git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3482 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_commands.html

@@ -323,12 +323,12 @@ of each style or click on the style itself for a full description:
 <TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_bond_break.html">bond/break</A></TD><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_coord_original.html">coord/original</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_move.html">move</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A> 
+<TR ALIGN="center"><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A> 
 </TD></TR></TABLE></DIV>
 
 <P>These are fix styles contributed by users, which can be used if

doc/Section_commands.txt

@@ -406,6 +406,7 @@ of each style or click on the style itself for a full description:
 "lineforce"_fix_lineforce.html,
 "msd"_fix_msd.html,
 "momentum"_fix_momentum.html,
+"move"_fix_move.html,
 "nph"_fix_nph.html,
 "npt"_fix_npt.html,
 "npt/asphere"_fix_npt_asphere.html,
@@ -445,8 +446,7 @@ of each style or click on the style itself for a full description:
 "wall/gran"_fix_wall_gran.html,
 "wall/lj126"_fix_wall.html,
 "wall/lj93"_fix_wall.html,
-"wall/reflect"_fix_wall_reflect.html,
+"wall/reflect"_fix_wall_reflect.html :tb(c=8,ea=c)
-"wiggle"_fix_wiggle.html :tb(c=8,ea=c)
 
 These are fix styles contributed by users, which can be used if
 "LAMMPS is built with the appropriate package"_Section_start.html#2_3.

doc/fix.html

@@ -130,6 +130,7 @@ list of fix styles available in LAMMPS:
 <LI><A HREF = "fix_lineforce.html">lineforce</A> - constrain atoms to move in a line
 <LI><A HREF = "fix_msd.html">msd</A> - compute mean-squared displacement      (i.e. diffusion coefficient)
 <LI><A HREF = "fix_momentum.html">momentum</A> - zero the linear and/or angular momentum   of a group of atoms
+<LI><A HREF = "fix_move.html">move</A> - move atoms in a prescribed fashion
 <LI><A HREF = "fix_nph.html">nph</A> - constant NPH time integration via Nose/Hoover
 <LI><A HREF = "fix_npt.html">npt</A> - constant NPT time integration via Nose/Hoover
 <LI><A HREF = "fix_npt_asphere.html">npt/asphere</A> - NPT for aspherical particles
@@ -168,8 +169,7 @@ list of fix styles available in LAMMPS:
 <LI><A HREF = "fix_wall_gran.html">wall/gran</A> - frictional wall(s) for granular simulations
 <LI><A HREF = "fix_wall_lj126.html">wall/lj126</A> - Lennard-Jones 12-6 wall
 <LI><A HREF = "fix_wall_lj93.html">wall/lj93</A> - Lennard-Jones 9-3 wall
-<LI><A HREF = "fix_wall_reflect.html">wall/reflect</A> - reflecting wall(s)
+<LI><A HREF = "fix_wall_reflect.html">wall/reflect</A> - reflecting wall(s) 
-<LI><A HREF = "fix_wiggle.html">wiggle</A> - oscillate walls and frozen atoms 
 </UL>
 <P>There are also additional fix styles submitted by users which are
 included in the LAMMPS distribution.  The list of these with links to

doc/fix.txt

@@ -129,6 +129,7 @@ list of fix styles available in LAMMPS:
      (i.e. diffusion coefficient)
 "momentum"_fix_momentum.html - zero the linear and/or angular momentum \
   of a group of atoms
+"move"_fix_move.html - move atoms in a prescribed fashion
 "nph"_fix_nph.html - constant NPH time integration via Nose/Hoover
 "npt"_fix_npt.html - constant NPT time integration via Nose/Hoover
 "npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
@@ -177,8 +178,7 @@ list of fix styles available in LAMMPS:
 "wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations
 "wall/lj126"_fix_wall_lj126.html - Lennard-Jones 12-6 wall
 "wall/lj93"_fix_wall_lj93.html - Lennard-Jones 9-3 wall
-"wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
+"wall/reflect"_fix_wall_reflect.html - reflecting wall(s) :ul
-"wiggle"_fix_wiggle.html - oscillate walls and frozen atoms :ul
 
