xmd.sgml

一个很好的分子动力学程序

CALC {expression..}
CLAMP [SEL] { temp cstep | OFF }
CMD nstep
CONSTRAIN OFF
CONSTRAIN { LINE | PLANE } xdir ydir zdir  xpnt ypnt zpnt
CONSTRAIN CAVITY  ELLIPSOID xc yc zc  xa ya za spring
CONSTRAIN CAVITY  SPHERE    xc yc zc  radius spring
COR file [ [ run ] step ]
DAMP { OFF | ON  [ [ formula [ formula .. ] ]   damp] }
DISP [SEL] { CLEAR | MOVE [scale] | READ n | REFCALC | SCALE scale }
DTIME dtime
DUP ndup xdisp ydisp zdisp
ECHO { ON | OFF }
ERASE file
ESAVE nskip file
EUNIT
EXTFORCE  { CLEAR | [ formula [ formula .. ] ]  fx fy fz }
EXTSPRING { CLEAR | [ formula [ formula .. ] ]  kx ky kz }
FIX {ON | OFF }
FIX       { ON | OFF }
FILL      ALIGN              x y z
FILL      BOUNDARY BOX       x1 y1 z1  x2 y2 z2
FILL      BOUNDARY SPHERE    radius xcenter ycenter zcenter
FILL      BOUNDARY CYLINDER  r length xc yc zc xorient yorient zorient
FILL      CELL
   ax ay az
   bx by bz
   cx cy cz
FILL      GO
FILL      MARGIN             margin
FILL      ORIENT             ax ay az  bx by bz  cx cy cz
FILL      PARTICLE n
   type x y z
 ....
ITEMP [SEL] temp [ X | Y | Z ]   [ X | Y | Z ] ...
LABEL nlabel
 ... (up to 8 lines)
MACRO name value
MACROF name format value
MASS mass
MC nstep dtemp
MOVE [ formula [ formula .. ] ] xdisp ydisp zdisp
NRANGE ratio
PARTICLE [ADD] np
 .. type x y z
PLOT BOND  {  OFF  |  ON  lo  hi  }
PLOT DEVICE { CANON | POSTSCRIPT }
PLOT DISP { ON | OFF | SCALE scale }
PLOT LAYER nlayer [ l1 [ l2 [ l3 .. ] ] ]
PLOT ORIENT { y/z z/y x/z z/x x/y y/x }
PLOT PAGE npage
PLOT SIZE xinch yinch
PLOT SYMBOL [FILL] [ RGB red green blue | HSB hue saturation brightness ]
  { NON | CIR | CRO | TRI | ITR | DIA | AST | SQU | NUM } radius
PLOT WRITE [SEL] [+]file
POSITION [ADD] np
 .. type x y z
POSVEL [ADD] np
 .. type x y z
POTENTIAL SET { EAM ntype | PAIR ntype | STILL | TERSOFF }
PRESSURE  ANDERSEN  xmass [ymass [zmass]] 
PRESSURE  CLAMP  bulkmodulus [cstep]  (bulk in units of MBAR)
PRESSURE  EXTERNAL pressureX [ pressureY [ pressureZ ] ] (Units of MBAR)
PRESSURE  { ISOTROPIC | ORTHORHOMBIC }
PRESSURE  OFF
PSTRAIN  e dx dy dz nx ny nz
QUENCH nstep [nquench]
RCV  file [ [run] step ]
READ file
REFSTEP [CLEAR | COPY | SWAP]
REMOVE
REPEAT nrepeat
 ... END
REPEAT { COR | RCV } filename [ step1 [ step2 ] ]
 ... END
ROTATE xaxis yaxis zaxis  xcenter ycenter zcenter  angle
RUN run
SCALE xscale [yscale [zscale]]
SCREW xburgers yburgers zburgers  xorg yorg zorg  [ xref yref zerf ]
SEED seed
SELECT  [AND | OR | NOT | XOR ]
 { ALL
 | BOX  x1 y1 z1 x2 y2 z2
 | EATOM lo hi
 | ELLIPSE xc yc zc xr yr zr
 | ILIST nlist
   i1 i2 i3 .....
 | INDEX i1 [i2 [iskip]]
 | NEAR n x y z
 | NONE
 | PLANE  xn yn zn  x1 y1 z1  x2 y2 z2
 | SET set
 | TAG tag
 | TYPE type 
 | VELOCITY [ ABS ] { X | Y | Z | MAG } lo hi
SELECT KEEP { ON | OFF }
SET { ADD | SUB | CLEAR } set
SIZE size
SSAVE nskip file
STATE
STEP step
STRESS THERMAL { ON | OFF }
SURFACE { ON | OFF } { X | Y | Z }   [ X | Y | Z | ON | OFF ]   ...
TAG tag
TYPE type
TYPELIST [ SEL ]  ntype
TYPENAME t1 name1 [ t2 name2 ] [ t3 name3 ] ... [tn namen]
VELOCITY {  LINEAR | ANGULAR } dx dy dz magnitude
VERBOSE  { ON | OFF }
WAVE      phase   dx dy dz   kx ky kz
WRITE     [SEL] COR  [+]fname
WRITE     [SEL] PDB  [+]fname
WRITE     [SEL] RCV  [+]fname
WRITE     [SEL] XMOL [+]fname
WRITE     [SEL] {ILIST | TYPELIST} [ [+]fname ]
WRITE     [SEL] [FILE [+]fname]  { STRESS }
WRITE     [SEL] [FILE [+]fname]  [AVG] [MIN] [MAX]
                                 { FORCE | PARTICLE | POSTVEL | VELOCITY }
WRITE     [SEL] [FILE [+]fname]  { DISP | EXTFORCE | EXTSPRING }
WRITE     [SEL] [FILE [+]fname]    EATOM
WRITE     [SEL] [FILE [+]fname]  { TEMP | EKIN | EPOT | ENERGY }
WRITE           [FILE [+]fname] RDF ntable rmin rmax [type1 type2]
WRITE           [FILE [+]fname] { BOX |  RUN | STEP }
WRITE     STATE fname
</verb>



