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Axel Kohlmeyer
2020-01-14 10:10:08 -05:00
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doc/src/fix_deposit.rst
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@ -57,6 +57,8 @@ Syntax
fix-ID = ID of :doc:`fix rigid/small <fix_rigid>` command
*shake* value = fix-ID
fix-ID = ID of :doc:`fix shake <fix_shake>` command
*orient* values = rx ry rz
rx,ry,rz = vector to randomly rotate an inserted molecule around
*units* value = *lattice* or *box*
lattice = the geometry is defined in lattice units
box = the geometry is defined in simulation box units
@ -236,6 +238,13 @@ sputtering process. E.g. the target point can be far away, so that
all incident particles strike the surface as if they are in an
incident beam of particles at a prescribed angle.
The *orient* keyword is only used when molecules are deposited. By
default, each molecule is inserted at a random orientation. If this
keyword is specified, then (rx,ry,rz) is used as an orientation
vector, and each inserted molecule is rotated around that vector with
a random value from zero to 2*PI. For a 2d simulation, rx = ry = 0.0
is required, since rotations can only be performed around the z axis.
The *id* keyword determines how atom IDs and molecule IDs are assigned
to newly deposited particles. Molecule IDs are only assigned if
molecules are being inserted. For the *max* setting, the atom and

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doc/txt/Packages_details.txt
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doc/txt/fix.txt
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@ -1,392 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
fix command :h3
[Syntax:]
fix ID group-ID style args :pre
ID = user-assigned name for the fix
group-ID = ID of the group of atoms to apply the fix to
style = one of a long list of possible style names (see below)
args = arguments used by a particular style :ul
[Examples:]
fix 1 all nve
fix 3 all nvt temp 300.0 300.0 0.01
fix mine top setforce 0.0 NULL 0.0 :pre
[Description:]
Set a fix that will be applied to a group of atoms. In LAMMPS, a
"fix" is any operation that is applied to the system during
timestepping or minimization. Examples include updating of atom
positions and velocities due to time integration, controlling
temperature, applying constraint forces to atoms, enforcing boundary
conditions, computing diagnostics, etc. There are hundreds of fixes
defined in LAMMPS and new ones can be added; see the
"Modify"_Modify.html doc page for details.
Fixes perform their operations at different stages of the timestep.
If 2 or more fixes operate at the same stage of the timestep, they are
invoked in the order they were specified in the input script.
The ID of a fix can only contain alphanumeric characters and
underscores.
Fixes can be deleted with the "unfix"_unfix.html command.
NOTE: The "unfix"_unfix.html command is the only way to turn off a
fix; simply specifying a new fix with a similar style will not turn
off the first one. This is especially important to realize for
integration fixes. For example, using a "fix nve"_fix_nve.html
command for a second run after using a "fix nvt"_fix_nh.html command
for the first run, will not cancel out the NVT time integration
invoked by the "fix nvt" command. Thus two time integrators would be
in place!
If you specify a new fix with the same ID and style as an existing
fix, the old fix is deleted and the new one is created (presumably
with new settings). This is the same as if an "unfix" command were
first performed on the old fix, except that the new fix is kept in the
same order relative to the existing fixes as the old one originally
was. Note that this operation also wipes out any additional changes
made to the old fix via the "fix_modify"_fix_modify.html command.
The "fix modify"_fix_modify.html command allows settings for some
fixes to be reset. See the doc page for individual fixes for details.
Some fixes store an internal "state" which is written to binary
restart files via the "restart"_restart.html or
"write_restart"_write_restart.html commands. This allows the fix to
continue on with its calculations 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. See the doc pages
for individual fixes for info on which ones can be restarted.
:line
Some fixes calculate one of three styles of quantities: global,
per-atom, or local, which can be used by other commands or output as
described below. A global quantity is one or more system-wide values,
e.g. the energy of a wall interacting with particles. A per-atom
quantity is one or more values per atom, e.g. the displacement vector
for each atom since time 0. Per-atom values are set to 0.0 for atoms
not in the specified fix group. Local quantities are calculated by
each processor based on the atoms it owns, but there may be zero or
more per atoms.
