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particles are defined or displaced, and whenever repeating boundary
conditions are created using the SURFACE command.  Because the repeating
boundary conditions can only be in the form of a rectangular box,  their
use enforces a orthonormal, tetragonal or cubic symmetry depending on
the box symmetry.
<P>
<P>
<H2><A NAME="ss6.11">6.11 Constraints</A>
</H2>

<P>It is possible to apply a variety of constraints to particles using the
CONSTRAIN command.  The first form of the command restricts particles to
motion along a line, or within a plane.  This constraint can be applied
individually to particles, each particle can have its own line or plane.
The second form of the constraint command imposes a spherical wall
around the particles.  Any particles which attempt to pass through the
wall are reflected back by a harmonic spring.  This can be used to
impose a pressure on a simulation - the resulting pressure can be
monitored by using the WRITE or SSAVE commands to display the system
stress.  Care must be taken with the choice of spring constant, if the
choice is too large then the motion integration may become unstable.  It
is recommended that before doing a production run, the user first do a
short run with no temperature clamp to insure that the total energy is
conserved (see discussion of under TIME STEP SIZE, page 3).
<P>
<P>
<H2><A NAME="implementation-run"></A> <A NAME="ss6.12">6.12 Run Identification</A>
</H2>

<P>Typically in research one will conduct a series of runs.  To aid in the
subsequent identification of a computer run, the user can assign a run
number 
(with the 
<A HREF="xmd-8.html#command-run">RUN command</A>) 
that will be stored in the STATE and RCV
files produced by XMD.  Furthermore every step is identified by a
number, starting with 0 for the first step (i.e. the particle
coordinates before the first integration step).  In addition to the
above output files, the step is also saved in the ESAVE, BSAVE and SSAVE
files.  Additional identification can be provided by a user specified
title, entered with the TITLE command.  The title is composed of 8 ASCII
strings each up to 80 characters long, it is stored in the STATE, RCV,
and COR files and is written out to the plot output.  The current value
of the run, step or title can be displayed into the standard output via
the WRITE RUN, WRITE STEP, or WRITE TITLE command.
<P>
<P>
<H2><A NAME="ss6.13">6.13 RCV File Format</A>
</H2>

<P>The RCV file format was originally designed for sending molecular
dynamics results (particle coordinates for various time steps) from
remote super computers to local workstations using normal phone lines.
Some computers would freely translate non-ASCII characters from one
value to another, so the RCV file format avoids these  characters.  The
resulting format uses standard ASCII text for miscellaneous data (i.e.
temperature, box size, time step, etc.) but the file format uses a type
of encoding for particle coordinates.  Although better schemes could be
implemented today, the RCV format persists because of the many utility
program written that require it.  The RCV file consists of one or more
equivalent sections, each containing coordinate data and other data for
a single simulation step.  Besides coordinate data each section contains
a 100 point histogram of the coordinate RDF (radial distribution
function). This was originally included in the RCV file because the RDF
was used regularly and calculating the RDF was too slow on PC class
workstations.  The RDF is calculated as the number of atom pairs whose
radii fall between 0 and twice the "unit cell distance".  This unit cell
distance can be an arbitrary number but is intended to be the unit cell
length of a BCC lattice of the same density as the system being
simulated.  The assumption about the identity of the "unit cell length"
is important only for some existing RCV analysis programs.  The RDF
function is encoded using the same encoding scheme as the particle
encoding.
<P>
<P>
<H3>Coordinate and RDF Encoding Scheme</H3>

<P>All the particle coordinates are mapped onto a range of integers from 0
to 9999.  For dimensions with repeating boundaries the integer 0
corresponds to a coordinate of 0, and the integer 9999 corresponds to a
coordinate equal to the box size.  For dimensions with free surfaces, 0
corresponds to the smallest  coordinate (which could be less than zero)
and 9999 corresponds to the largest.  Each resulting integer is coded as
a pair of ASCII characters.  Each ASCII character serves as a single
digit in a base 100 representation and ranges from 0 to 99.  The first
digit (call it i) is the low order digit, the second (call it j) is the
high order digit, so that the resulting integer is 100*j+i.  The ASCII
characters 27 to 126 are mapped into the digits 0 to 99.
<P>
<P>When coding dimensions with free surfaces the box size becomes the
distance between the smallest and greatest coordinate.  In addition a
second value is stored in ASCII format: the translation.  This number is
subtracted from 0 or the box size to obtain the smallest or greatest
coordinate respectively.  The x, y and z coordinates of each particle
are stored sequentially, up to 13 particles (or 39 coordinates or 78
characters) per line.  The encoding for the RDF is very similar, the
main difference being that (1) only 100 points are encoded (the points
of the RDF) and (2) the integers 0 to 9999 are mapped onto the interval
from 0 to MAXTABLE, where MAXTABLE is the maximum value of the RDF.
<P>
<P>
<P>
<H2><A NAME="ss6.14">6.14 COR File Format</A>
</H2>

