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

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sjplimp
2009-12-03 17:57:33 +00:00
parent 69d350af34
commit f62d15de78
14 changed files with 495 additions and 62 deletions
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12
doc/Section_commands.html
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@ -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_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_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_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_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_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_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.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_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_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_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_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

4
doc/Section_commands.txt
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@ -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,
"wiggle"_fix_wiggle.html :tb(c=8,ea=c)
"wall/reflect"_fix_wall_reflect.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.

2
doc/fix.html
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@ -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
@ -169,7 +170,6 @@ list of fix styles available in LAMMPS:
<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_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

4
doc/fix.txt
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@ -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)
"wiggle"_fix_wiggle.html - oscillate walls and frozen atoms :ul
"wall/reflect"_fix_wall_reflect.html - reflecting wall(s) :ul
There are also additional fix styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to

5
doc/fix_coord_original.html
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@ -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
atom. The per-atom values be accessed on any timestep.
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>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

5
doc/fix_coord_original.txt
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@ -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
atom. The per-atom values be accessed on any timestep.
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.
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

17
doc/fix_gravity.html
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@ -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>
and <I>phi_grad</I> are ignored.
is phi,theta at the beginning of the simulation. For 2d systems,
<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
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 minimization</A>.
commands</A>.
</P>
<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>

15
doc/fix_gravity.txt
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@ -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}
and {phi_grad} are ignored.
is phi,theta at the beginning of the simulation. For 2d systems,
{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
used with the {start/stop} keywords of the "run"_run.html command.
commands"_Section_howto.html#4_15.
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

206
doc/fix_move.html Normal file
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@ -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>

195
doc/fix_move.txt Normal file
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@ -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.

23
doc/fix_wall_gran.html
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@ -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
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
set to the derivative of this expression.
<P>where <I>pos0</I> is the position at the beginning of the simulation, <I>A</I>
is the <I>amplitude</I>, <I>omega</I> is 2 PI / <I>period</I>, and <I>delta</I> is the
elapsed time since the beginning of the simulatoin. The velocity of
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
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 minimization</A>.
commands</A>.
</P>
<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>

21
doc/fix_wall_gran.txt
View File

@ -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
the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the
elapsed time since the fix was specified. The velocity of the wall is
set to the derivative of this expression.
where {pos0} is the position at the beginning of the simulation, {A}
is the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the
elapsed time since the beginning of the simulatoin. The velocity of
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
used with the {start/stop} keywords of the "run"_run.html command.
commands"_Section_howto.html#4_15.
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

23
doc/variable.html
View File

@ -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 = "compute.html">compute</A> to calculate their values such as "temp" or
"press", use computes stored and invoked by the thermo_style command.
This means that you can only use those keywords in a variable if the
style you are using with the thermo_style command (and the thermo
keywords associated with that style) also define and use the needed
compute. Note that some thermo keywords use a compute indirectly to
calculate their value (e.g. the enthalpy keyword uses temp, pe, and
pressure). If a variable is evaluated in an input script (not during
a run), then the values accessed by the thermo keyword must be
current. See the discussion below about "Variable Accuracy".
<A HREF = "thermo_style.html">thermo_style custom</A> command. Thermo keywords that
require a <A HREF = "compute.html">compute</A> to calculate their values such as
"temp" or "press", use computes stored and invoked by the
<A HREF = "thermo_style.html">thermo_style</A> command. This means that you can
only use those keywords in a variable if the style you are using with
the thermo_style command (and the thermo keywords associated with that
style) also define and use the needed compute. Note that some thermo
keywords use a compute indirectly to calculate their value (e.g. the
enthalpy keyword uses temp, pe, and pressure). If a variable is
evaluated in an input script (not during a run), then the values
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

23
doc/variable.txt
View File

@ -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
"compute"_compute.html to calculate their values such as "temp" or
"press", use computes stored and invoked by the thermo_style command.
This means that you can only use those keywords in a variable if the
style you are using with the thermo_style command (and the thermo
keywords associated with that style) also define and use the needed
compute. Note that some thermo keywords use a compute indirectly to
calculate their value (e.g. the enthalpy keyword uses temp, pe, and
pressure). If a variable is evaluated in an input script (not during
a run), then the values accessed by the thermo keyword must be
current. See the discussion below about "Variable Accuracy".
"thermo_style custom"_thermo_style.html command. Thermo keywords that
require a "compute"_compute.html to calculate their values such as
"temp" or "press", use computes stored and invoked by the
"thermo_style"_thermo_style.html command. This means that you can
only use those keywords in a variable if the style you are using with
the thermo_style command (and the thermo keywords associated with that
style) also define and use the needed compute. Note that some thermo
keywords use a compute indirectly to calculate their value (e.g. the
enthalpy keyword uses temp, pe, and pressure). If a variable is
evaluated in an input script (not during a run), then the values
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