forked from lijiext/lammps
259 lines
12 KiB
Plaintext
259 lines
12 KiB
Plaintext
"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 command :h3
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[Syntax:]
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fix ID group-ID style args :pre
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ID = user-assigned name for the fix
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group-ID = ID of the group of atoms to apply the fix to
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style = one of a long list of possible style names (see below)
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args = arguments used by a particular style :ul
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[Examples:]
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fix 1 all nve
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fix 3 all nvt 300.0 300.0 0.01
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fix mine top setforce 0.0 NULL 0.0 :pre
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[Description:]
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Set a fix that will be applied to a group of atoms. In LAMMPS, a
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"fix" is any operation that is applied to the system during
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timestepping or minimization. Examples include updating of atom
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positions and velocities due to time integration, controlling
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temperature, applying constraint forces to atoms, enforcing boundary
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conditions, computing diagnostics, etc. There are dozens of fixes
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defined in LAMMPS and new ones can be added; see "this
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section"_Section_modify.html for a discussion.
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Fixes perform their operations at different stages of the timestep.
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If 2 or more fixes operate at the same stage of the timestep, they are
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invoked in the order they were specified in the input script.
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The ID of a fix can only contain alphanumeric characters and
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underscores.
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Fixes can be deleted with the "unfix"_unfix.html command.
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IMPORTANT NOTE: The "unfix"_unfix.html command is the only way to turn
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off a fix; simply specifying a new fix with a similar style will not
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turn off the first one. This is especially important to realize for
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integration fixes. For example, using a "fix nve"_fix_nve.html
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command for a second run after using a "fix nvt"_fix_nh.html command
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for the first run, will not cancel out the NVT time integration
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invoked by the "fix nvt" command. Thus two time integrators would be
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in place!
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If you specify a new fix with the same ID and style as an existing
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fix, the old fix is deleted and the new one is created (presumably
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with new settings). This is the same as if an "unfix" command were
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first performed on the old fix, except that the new fix is kept in the
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same order relative to the existing fixes as the old one originally
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was. Note that this operation also wipes out any additional changes
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made to the old fix via the "fix_modify"_fix_modify.html command.
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The "fix modify"_fix_modify.html command allows settings for some
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fixes to be reset. See the doc page for individual fixes for details.
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Some fixes store an internal "state" which is written to binary
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restart files via the "restart"_restart.html or
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"write_restart"_write_restart.html commands. This allows the fix to
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continue on with its calculations in a restarted simulation. 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. See the doc pages
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for individual fixes for info on which ones can be restarted.
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:line
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Some fixes calculate one of three styles of quantities: global,
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per-atom, or local, which can be used by other commands or output as
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described below. A global quantity is one or more system-wide values,
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e.g. the energy of a wall interacting with particles. A per-atom
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quantity is one or more values per atom, e.g. the displacement vector
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for each atom since time 0. Per-atom values are set to 0.0 for atoms
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not in the specified fix group. Local quantities are calculated by
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each processor based on the atoms it owns, but there may be zero or
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more per atoms.
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Note that a single fix may produces either global or per-atom or local
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quantities (or none at all), but never more than one of these.
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Global, per-atom, and local quantities each come in three kinds: a
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single scalar value, a vector of values, or a 2d array of values. The
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doc page for each fix describes the style and kind of values it
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produces, e.g. a per-atom vector. Some fixes produce more than one
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kind of a single style, e.g. a global scalar and a global vector.
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When a fix quantity is accessed, as in many of the output commands
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discussed below, it can be referenced via the following bracket
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notation, where ID is the ID of the fix:
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f_ID | entire scalar, vector, or array
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f_ID\[I\] | one element of vector, one column of array
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f_ID\[I\]\[J\] | one element of array :tb(s=|)
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In other words, using one bracket reduces the dimension of the
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quantity once (vector -> scalar, array -> vector). Using two brackets
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reduces the dimension twice (array -> scalar). Thus a command that
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uses scalar fix values as input can also process elements of a vector
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or array.
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Note that commands and "variables"_variable.html which use fix
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quantities typically do not allow for all kinds, e.g. a command may
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require a vector of values, not a scalar. This means there is no
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ambiguity about referring to a fix quantity as f_ID even if it
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produces, for example, both a scalar and vector. The doc pages for
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various commands explain the details.
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:line
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In LAMMPS, the values generated by a fix can be used in several ways:
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Global values can be output via the "thermo_style
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custom"_thermo_style.html or "fix ave/time"_fix_ave_time.html command.
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Or the values can be referenced in a "variable equal"_variable.html or
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"variable atom"_variable.html command. :ulb,l
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Per-atom values can be output via the "dump custom"_dump.html command
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or the "fix ave/spatial"_fix_ave_spatial.html command. Or they can be
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time-averaged via the "fix ave/atom"_fix_ave_atom.html command or
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reduced by the "compute reduce"_compute_reduce.html command. Or the
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per-atom values can be referenced in an "atom-style
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variable"_variable.html. :l
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Local values can be reduced by the "compute
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reduce"_compute_reduce.html command, or histogrammed by the "fix
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ave/histo"_fix_ave_histo.html command. :l,ule
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See this "howto section"_Section_howto.html#4_15 for a summary of
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various LAMMPS output options, many of which involve fixes.
