git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5530 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/set.html

@@ -21,7 +21,7 @@
 
 <LI>one or more keyword/value pairs may be appended 
 
-<LI>keyword = <I>type</I> or <I>type/fraction</I> or <I>mol</I> or 	  <I>x</I> or <I>y</I> or <I>z</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or           <I>charge</I> or <I>dipole</I> or <I>dipole/random</I> or <I>quat/random</I> or 	  <I>diameter</I> or <I>density</I> or <I>volume</I> or <I>image</I> or
+<LI>keyword = <I>type</I> or <I>type/fraction</I> or <I>mol</I> or <I>x</I> or <I>y</I> or <I>z</I> or           <I>charge</I> or <I>dipole</I> or <I>dipole/random</I> or <I>quat/random</I> or 	  <I>diameter</I> or <I>density</I> or <I>volume</I> or <I>image</I> or
 	  <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> 
 
 <PRE>  <I>type</I> value = atom type
@@ -31,7 +31,6 @@
     seed = random # seed (positive integer)
   <I>mol</I> value = molecule ID
   <I>x</I>,<I>y</I>,<I>z</I> value = atom coordinate (distance units)
-  <I>vx</I>,<I>vy</I>,<I>vz</I> value = velocity component (velocity units)
   <I>charge</I> value = atomic charge (charge units)
   <I>dipole</I> values = x y z
     x,y,z = orientation of dipole moment vector
@@ -60,7 +59,7 @@
 set group solvent type/fraction 2 0.5 12393
 set group edge bond 4
 set region half charge 0.5
-set atom 100 x 0.5 vx 1.0
+set atom 100 x 0.5 y 1.0
 set atom 1492 type 3 
 </PRE>
 <P><B>Description:</B>
@@ -105,10 +104,9 @@ used.
 style</A> being used must support the use of molecule
 IDs.
 </P>
-<P>Keywords <I>x</I>, <I>y</I>, <I>z</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, and <I>charge</I> set the
+<P>Keywords <I>x</I>, <I>y</I>, <I>z</I>, and <I>charge</I> set the coordinates or charge of
-coordinates, velocity, or charge of all selected atoms.  For <I>charge</I>,
+all selected atoms.  For <I>charge</I>, the <A HREF = "atom_style.html">atom style</A>
-the <A HREF = "atom_style.html">atom style</A> being used must support the use of
+being used must support the use of atomic charge.
-atomic charge.
 </P>
 <P>Keyword <I>dipole</I> uses the specified x,y,z values as components of a
 vector to set as the orientation of the dipole moment vectors of the

doc/set.txt

@@ -15,8 +15,7 @@ set style ID keyword values ... :pre
 style = {atom} or {group} or {region} :ulb,l
 ID = atom ID or group ID or region ID :l
 one or more keyword/value pairs may be appended :l
-keyword = {type} or {type/fraction} or {mol} or \
+keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
-	  {x} or {y} or {z} or {vx} or {vy} or {vz} or \
           {charge} or {dipole} or {dipole/random} or {quat/random} or \
 	  {diameter} or {density} or {volume} or {image} or
 	  {bond} or {angle} or {dihedral} or {improper} :l
@@ -27,7 +26,6 @@ keyword = {type} or {type/fraction} or {mol} or \
     seed = random # seed (positive integer)
   {mol} value = molecule ID
   {x},{y},{z} value = atom coordinate (distance units)
-  {vx},{vy},{vz} value = velocity component (velocity units)
   {charge} value = atomic charge (charge units)
   {dipole} values = x y z
     x,y,z = orientation of dipole moment vector
@@ -55,7 +53,7 @@ set group solvent type 2
 set group solvent type/fraction 2 0.5 12393
 set group edge bond 4
 set region half charge 0.5
-set atom 100 x 0.5 vx 1.0
+set atom 100 x 0.5 y 1.0
 set atom 1492 type 3 :pre
 
 [Description:]
@@ -100,10 +98,9 @@ Keyword {mol} sets the molecule ID for all selected atoms.  The "atom
 style"_atom_style.html being used must support the use of molecule
 IDs.
 