 There are also additional fix styles submitted by users which are
 included in the LAMMPS distribution.  The list of these with links to

doc/fix_coord_original.html

@@ -59,8 +59,9 @@ fix.
 </P>
 <P>This fix produces a per-atom vector which can be accessed by various
 <A HREF = "Section_howto.html#4_15">output commands</A>.  The length of the vector
-for each atom is 3, and the components store the x,y,z coords of each
+for each atom is 3, and the components store the original unwrapped
-atom.  The per-atom values be accessed on any timestep.
+x,y,z coords of each atom.  The per-atom values be accessed on any
+timestep.
 </P>
 <P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
 the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy

doc/fix_coord_original.txt

@@ -56,8 +56,9 @@ fix.
 
 This fix produces a per-atom vector which can be accessed by various
 "output commands"_Section_howto.html#4_15.  The length of the vector
-for each atom is 3, and the components store the x,y,z coords of each
+for each atom is 3, and the components store the original unwrapped
-atom.  The per-atom values be accessed on any timestep.
+x,y,z coords of each atom.  The per-atom values be accessed on any
+timestep.
 
 No parameter of this fix can be used with the {start/stop} keywords of
 the "run"_run.html command.  This fix is not invoked during "energy

doc/fix_gravity.html

@@ -79,8 +79,9 @@ 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 time the fix is specified.  For 2d systems, <I>phi</I>
+is phi,theta at the beginning of the simulation.  For 2d systems,
-and <I>phi_grad</I> are ignored.
+<I>phi</I> and <I>phi_grad</I> are ignored.  See the note below about making the
+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.
@@ -91,9 +92,15 @@ 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>.  No parameter of this fix can be
+commands</A>.  
-used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+</P>
-This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+<P>This fix can change the direction of the gravity vector, due to the
+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

@@ -71,8 +71,9 @@ 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 time the fix is specified.  For 2d systems, {phi}
+is phi,theta at the beginning of the simulation.  For 2d systems,
-and {phi_grad} are ignored.
+{phi} and {phi_grad} are ignored.  See the note below about making the
+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.
@@ -83,8 +84,14 @@ 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.  No parameter of this fix can be
+commands"_Section_howto.html#4_15.  
-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

