git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3484 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_gravity.html

@@ -79,9 +79,8 @@ the gradient arguments are in full rotations per time unit.  E.g. a
 timestep of 0.001 and a gradient of 0.1 means the acceleration vector
 would rotate thru 360 degrees every 10,000 timesteps.  For the
 time-dependent case, the initial direction of the acceleration vector
-is phi,theta at the beginning of the simulation.  For 2d systems,
+is set to phi,theta when the fix is specified and evolves thereafter.
-<I>phi</I> and <I>phi_grad</I> are ignored.  See the note below about making the
+For 2d systems, <I>phi</I> and <I>phi_grad</I> are ignored.
-acceleration vector rotate continuously across multiple runs.
 </P>
 <P>Style <I>vector</I> imposes an acceleration in the vector direction given
 by (x,y,z).  For 2d systems, the z component is ignored.
@@ -92,15 +91,9 @@ by (x,y,z).  For 2d systems, the z component is ignored.
 files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
 are relevant to this fix.  No global scalar or vector or per-atom
 quantities are stored by this fix for access by various <A HREF = "Section_howto.html#4_15">output
-commands</A>.  
+commands</A>.  No parameter of this fix can be
-</P>
+used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
-<P>This fix can change the direction of the gravity vector, due to the
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
-time-dependent <I>gradient</I> keyword, continuously over multiple runs,
-using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command.
-If you do not do this, the direction of the gravity vector will be
-reset to its initial value at the beginning of each run.
-</P>
-<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/fix_gravity.txt

@@ -71,9 +71,8 @@ the gradient arguments are in full rotations per time unit.  E.g. a
 timestep of 0.001 and a gradient of 0.1 means the acceleration vector
 would rotate thru 360 degrees every 10,000 timesteps.  For the
 time-dependent case, the initial direction of the acceleration vector
-is phi,theta at the beginning of the simulation.  For 2d systems,
+is set to phi,theta when the fix is specified and evolves thereafter.
-{phi} and {phi_grad} are ignored.  See the note below about making the
+For 2d systems, {phi} and {phi_grad} are ignored.
-acceleration vector rotate continuously across multiple runs.
 
 Style {vector} imposes an acceleration in the vector direction given
 by (x,y,z).  For 2d systems, the z component is ignored.
@@ -84,14 +83,8 @@ No information about this fix is written to "binary restart
 files"_restart.html.  None of the "fix_modify"_fix_modify.html options
 are relevant to this fix.  No global scalar or vector or per-atom
 quantities are stored by this fix for access by various "output
-commands"_Section_howto.html#4_15.  
+commands"_Section_howto.html#4_15.  No parameter of this fix can be
-
+used with the {start/stop} keywords of the "run"_run.html command.
-This fix can change the direction of the gravity vector, due to the
-time-dependent {gradient} keyword, continuously over multiple runs,
-using the {start} and {stop} keywords of the "run"_run.html command.
-If you do not do this, the direction of the gravity vector will be
-reset to its initial value at the beginning of each run.
-
 This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:] none

doc/fix_move.html

@@ -87,8 +87,8 @@ notation as
 </PRE>
 <P>where <I>X0</I> = (x0,y0,z0) is their position at the time the fix is
 specified, <I>V</I> is the specified velocity vector with components
-(Vx,Vy,Vz), and <I>delta</I> is the time elapsed since the beginning of the
+(Vx,Vy,Vz), and <I>delta</I> is the time elapsed since the fix was
-simulation.  This style also sets the velocity of each atom to V =
+specified.  This style also sets the velocity of each atom to V =
 (Vx,Vy,Vz).  If any of the velocity components is specified as NULL,
 then the position and velocity of that component is time integrated
 the same as the <A HREF = "fix_nve.html">fix nve</A> command would perform, using
@@ -103,9 +103,9 @@ notation as
 <P>where <I>X0</I> = (x0,y0,z0) is their position at the time the fix is
 specified, <I>A</I> is the specified amplitude vector with components
 (Ax,Ay,Az), <I>omega</I> is 2 PI / <I>period</I>, and <I>delta</I> is the time
-elapsed since the beginning of the simulation.  This style also sets
+elapsed since the fix was specified.  This style also sets the
-the velocity of each atom to the time derivative of this expression.
+velocity of each atom to the time derivative of this expression.  If
-If any of the amplitude components is specified as NULL, then the
+any of the amplitude components is specified as NULL, then the
 position and velocity of that component is time integrated the same as
 the <A HREF = "fix_nve.html">fix nve</A> command would perform, using the
 corresponding force component on the atom.
@@ -187,11 +187,9 @@ for each atom is 3, and the components store the original unwrapped
 x,y,z coords of each atom.  The per-atom values be accessed on any
 timestep.
 </P>
-<P>This fix can move atoms continously over multiple runs, using the
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
-<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command.  See the
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
-<A HREF = "run.html">run</A> command for details of how to do this.
+minimization</A>.
-</P>
-<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/fix_move.txt

