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一个很好的分子动力学程序

this will change the current particle state, and the particle state
after this command runs will be the last step in the COR file.  The name
of the file is file, and the beginning step1 and ending step2 step
number may be specified.  This is the step number assigned when the COR
file was written.  For example the COR file may have the steps 100, 200,
300, etc.  The step numbers do not indicate the sequence of steps.  For
example, a value of 5 means step 5, not the fifth step - it could even
be the first step.  If the ending step is omitted then all steps are
read to the end of the file.  If the beginning step is omitted, then the
command starts with the first step in the file.
<P>
<P>
<DT><B>ROTATE xaxis yaxis zaxis  xcenter ycenter zcenter  angle</B><DD><P>This command rotates the selected particles
about the specified axis by the given angle (in degrees).  The axis
direction is given by the vector xaxis yaxis zaxis (the magnitude of the
vector is ignored).  The coordinates xcenter ycenter zcenter locate the
axis in space by specifying a point which the axis must pass through.
The rotation follows the &quot; right hand rule &quot;, meaning that when
the thumb of one's right hand points in the direction of the axis the
remaining fingers, when curled, point in the direction of a positive
rotation.
<P>
<P>
<A NAME="command-run"></A> <DT><B>RUN run</B><DD><P>Sets the run number to run.  Used by PLOT, STATE and WRITE RCV (see
section on 
<A HREF="xmd-6.html#implementation-run">run identification</A>).
<P>
<DT><B>SCALE xscale [yscale [zscale]]</B><DD><P>Scales the box and particles by xscale, yscale and zscale respectively
in the x, y and z directions.  If zscale is omitted it is set to the
yscale, similarly if yscale is omitted it is set to xscale.
<P>
<P>
<DT><B>SCREW xburgers yburgers zburgers  xorg yorg zorg  [ xref yref zref ]</B><DD><P>Apply displacements to selected particles to form a screw dislocation in
a previously perfect lattice. xburgers, yburgers, zburgers, are the
components of the burgers vector. xorg, yorg, zorg, specify a point
through which the screw line passes.  The optional xref, yref, zref,
specify a reference direction non-parallel to the burgers vector (which
is also the direction of the screw dislocation line).  This reference
together with the screw dislocation line defines the reference plane.
All atoms within this reference plane undergo zero displacement.  If no
reference direction is specified, an arbitrary one is used.  The
displacement of each atom is given by
<P>
<BLOCKQUOTE><CODE>
<PRE>
di = b * sin(ai)
</PRE>
</CODE></BLOCKQUOTE>
<P>where di is the atom displacement, ai is the angle made with the
reference plane by the line joining the atom i and the origin point, and
b is the burgers vector.
<P>
<DT><B>SEED seed</B><DD><P>Set the random number generator to seed.  The random number generator is
used by ITEMP as well as for random moves by MC command.
<P>
<P>
<P>
<A NAME="command-select"></A> <DT><B>SELECT</B><DD><P>
<P>The full form of the SELECT command with all possible options is
<BLOCKQUOTE><CODE>
<PRE>
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]]
 | LAYER {x|y|z} nlayer l1 [l2  [l3 [..] ] ]
 | NEAR n x y z
 | PLANE xn yn zn  x1 y1 z1  x2 y2 z2
 | SET set
 | TAG tag
 | TYPE type 
 | VELOCITY [ ABS ] { X | Y| Z | MAG } lo hi }
</PRE>
</CODE></BLOCKQUOTE>
<P>
<P>This command selects a subset of particles according to the given
criteria.  AND selects only those particles that have been both
previously selected or fit the current criteria.  OR selects particles
that belong to either group.  NOT selects those particles which do not
fit the given criteria.  XOR selects those particles have been
previously selected or which fit the current criteria, but not both.
<P>
<DL>
<P>
<DT><B> ALL </B><DD><P>selects all particles.
<P>
<DT><B> BOX  x1 y1 z1  x2 y2 z2 </B><DD><P>selects all particles within a box whose opposite corners are (x1,y1,z1)
and (x2,y2,z2).
<P>
<DT><B> EATOM lo hi</B><DD><P>selects all atoms whose potential energy falls between lo and hi, where
the units are those specified by the EUNIT command (default is ergs).
