forked from lijiext/lammps
282 lines
13 KiB
Plaintext
282 lines
13 KiB
Plaintext
.. index:: fix pour
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fix pour 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 pour N type seed keyword values ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* pour = style name of this fix command
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* N = # of particles to insert
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* type = atom type to assign to inserted particles (offset for molecule insertion)
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* seed = random # seed (positive integer)
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* one or more keyword/value pairs may be appended to args
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* keyword = *region* or *diam* or *vol* or *rate* or *dens* or *vel* or *mol* or *rigid* or *shake* or *ignore*
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.. parsed-literal::
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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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*diam* values = dstyle args
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dstyle = *one* or *range* or *poly*
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*one* args = D
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D = single diameter for inserted particles (distance units)
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*range* args = Dlo Dhi
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Dlo,Dhi = range of diameters for inserted particles (distance units)
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*poly* args = Npoly D1 P1 D2 P2 ...
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Npoly = # of (D,P) pairs
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D1,D2,... = diameter for subset of inserted particles (distance units)
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P1,P2,... = percentage of inserted particles with this diameter (0-1)
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*id* values = idflag
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idflag = *max* or *next* = how to choose IDs for inserted particles and molecules
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*vol* values = fraction Nattempt
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fraction = desired volume fraction for filling insertion volume
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Nattempt = max # of insertion attempts per particle
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*rate* value = V
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V = z velocity (3d) or y velocity (2d) at which
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insertion volume moves (velocity units)
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*dens* values = Rholo Rhohi
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Rholo,Rhohi = range of densities for inserted particles (mass/volume units)
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*vel* values (3d) = vxlo vxhi vylo vyhi vz
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*vel* values (2d) = vxlo vxhi vy
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vxlo,vxhi = range of x velocities for inserted particles (velocity units)
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vylo,vyhi = range of y velocities for inserted particles (velocity units)
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vz = z velocity (3d) assigned to inserted particles (velocity units)
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vy = y velocity (2d) assigned to inserted particles (velocity units)
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*mol* value = template-ID
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template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
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*molfrac* values = f1 f2 ... fN
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f1 to fN = relative probability of creating each of N molecules in template-ID
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*rigid* value = fix-ID
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fix-ID = ID of :doc:`fix rigid/small <fix_rigid>` command
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*shake* value = fix-ID
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fix-ID = ID of :doc:`fix shake <fix_shake>` command
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*ignore* value = none
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skip any line or triangle particles when detecting possible
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overlaps with inserted particles
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Examples
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""""""""
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.. parsed-literal::
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fix 3 all pour 1000 2 29494 region myblock
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fix 2 all pour 10000 1 19985583 region disk vol 0.33 100 rate 1.0 diam range 0.9 1.1
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fix 2 all pour 10000 1 19985583 region disk diam poly 2 0.7 0.4 1.5 0.6
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fix ins all pour 500 1 4767548 vol 0.8 10 region slab mol object rigid myRigid
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Description
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"""""""""""
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Insert finite-size particles or molecules into the simulation box
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every few timesteps within a specified region until N particles or
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molecules have been inserted. This is typically used to model the
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pouring of granular particles into a container under the influence of
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gravity. For the remainder of this doc page, a single inserted atom
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or molecule is referred to as a "particle".
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If inserted particles are individual atoms, they are assigned the
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specified atom type. If they are molecules, the type of each atom in
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the inserted molecule is specified in the file read by the
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:doc:`molecule <molecule>` command, and those values are added to the
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specified atom type. E.g. if the file specifies atom types 1,2,3, and
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those are the atom types you want for inserted molecules, then specify
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*type* = 0. If you specify *type* = 2, the in the inserted molecule
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will have atom types 3,4,5.
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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 pour command
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(which can also be "all").
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This command must use the *region* keyword to define an insertion
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volume. The specified region must have been previously defined with a
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:doc:`region <region>` command. It must be of type *block* or a z-axis
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*cylinder* and must be defined with side = *in*. The cylinder style
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of region can only be used with 3d simulations.
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Individual atoms are inserted, unless the *mol* keyword is used. It
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specifies a *template-ID* previously defined using the
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:doc:`molecule <molecule>` command, which reads a file that defines the
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molecule. The coordinates, atom types, center-of-mass, moments of
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inertia, etc, as well as any bond/angle/etc and special neighbor
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information for the molecule can be specified in the molecule file.
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See the :doc:`molecule <molecule>` command for details. The only
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settings required to be in this file are the coordinates and types of
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atoms in the molecule.
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If the molecule template contains more than one molecule, the relative
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probability of depositing each molecule can be specified by the
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*molfrac* keyword. N relative probablities, each from 0.0 to 1.0, are
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specified, where N is the number of molecules in the template. Each
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time a molecule is inserted, a random number is used to sample from
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the list of relative probabilities. The N values must sum to 1.0.
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If you wish to insert molecules via the *mol* keyword, that will be
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treated as rigid bodies, use the *rigid* keyword, specifying as its
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value the ID of a separate :doc:`fix rigid/small <fix_rigid_small>`
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command which also appears in your input script.
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If you wish to insert molecules via the *mol* keyword, that will have
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their bonds or angles constrained via SHAKE, use the *shake* keyword,
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specifying as its value the ID of a separate :doc:`fix shake <fix_shake>` command which also appears in your input script.