@@ -78,8 +78,8 @@ X(t) = X0 + V * delta :pre
 
 where {X0} = (x0,y0,z0) is their position at the time the fix is
 specified, {V} is the specified velocity vector with components
-(Vx,Vy,Vz), and {delta} is the time elapsed since the beginning of the
+(Vx,Vy,Vz), and {delta} is the time elapsed since the fix was
-simulation.  This style also sets the velocity of each atom to V =
+specified.  This style also sets the velocity of each atom to V =
 (Vx,Vy,Vz).  If any of the velocity components is specified as NULL,
 then the position and velocity of that component is time integrated
 the same as the "fix nve"_fix_nve.html command would perform, using
@@ -94,9 +94,9 @@ X(t) = X0 + A sin(omega*delta) :pre
 where {X0} = (x0,y0,z0) is their position at the time the fix is
 specified, {A} is the specified amplitude vector with components
 (Ax,Ay,Az), {omega} is 2 PI / {period}, and {delta} is the time
-elapsed since the beginning of the simulation.  This style also sets
+elapsed since the fix was specified.  This style also sets the
-the velocity of each atom to the time derivative of this expression.
+velocity of each atom to the time derivative of this expression.  If
-If any of the amplitude components is specified as NULL, then the
+any of the amplitude components is specified as NULL, then the
 position and velocity of that component is time integrated the same as
 the "fix nve"_fix_nve.html command would perform, using the
 corresponding force component on the atom.
@@ -178,11 +178,9 @@ for each atom is 3, and the components store the original unwrapped
 x,y,z coords of each atom.  The per-atom values be accessed on any
 timestep.
 
-This fix can move atoms continously over multiple runs, using the
+No parameter of this fix can be used with the {start/stop} keywords of
-{start} and {stop} keywords of the "run"_run.html command.  See the
+the "run"_run.html command.  This fix is not invoked during "energy
-"run"_run.html command for details of how to do this.
+minimization"_minimize.html.
-
-This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:] none
 