Important:  This command uses the energies which last calculated for the
atoms when the commands WRITE ENERGY, WRITE EATOM, CMD, QUENCH or MC
where executed.  This command will NOT re-calculate the energies.
<P>
<DT><B> ELLIPSE xc yc zc xr yr zr</B><DD><P>selects those particles within an ellipse centered on (xc,yc,zc) and
whose axes are (xr,yr,zr).
<P>
<DT><B> ILIST nlist /  i1 i2 i3 ... </B><DD><P>selects all particles whose indices are listed.  nlist is the number of
indices in the list.  The list of indices is placed on the subsequent
lines.
<P>
<DT><B> INDEX i1 [i2 [iskip]] </B><DD><P>selects particles numbered from i1 to i2.  If i2 is omitted then only
particle i1 is selected.  If iskip is included then only every iskip'th
particle starting at i1 and not exceeding i2 is selected.
<P>
<DT><B> LAYER {x|y|z} nlayer l1 [l2  [l3 [..] ] ] </B><DD><P>divides the simulation into nlayer layers in the x, y, or z direction
and selects those atoms in layer(s) l1, l2, ...  If there are repeating
boundary conditions then it divides the box into nlayers, otherwise it
divides the space between the maximum and minimum particles in the
selected direction.
<P>
<DT><B> NEAR n x y z </B><DD><P>selects n nearest particles to the point (x,y,z).
<P>
<DT><B> PLANE xn yn zn  x1 y1 z1  x2 y2 z2 </B><DD><P>selects particles between two parallel planes.  The planes are normal to
the vector (xn,yn,zn).  The two planes pass through the points
(x1,y1,z1) and (x2,y2,z2) respectively.
<P>
<DT><B> SET set </B><DD><P>selects all particles in specified set (set value ranges from 1 to 8).
<P>
<DT><B> TAG tag </B><DD><P>selects all particles with specified tag value (values range from 0 to 255).
<P>
<DT><B> TYPE type  </B><DD><P>chooses all particles of type type.
<P>
<DT><B> VELOCITY [ ABS ] { X | Y| Z | MAG } lo hi </B><DD><P>chooses particles with velocities between lo and hi.  
One can use the X, Y or Z components of the velocity, in which
case one can also use the ABS option to query the absolute value of 
the velocity.  The MAG option compares the magnitude of the velocity, 
in which case the ABS option is irrelevant.  The units for X, Y, Z and
MAG are centimeters per second.
<P>
</DL>
<P>
<P>
<DT><B>SELECT KEEP { ON | OFF }</B><DD><P>Determines if SELECT, SET and TAG info is forgotton (OFF) or remembered
(ON) when coordinates are read with the COR or RCV commands.  The default
is OFF.  For further discussion see section
<A HREF="xmd-6.html#particle-selection">Particle Selection</A>.
<P>
<P>
<P>
<P>
<P>
<P>
<DT><B>SET { ADD | SUB | CLEAR } set</B><DD><P>Either adds or subtracts (ADD or SUB) selected particles from set number set
(which can range between 1 and 12).  The CLEAR option resets the specified set
to be empty.
<P>
<P>
<DT><B>SIZE size</B><DD><P>Sets the size of a jump used by MC.  Units are angstroms.
<P>
<P>
<DT><B>SSAVE nskip file</B><DD><P>Causes the average internal scaled stress per particle (not the true stress) to be written to file every nskip
steps.  The data file is a text file with 7 columns.  The first column is the step number, the following six
columns are the Voight scaled stresses per atom in units of ergs.  To obtain the true Voight stresses from the
scale stresses, you must divide by the volume per atom.  The program does not do this automatically, because
when there are free surfaces and/or lattice voids the volume per atom is not well defined.
SSAVE works when using EAM and PAIR potentials, but does not currently work for the Tersoff potential.
<P>
<P>
<DT><B>STATE file</B><DD><P>Reads current state of CMD and MC simulation in the file file (where the
file was created with the WRITE STATE command).
<P>
<P>
<DT><B>STEP step</B><DD><P>Sets the step number to step.  Used by PLOT, STATE, ESAVE and WRITE RCV (see WRITE below,
page 23).
