260 lines
11 KiB
ReStructuredText
260 lines
11 KiB
ReStructuredText
.. index:: fix meso/move
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fix meso/move command
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=====================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID meso/move style args keyword values ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* meso/move = style name of this fix command
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* style = *linear* or *wiggle* or *rotate* or *variable*
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.. parsed-literal::
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*linear* args = Vx Vy Vz
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Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
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*wiggle* args = Ax Ay Az period
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Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
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period = period of oscillation (time units)
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*rotate* args = Px Py Pz Rx Ry Rz period
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Px,Py,Pz = origin point of axis of rotation (distance units)
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Rx,Ry,Rz = axis of rotation vector
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period = period of rotation (time units)
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*variable* args = v_dx v_dy v_dz v_vx v_vy v_vz
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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
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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
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* zero or more keyword/value pairs may be appended
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* keyword = *units*
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.. parsed-literal::
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*units* value = *box* or *lattice*
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 1 boundary meso/move wiggle 3.0 0.0 0.0 1.0 units box
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fix 2 boundary meso/move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
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fix 2 boundary meso/move variable v_myx v_myy NULL v_VX v_VY NULL
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Description
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"""""""""""
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Perform updates of position, velocity, internal energy and local
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density for mesoscopic particles in the group each timestep using the
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specified settings or formulas, without regard to forces on the
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particles. This can be useful for boundary, solid bodies or other
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particles, whose movement can influence nearby particles.
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The operation of this fix is exactly like that described by the
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:doc:`fix move <fix_move>` command, except that particles' density,
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internal energy and extrapolated velocity are also updated.
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.. note::
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The particles affected by this fix should not be time integrated by
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other fixes (e.g. :doc:`fix sph <fix_sph>`, :doc:`fix
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sph/stationary <fix_sph_stationary>`), since that will change their
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positions and velocities twice.
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.. note::
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As particles move due to this fix, they will pass through periodic
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boundaries and be remapped to the other side of the simulation box,
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just as they would during normal time integration (e.g. via the
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:doc:`fix sph <fix_sph>` command). It is up to you to decide
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whether periodic boundaries are appropriate with the kind of
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particle motion you are prescribing with this fix.
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.. note::
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As discussed below, particles are moved relative to their initial
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position at the time the fix is specified. These initial coordinates
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are stored by the fix in "unwrapped" form, by using the image flags
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associated with each particle. See the :doc:`dump custom <dump>` command
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for a discussion of "unwrapped" coordinates. See the Atoms section of
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the :doc:`read_data <read_data>` command for a discussion of image flags
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and how they are set for each particle. You can reset the image flags
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(e.g. to 0) before invoking this fix by using the :doc:`set image <set>`
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command.
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----------
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The *linear* style moves particles at a constant velocity, so that their
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position *X* = (x,y,z) as a function of time is given in vector
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notation as
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.. parsed-literal::
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X(t) = X0 + V \* delta
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where *X0* = (x0,y0,z0) is their position at the time the fix is
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specified, *V* is the specified velocity vector with components
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(Vx,Vy,Vz), and *delta* is the time elapsed since the fix was
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specified. This style also sets the velocity of each particle to V =
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(Vx,Vy,Vz). If any of the velocity components is specified as NULL,
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then the position and velocity of that component is time integrated
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the same as the :doc:`fix sph <fix_sph>` command would perform, using
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the corresponding force component on the particle.
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Note that the *linear* style is identical to using the *variable*
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style with an :doc:`equal-style variable <variable>` that uses the
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vdisplace() function. E.g.
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.. code-block:: LAMMPS
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variable V equal 10.0
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variable x equal vdisplace(0.0,$V)
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fix 1 boundary move variable v_x NULL NULL v_V NULL NULL
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The *wiggle* style moves particles in an oscillatory fashion, so that
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their position *X* = (x,y,z) as a function of time is given in vector
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notation as
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.. parsed-literal::
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X(t) = X0 + A sin(omega\*delta)
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where *X0* = (x0,y0,z0) is their position at the time the fix is
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specified, *A* is the specified amplitude vector with components
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(Ax,Ay,Az), *omega* is 2 PI / *period*\ , and *delta* is the time
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elapsed since the fix was specified. This style also sets the
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velocity of each particle to the time derivative of this expression.
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If any of the amplitude components is specified as NULL, then the
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position and velocity of that component is time integrated the same as
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the :doc:`fix sph <fix_sph>` command would perform, using the
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corresponding force component on the particle.
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Note that the *wiggle* style is identical to using the *variable*
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style with :doc:`equal-style variables <variable>` that use the
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swiggle() and cwiggle() functions. E.g.