doc/fix_wall.html

@@ -34,7 +34,10 @@
     cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
   <I>vel</I> value = v
     v = velocity of wall in perpendicular direction (velocity units)
-  <I>wiggle</I> values = amplitude period
+  <I>wiggle/sin</I> values = amplitude period
+    amplitude = size of oscillation (distance units)
+    period = time of oscillation (time units)
+  <I>wiggle/cos</I> values = amplitude period
     amplitude = size of oscillation (distance units)
     period = time of oscillation (time units)
   <I>units</I> value = <I>lattice</I> or <I>box</I>
@@ -102,42 +105,39 @@ in the wall.
 <P>If the <I>vel</I> keyword is specified, the position of all walls will move
 during the simulation in a perpendicular direction, based on their
 initial <I>coord</I> position, the specified velocity <I>vel</I>, and the time
-elapsed since the beginning of the simulation.  See the note below
+elapsed since the fix was specified.  A positive velocity means each
-about making a wall move continuously across multiple runs.  A
+wall moves inward, towards the center of the box.  I.e. an <I>xlo</I> wall
-positive velocity means each wall moves inward, towards the center of
+will move in the +x direction and an <I>xhi</I> wall will move in the -x
-the box.  I.e. an <I>xlo</I> wall will move in the +x direction and an
+direction.  A negative velocity means each wall moves outward, away
-<I>xhi</I> wall will move in the -x direction.  A negative velocity means
+from the center of the box.  If you want different walls to move with
-each wall moves outward, away from the center of the box.  If you want
+different velocities, then you need to use multiple fix wall commands.
-different walls to move with different velocities, then you need to
-use multiple fix wall commands.
 </P>
 <P>If the <I>wiggle/sin</I> keyword is specified, the position of all walls
 will oscillate sinusoidally during the simulation in the perpendicular
 direction, according to the equation:
 </P>
-<PRE>position = pos0 + A sin(omega*delta) 
+<PRE>position = coord + A sin(omega*delta) 
 </PRE>
 <P>If the <I>wiggle/cos</I> keyword is specified, the position of all walls
 will oscillate sinusoidally during the simulation in the perpendicular
 direction, according to the equation:
 </P>
-<PRE>position = pos0 + A (1 - cos(omega*delta)) 
+<PRE>position = coord + A (1 - cos(omega*delta)) 
 </PRE>
-<P>In both cases, <I>pos0</I> is the position at the beginning of the
+<P>In both cases, <I>coord</I> is the specified initial position of the wall,
-simulation, <I>A</I> is the <I>amplitude</I>, <I>omega</I> is 2 PI / <I>period</I>, and
+<I>A</I> is the <I>amplitude</I>, <I>omega</I> is 2 PI / <I>period</I>, and <I>delta</I> is the
-<I>delta</I> is the time elapsed since the beginning of the simulation.
+time elapsed since the fix was specified.  A positive amplitude means
-See the note below about making a wall oscillate continuously across
+each wall initially moves inward, towards the center of the box.
-multiple runs.  A positive amplitude means each wall initially moves
+I.e. an <I>xlo</I> wall will move initially in the +x direction and an
-inward, towards the center of the box.  I.e. an <I>xlo</I> wall will move
+<I>xhi</I> wall will move initially in the -x direction.  A negative
-initially in the +x direction and an <I>xhi</I> wall will move initially in
+velocity means each wall moves initially outward, away from the center
-the -x direction.  A negative velocity means each wall moves initially
+of the box.  Note that the <I>wiggle/sin</I> option oscillates with
-outward, away from the center of the box.  Note that the <I>wiggle/sin</I>
+amplitude <I>A</I> around the pos0 position and the velocity of the wall is
-option oscillates with amplitude <I>A</I> around the pos0 position and the
+a maximum at time 0.  By contrast, for the <I>wiggle/cos</I> option the
-velocity of the wall is a maximum at time 0.  By contrast, for the
+wall moves up to <I>2A</I> away from pos0 in one direction and the velocity
-<I>wiggle/cos</I> option the wall moves up to <I>2A</I> away from pos0 in one
+of the wall is 0 at time 0.  If you want different walls to oscillate
-direction and the velocity of the wall is 0 at time 0.  If you want
+with different amplitudes or periods, then you need to use multiple
-different walls to oscillate with different amplitudes or periods,
+fix wall commands.
-then you need to use multiple fix wall commands.
 </P>
 <P>The <I>units</I> keyword determines the meaning of the distance units used
 to define the position of the wall and its velocity and wiggle
@@ -175,11 +175,8 @@ corresponding wall is defined.  Note that an outward force on a wall
 will be a negative value for <I>lo</I> walls and a positive value for <I>hi</I>
 walls.
 </P>
-<P>This fix can change the position of each wall, due to the <I>vel</I> or
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
-<I>wiggle</I> keywords, continuously over multiple runs, using the <I>start</I>
+the <A HREF = "run.html">run</A> command.
-and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command.  If you do not do
-this, the wall position will be reset to <I>coord</I> at the beginning of
-each run.
 </P>
 <P>The forces due to this fix are imposed during an energy minimization,
 invoked by the <A HREF = "minimize.html">minimize</A> command.
@@ -193,7 +190,8 @@ being minimized), you MUST enable the <A HREF = "fix_modify.html">fix_modify</A>
 </P>
 <P>Any dimension (xyz) that has a wall must be non-periodic.
 </P>
-<P>You cannot use both the <I>vel</I> and <I>wiggle</I> keywords together.
+<P>You cannot use both the <I>vel</I> and either of the <I>wiggle</I> keywords
+together.
 </P>
 <P><B>Related commands:</B>
 </P>