Note that a single fix can produce either global or per-atom or local
quantities (or none at all), but not both global and per-atom. It can
produce local quantities in tandem with global or per-atom quantities.
The fix doc page will explain.
Global, per-atom, and local quantities each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The
doc page for each fix describes the style and kind of values it
produces, e.g. a per-atom vector. Some fixes produce more than one
kind of a single style, e.g. a global scalar and a global vector.
When a fix quantity is accessed, as in many of the output commands
discussed below, it can be referenced via the following bracket
notation, where ID is the ID of the fix:
f_ID | entire scalar, vector, or array
f_ID\[I\] | one element of vector, one column of array
f_ID\[I\]\[J\] | one element of array :tb(s=|)
In other words, using one bracket reduces the dimension of the
quantity once (vector -> scalar, array -> vector). Using two brackets
reduces the dimension twice (array -> scalar). Thus a command that
uses scalar fix values as input can also process elements of a vector
or array.
Note that commands and "variables"_variable.html which use fix
quantities typically do not allow for all kinds, e.g. a command may
require a vector of values, not a scalar. This means there is no
ambiguity about referring to a fix quantity as f_ID even if it
produces, for example, both a scalar and vector. The doc pages for
various commands explain the details.
:line
In LAMMPS, the values generated by a fix can be used in several ways:
Global values can be output via the "thermo_style
custom"_thermo_style.html or "fix ave/time"_fix_ave_time.html command.
Or the values can be referenced in a "variable equal"_variable.html or
"variable atom"_variable.html command. :ulb,l
Per-atom values can be output via the "dump custom"_dump.html command.
Or they can be time-averaged via the "fix ave/atom"_fix_ave_atom.html
command or reduced by the "compute reduce"_compute_reduce.html
command. Or the per-atom values can be referenced in an "atom-style
variable"_variable.html. :l
Local values can be reduced by the "compute
reduce"_compute_reduce.html command, or histogrammed by the "fix
ave/histo"_fix_ave_histo.html command. :l
:ule
See the "Howto output"_Howto_output.html doc page for a summary of
various LAMMPS output options, many of which involve fixes.
The results of fixes that calculate global quantities can be either
"intensive" or "extensive" values. Intensive means the value is
independent of the number of atoms in the simulation,
e.g. temperature. Extensive means the value scales with the number of
atoms in the simulation, e.g. total rotational kinetic energy.
"Thermodynamic output"_thermo_style.html will normalize extensive
values by the number of atoms in the system, depending on the
"thermo_modify norm" setting. It will not normalize intensive values.
If a fix value is accessed in another way, e.g. by a
"variable"_variable.html, you may want to know whether it is an
intensive or extensive value. See the doc page for individual fixes
for further info.
:line
Each fix style has its own doc page which describes its arguments and
what it does, as listed below. Here is an alphabetic list of fix
styles available in LAMMPS. They are also listed in more compact form
on the "Commands fix"_Commands_fix.html doc page.
There are also additional accelerated fix styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands fix"_Commands_fix.html doc
page are followed by one or more of (g,i,k,o,t) to indicate which
accelerated styles exist.