@@ -0,0 +1,206 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> 
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix move command 
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID move style args keyword values ... 
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command 
+
+<LI>move = style name of this fix command 
+
+<LI>style = <I>linear</I> or <I>wiggle</I> or <I>rotate</I> or <I>variable</I> 
+
+<PRE>  <I>linear</I> args = Vx Vy Vz
+    Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
+  <I>wiggle</I> args = Ax Ay Az period
+    Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
+    period = period of oscillation (time units)
+  <I>rotate</I> args = Px Py Pz Rx Ry Rz period
+    Px,Py,Pz = origin point of axis of rotation (distance units)
+    Rx,Ry,Rz = axis of rotation vector
+    period = period of rotation (time units)
+  <I>variable</I> args = v_dx v_dy v_dz v_vx v_vy v_vz
+    v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
+    v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL 
+</PRE>
+<LI>zero or more keyword/value pairs may be appended 
+
+<LI>keyword = <I>units</I> 
+
+<PRE>  <I>units</I> value = <I>box</I> or <I>lattice</I> 
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
+fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
+fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL 
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform updates of position and velocity for atoms in the group each
+timestep using the specified settings or formulas, without regard to
+forces on the atoms.  This can be useful for boundary or other atoms,
+whose movement can influence nearby atoms.
+</P>
+<P>IMPORTANT NOTE: The atoms affected by this fix should not normally be
+time integrated by other fixes (e.g. <A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nvt.html">fix
+nvt</A>), since that will change their positions and
+velocities twice.
+</P>
+<P>IMPORTANT NOTE: As atoms move due to this fix, they will pass thru
+periodic boundaries and be remapped to the other side of the
+simulation box, just as they would during normal time integration
+(e.g. via the <A HREF = "fix_nve.html">fix nve</A> command).  It is up to you to
+decide whether periodic boundaries are appropriate with the kind of
+atom motion you are prescribing with this fix.
+</P>
+<P>IMPORTANT NOTE: As dicsussed below, atoms are moved relative to their
+initial position at the time the fix is specified.  These initial
+coordinates are stored by the fix in "unwrapped" form, by using the
+image flags associated with each atom.  See the <A HREF = "dump.html">dump
+custom</A> command for a discussion of "unwrapped" coordinates.
+See the Atoms section of the <A HREF = "read_data.html">read_data</A> command for a
+discussion of image flags and how they are set for each atom.  You can
+reset the image flags (e.g. to 0) before invoking this fix by using
+the <A HREF = "set.html">set image</A> command.
+</P>
+<HR>
+
+<P>The <I>linear</I> style moves atoms at a constant velocity, so that their
+position <I>X</I> = (x,y,z) as a function of time is given in vector
+notation as
+</P>
+<PRE>X(t) = X0 + V * delta 
+</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
+simulation.  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
+the corresponding force component on the atom.
+</P>
+<P>The <I>wiggle</I> style moves atoms in an oscillatory fashion, so that
+their position <I>X</I> = (x,y,z) as a function of time is given in vector
+notation as
+</P>
+<PRE>X(t) = X0 + A sin(omega*delta) 
+</PRE>
+<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
+the velocity of each atom to the time derivative of this expression.
+If 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.
+</P>
+<P>The <I>rotate</I> style rotates atoms around a rotation axis <I>R</I> =
+(Rx,Ry,Rz) that goes thru a point <I>P</I> = (Px,Py,Pz).  The <I>period</I> of
+the rotation is also specified.  This style also sets the velocity of
+each atom to (omega cross Rperp) where omega is its angular velocity
+around the rotation axis and Rperp is a perpendicular vector from the
+rotation axis to the atom.  If the defined
+<A HREF = "atom_style.html">atom_style</A> assigns an angular velocity to each atom,
+then each atom's angular velocity is also set to omega.
+</P>
+<P>The <I>variable</I> style allows the position and velocity components of
+each atom to be set by formulas specified via the
+<A HREF = "variable.html">variable</A> command.  Each of the 6 variables is
+specified as an argument to the fix as v_name, where <I>name</I> is the
+name of the variable that appears elsewhere in the input script.
+</P>
+<P>Each variable must be of either the <I>equal</I> or <I>atom</I> style.
+<I>Equal</I>-style variables compute a single numeric quantity, that can be
+a function of the timestep as well as of other simulation values.
+<I>Atom</I>-style variables compute a numeric quantity for each atom, that
+can be a function per-atom quantities, such as the atom's position, as
+well as of the timestep and other simulation values.  See the
+<A HREF = "variable.html">variable</A> command for details.
+</P>
+<P>The first 3 variables (v_dx,v_dy,v_dz) specified for the <I>variable</I>
+style are used to calculate a displacement from the atom's original
+position at the time the fix was specified.  The second 3 variables
+(v_vx,v_vy,v_vz) specified are used to compute a velocity for each
+atom.
+</P>
+<P>Any of the 6 variables can be specified as NULL.  If both the
+displacement and velocity variables for a particular x,y,z component
+are 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.  If only the velocity variable for a component is specified as
+NULL, then the displacement variable will be used to set the position
+of the atom, and its velocity component will not be changed.  If only
+the displacement variable for a component is specified as NULL, then
+the velocity variable will be used to set the velocity of the atom,
+and the position of the atom will be time integrated using that
+velocity.
+</P>
+<P>The <I>units</I> keyword determines the meaning of the distance units used
+to define the <I>linear</I> velocity and <I>wiggle</I> amplitude and <I>rotate</I>
+origin.  This setting is ignored for the <I>variable</I> style.  A <I>box</I>
+value selects standard units as defined by the <A HREF = "units.html">units</A>
+command, e.g. velocity in Angstroms/fmsec and amplitude and position
+in Angstroms for units = real.  A <I>lattice</I> value means the velocity
+units are in lattice spacings per time and the amplitude and position
+are in lattice spacings.  The <A HREF = "lattice.html">lattice</A> command must have
+been previously used to define the lattice spacing.  Each of these 3
+quantities may be dependent on the x,y,z dimension, since the lattice
+spacings can be different in x,y,z.
+</P>
+<P>For <A HREF = "run_style.html">rRESPA time integration</A>, this fix adjusts the
+position and velocity of atoms on the outermost rRESPA level.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the original coordinates of moving atoms to <A HREF = "restart.html">binary
+restart files</A>, so that the motion can be continuous in a
+restarted simulation.  See the <A HREF = "read_restart.html">read_restart</A>
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix.  
+</P>
+<P>This fix produces a per-atom vector which can be accessed by various
+<A HREF = "Section_howto.html#4_15">output commands</A>.  The length of the vector
+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
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command.  See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<P>The option default is units = lattice.
+</P>
+</HTML>