<P>
<P>
<DT><B>STRESS THERMAL { ON | OFF }</B><DD><P>
<P>Most (all?) thermodynamics texts include the a term in the 
atomic velocities (the 'virial') when calculating the internal
stress.  By default XMD does not include this term, but includes
only the internal stress which arises directly from the force.
If you wish to include the virial term, then use the command
<BLOCKQUOTE><CODE>
<PRE>
   STRESS THERMAL ON 
</PRE>
</CODE></BLOCKQUOTE>

This is a controversial issue, I think it can be resolved
by considering the internal stress and thermal expansion of
a perfectly harmonic solid.  Such a solid DOES NOT expand
with increasing temperature, but it would expand if the
virial term were correct.
Anyway, there's probably a paper in this somewhere :)
<P>
<P>
<P>
<DT><B>SURFACE { ON | OFF } { X | Y | Z } [X|Y|Z|ON|OFF] ...</B><DD><P>
<P>Determines whether a free surface or repeating boundary condition is
used with the MC and CMD simulations (see page 7).  SURFACE ON X Y Z
creates a free surface in the x, y and z directions.  SURFACE OFF X Y ON
Z creates a free surface in the z direction and repeating boundary
conditions in the x and y directions.  By default repeating boundary
conditions exist in all three directions.  When there is a free surface
the box dimension is ignored for that dimension.
<P>
<P>
<DT><B>TAG tag</B><DD><P>
<P>Sets tag value for selected atoms.  Every atom can have a tag value between 0
and 255.  The default value is 0.  Tag values are used similar to sets, but
where a single atom can belong to any combination of sets, a single atom can
only have one tag value.  Thus if atoms are grouped by their tag values, each
atom can belong to only one group.  You can select atoms according to their
tag value with the SELECT command.
<P>
<P>
<DT><B>TYPE type</B><DD><P>
<P>Sets type value for selected atoms.  The properties of each atom type
is controlled by the potential model.
<P>
<P>
<DT><B>TYPELIST [SEL] ntype</B><DD><P>
<P>Reads ntype number of types from input lines following command.  These
types are assigned existing particles (or selected particles).  ntype
can be either less or more than the number of particles (or selected
particles).  If less, then only the first ntype particles are changes.
If more, then the extra types read in are ignored.
<P>
<P>
<DT><B>TYPENAME t1 name1 [ t2 name2 ] [ t3 name3 ] ... [tn namen]</B><DD><P>
<P>Associates the type number t1 (or t2, etc.)  with the element name name1 (or name2, etc.).  This is
typically used to assign element abbreviations (such as FE, NA) to be used in place of type numbers for certain
output formats (currently WRITE XMOL and WRITE PDB).
<P>
<P>
<DT><B>VELOCITY {  LINEAR | ANGULAR} dx dy dz magnitude</B><DD><P>
<P>Sets the total linear or angular velocity for the selected
particles.  For the linear case, (dx, dy, dz) determines the direction
of the velocity, and magnitude is the magnitude of the velocity (in
centimeters per second).
<P>
<P>For the angular case, (dx,dy,dz) is the direction of the rotational
axis, and magnitude is the angular velocity (in radians per second).
The axis is positioned through the center of mass of the selected
particles.  The direction of positive angular velocity follows the right
hand rule:  if the thumb of the right hand is pointed along the axis,
then the curled fingers of that hand indicate the direction of positive
rotation.
<P>
<P>
<DT><B>VERBOSE { ON | OFF }</B><DD><P>
<P>Turns output comments on or off.  At present, only the  WRITE ATOM
command produces comments.
<P>
<P>
<DT><B>WAVE phase dx dy dz kx ky kz</B><DD><P>Displaces the selected particles by a wave.  
The new position of each particle is
<P>
<BLOCKQUOTE><CODE>
<PRE>
 r' = r + d  sin (k &middot; r)
</PRE>
</CODE></BLOCKQUOTE>
<P>where d is the wave vector (dx,dy,dz) and k is (kx,ky,kz). r is the
original particle coordinate measured from the origin and  r' is
the new particle coordinate.
<P>
</DL>
<P>
<P>
<P>
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