"adapt"_fix_adapt.html - change a simulation parameter over time
"adapt/fep"_fix_adapt_fep.html - enhanced version of fix adapt
"addforce"_fix_addforce.html - add a force to each atom
"addtorque"_fix_addtorque.html - add a torque to a group of atoms
"append/atoms"_fix_append_atoms.html - append atoms to a running simulation
"atc"_fix_atc.html - initiates a coupled MD/FE simulation
"atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping
"ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities
"ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities
"ave/correlate"_fix_ave_correlate.html - compute/output time correlations
"ave/correlate/long"_fix_ave_correlate_long.html -
"ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms
"ave/histo/weight"_fix_ave_histo.html - weighted version of fix ave/histo
"ave/time"_fix_ave_time.html - compute/output global time-averaged quantities
"aveforce"_fix_aveforce.html - add an averaged force to each atom
"balance"_fix_balance.html - perform dynamic load-balancing
"bocs"_fix_bocs.html - NPT style time integration with pressure correction
"bond/break"_fix_bond_break.html - break bonds on the fly
"bond/create"_fix_bond_create.html - create bonds on the fly
"bond/react"_fix_bond_react.html - apply topology changes to model reactions
"bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping
"box/relax"_fix_box_relax.html - relax box size during energy minimization
"client/md"_fix_client_md.html - MD client for client/server simulations
"cmap"_fix_cmap.html - enables CMAP cross-terms of the CHARMM force field
"colvars"_fix_colvars.html - interface to the collective variables "Colvars" library
"controller"_fix_controller.html - apply control loop feedback mechanism
"deform"_fix_deform.html - change the simulation box size/shape
"deposit"_fix_deposit.html - add new atoms above a surface
"dpd/energy"_fix_dpd_energy.html - constant energy dissipative particle dynamics
"drag"_fix_drag.html - drag atoms towards a defined coordinate
"drude"_fix_drude.html - part of Drude oscillator polarization model
"drude/transform/direct"_fix_drude_transform.html - part of Drude oscillator polarization model
"drude/transform/inverse"_fix_drude_transform.html - part of Drude oscillator polarization model
"dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces
"edpd/source"_fix_dpd_source.html - add heat source to eDPD simulations
"efield"_fix_efield.html - impose electric field on system
"ehex"_fix_ehex.html - enhanced heat exchange algorithm
"electron/stopping"_fix_electron_stopping.html - electronic stopping power as a friction force
"enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
"eos/cv"_fix_eos_cv.html -
"eos/table"_fix_eos_table.html -
"eos/table/rx"_fix_eos_table_rx.html -
"evaporate"_fix_evaporate.html - remove atoms from simulation periodically
"external"_fix_external.html - callback to an external driver program
"ffl"_fix_ffl.html - apply a Fast-Forward Langevin equation thermostat
"filter/corotate"_fix_filter_corotate.html - implement corotation filter to allow larger timesteps with r-RESPA
"flow/gauss"_fix_flow_gauss.html - Gaussian dynamics for constant mass flux
"freeze"_fix_freeze.html - freeze atoms in a granular simulation
"gcmc"_fix_gcmc.html - grand canonical insertions/deletions
"gld"_fix_gld.html - generalized Langevin dynamics integrator
"gle"_fix_gle.html - generalized Langevin equation thermostat
"gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
"grem"_fix_grem.html - implements the generalized replica exchange method
"halt"_fix_halt.html - terminate a dynamics run or minimization
"heat"_fix_heat.html - add/subtract momentum-conserving heat
"hyper/global"_fix_hyper_global.html - global hyperdynamics
"hyper/local"_fix_hyper_local.html - local hyperdynamics
"imd"_fix_imd.html - implements the "Interactive MD" (IMD) protocol
"indent"_fix_indent.html - impose force due to an indenter
"ipi"_fix_ipi.html - enable LAMMPS to run as a client for i-PI path-integral simulations
"langevin"_fix_langevin.html - Langevin temperature control
"langevin/drude"_fix_langevin_drude.html - Langevin temperature control of Drude oscillators
"langevin/eff"_fix_langevin_eff.html - Langevin temperature control for the electron force field model
"langevin/spin"_fix_langevin_spin.html - Langevin temperature control for a spin or spin-lattice system
"latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code
"lb/fluid"_fix_lb_fluid.html -
"lb/momentum"_fix_lb_momentum.html -
"lb/pc"_fix_lb_pc.html -
"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html -
"lb/viscous"_fix_lb_viscous.html -
"lineforce"_fix_lineforce.html - constrain atoms to move in a line