doc/fix_move.txt

@@ -0,0 +1,195 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix move command :h3
+
+[Syntax:]
+
+fix ID group-ID move style args keyword values ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+move = style name of this fix command :l
+style = {linear} or {wiggle} or {rotate} or {variable} :l
+  {linear} args = Vx Vy Vz
+    Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
+  {wiggle} args = Ax Ay Az period
+    Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
+    period = period of oscillation (time units)
+  {rotate} args = Px Py Pz Rx Ry Rz period
+    Px,Py,Pz = origin point of axis of rotation (distance units)
+    Rx,Ry,Rz = axis of rotation vector
+    period = period of rotation (time units)
+  {variable} args = v_dx v_dy v_dz v_vx v_vy v_vz
+    v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
+    v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL :pre
+
+zero or more keyword/value pairs may be appended :l
+keyword = {units} :l
+  {units} value = {box} or {lattice} :pre
+:ule
+
+[Examples:]
+
+fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
+fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
+fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL :pre
+
+[Description:]
+
+Perform updates of position and velocity for atoms in the group each
+timestep using the specified settings or formulas, without regard to
+forces on the atoms.  This can be useful for boundary or other atoms,
+whose movement can influence nearby atoms.
+
+IMPORTANT NOTE: The atoms affected by this fix should not normally be
+time integrated by other fixes (e.g. "fix nve"_fix_nve.html, "fix
+nvt"_fix_nvt.html), since that will change their positions and
+velocities twice.
+
+IMPORTANT NOTE: As atoms move due to this fix, they will pass thru
+periodic boundaries and be remapped to the other side of the
+simulation box, just as they would during normal time integration
+(e.g. via the "fix nve"_fix_nve.html command).  It is up to you to
+decide whether periodic boundaries are appropriate with the kind of
+atom motion you are prescribing with this fix.
+
+IMPORTANT NOTE: As dicsussed below, atoms are moved relative to their
+initial position at the time the fix is specified.  These initial
+coordinates are stored by the fix in "unwrapped" form, by using the
+image flags associated with each atom.  See the "dump
+custom"_dump.html command for a discussion of "unwrapped" coordinates.
+See the Atoms section of the "read_data"_read_data.html command for a
+discussion of image flags and how they are set for each atom.  You can
+reset the image flags (e.g. to 0) before invoking this fix by using
+the "set image"_set.html command.
+
+:line
+
+The {linear} style moves atoms at a constant velocity, so that their
+position {X} = (x,y,z) as a function of time is given in vector
+notation as
+
+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
+simulation.  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
+the corresponding force component on the atom.
+
+The {wiggle} style moves atoms in an oscillatory fashion, so that
+their position {X} = (x,y,z) as a function of time is given in vector
+notation as
+
+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
+the velocity of each atom to the time derivative of this expression.
+If 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.
+
+The {rotate} style rotates atoms around a rotation axis {R} =
+(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz).  The {period} of
+the rotation is also specified.  This style also sets the velocity of
+each atom to (omega cross Rperp) where omega is its angular velocity
+around the rotation axis and Rperp is a perpendicular vector from the
+rotation axis to the atom.  If the defined
+"atom_style"_atom_style.html assigns an angular velocity to each atom,
+then each atom's angular velocity is also set to omega.
+
+The {variable} style allows the position and velocity components of
+each atom to be set by formulas specified via the
+"variable"_variable.html command.  Each of the 6 variables is
+specified as an argument to the fix as v_name, where {name} is the
+name of the variable that appears elsewhere in the input script.
+
+Each variable must be of either the {equal} or {atom} style.
+{Equal}-style variables compute a single numeric quantity, that can be
+a function of the timestep as well as of other simulation values.
+{Atom}-style variables compute a numeric quantity for each atom, that
+can be a function per-atom quantities, such as the atom's position, as
+well as of the timestep and other simulation values.  See the
+"variable"_variable.html command for details.
+
+The first 3 variables (v_dx,v_dy,v_dz) specified for the {variable}
+style are used to calculate a displacement from the atom's original
+position at the time the fix was specified.  The second 3 variables
+(v_vx,v_vy,v_vz) specified are used to compute a velocity for each
+atom.
+
+Any of the 6 variables can be specified as NULL.  If both the
+displacement and velocity variables for a particular x,y,z component
+are 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.  If only the velocity variable for a component is specified as
+NULL, then the displacement variable will be used to set the position
+of the atom, and its velocity component will not be changed.  If only
+the displacement variable for a component is specified as NULL, then
+the velocity variable will be used to set the velocity of the atom,
+and the position of the atom will be time integrated using that
+velocity.
+
+The {units} keyword determines the meaning of the distance units used
+to define the {linear} velocity and {wiggle} amplitude and {rotate}
+origin.  This setting is ignored for the {variable} style.  A {box}
+value selects standard units as defined by the "units"_units.html
+command, e.g. velocity in Angstroms/fmsec and amplitude and position
+in Angstroms for units = real.  A {lattice} value means the velocity
+units are in lattice spacings per time and the amplitude and position
+are in lattice spacings.  The "lattice"_lattice.html command must have
+been previously used to define the lattice spacing.  Each of these 3
+quantities may be dependent on the x,y,z dimension, since the lattice
+spacings can be different in x,y,z.
+
+For "rRESPA time integration"_run_style.html, this fix adjusts the
+position and velocity of atoms on the outermost rRESPA level.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+This fix writes the original coordinates of moving atoms to "binary
+restart files"_restart.html, so that the motion can be continuous in a
+restarted simulation.  See the "read_restart"_read_restart.html
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+None of the "fix_modify"_fix_modify.html options are relevant to this
+fix.  
+
+This fix produces a per-atom vector which can be accessed by various
+"output commands"_Section_howto.html#4_15.  The length of the vector
+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
+{start} and {stop} keywords of the "run"_run.html command.  See the
+"run"_run.html command for details of how to do this.
+
+This fix is not invoked during "energy minimization"_minimize.html.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"fix nve"_fix_nve.html
+
+[Default:] none
+
+The option default is units = lattice.