<P>The COR file format is a replacement for the RCV file format.  Its
design was not restricted by the requirement to send files over normal
phone lines.  The primary differences between the COR and RCV formats
are
<P>
<UL>
<LI>  the COR file stores the atom types along with the coordinates,
</LI>
<LI>  the particle coordinates are stored as two byte integers (i.e.
integers between 0 and 65355).
</LI>
<LI>  the RDF is not stored in the COR file and
</LI>
<LI>  the COR file uses non-ascii characters, consequently it is
difficult (or impossible) to edit with a typical text editor.  Other
information stored in a COR file
</LI>
<LI>  Number of particles,
</LI>
<LI>  Boundary conditions,
</LI>
<LI>  Run and Step Number,
</LI>
<LI>  Title,
</LI>
<LI>  Energies - Kinetic, Potential, Total and "Bath".
</LI>
</UL>
<P>
<P>
<P>
<H2><A NAME="ss6.15">6.15 Atom Plots</A>
</H2>

<P>XMD can produce graphical output of the simulation atoms.  This is done
with the PLOT commands.  With these commands you can
<P>
<UL>
<LI> assign various symbols, sizes and colors to atoms,
</LI>
<LI> select the orientation of the plot,
</LI>
<LI> set the number of pages,
</LI>
<LI> plot 'tails' (lines which emanate from each atom to show their motion),
</LI>
<LI> plot bonds (lines connecting atoms within a certain distance from
one another),
</LI>
<LI> set the output destination (typically a file or device) and
format (typically Postscript).
</LI>
</UL>
<P>
<P>
<P>
<H2><A NAME="ss6.16">6.16 REPEAT Command</A>
</H2>

<P>Often XMD simulations involve repeating blocks of instructions.
To make these easier to handle there is the REPEAT command.
The REPEAT command is a simple loop command that looks like this,
<BLOCKQUOTE><CODE>
<PRE>
repeat 10
   cmd 100
   write cor +femelt.cor
end
</PRE>
</CODE></BLOCKQUOTE>

All commands between the REPEAT and the END are repeated 10 times in
this example.  You can even have REPEAT commands within other REPEAT
commands.
<P>
<P>
<P>
<H2><A NAME="implementation-calc"></A> <A NAME="ss6.17">6.17 Built-in Calculator </A>
</H2>

<P>A useful feature of XMD is the built-in line calculator.  It can be used
in two ways.  You can use expressions such as <CODE>sqrt(2)</CODE> in place
of a number for any XMD command.  For example, you can have the commmand
<BLOCKQUOTE><CODE>
<PRE>
fill cell  sqrt(2)/2 0 0   0 sqrt(2)/2 0   0 0 1
</PRE>
</CODE></BLOCKQUOTE>

and the value of sqrt(2) will be used
the <CODE>FILL CELL</CODE> command.
Note that you cannot have any spaces in these expressions when
used this way, otherwise the expression will be considered to
be two (or more) separate values.
<P>The calculator can also be used to set values.  We could have
written the above command as
<BLOCKQUOTE><CODE>
<PRE>
fill cell  x=sqrt(2)/2 0 0  0 x 0  0 0 1
</PRE>
</CODE></BLOCKQUOTE>

Thisi will set the varible X to sqrt(2)/2 and use this value
for the first number.  Then, it will use this value of X to
set the 5'th number on the line.
<P>You can also use the command CALC to perform calculations on
variables
(see the section on the 
<A HREF="xmd-8.html#command-calc">CALC command</A>).
This is especially useful when used with the REPEAT
command, for example
<BLOCKQUOTE><CODE>
<PRE>
calc TEMP=100
repeat 5
   itemp TEMP
   cmd   100
   write cor +fetest.cor
   calc  TEMP = TEMP + 100
end
</PRE>
</CODE></BLOCKQUOTE>

Here we are simulating at system at increasing temperatures, starting
with 100 Kelvin and increasing to 500 Kelvin.
Note that in the CALC command you do not need to remove spaces
as you did in the first two examples.  Also, variables are
case insensitive, <CODE>temp</CODE> means the same as <CODE>TEMP</CODE>.
Variables set at one place in the program, either by the CALC
command or within other commands as in the first two examples,
are available for the remainder of the program (except for the
limited exception covered in the next paragraph).
<P>Some commands offer an additional capability.
The commands MOVE, DAMP, EXTFORCE and EXTSPRING interpret the
variables X, Y and Z in a special manner (and as a consequence,
if you used variables named X, Y or Z previously, they are
not available for this command).  These commands apply changes
to each individual atom.  You can use the special X, Y and Z
variables to make these changes a function of the atom's position.
See the
<A HREF="xmd-8.html#command-move">MOVE command</A>
for an example.
See the MOVE command for an example.
<P>
<P>
<P>
<H2><A NAME="implementation-macros"></A> <A NAME="ss6.18">6.18 Macros </A>
</H2>

<P>XMD allows the use of &quot;Macros&quot;.  The first use is to
allow options to be set from the command line.  For example, if