"manifoldforce"_fix_manifoldforce.html - restrain atoms to a manifold during minimization
"meso"_fix_meso.html - time integration for SPH/DPDE particles
"meso/move"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion
"meso/stationary"_fix_meso_stationary.html -
"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
"mscg"_fix_mscg.html - apply MSCG method for force-matching to generate coarse grain models
"msst"_fix_msst.html - multi-scale shock technique (MSST) integration
"mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm
"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algorithm
"mvv/tdpd"_fix_mvv_dpd.html - constant temperature DPD using the modified velocity-Verlet algorithm
"neb"_fix_neb.html - nudged elastic band (NEB) spring forces
"nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
"nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles
"nph/body"_fix_nph_body.html - NPH for body particles
"nph/eff"_fix_nh_eff.html - NPH for nuclei and electrons in the electron force field model
"nph/sphere"_fix_nph_sphere.html - NPH for spherical particles
"nphug"_fix_nphug.html - constant-stress Hugoniostat integration
"npt"_fix_nh.html - constant NPT time integration via Nose/Hoover
"npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
"npt/body"_fix_npt_body.html - NPT for body particles
"npt/eff"_fix_nh_eff.html - NPT for nuclei and electrons in the electron force field model
"npt/sphere"_fix_npt_sphere.html - NPT for spherical particles
"npt/uef"_fix_nh_uef.html - NPT style time integration with diagonal flow
"nve"_fix_nve.html - constant NVE time integration
"nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles
"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces
"nve/awpmd"_fix_nve_awpmd.html - NVE for the Antisymmetrized Wave Packet Molecular Dynamics model
"nve/body"_fix_nve_body.html - NVE for body particles
"nve/dot"_fix_nve_dot.html - rigid body constant energy time integrator for coarse grain models
"nve/dotc/langevin"_fix_nve_dotc_langevin.html - Langevin style rigid body time integrator for coarse grain models
"nve/eff"_fix_nve_eff.html - NVE for nuclei and electrons in the electron force field model
"nve/limit"_fix_nve_limit.html - NVE with limited step length
"nve/line"_fix_nve_line.html - NVE for line segments
"nve/manifold/rattle"_fix_nve_manifold_rattle.html -
"nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
"nve/sphere"_fix_nve_sphere.html - NVE for spherical particles
"nve/spin"_fix_nve_spin.html - NVE for a spin or spin-lattice system
"nve/tri"_fix_nve_tri.html - NVE for triangles
"nvk"_fix_nvk.html - constant kinetic energy time integration
"nvt"_fix_nh.html - NVT time integration via Nose/Hoover
"nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
"nvt/body"_fix_nvt_body.html - NVT for body particles
"nvt/eff"_fix_nh_eff.html - NVE for nuclei and electrons in the electron force field model
"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html -
"nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
"nvt/sllod/eff"_fix_nvt_sllod_eff.html - NVT for NEMD with SLLOD equations for the electron force field model
"nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles
"nvt/uef"_fix_nh_uef.html - NVT style time integration with diagonal flow
"oneway"_fix_oneway.html - constrain particles on move in one direction
"orient/bcc"_fix_orient.html - add grain boundary migration force for BCC
"orient/fcc"_fix_orient.html - add grain boundary migration force for FCC
"phonon"_fix_phonon.html - calculate dynamical matrix from MD simulations
"pimd"_fix_pimd.html - Feynman path integral molecular dynamics
"planeforce"_fix_planeforce.html - constrain atoms to move in a plane
"plumed"_fix_plumed.html - wrapper on PLUMED free energy library
"poems"_fix_poems.html - constrain clusters of atoms to move as coupled rigid bodies
"pour"_fix_pour.html - pour new atoms/molecules into a granular simulation domain
"precession/spin"_fix_precession_spin.html -
"press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat
"print"_fix_print.html - print text and variables during a simulation
"property/atom"_fix_property_atom.html - add customized per-atom values
"python/invoke"_fix_python_invoke.html - call a Python function during a simulation
"python/move"_fix_python_move.html - call a Python function during a simulation run
"qbmsst"_fix_qbmsst.html - quantum bath multi-scale shock technique time integrator
"qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential
"qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method
"qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer
"qeq/point"_fix_qeq.html - charge equilibration via point method