doc/fix_wall.txt

@@ -25,7 +25,10 @@ keyword = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} or {vel} or {wiggle
     cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
   {vel} value = v
     v = velocity of wall in perpendicular direction (velocity units)
-  {wiggle} values = amplitude period
+  {wiggle/sin} values = amplitude period
+    amplitude = size of oscillation (distance units)
+    period = time of oscillation (time units)
+  {wiggle/cos} values = amplitude period
     amplitude = size of oscillation (distance units)
     period = time of oscillation (time units)
   {units} value = {lattice} or {box}
@@ -92,42 +95,39 @@ in the wall.
 If the {vel} keyword is specified, the position of all walls will move
 during the simulation in a perpendicular direction, based on their
 initial {coord} position, the specified velocity {vel}, and the time
-elapsed since the beginning of the simulation.  See the note below
+elapsed since the fix was specified.  A positive velocity means each
-about making a wall move continuously across multiple runs.  A
+wall moves inward, towards the center of the box.  I.e. an {xlo} wall
-positive velocity means each wall moves inward, towards the center of
+will move in the +x direction and an {xhi} wall will move in the -x
-the box.  I.e. an {xlo} wall will move in the +x direction and an
+direction.  A negative velocity means each wall moves outward, away
-{xhi} wall will move in the -x direction.  A negative velocity means
+from the center of the box.  If you want different walls to move with
-each wall moves outward, away from the center of the box.  If you want
+different velocities, then you need to use multiple fix wall commands.
-different walls to move with different velocities, then you need to
-use multiple fix wall commands.
 
 If the {wiggle/sin} keyword is specified, the position of all walls
 will oscillate sinusoidally during the simulation in the perpendicular
 direction, according to the equation:
 
-position = pos0 + A sin(omega*delta) :pre
+position = coord + A sin(omega*delta) :pre
 
 If the {wiggle/cos} keyword is specified, the position of all walls
 will oscillate sinusoidally during the simulation in the perpendicular
 direction, according to the equation:
 
-position = pos0 + A (1 - cos(omega*delta)) :pre
+position = coord + A (1 - cos(omega*delta)) :pre
 
-In both cases, {pos0} is the position at the beginning of the
+In both cases, {coord} is the specified initial position of the wall,
-simulation, {A} is the {amplitude}, {omega} is 2 PI / {period}, and
+{A} is the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the
-{delta} is the time elapsed since the beginning of the simulation.
+time elapsed since the fix was specified.  A positive amplitude means
-See the note below about making a wall oscillate continuously across
+each wall initially moves inward, towards the center of the box.
-multiple runs.  A positive amplitude means each wall initially moves
+I.e. an {xlo} wall will move initially in the +x direction and an
-inward, towards the center of the box.  I.e. an {xlo} wall will move
+{xhi} wall will move initially in the -x direction.  A negative
-initially in the +x direction and an {xhi} wall will move initially in
+velocity means each wall moves initially outward, away from the center
-the -x direction.  A negative velocity means each wall moves initially
+of the box.  Note that the {wiggle/sin} option oscillates with
-outward, away from the center of the box.  Note that the {wiggle/sin}
+amplitude {A} around the pos0 position and the velocity of the wall is
-option oscillates with amplitude {A} around the pos0 position and the
+a maximum at time 0.  By contrast, for the {wiggle/cos} option the
-velocity of the wall is a maximum at time 0.  By contrast, for the
+wall moves up to {2A} away from pos0 in one direction and the velocity
-{wiggle/cos} option the wall moves up to {2A} away from pos0 in one
+of the wall is 0 at time 0.  If you want different walls to oscillate
-direction and the velocity of the wall is 0 at time 0.  If you want
+with different amplitudes or periods, then you need to use multiple
-different walls to oscillate with different amplitudes or periods,
+fix wall commands.
-then you need to use multiple fix wall commands.
 
 The {units} keyword determines the meaning of the distance units used
 to define the position of the wall and its velocity and wiggle
@@ -165,11 +165,8 @@ corresponding wall is defined.  Note that an outward force on a wall
 will be a negative value for {lo} walls and a positive value for {hi}
 walls.
 