-Keywords {x}, {y}, {z}, {vx}, {vy}, {vz}, and {charge} set the
+Keywords {x}, {y}, {z}, and {charge} set the coordinates or charge of
-coordinates, velocity, or charge of all selected atoms.  For {charge},
+all selected atoms.  For {charge}, the "atom style"_atom_style.html
-the "atom style"_atom_style.html being used must support the use of
+being used must support the use of atomic charge.
-atomic charge.
 
 Keyword {dipole} uses the specified x,y,z values as components of a
 vector to set as the orientation of the dipole moment vectors of the

doc/velocity.html

@@ -24,6 +24,7 @@
     seed = random # seed (positive integer)
   <I>set</I> args = vx vy vz
     vx,vy,vz = velocity value or NULL (velocity units)
+    any of vx,vy,vz van be a variable (see below)
   <I>scale</I> arg = temp
     temp = temperature value (temperature units)
   <I>ramp</I> args = vdim vlo vhi dim clo chi
@@ -52,7 +53,7 @@
 <P><B>Examples:</B>
 </P>
 <PRE>velocity all create 300.0 4928459 rot yes dist gaussian
-velocity border set NULL 4.0 3.0 sum yes units box
+velocity border set NULL 4.0 v_vz sum yes units box
 velocity flow scale 300.0
 velocity flow ramp vx 0.0 5.0 y 5 25 temp mytemp
 velocity all zero linear 
@@ -69,7 +70,20 @@ number generator with the specified seed as the specified temperature.
 </P>
 <P>The <I>set</I> style sets the velocities of all atoms in the group to the
 specified values.  If any component is specified as NULL, then it is
-not set.
+not set.  Any of the vx,vy,vz velocity components can be specified as
+an equal-style or atom-style <A HREF = "variable.html">variable</A>.  If the value
+is a variable, it should be specified as v_name, where name is the
+variable name.  In this case, the variable will be evaluated, and its
+value used to determine the velocity component.
+</P>
+<P>Equal-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters or other parameters.
+</P>
+<P>Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates.  Thus it is easy to specify a spatially-dependent
+velocity field.
 </P>
 <P>The <I>scale</I> style computes the current temperature of the group of
 atoms and then rescales the velocities to the specified temperature.

doc/velocity.txt

@@ -19,6 +19,7 @@ style = {create} or {set} or {scale} or {ramp} or {zero} :l
     seed = random # seed (positive integer)
   {set} args = vx vy vz
     vx,vy,vz = velocity value or NULL (velocity units)
+    any of vx,vy,vz van be a variable (see below)
   {scale} arg = temp
     temp = temperature value (temperature units)
   {ramp} args = vdim vlo vhi dim clo chi
@@ -44,7 +45,7 @@ keyword = {dist} or {sum} or {mom} or {rot} or {temp} or {loop} or {units} :l
 [Examples:]
 
 velocity all create 300.0 4928459 rot yes dist gaussian
-velocity border set NULL 4.0 3.0 sum yes units box
+velocity border set NULL 4.0 v_vz sum yes units box
 velocity flow scale 300.0
 velocity flow ramp vx 0.0 5.0 y 5 25 temp mytemp
 velocity all zero linear :pre
@@ -61,7 +62,20 @@ number generator with the specified seed as the specified temperature.
 
 The {set} style sets the velocities of all atoms in the group to the
 specified values.  If any component is specified as NULL, then it is
-not set.
+not set.  Any of the vx,vy,vz velocity components can be specified as
+an equal-style or atom-style "variable"_variable.html.  If the value
+is a variable, it should be specified as v_name, where name is the
+variable name.  In this case, the variable will be evaluated, and its
+value used to determine the velocity component.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include "thermo_style"_thermo_style.html command
+keywords for the simulation box parameters or other parameters.
+
+Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates.  Thus it is easy to specify a spatially-dependent
+velocity field.
 
 The {scale} style computes the current temperature of the group of
 atoms and then rescales the velocities to the specified temperature.