"qeq/reax"_fix_qeq_reax.html - charge equilibration for ReaxFF potential
"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method
"qeq/slater"_fix_qeq.html - charge equilibration via Slater method
"qmmm"_fix_qmmm.html - functionality to enable a quantum mechanics/molecular mechanics coupling
"qtb"_fix_qtb.html - implement quantum thermal bath scheme
"rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
"reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information
"reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information
"recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
"restrain"_fix_restrain.html - constrain a bond, angle, dihedral
"rhok"_fix_rhok.html - add bias potential for long-range ordered systems
"rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration
"rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration
"rigid/nph/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPH integration
"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPT integration
"rigid/npt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration
"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
"rigid/nve/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration
"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVT integration
"rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration
"rx"_fix_rx.html -
"saed/vtk"_fix_saed_vtk.html -
"setforce"_fix_setforce.html - set the force on each atom
"shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
"shardlow"_fix_shardlow.html - integration of DPD equations of motion using the Shardlow splitting
"smd"_fix_smd.html - applied a steered MD force to a group
"smd/adjust_dt"_fix_smd_adjust_dt.html -
"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html -
"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html -
"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html -
"smd/setvel"_fix_smd_setvel.html -
"smd/wall_surface"_fix_smd_wall_surface.html -
"spring"_fix_spring.html - apply harmonic spring force to group of atoms
"spring/chunk"_fix_spring_chunk.html - apply harmonic spring force to each chunk of atoms
"spring/rg"_fix_spring_rg.html - spring on radius of gyration of group of atoms
"spring/self"_fix_spring_self.html - spring from each atom to its origin
"srd"_fix_srd.html - stochastic rotation dynamics (SRD)
"store/force"_fix_store_force.html - store force on each atom
"store/state"_fix_store_state.html - store attributes for each atom
"tdpd/source"_fix_dpd_source.html -
"temp/berendsen"_fix_temp_berendsen.html - temperature control by Berendsen thermostat
"temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics
"temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics
"temp/rescale"_fix_temp_rescale.html - temperature control by velocity rescaling
"temp/rescale/eff"_fix_temp_rescale_eff.html - temperature control by velocity rescaling in the electron force field model
"tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method
"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
"ti/spring"_fix_ti_spring.html -
"tmd"_fix_tmd.html - guide a group of atoms to a new configuration
"ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling
"ttm/mod"_fix_ttm.html - enhanced two-temperature model with additional options
"tune/kspace"_fix_tune_kspace.html - auto-tune KSpace parameters
"vector"_fix_vector.html - accumulate a global vector every N timesteps
"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for viscosity calculation
"viscous"_fix_viscous.html - viscous damping for granular simulations
"wall/body/polygon"_fix_wall_body_polygon.html -
"wall/body/polyhedron"_fix_wall_body_polyhedron.html -
"wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles
"wall/ees"_fix_wall_ees.html - wall for ellipsoidal particles
"wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations
"wall/gran/region"_fix_wall_gran_region.html -
"wall/harmonic"_fix_wall.html - harmonic spring wall
"wall/lj1043"_fix_wall.html - Lennard-Jones 10-4-3 wall
"wall/lj126"_fix_wall.html - Lennard-Jones 12-6 wall
"wall/lj93"_fix_wall.html - Lennard-Jones 9-3 wall
"wall/morse"_fix_wall.html - Morse potential wall
"wall/piston"_fix_wall_piston.html - moving reflective piston wall
"wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
"wall/region"_fix_wall_region.html - use region surface as wall
"wall/region/ees"_fix_wall_ees.html - use region surface as wall for ellipsoidal particles
"wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul
[Restrictions:]
Some fix styles are part of specific packages. They are only enabled
if LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info. The doc pages for
individual fixes tell if it is part of a package.