-This fix can change the position of each wall, due to the {vel} or
+No parameter of this fix can be used with the {start/stop} keywords of
-{wiggle} keywords, continuously over multiple runs, using the {start}
+the "run"_run.html command.
-and {stop} keywords of the "run"_run.html command.  If you do not do
-this, the wall position will be reset to {coord} at the beginning of
-each run.
 
 The forces due to this fix are imposed during an energy minimization,
 invoked by the "minimize"_minimize.html command.
@@ -183,7 +180,8 @@ being minimized), you MUST enable the "fix_modify"_fix_modify.html
 
 Any dimension (xyz) that has a wall must be non-periodic.
 
-You cannot use both the {vel} and {wiggle} keywords together.
+You cannot use both the {vel} and either of the {wiggle} keywords
+together.
 
 [Related commands:]
 

doc/fix_wall_gran.html

@@ -125,13 +125,12 @@ is perpendicular to the wall, it is more of a shaking motion.  A
 <P>Each timestep, the position of a wiggled wall in the appropriate <I>dim</I>
 is set according to this equation:
 </P>
-<PRE>position = pos0 + A - A cos (omega * delta) 
+<PRE>position = coord + A - A cos (omega * delta) 
 </PRE>
-<P>where <I>pos0</I> is the position at the beginning of the simulation, <I>A</I>
+<P>where <I>coord</I> is the specified initial position of the wall, <I>A</I> is
-is the <I>amplitude</I>, <I>omega</I> is 2 PI / <I>period</I>, and <I>delta</I> is the
+the <I>amplitude</I>, <I>omega</I> is 2 PI / <I>period</I>, and <I>delta</I> is the time
-elapsed time since the beginning of the simulatoin.  The velocity of
+elapsed since the fix was specified.  The velocity of the wall is set
-the wall is set to the derivative of this expression.  See the note
+to the derivative of this expression.
-below about making a wall oscillate continuously across multiple runs.
 </P>
 <P>For the <I>shear</I> keyword, the wall moves continuously in the specified
 dimension with velocity <I>vshear</I>.  The dimension must be tangential to
@@ -156,15 +155,9 @@ uninterrupted fashion.
 <P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
 fix.  No global scalar or vector or per-atom quantities are stored by
 this fix for access by various <A HREF = "Section_howto.html#4_15">output
-commands</A>. 
+commands</A>.  No parameter of this fix can be
-</P>
+used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
-<P>This fix can change the position and velocity of the wall(s), due to
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
-the <I>wiggle</I> keyword, continuously over multiple runs, using the
-<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command.  If you do
-not do this, the wall position and velocity will be reset to its
-initial values at the beginning of each run.
-</P>
-<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
 </P>
 <P><B>Restrictions:</B>
 </P>

doc/fix_wall_gran.txt

@@ -108,13 +108,12 @@ is perpendicular to the wall, it is more of a shaking motion.  A
 Each timestep, the position of a wiggled wall in the appropriate {dim}
 is set according to this equation:
 
-position = pos0 + A - A cos (omega * delta) :pre
+position = coord + A - A cos (omega * delta) :pre
 
-where {pos0} is the position at the beginning of the simulation, {A}
+where {coord} is the specified initial position of the wall, {A} is
-is the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the
+the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the time
-elapsed time since the beginning of the simulatoin.  The velocity of
+elapsed since the fix was specified.  The velocity of the wall is set
-the wall is set to the derivative of this expression.  See the note
+to the derivative of this expression.
-below about making a wall oscillate continuously across multiple runs.
 
 For the {shear} keyword, the wall moves continuously in the specified
 dimension with velocity {vshear}.  The dimension must be tangential to
@@ -139,14 +138,8 @@ uninterrupted fashion.
 None of the "fix_modify"_fix_modify.html options are relevant to this
 fix.  No global scalar or vector or per-atom quantities are stored by
 this fix for access by various "output
-commands"_Section_howto.html#4_15. 
+commands"_Section_howto.html#4_15.  No parameter of this fix can be
-
+used with the {start/stop} keywords of the "run"_run.html command.
-This fix can change the position and velocity of the wall(s), due to
-the {wiggle} keyword, continuously over multiple runs, using the
-{start} and {stop} keywords of the "run"_run.html command.  If you do
-not do this, the wall position and velocity will be reset to its
-initial values at the beginning of each run.
-
 This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:]