform actions on selected atoms, such as moving them (MOVE),
inserting defects (SCREW, WAVE), setting atom type (TYPE), setting atom
mass (MASS), rotating selected atoms (ROTATE), etc.

<item>
Some commands (MOVE, DAMP, EXTFORCE and EXTSPRING) allow input values
to be a function of atomic coordinates.
</itemize>


<tag> Program Output </tag>
<itemize>

<item>
Save the complete simulation state for later continuation (WRITE STATE
command).

<item>
Accumulate system energies (ESAVE and WRITE ENERGY commands), atomic
stress (SSAVE and WRITE STRESS commands), atom coordinates (WRITE
PARTICLE command) and other information to text files during simulation.

<item>
Coordinates can be stored in special compact format (RCV or COR
commands) for later use with companion programs such as WMOVIEC which
produces movies.

<item>
Save atomic coordinates in a Protein Data Bank file for use with
display software such as MSI's Cerius2 (WRITE PDB command),
or standard XYZ format (WRITE XYZ command).

<item>
Built-in plotting routines for plotting atom configuration in color on
a Postscript device (PLOT command).

</itemize>

</descrip>



<!--
************************************************************************
Introduction
************************************************************************
-->


<sect> Introduction

<p>

XMD is a program which performs Computer Molecular Dynamics (CMD)
simulations.  It can use Embedded Atom Method (EAM) potentials, pair
potentials, Tersoff's silicon-carbon potential [1], or
Stillinger-Weber's Silicon potential [2].
With XMD you can
generate specific lattice structures.  With these lattice structures
you can
perform calculations using both static (energies or forces) and dynamic
(molecular dynamics).  XMD reads a command file which describes a
an initial atomic system,
the simulation to be performed, and the output desired.  This
command file is a normal text file (a file that can be read by a normal
text editor).  Normal text files are also used for recording energies
during the course of a simulation.  Special format files (files than
cannot be used with text editors) are used for storing the particle
coordinates (RCV files) and the complete CMD state (STA files).



<!--
************************************************************************
File Formats
************************************************************************
-->

<sect> File Formats

<p>

A variety of file formats can be used with XMD.

<descrip>

<tag> Input File </tag>
XMD's main input is a text file.  This file contains commands
(described below) which control the simulation.  This file is
required.

<tag> Output File </tag>
The output file is also a text file.  It contains the messages
generated by the commands in the input file.  An output file
is always generated.

<tag> Energy / Stress / Box / Trajectory </tag>
These four types of files are also text files.
They are optional and contain information generated during a
dynamics simulation.  They are controlled by the commands
ESAVE, SSAVE, BSAVE and TSAVE (see below).

<tag> COR / RCV </tag>
There are special format files (not Text files) that contain
atom positions as a function of time.  They are written by
the <tt>WRITE COR</tt> and <tt>WRITE RCV</tt> commands.  They
can be read by XMD or by other support programs such as MSD, WMOVIEC,
STRAIN, etc (see section on auxillary program below).

<tag> XYZ / PDB </tag>
Like the previous pair of files, these contain atoms positions.
They are files that can be read by a variety of third party programs.
They are created by the <tt>WRITE XYZ</tt> and <tt>WRITE PDB</tt> commands.

<tag> STATE </tag>
This file is a machine file which contain information needed to
continue a simulation exactly.  It is written and read with the
<tt>WRITE STATE</tt> and <tt>STATE</tt> commands.

</descrip>


<!-- 
************************************************************************
Usage
************************************************************************
-->

<sect> Usage

<p>

The methods used to invoke XMD depend on the specific computer
environment.  At present XMD has been ported to UNIX and the IBM PC
under DOS.  Under these environments the command used is

<tscreen><verb>
xmd  infile [ &dollar;1 &dollar;2 &dollar;3 .. &dollar;9 ] >  outfile
</verb></tscreen>

The parameters infile and outfile are to be replaced by the names of
your input and output file.  The > is the "IO redirection" symbol under
both DOS and UNIX, and it causes the output file to be written to
outfile.  If the > symbol and the outfile are omitted, the output is
printed on the screen.  Under DOS, the user must wait for this command
to finish before another can be run.  Under UNIX, one can enter either

<tscreen><verb>
nohup  XMD  infile  >  outfile  &
</verb></tscreen>

on the IBM Risc 6000 using the AIX operating system, or

<tscreen><verb>
xmd  infile  >  outfile  &
</verb></tscreen>

under Linux and other Unix's.  These commands will run XMD in
"background" mode.  That is, while the program is running, you will be
able to run other commands and programs as well.  Both nohup and
&amp are
special to UNIX.

<p>
You can include up to 9 optional parameters after the input file
name denoted as &dollar;1, &dollar;2, .. &dollar;9 in the example above.
These strings will be substituted for
the strings &dollar;1, &dollar;2, &dollar;3, .. &dollar;9 in the input file.
This allows you to leave some input file parameters unspecified
until you run it.  For example, if you would like to run a
simulation at a variety of temperatures, you can put the string
&quot &dollar;1 &quot where XMD expects to see a temperature value.
Then when you run the program, you can enter

<tscreen><verb>
xmd infile 100 > outfile
</verb></tscreen>

for one run, then

<tscreen><verb>
xmd infile 200 > outfile