[Related commands:]
"unfix"_unfix.html, "fix_modify"_fix_modify.html
[Default:] none

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doc/txt/fix_deposit.txt
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@ -1,295 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
fix deposit command :h3
[Syntax:]
fix ID group-ID deposit N type M seed keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
deposit = style name of this fix command :l
N = # of atoms or molecules to insert :l
type = atom type to assign to inserted atoms (offset for molecule insertion) :l
M = insert a single atom or molecule every M steps :l
seed = random # seed (positive integer) :l
one or more keyword/value pairs may be appended to args :l
keyword = {region} or {id} or {global} or {local} or {near} or {gaussian} or {attempt} or {rate} or {vx} or {vy} or {vz} or {mol} or {rigid} or {shake} or {units} :l
{region} value = region-ID
region-ID = ID of region to use as insertion volume
{id} value = {max} or {next}
max = atom ID for new atom(s) is max ID of all current atoms plus one
next = atom ID for new atom(s) increments by one for every deposition
{global} values = lo hi
lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units)
{local} values = lo hi delta
lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units)
delta = lateral distance within which a neighbor is considered "nearby" (distance units)
{near} value = R
R = only insert atom/molecule if further than R from existing particles (distance units)
{gaussian} values = xmid ymid zmid sigma
xmid,ymid,zmid = center of the gaussian distribution (distance units)
sigma = width of gaussian distribution (distance units)
{attempt} value = Q
Q = attempt a single insertion up to Q times
{rate} value = V
V = z velocity (y in 2d) at which insertion volume moves (velocity units)
{vx} values = vxlo vxhi
vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units)
{vy} values = vylo vyhi
vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units)
{vz} values = vzlo vzhi
vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
{target} values = tx ty tz
tx,ty,tz = location of target point (distance units)
{mol} value = template-ID
template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
{molfrac} values = f1 f2 ... fN
f1 to fN = relative probability of creating each of N molecules in template-ID
{rigid} value = fix-ID
fix-ID = ID of "fix rigid/small"_fix_rigid.html command
{shake} value = fix-ID
fix-ID = ID of "fix shake"_fix_shake.html command
{units} value = {lattice} or {box}
lattice = the geometry is defined in lattice units
box = the geometry is defined in simulation box units :pre
:ule
[Examples:]
fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box
fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8
fix 4 sputter deposit 1000 2 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice
fix 5 insert deposit 200 2 100 777 region disk gaussian 5.0 5.0 9.0 1.0 units box :pre
[Description:]
Insert a single atom or molecule into the simulation domain every M
timesteps until N atoms or molecules have been inserted. This is
useful for simulating deposition onto a surface. For the remainder of
this doc page, a single inserted atom or molecule is referred to as a
"particle".
If inserted particles are individual atoms, they are assigned the
specified atom type. If they are molecules, the type of each atom in
the inserted molecule is specified in the file read by the
"molecule"_molecule.html command, and those values are added to the
specified atom type. E.g. if the file specifies atom types 1,2,3, and
those are the atom types you want for inserted molecules, then specify
{type} = 0. If you specify {type} = 2, the in the inserted molecule
will have atom types 3,4,5.
All atoms in the inserted particle are assigned to two groups: the
default group "all" and the group specified in the fix deposit command
(which can also be "all").
If you are computing temperature values which include inserted
particles, you will want to use the
"compute_modify"_compute_modify.html dynamic option, which insures the
current number of atoms is used as a normalizing factor each time the
temperature is computed.