<!--
************************************************************************
Commands
************************************************************************
-->

<sect> Commands

<p>

<descrip>

<tag> \ (backslash)</tag>
This is not really a command, but a special character which can be used
to extend a command onto multiple lines.  When the last character in a
command is a &quot \ &quot , then the next line appended to the end of
the current line.  A command can span multiple lines, but it is limited
to 1024 characters (typically between 12 and 20 lines).

<tag> &num (pound sign) </tag>

<p>

<tag> * (asterisk) </tag>
Used for commenting instruction files.  Lines whose first non-blank
character is an asterisk or a pound sign will be ignored.


<label id="command-box">
<tag>BOX [SCALE] xbox ybox zbox</tag>

Specifies the box size (in angstroms).  The box size is relevant when
(1) performing a calculation with repeating boundary conditions (see
option SURFACE) and (2) when writing a RCV file (see RCV).  If the
option scale is chosen then any existing coordinates will be re-scaled
(relative to the previous box size) to fit the new box.


<tag>BSAVE nskip file</tag>

Causes  CMD simulations to save the step number and the x, y and z box
sizes every nskip steps in file.  This is useful for monitering the box
size when using the PRESSURE command which allows the box size to
change.


<label id="command-calc">
<tag>CALC {expression..} </tag>

CALC is a rich command which provides a simple computational language.
For instance if the command

<tscreen><verb>
CALC  x = 2^(1/3)
</verb></tscreen>

is given, then a variable x is created that is set equal to 2 to the 1/3
power.  Later one could have a command

<tscreen><verb>
SCALE x
</verb></tscreen>

which would scale all the particles (and box) by 2^(1/3).  This variable can also be written out with the
statement

<tscreen><verb>
WRITE X
</verb></tscreen>

(see the WRITE string command below).
Furthermore in all commands which require a number, an algebraic
expression may be used (provided there are no embedded blanks).  Thus
you could also have the command

<tscreen><verb>
SCALE 2^(1/3)
</verb></tscreen>

The allowed operators are: + - * / ^ ( ) =
<p>
There are also allowed functions which are: sin() cos() tan() exp()
log() log10() acos() asin() atan() abs() sqrt() int() rand().
The functions sin(x), cos(x) and tan(x) expect angle x to be in 
radians.
The functions asin(x), acos(x) and atan(x) return the angle in units of
radians.
The function exp(x) return e^x.
The function log(x) returns log base e of x,
log10(x) returns log base 10.
The function abs(x) returns the absolute value of x.
The function sqrt(x) returns the square root of x.
The function int(x) returns the integer portion of x.
The function rand(x) returns a random number from the uniform
distribution between 0 and x.
<p>
There are two built in constants: pi and e.
<p>
There can be up to 128 variables set created in one program.
See more on CALC under the section on 
<ref id="implementation-calc" name="implementation">.