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.. code-block:: LAMMPS
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variable A equal 10.0
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variable T equal 5.0
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variable omega equal 2.0*PI/$T
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variable x equal swiggle(0.0,$A,$T)
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variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
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fix 1 boundary move variable v_x NULL NULL v_v NULL NULL
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The *rotate* style rotates particles around a rotation axis *R* =
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(Rx,Ry,Rz) that goes through a point *P* = (Px,Py,Pz). The *period* of
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the rotation is also specified. The direction of rotation for the
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particles around the rotation axis is consistent with the right-hand
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rule: if your right-hand thumb points along *R*\ , then your fingers wrap
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around the axis in the direction of rotation.
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This style also sets the velocity of each particle to (omega cross
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Rperp) where omega is its angular velocity around the rotation axis and
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Rperp is a perpendicular vector from the rotation axis to the particle.
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The *variable* style allows the position and velocity components of
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each particle to be set by formulas specified via the
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:doc:`variable <variable>` command. Each of the 6 variables is
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specified as an argument to the fix as v_name, where name is the
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variable name that is defined elsewhere in the input script.
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Each variable must be of either the *equal* or *atom* style.
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*Equal*\ -style variables compute a single numeric quantity, that can be
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a function of the timestep as well as of other simulation values.
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*Atom*\ -style variables compute a numeric quantity for each particle, that
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can be a function per-atom quantities, such as the particle's position, as
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well as of the timestep and other simulation values. Note that this
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fix stores the original coordinates of each particle (see note below) so
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that per-atom quantity can be used in an atom-style variable formula.
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See the :doc:`variable <variable>` command for details.
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The first 3 variables (v_dx,v_dy,v_dz) specified for the *variable*
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style are used to calculate a displacement from the particle's original
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position at the time the fix was specified. The second 3 variables
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(v_vx,v_vy,v_vz) specified are used to compute a velocity for each
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particle.
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Any of the 6 variables can be specified as NULL. If both the
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displacement and velocity variables for a particular x,y,z component
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are specified as NULL, then the position and velocity of that
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component is time integrated the same as the :doc:`fix sph <fix_sph>`
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command would perform, using the corresponding force component on the
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particle. If only the velocity variable for a component is specified
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as NULL, then the displacement variable will be used to set the
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position of the particle, and its velocity component will not be
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changed. If only the displacement variable for a component is
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specified as NULL, then the velocity variable will be used to set the
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velocity of the particle, and the position of the particle will be
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time integrated using that velocity.
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The *units* keyword determines the meaning of the distance units used
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to define the *linear* velocity and *wiggle* amplitude and *rotate*
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origin. This setting is ignored for the *variable* style. A *box*
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value selects standard units as defined by the :doc:`units <units>`
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command, e.g. velocity in Angstroms/fs and amplitude and position
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in Angstroms for units = real. A *lattice* value means the velocity
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units are in lattice spacings per time and the amplitude and position
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are in lattice spacings. The :doc:`lattice <lattice>` command must have
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been previously used to define the lattice spacing. Each of these 3
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quantities may be dependent on the x,y,z dimension, since the lattice
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spacings can be different in x,y,z.
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----------
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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This fix writes the original coordinates of moving particles to :doc:`binary restart files <restart>`, as well as the initial timestep, so that
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the motion can be continuous in a restarted simulation. See the
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:doc:`read_restart <read_restart>` command for info on how to re-specify
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a fix in an input script that reads a restart file, so that the
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operation of the fix continues in an uninterrupted fashion.
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.. note::
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Because the move positions are a function of the current
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timestep and the initial timestep, you cannot reset the timestep to a
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different value after reading a restart file, if you expect a fix move
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command to work in an uninterrupted fashion.
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None of the :doc:`fix_modify <fix_modify>` options are relevant to this
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fix.
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This fix produces a per-atom array which can be accessed by various
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:doc:`output commands <Howto_output>`. The number of columns for each
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atom is 3, and the columns store the original unwrapped x,y,z coords
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of each particle. The per-atom values can be accessed on any timestep.
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command.
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This fix is not invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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This fix is part of the USER-SDPD package. It is only enabled if
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LAMMPS was built with that package. See the :doc:`Build package
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<Build_package>` doc page for more info.
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This fix requires that atoms store density and internal energy as
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defined by the :doc:`atom_style sph <atom_style>` command.
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All particles in the group must be mesoscopic SPH/SDPD particles.
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Related commands
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""""""""""""""""
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:doc:`fix move <fix_move>`, :doc:`fix sph <fix_sph>`,
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:doc:`displace_atoms <displace_atoms>`
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Default
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"""""""
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The option default is units = lattice.
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