Care must be taken that inserted particles are not too near existing
atoms, using the options described below. When inserting particles
above a surface in a non-periodic box (see the
"boundary"_boundary.html command), the possibility of a particle
escaping the surface and flying upward should be considered, since the
particle may be lost or the box size may grow infinitely large. A
"fix wall/reflect"_fix_wall_reflect.html command can be used to
prevent this behavior. Note that if a shrink-wrap boundary is used,
it is OK to insert the new particle outside the box, however the box
will immediately be expanded to include the new particle. When
simulating a sputtering experiment it is probably more realistic to
ignore those atoms using the "thermo_modify"_thermo_modify.html
command with the {lost ignore} option and a fixed
"boundary"_boundary.html.
The fix deposit command must use the {region} keyword to define an
insertion volume. The specified region must have been previously
defined with a "region"_region.html command. It must be defined with
side = {in}.
NOTE: LAMMPS checks that the specified region is wholly inside the
simulation box. It can do this correctly for orthonormal simulation
boxes. However for "triclinic boxes"_Howto_triclinic.html, it only
tests against the larger orthonormal box that bounds the tilted
simulation box. If the specified region includes volume outside the
tilted box, then an insertion will likely fail, leading to a "lost
atoms" error. Thus for triclinic boxes you should insure the
specified region is wholly inside the simulation box.
The locations of inserted particles are taken from uniform distributed
random numbers, unless the {gaussian} keyword is used. Then the
individual coordinates are taken from a gaussian distribution of
width {sigma} centered on {xmid,ymid,zmid}.
Individual atoms are inserted, unless the {mol} keyword is used. It
specifies a {template-ID} previously defined using the
"molecule"_molecule.html command, which reads files that define one or
more molecules. The coordinates, atom types, charges, etc, as well as
any bond/angle/etc and special neighbor information for the molecule
can be specified in the molecule file. See the
"molecule"_molecule.html command for details. The only settings
required to be in each file are the coordinates and types of atoms in
the molecule.
If the molecule template contains more than one molecule, the relative
probability of depositing each molecule can be specified by the
{molfrac} keyword. N relative probabilities, each from 0.0 to 1.0, are
specified, where N is the number of molecules in the template. Each
time a molecule is deposited, a random number is used to sample from
the list of relative probabilities. The N values must sum to 1.0.
If you wish to insert molecules via the {mol} keyword, that will be
treated as rigid bodies, use the {rigid} keyword, specifying as its
value the ID of a separate "fix rigid/small"_fix_rigid.html
command which also appears in your input script.
NOTE: If you wish the new rigid molecules (and other rigid molecules)
to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html
or "fix rigid/small/npt"_fix_rigid.html, then you need to use the
"fix_modify dynamic/dof yes" command for the rigid fix. This is to
inform that fix that the molecule count will vary dynamically.
If you wish to insert molecules via the {mol} keyword, that will have
their bonds or angles constrained via SHAKE, use the {shake} keyword,
specifying as its value the ID of a separate "fix
shake"_fix_shake.html command which also appears in your input script.
Each timestep a particle is inserted, the coordinates for its atoms
are chosen as follows. For insertion of individual atoms, the
"position" referred to in the following description is the coordinate
of the atom. For insertion of molecule, the "position" is the
geometric center of the molecule; see the "molecule"_molecule.html doc
page for details. A random rotation of the molecule around its center
point is performed, which determines the coordinates all the
individual atoms.
A random position within the region insertion volume is generated. If
neither the {global} or {local} keyword is used, the random position
is the trial position. If the {global} keyword is used, the random
x,y values are used, but the z position of the new particle is set
above the highest current atom in the simulation by a distance
randomly chosen between lo/hi. (For a 2d simulation, this is done for
the y position.) If the {local} keyword is used, the z position is
set a distance between lo/hi above the highest current atom in the
simulation that is "nearby" the chosen x,y position. In this context,
"nearby" means the lateral distance (in x,y) between the new and old
particles is less than the {delta} setting.
