2006-12-13 08:37:25 +08:00
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix deposit command :h3
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[Syntax:]
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fix ID group-ID deposit N type M seed keyword values ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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deposit = style name of this fix command :l
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N = # of atoms or molecules to insert :l
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type = atom type to assign to inserted atoms (for atom insertion) :l
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M = insert a single atom or molecule every M steps :l
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seed = random # seed (positive integer) :l
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one or more keyword/value pairs may be appended to args :l
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keyword = {region} or {mol} or {id} or {global} or {local} or {near} or {attempt} or {rate} or {vx} or {vy} or {vz} or {units} :l
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{region} value = region-ID
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region-ID = ID of region to use as insertion volume
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{mol} value = template-ID
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template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
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{id} value = {max} or {next}
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max = atom ID for new atom(s) is max ID of all current atoms plus one
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next = atom ID for new atom(s) increments by one for every deposition
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{global} values = lo hi
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lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units)
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{local} values = lo hi delta
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lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units)
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delta = lateral distance within which a neighbor is considered "nearby" (distance units)
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{near} value = R
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R = only insert atom/molecule if further than R from existing particles (distance units)
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{attempt} value = Q
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Q = attempt a single insertion up to Q times
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{rate} value = V
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V = z velocity (y in 2d) at which insertion volume moves (velocity units)
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{vx} values = vxlo vxhi
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vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units)
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{vy} values = vylo vyhi
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vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units)
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{vz} values = vzlo vzhi
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vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
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{target} values = tx ty tz
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tx,ty,tz = location of target point (distance units)
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{units} value = {lattice} or {box}
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lattice = the geometry is defined in lattice units
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box = the geometry is defined in simulation box units :pre
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:ule
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[Examples:]
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fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box
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fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8
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fix 4 sputter deposit 1000 2 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice :pre
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[Description:]
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Insert a single atom or molecule into the simulation domain every M
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timesteps until N atoms or molecules have been inserted. This is
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useful for simulating deposition onto a surface. For the remainder of
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this doc page, a single inserted atom or molecule is referred to as a
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"particle".
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If inserted particles are individual atoms, they are assigned the
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specified atom type. For molecules the specified type is ignored, and
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the type of each atom in the inserted molecule is specified in the
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file read by the "molecule"_molecule.html command.
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All atoms in the inserted particle are assigned to two groups: the
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default group "all" and the group specified in the fix deposit command
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(which can also be "all").
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If you are computing temperature values which include inserted
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particles, you will want to use the
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"compute_modify"_compute_modify.html dynamic option, which insures the
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current number of atoms is used as a normalizing factor each time the
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temperature is computed.
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Care must be taken that inserted particles are not too near existing
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atoms, using the options described below. When inserting particles
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above a surface in a non-periodic box (see the
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"boundary"_boundary.html command), the possibility of a particle
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escaping the surface and flying upward should be considered, since the
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particle may be lost or the box size may grow infinitely large. A
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"fix wall/reflect"_fix_wall_reflect.html command can be used to
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prevent this behavior. Note that if a shrink-wrap boundary is used,
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it is OK to insert the new particle outside the box, however the box
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will immediately be expanded to include the new particle. When
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simulating a sputtering experiment it is probably more realistic to
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ignore those atoms using the "thermo_modify"_thermo_modify.html
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command with the {lost ignore} option and a fixed
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"boundary"_boundary.html.
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The fix deposit command must use the {region} keyword to define an
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insertion volume. The specified region must have been previously
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defined with a "region"_region.html command. It must be defined with
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side = {in}.
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Individual atoms are inserted, unless the {mol} keyword is used. It
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specifies a previously defined {template-ID} used by the
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"molecule"_molecule.html command which reads a file that defines the
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molecule. The coordinates, atom types, charges, etc, as well as any
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bond/angle/etc information for the molecule must be specified in the
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molecule file. See the "molecule"_molecule.html command for details.
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The only required settings from this file are the coordinates and
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types of atoms in the molecule.
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Each timestep a particle is inserted, the coordinates for its atoms
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are chosen as follows. For insertion of individual atoms, the
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"position" referred to in the following description is the coordinate
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of the atom. For insertion of molecule, the "position" is the
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geometric center of the molecule; see the (molecule"_molecule.html doc
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page for details. A random rotation of the molecule around its center
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point is performed, which determines the coordinates all the
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individual atoms.