doc/fix_wall_gran.html

@@ -127,10 +127,11 @@ is set according to this equation:
 </P>
 <PRE>position = pos0 + A - A cos (omega * delta) 
 </PRE>
-<P>where <I>pos0</I> is the position at the time the fix was specified, <I>A</I> is
+<P>where <I>pos0</I> is the position at the beginning of the simulation, <I>A</I>
-the <I>amplitude</I>, <I>omega</I> is 2 PI / <I>period</I>, and <I>delta</I> is the
+is the <I>amplitude</I>, <I>omega</I> is 2 PI / <I>period</I>, and <I>delta</I> is the
-elapsed time since the fix was specified.  The velocity of the wall is
+elapsed time since the beginning of the simulatoin.  The velocity of
-set to the derivative of this expression.
+the wall is set to the derivative of this expression.  See the note
+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
@@ -155,9 +156,15 @@ 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>.  No parameter of this fix can be
+commands</A>. 
-used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+</P>
-This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+<P>This fix can change the position and velocity of the wall(s), due to
+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>
@@ -169,7 +176,7 @@ LAMMPS</A> section for more info.
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "fix_wiggle.html<A HREF = "pair_gran.html">>fix_wiggle</A>, pair_style granular</A>
+<P><A HREF = "fix_wiggle.html">fix_wiggle</A>, <A HREF = "pair_gran.html">pair_style granular</A>
 </P>
 <P><B>Default:</B> none
 </P>

doc/fix_wall_gran.txt

@@ -110,10 +110,11 @@ is set according to this equation:
 
 position = pos0 + A - A cos (omega * delta) :pre
 
-where {pos0} is the position at the time the fix was specified, {A} is
+where {pos0} is the position at the beginning of the simulation, {A}
-the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the
+is the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the
-elapsed time since the fix was specified.  The velocity of the wall is
+elapsed time since the beginning of the simulatoin.  The velocity of
-set to the derivative of this expression.
+the wall is set to the derivative of this expression.  See the note
+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
@@ -138,8 +139,14 @@ 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.  No parameter of this fix can be
+commands"_Section_howto.html#4_15. 
-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:]
@@ -152,6 +159,6 @@ Any dimension (xyz) that has a granular wall must be non-periodic.
 
