git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@774 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/change_box.html

@@ -47,11 +47,14 @@ orthogonal box.
 </P>
 <P><B>Restrictions:</B>
 </P>
-<P>When this command is used, no <A HREF = "dump.html">dumps</A> can be defined, nor
-can <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> or <A HREF = "fix_deform.html">fix
-deform</A> be defined.  This is because these commands
-test whether the simulation box is orthogonal or not when they are
-first issued.
+<P>At the point in the input script when this command is issued, no
+<A HREF = "dump.html">dumps</A> can be active, nor can a <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A> or <A HREF = "fix_deform.html">fix deform</A> be
+active.  This is because these commands test whether the simulation
+box is orthogonal when they are first issued.  Note that these
+commmands can appear in your script before a change_box command is
+issued, so long as an <A HREF = "undump.html">undump</A> or <A HREF = "unfix.html">unfix</A>
+command is also used to turn them off.
 </P>
 <P><B>Related commands:</B> none
 </P>

doc/change_box.txt

@@ -43,11 +43,14 @@ orthogonal box.
 
 [Restrictions:]
 
-When this command is used, no "dumps"_dump.html can be defined, nor
-can "fix ave/spatial"_fix_ave_spatial.html or "fix
-deform"_fix_deform.html be defined.  This is because these commands
-test whether the simulation box is orthogonal or not when they are
-first issued.
+At the point in the input script when this command is issued, no
+"dumps"_dump.html can be active, nor can a "fix
+ave/spatial"_fix_ave_spatial.html or "fix deform"_fix_deform.html be
+active.  This is because these commands test whether the simulation
+box is orthogonal when they are first issued.  Note that these
+commmands can appear in your script before a change_box command is
+issued, so long as an "undump"_undump.html or "unfix"_unfix.html
+command is also used to turn them off.
 
 [Related commands:] none
 

doc/compute_temp_deform.html

@@ -46,13 +46,13 @@ velocity which is used to compute the temperature.
 </P>
 <P>IMPORTANT NOTE: <A HREF = "fix_deform.html">Fix deform</A> has an option for
 remapping either atom coordinates or velocities to the changing
-simulation box.  To use this compute, the fix should NOT remap atom
+simulation box.  To use this compute, fix deform should NOT remap atom
 positions, but rather should let atoms respond to the changing box by
 adjusting their own velocities (or let fix deform remap the atom
-velocities).  If the fix does remap atom positions, their velocity is
-not changed, and thus they do not have the streaming velocity assumed
-by this compute.  LAMMPS will warn you if this setting is not
-consistent.
+velocities).  If fix deform does remap atom positions, their velocity
+is not changed, and thus they do not have the streaming velocity
+assumed by this compute.  LAMMPS will warn you if the fix deform
+setting is not consistent with this compute.
 </P>
 <P>The temperature is calculated by the formula KE = dim/2 N k T, where
 KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),

doc/compute_temp_deform.txt

@@ -43,13 +43,13 @@ velocity which is used to compute the temperature.
 
 IMPORTANT NOTE: "Fix deform"_fix_deform.html has an option for
 remapping either atom coordinates or velocities to the changing
-simulation box.  To use this compute, the fix should NOT remap atom
+simulation box.  To use this compute, fix deform should NOT remap atom
 positions, but rather should let atoms respond to the changing box by
 adjusting their own velocities (or let fix deform remap the atom
-velocities).  If the fix does remap atom positions, their velocity is
-not changed, and thus they do not have the streaming velocity assumed
-by this compute.  LAMMPS will warn you if this setting is not
-consistent.
+velocities).  If fix deform does remap atom positions, their velocity
+is not changed, and thus they do not have the streaming velocity
+assumed by this compute.  LAMMPS will warn you if the fix deform
+setting is not consistent with this compute.
 
 The temperature is calculated by the formula KE = dim/2 N k T, where
 KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),

doc/fix_deform.html

@@ -50,9 +50,8 @@
         V = change tilt factor at this velocity (distance/time units),
 	    effectively an engineering shear strain rate
       <I>erate</I> value = R
-        R = engineering shear strain rate (1/time units) 
-</PRE>
-<PRE>      <I>trate</I> value = R
+        R = engineering shear strain rate (1/time units)
+      <I>trate</I> value = R
         R = true shear strain rate (1/time units) 
 </PRE>
 <LI>zero or more keyword/value pairs may be appended 
@@ -337,10 +336,9 @@ used.  This is because <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> adjusts
 atom positions and velocities to provide a velocity profile that
 matches the changing box size/shape.  Thus atom coordinates should NOT
 be remapped by fix deform, but velocities SHOULD be when atoms cross
-periodic boundaries, since when atoms cross periodic boundaries since
-that is consistent with maintaining the velocity profile created by
-fix nvt/sllod.  LAMMPS will warn you if this settings is not
-consistent.
+periodic boundaries, since that is consistent with maintaining the
+velocity profile already created by fix nvt/sllod.  LAMMPS will warn
+you if the <I>remap</I> setting is not consistent with fix nvt/sllod.
 </P>
 <P>The <I>units</I> keyword determines the meaning of the distance units used
 to define various arguments.  A <I>box</I> value selects standard distance

doc/fix_deform.txt

@@ -43,7 +43,7 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
         V = change tilt factor at this velocity (distance/time units),
 	    effectively an engineering shear strain rate
       {erate} value = R
-        R = engineering shear strain rate (1/time units) :pre
+        R = engineering shear strain rate (1/time units)
       {trate} value = R
         R = true shear strain rate (1/time units) :pre
 
@@ -326,10 +326,9 @@ used.  This is because "fix nvt/sllod"_fix_nvt_sllod.html adjusts the
 atom positions and velocities to provide a velocity profile that
 matches the changing box size/shape.  Thus atom coordinates should NOT
 be remapped by fix deform, but velocities SHOULD be when atoms cross
-periodic boundaries, since when atoms cross periodic boundaries since
-that is consistent with maintaining the velocity profile created by
-fix nvt/sllod.  LAMMPS will warn you if this settings is not
-consistent.
+periodic boundaries, since that is consistent with maintaining the
+velocity profile already created by fix nvt/sllod.  LAMMPS will warn
+you if the {remap} setting is not consistent with fix nvt/sllod.
 
 The {units} keyword determines the meaning of the distance units used
 to define various arguments.  A {box} value selects standard distance