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A random position within the region insertion volume is generated. If
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neither the {global} or {local} keyword is used, the random position
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is the trial position. If the {global} keyword is used, the random
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x,y values are used, but the z position of the new particle is set
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above the highest current atom in the simulation by a distance
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randomly chosen between lo/hi. (For a 2d simulation, this is done for
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the y position.) If the {local} keyword is used, the z position is
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set a distance between lo/hi above the highest current atom in the
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simulation that is "nearby" the chosen x,y position. In this context,
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"nearby" means the lateral distance (in x,y) between the new and old
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particles is less than the {delta} setting.
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Once a trial x,y,z position has been selected, the insertion is only
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performed if no current atom in the simulation is within a distance R
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of any atom in the new particle. Note that the default value for R is
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0.0, which will allow atoms to strongly overlap if you are inserting
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where other atoms are present. This distance test is performed
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independently for each atom in an inserted molecule, based on the
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randomly rotated configuration of the molecule. If this test fails, a
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new random position within the insertion volume is chosen and another
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trial is made. Up to Q attempts are made. If the particle is not
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successfully inserted, LAMMPS prints a warning message.
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The {rate} option moves the insertion volume in the z direction (3d)
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or y direction (2d). This enables particles to be inserted from a
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successively higher height over time. Note that this parameter is
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ignored if the {global} or {local} keywords are used, since those
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options choose a z-coordinate for insertion independently.
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The vx, vy, and vz components of velocity for the inserted particle
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are set using the values specified for the {vx}, {vy}, and {vz}
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keywords. Note that normally, new particles should be a assigned a
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negative vertical velocity so that they move towards the surface. For
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molecules, the same velocity is given to every particle (no rotation
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or bond vibration).
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If the {target} option is used, the velocity vector of the inserted
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particle is changed so that it points from the insertion position
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towards the specified target point. The magnitude of the velocity is
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unchanged. This can be useful, for example, for simulating a
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sputtering process. E.g. the target point can be far away, so that
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all incident particles strike the surface as if they are in an
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incident beam of particles at a prescribed angle.
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The {id} keyword determines how atom IDs and molecule IDs are assigned
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to newly deposited particles. Molecule IDs are only assigned if
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molecules are being inserted. For the {max} setting, the atom and
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molecule IDs of all current atoms are checked. Atoms in the new
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particle are assigned IDs starting with the current maximum plus one.
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If a molecule is inserted it is assigned an ID = current maximum plus
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one. This means that if particles leave the system, the new IDs may
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replace the lost ones. For the {next} setting, the maximum ID of any
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atom and molecule is stored at the time the fix is defined. Each time
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a new particle is added, this value is incremented to assign IDs to
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the new atom(s) or molecule. Thus atom and molecule IDs for deposited
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particles will be consecutive even if particles leave the system over
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time.
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The {units} keyword determines the meaning of the distance units used
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for the other deposition parameters. A {box} value selects standard
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distance units as defined by the "units"_units.html command,
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e.g. Angstroms for units = real or metal. A {lattice} value means the
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distance units are in lattice spacings. The "lattice"_lattice.html
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command must have been previously used to define the lattice spacing.
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Note that the units choice affects all the keyword values that have
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units of distance or velocity.
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2007-10-11 06:28:11 +08:00
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[Restart, fix_modify, output, run start/stop, minimize info:]
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2007-06-26 08:03:39 +08:00
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2007-10-13 01:37:26 +08:00
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This fix writes the state of the deposition to "binary restart
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files"_restart.html. This includes information about how many
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particles have been depositied, the random number generator seed, the
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next timestep for deposition, etc. See the
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"read_restart"_read_restart.html 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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None of the "fix_modify"_fix_modify.html options are relevant to this
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fix. No global or per-atom quantities are stored by this fix for
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2011-08-26 01:01:01 +08:00
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access by various "output commands"_Section_howto.html#howto_15. No
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2010-04-03 00:51:06 +08:00
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parameter of this fix can be used with the {start/stop} keywords of
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the "run"_run.html command. This fix is not invoked during "energy
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minimization"_minimize.html.
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2010-01-12 05:17:23 +08:00
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[Restrictions:]
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The specified insertion region cannot be a "dynamic" region, as
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defined by the "region"_region.html command.
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[Related commands:]
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"fix_pour"_fix_pour.html, "region"_region.html
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[Default:]
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Insertions are performed for individual atoms, i.e. no {mol} setting
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is defined. Additional option defaults are id = max, delta = 0.0,
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near = 0.0, attempt = 10, rate = 0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz =
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0.0 0.0, and units = lattice.
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