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Each timestep particles are inserted, they are placed randomly inside
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the insertion volume so as to mimic a stream of poured particles. If
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they are molecules they are also oriented randomly. Each atom in the
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particle is tested for overlaps with existing particles, including
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effects due to periodic boundary conditions if applicable. If an
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overlap is detected, another random insertion attempt is made; see the
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*vol* keyword discussion below. The larger the volume of the
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insertion region, the more particles that can be inserted at any one
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timestep. Particles are inserted again after enough time has elapsed
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that the previously inserted particles fall out of the insertion
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volume under the influence of gravity. Insertions continue every so
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many timesteps until the desired # of particles has been inserted.
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.. note::
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If you are monitoring the temperature of a system where the
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particle count is changing due to adding particles, you typically
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should use the :doc:`compute_modify dynamic yes <compute_modify>`
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command for the temperature compute you are using.
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----------
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All other keywords are optional with defaults as shown below.
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The *diam* option is only used when inserting atoms and specifes the
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diameters of inserted particles. There are 3 styles: *one*, *range*,
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or *poly*. For *one*, all particles will have diameter *D*. For
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*range*, the diameter of each particle will be chosen randomly and
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uniformly between the specified *Dlo* and *Dhi* bounds. For *poly*, a
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series of *Npoly* diameters is specified. For each diameter a
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percentage value from 0.0 to 1.0 is also specified. The *Npoly*
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percentages must sum to 1.0. For the example shown above with "diam 2
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0.7 0.4 1.5 0.6", all inserted particles will have a diameter of 0.7
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or 1.5. 40% of the particles will be small; 60% will be large.
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Note that for molecule insertion, the diameters of individual atoms in
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the molecule can be specified in the file read by the
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:doc:`molecule <molecule>` command. If not specified, the diameter of
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each atom in the molecule has a default diameter of 1.0.
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The *id* option has two settings which are used to determine the atom
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or molecule IDs to assign to inserted particles/molecules. In both
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cases a check is done of the current system to find the maximum
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current atom and molecule ID of any existing particle. Newly inserted
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particles and molecules are assigned IDs that increment those max
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values. For the *max* setting, which is the default, this check is
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done at every insertion step, which allows for particles to leave the
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system, and their IDs to potentially be re-used. For the *next*
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setting this check is done only once when the fix is specified, which
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can be more efficient if you are sure particles will not be added in
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some other way.
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The *vol* option specifies what volume fraction of the insertion
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volume will be filled with particles. For particles with a size
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specified by the *diam range* keyword, they are assumed to all be of
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maximum diamter *Dhi* for purposes of computing their contribution to
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the volume fraction.
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The higher the volume fraction value, the more particles are inserted
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each timestep. Since inserted particles cannot overlap, the maximum
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volume fraction should be no higher than about 0.6. Each timestep
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particles are inserted, LAMMPS will make up to a total of M tries to
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insert the new particles without overlaps, where M = # of inserted
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particles * Nattempt. If LAMMPS is unsuccessful at completing all
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insertions, it prints a warning.
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The *dens* and *vel* options enable inserted particles to have a range
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of densities or xy velocities. The specific values for a particular
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inserted particle will be chosen randomly and uniformly between the
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specified bounds. Internally, the density value for a particle is
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converted to a mass, based on the radius (volume) of the particle.
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The *vz* or *vy* value for option *vel* assigns a z-velocity (3d) or
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y-velocity (2d) to each inserted particle.
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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 pouring particles from a
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successively higher height over time.
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The *ignore* option is useful when running a simulation that used line
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segment (2d) or triangle (3d) particles, typically to define
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boundaries for spherical granular particles to interact with. See the
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:doc:`atom_style line or tri <atom_style>` command for details. Lines
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and triangles store their size, and if the size is large it may
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overlap (in a spherical sense) with the insertion region, even if the
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line/triangle is oriented such that there is no actual overlap. This
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can prevent particles from being inserted. The *ignore* keyword
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causes the overlap check to skip any line or triangle particles.
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Obviously you should only use it if there is in fact no overlap of the
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line or triangle particles with the insertion region.
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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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No information about this fix is written to :doc:`binary restart files <restart>`. This means you must be careful when restarting a
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pouring simulation, when the restart file was written in the middle of
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the pouring operation. Specifically, you should use a new fix pour
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command in the input script for the restarted simulation that
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continues the operation. You will need to adjust the arguments of the
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original fix pour command to do this.
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Also note that because the state of the random number generator is not
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saved in restart files, you cannot do "exact" restarts with this fix,
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where the simulation continues on the same as if no restart had taken
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place. However, in a statistical sense, a restarted simulation should
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produce the same behavior if you adjust the fix pour parameters
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appropriately.
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None of the :doc:`fix_modify <fix_modify>` 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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access by various :ref:`output commands <howto_15>`. No
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parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. 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 GRANULAR package. It is only enabled if
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LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
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For 3d simulations, a gravity fix in the -z direction must be defined
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for use in conjunction with this fix. For 2d simulations, gravity
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must be defined in the -y direction.
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The specified insertion region cannot be a "dynamic" region, as
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defined by the :doc:`region <region>` command.
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Related commands
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""""""""""""""""
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:doc:`fix deposit <fix_deposit>`, :doc:`fix gravity <fix_gravity>`,
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:doc:`region <region>`
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Default
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"""""""
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Insertions are performed for individual particles, i.e. no *mol*
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setting is defined. If the *mol* keyword is used, the default for
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*molfrac* is an equal probabilities for all molecules in the template.
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Additional option defaults are diam = one 1.0, dens = 1.0 1.0, vol =
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0.25 50, rate = 0.0, vel = 0.0 0.0 0.0 0.0 0.0 (for 3d), vel = 0.0 0.0 0.0
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(for 2d), and id = max.
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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