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The results of fixes that calculate global quantities can be either
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"intensive" or "extensive" values. Intensive means the value is
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independent of the number of atoms in the simulation,
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e.g. temperature. Extensive means the value scales with the number of
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atoms in the simulation, e.g. total rotational kinetic energy.
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"Thermodynamic output"_thermo_style.html will normalize extensive
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values by the number of atoms in the system, depending on the
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"thermo_modify norm" setting. It will not normalize intensive values.
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If a fix value is accessed in another way, e.g. by a
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"variable"_variable.html, you may want to know whether it is an
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intensive or extensive value. See the doc page for individual fixes
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for further info.
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:line
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Each fix style has its own documentation page which describes its
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arguments and what it does, as listed below. Here is an alphabetic
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list of fix styles available in LAMMPS:
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"addforce"_fix_addforce.html - add a force to each atom
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"aveforce"_fix_aveforce.html - add an averaged force to each atom
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"ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities
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"ave/histo"_fix_ave_atom.html - compute/output time-averaged histograms
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"ave/spatial"_fix_ave_spatial.html - compute/output time-averaged per-atom quantities by layer
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"ave/time"_fix_ave_time.html - compute/output global time-averaged quantities
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"bond/break"_fix_bond_break.html - break bonds on the fly
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"bond/create"_fix_bond_create.html - create bonds on the fly
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"bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping
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"box/relax"_fix_box_relax.html - relax box size during energy minimization
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"deform"_fix_deform.html - change the simulation box size/shape
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"deposit"_fix_deposit.html - add new atoms above a surface
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"drag"_fix_drag.html - drag atoms towards a defined coordinate
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"dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces
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"efield"_fix_efield.html - impose electric field on system
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"enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
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"evaporate"_fix_evaporate.html - remove atoms from simulation periodically
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"freeze"_fix_freeze.html - freeze atoms in a granular simulation
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"gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
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"heat"_fix_heat.html - add/subtract momentum-conserving heat
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"indent"_fix_indent.html - impose force due to an indenter
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"langevin"_fix_langevin.html - Langevin temperature control
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"lineforce"_fix_lineforce.html - constrain atoms to move in a line
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"momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms
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"move"_fix_move.html - move atoms in a prescribed fashion
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"nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
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"nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles
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"nph/sphere"_fix_nph_sphere.html - NPH for spherical particles
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"npt"_fix_nh.html - constant NPT time integration via Nose/Hoover
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"npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
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"npt/sphere"_fix_npt_sphere.html - NPT for spherical particles
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"nve"_fix_nve.html - constant NVE time integration
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"nve/asphere"_fix_nve_asphere.html - NVT for aspherical particles
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"nve/limit"_fix_nve_limit.html - NVE with limited step length
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"nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
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"nve/sphere"_fix_nve_sphere.html - NVT for spherical particles
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"nvt"_fix_nh.html - constant NVT time integration via Nose/Hoover
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"nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
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"nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
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"nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles
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"orient/fcc"_fix_orient_fcc.html - add grain boundary migration force
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"planeforce"_fix_planeforce.html - constrain atoms to move in a plane
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"poems"_fix_poems.html - constrain clusters of atoms to move \
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as coupled rigid bodies
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"pour"_fix_pour.html - pour new atoms into a granular simulation domain
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"press/berendsen"_fix_press_berendsen.html - pressure control by \
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Berendsen barostat
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"print"_fix_print.html - print text and variables during a simulation
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"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information \
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"recenter"_fix_recenter.html - constrain the center-of-mass position \
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of a group of atoms
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"rigid"_fix_rigid.html - constrain one or more clusters of atoms to \
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move as a rigid body with NVE integration
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"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to \
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move as a rigid body with alternate NVE integration
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"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to \
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move as a rigid body with NVT integration
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"setforce"_fix_setforce.html - set the force on each atom
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"shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
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"spring"_fix_spring.html - apply harmonic spring force to group of atoms
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"spring/rg"_fix_spring_rg.html - spring on radius of gyration of \
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group of atoms
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"spring/self"_fix_spring_self.html - spring from each atom to its origin
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"store/coord"_fix_store_coord.html - store coords of each atom
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"store/force"_fix_store_force.html - store force on each atom
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"temp/berendsen"_fix_temp_berendsen.html - temperature control by \
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Berendsen thermostat
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"temp/rescale"_fix_temp_rescale.html - temperature control by \
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velocity rescaling
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"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for \
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thermal conductivity calculation
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"tmd"_fix_tmd.html - guide a group of atoms to a new configuration
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"ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling
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"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for \
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viscosity calculation
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"viscous"_fix_viscous.html - viscous damping for granular simulations
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"wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles
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"wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations
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"wall/harmonic"_fix_wall.html - harmonic spring wall
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"wall/lj126"_fix_wall.html - Lennard-Jones 12-6 wall
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"wall/lj93"_fix_wall.html - Lennard-Jones 9-3 wall
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"wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
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"wall/region"_fix_wall_region.html - use region surface as wall :ul
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There are also additional fix styles submitted by users which are
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included in the LAMMPS distribution. The list of these with links to
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the individual styles are given in the fix section of "this
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page"_Section_commands.html#3_5.
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[Restrictions:]
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Some fix styles are part of specific packages. They are only enabled
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if LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#2_3 section for more info on packages. The
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doc pages for individual fixes tell if it is part of a package.
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[Related commands:]
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"unfix"_unfix.html, "fix_modify"_fix_modify.html
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[Default:] none
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