<tag>CLAMP [SEL] {temp [cstep] | OFF }</tag>

Maintains the temperature for both MC and CMD simulations.  For the MC
<tt>temp</tt> is used as the Boltzmann temperature and cstep is ignored.
<p>
For the CMD the particles velocities are scaled by
(T/<tt>temp</tt>)(1/(2*<tt>cstep</tt>))
at each CMD time step.  Here T is the instantaneous system temperature.
The application of this factor has the effect of forcing the particle
velocities to a value appropriate for the temperature <tt>temp</tt>.
The parameter cstep is used to control the rapidity at which the target
temperature is approached.  If temp is set to -1, then no temperature
clamp is used (this would be an adiabatic system).  See section on
Temperature Control.
<p>
XMD can maintain up to 4 separate particle groups at different
temperatures.  When the SEL option is used, the <tt>temp</tt> and
<tt>cstep</tt> or the OFF setting is applied to the selected particles,
the CLAMP settings for all other particles remain unchanged.
When the CLAMP command is given without the SEL option, then all
particles are set the same.


<tag> CLAMP INFO</tag>
This prints information about the up to 4 separate clamp settings.


<tag>CMD nstep</tag>
Initiates a CMD simulation for nstep time steps.
If ESAVE, BSAVE, SSAVE or TSAVE have been
implemented then the corresponding data will be written to disk.
Commands which directly affect the course of the CMD simulation are
CLAMP, CONSTRAIN, DAMP, DTIME, EXTFORCE, EXTSPRING, FIX, MASS, and SURFACE;
as well as the particle types and coordinates as determined by PARTICLE,
TYPE and STATE; and the interatomic potential as determined by POTSTATE
and POTENTIAL commands.


<tag>CONSTRAIN OFF  |  {LINE | PLANE} xdir ydir zdir  xpnt ypnt zpnt</tag>
Applies (LINE or PLANE) or removes (OFF) a constraint to the selected
particles.  The LINE and PLANE constraints force a particle to remain on
a line or plane, regardless of the forces it experiences.  In practice
this is done by ignoring any forces which are normal to the line or
plane.  The values xdir, ydir, zdir specify either the line direction or
the plane normal.  The values xpnt, ypnt, zpnt specify a coordinate
within the line or plane (it can be any one of many coordinates) - this
is necessary to locate the line or plane somewhere in space.


<tag>CONSTRAIN CAVITY ELLIPSOID  spring  xcenter ycenter zcenter  xaxis
yaxis zaxis</tag>
<p>


<tag>CONSTRAIN CAVITY SPHERE       spring  xcenter ycenter zcenter
radius</tag>

This command places an ellipsoidal &quot cavity &quot in the
simulation.  The cavity walls reflect particles.  When a particle passes
into a wall it experiences a spring force pushing back out.  The force
is equal to
<tscreen><verb>
F = &frac12 * spring * dq &sup2
</verb></tscreen>
where
<tt>dq</tt>
is the normal distance from wall to the particle, and
<tt>spring</tt>
is the spring constant.  Once the particle passes back out of the wall,
it no longer feels the force.  Only one cavity can be present in a
simulation.  All particles will be affected by the wall.
(xcenter,ycenter,zcenter) specifies the center of the cavity.  For a
spherical cavity, radius is the radius.  For an ellipsoidal cavity,
(xaxis,yaxis,zaxis) are the x,y,z half-axis, analogous to spherical
radii.  They measure the distance from the ellipsoid center to the
ellipsoid wall in the x,y,z directions.
Please note the following things about the CONSTRAIN CAVITY command.
<itemize>
<item>
(1)  Only one cavity can be present in a simulation.
<item>
(2) The cavity is affected by the SCALE command.  If the SCALE command
scales non-uniformly (difference scale in x, y and z directions) then
the an initially spherical cavity will become an ellipsoid, the
same as if it had been made with the CONSTRAIN CAVITY ELLIPSOID command
above.
<item>
(3) The cavity does know about repeating boundary conditions, so it can
overlap the box.
<item>
(4) The ellipsoid cavity can only be orientated with its axis along the
x, y and z directions.
<item>
(5)  A spring constant that is too large will cause instability in the
integration algorithm, the same kind of instability as having a time
step too large.  As a rough guide, make sure that spring satisfies the
following relation,
<tscreen><verb>
k = 4 pi&sup2; m / t&sup2;
</verb></tscreen>
where
k is the spring constant,
m is the mass in grams of the lightest particle in the simulation,
and t is the time step size in seconds.
</itemize>


<tag>COR file [ [run] step]</tag>

Reads a COR step from file.  If step is specified then the data for that
step is read; otherwise the first step in the file is read.  If step is
not in the file then an error message is given and the program
continues.  If run is specified (which implies that step is also
specified) then only the data that belongs to the run and step are read.
If step is specified without run, and two COR steps have the