 [Related commands:]
 
-"fix_wiggle"_fix_wiggle.html, pair_style granular"_pair_gran.html
+"fix_wiggle"_fix_wiggle.html, "pair_style granular"_pair_gran.html
 
 [Default:] none

doc/variable.html

@@ -267,17 +267,18 @@ can use formula elements that produce either global values or per-atom
 values.
 </P>
 <P>The thermo keywords allowed in a formula are those defined by the
-"thermo_style custom" command.  Thermo keywords that require a
+<A HREF = "thermo_style.html">thermo_style custom</A> command.  Thermo keywords that
-<A HREF = "compute.html">compute</A> to calculate their values such as "temp" or
+require a <A HREF = "compute.html">compute</A> to calculate their values such as
-"press", use computes stored and invoked by the thermo_style command.
+"temp" or "press", use computes stored and invoked by the
-This means that you can only use those keywords in a variable if the
+<A HREF = "thermo_style.html">thermo_style</A> command.  This means that you can
-style you are using with the thermo_style command (and the thermo
+only use those keywords in a variable if the style you are using with
-keywords associated with that style) also define and use the needed
+the thermo_style command (and the thermo keywords associated with that
-compute.  Note that some thermo keywords use a compute indirectly to
+style) also define and use the needed compute.  Note that some thermo
-calculate their value (e.g. the enthalpy keyword uses temp, pe, and
+keywords use a compute indirectly to calculate their value (e.g. the
-pressure).  If a variable is evaluated in an input script (not during
+enthalpy keyword uses temp, pe, and pressure).  If a variable is
-a run), then the values accessed by the thermo keyword must be
+evaluated in an input script (not during a run), then the values
-current.  See the discussion below about "Variable Accuracy".
+accessed by the thermo keyword must be current.  See the discussion
+below about "Variable Accuracy".
 </P>
 <P>Math operations are written in the usual way, where the "x" and "y" in
 the examples above can be another section of the formula.  Operators

doc/variable.txt

@@ -263,17 +263,18 @@ can use formula elements that produce either global values or per-atom
 values.
 
 The thermo keywords allowed in a formula are those defined by the
-"thermo_style custom" command.  Thermo keywords that require a
+"thermo_style custom"_thermo_style.html command.  Thermo keywords that
-"compute"_compute.html to calculate their values such as "temp" or
+require a "compute"_compute.html to calculate their values such as
-"press", use computes stored and invoked by the thermo_style command.
+"temp" or "press", use computes stored and invoked by the
-This means that you can only use those keywords in a variable if the
+"thermo_style"_thermo_style.html command.  This means that you can
-style you are using with the thermo_style command (and the thermo
+only use those keywords in a variable if the style you are using with
-keywords associated with that style) also define and use the needed
+the thermo_style command (and the thermo keywords associated with that
-compute.  Note that some thermo keywords use a compute indirectly to
+style) also define and use the needed compute.  Note that some thermo
-calculate their value (e.g. the enthalpy keyword uses temp, pe, and
+keywords use a compute indirectly to calculate their value (e.g. the
-pressure).  If a variable is evaluated in an input script (not during
+enthalpy keyword uses temp, pe, and pressure).  If a variable is
-a run), then the values accessed by the thermo keyword must be
+evaluated in an input script (not during a run), then the values
-current.  See the discussion below about "Variable Accuracy".
+accessed by the thermo keyword must be current.  See the discussion
+below about "Variable Accuracy".
 
 Math operations are written in the usual way, where the "x" and "y" in
 the examples above can be another section of the formula.  Operators