Once a trial x,y,z position has been selected, the insertion is only
performed if no current atom in the simulation is within a distance R
of any atom in the new particle, including the effect of periodic
boundary conditions if applicable. R is defined by the {near}
keyword. Note that the default value for R is 0.0, which will allow
atoms to strongly overlap if you are inserting where other atoms are
present. This distance test is performed independently for each atom
in an inserted molecule, based on the randomly rotated configuration
of the molecule. If this test fails, a new random position within the
insertion volume is chosen and another trial is made. Up to Q
attempts are made. If the particle is not successfully inserted,
LAMMPS prints a warning message.
NOTE: If you are inserting finite size particles or a molecule or
rigid body consisting of finite-size particles, then you should
typically set R larger than the distance at which any inserted
particle may overlap with either a previously inserted particle or an
existing particle. LAMMPS will issue a warning if R is smaller than
this value, based on the radii of existing and inserted particles.
The {rate} option moves the insertion volume in the z direction (3d)
or y direction (2d). This enables particles to be inserted from a
successively higher height over time. Note that this parameter is
ignored if the {global} or {local} keywords are used, since those
options choose a z-coordinate for insertion independently.
The vx, vy, and vz components of velocity for the inserted particle
are set using the values specified for the {vx}, {vy}, and {vz}
keywords. Note that normally, new particles should be a assigned a
negative vertical velocity so that they move towards the surface. For
molecules, the same velocity is given to every particle (no rotation
or bond vibration).
If the {target} option is used, the velocity vector of the inserted
particle is changed so that it points from the insertion position
towards the specified target point. The magnitude of the velocity is
unchanged. This can be useful, for example, for simulating a
sputtering process. E.g. the target point can be far away, so that
all incident particles strike the surface as if they are in an
incident beam of particles at a prescribed angle.
The {id} keyword determines how atom IDs and molecule IDs are assigned
to newly deposited particles. Molecule IDs are only assigned if
molecules are being inserted. For the {max} setting, the atom and
molecule IDs of all current atoms are checked. Atoms in the new
particle are assigned IDs starting with the current maximum plus one.
If a molecule is inserted it is assigned an ID = current maximum plus
one. This means that if particles leave the system, the new IDs may
replace the lost ones. For the {next} setting, the maximum ID of any
atom and molecule is stored at the time the fix is defined. Each time
a new particle is added, this value is incremented to assign IDs to
the new atom(s) or molecule. Thus atom and molecule IDs for deposited
particles will be consecutive even if particles leave the system over
time.
The {units} keyword determines the meaning of the distance units used
for the other deposition parameters. A {box} value selects standard
distance units as defined by the "units"_units.html command,
e.g. Angstroms for units = real or metal. A {lattice} value means the
distance units are in lattice spacings. The "lattice"_lattice.html
command must have been previously used to define the lattice spacing.
Note that the units choice affects all the keyword values that have
units of distance or velocity.
NOTE: If you are monitoring the temperature of a system where the atom
count is changing due to adding particles, you typically should use
the "compute_modify dynamic yes"_compute_modify.html command for the
temperature compute you are using.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the state of the deposition to "binary restart
files"_restart.html. This includes information about how many
particles have been deposited, the random number generator seed, the
next timestep for deposition, etc. 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.
NOTE: For this to work correctly, the timestep must [not] be changed
after reading the restart with "reset_timestep"_reset_timestep.html.
The fix will try to detect it and stop with an error.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
access by various "output commands"_Howto_output.html. 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
minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
was built with that package. See the "Build
package"_Build_package.html doc page for more info.
The specified insertion region cannot be a "dynamic" region, as
defined by the "region"_region.html command.
[Related commands:]
"fix pour"_fix_pour.html, "region"_region.html
[Default:]
Insertions are performed for individual atoms, i.e. no {mol} setting
is defined. If the {mol} keyword is used, the default for {molfrac}
is an equal probabilities for all molecules in the template.
Additional option defaults are id = max, delta = 0.0, near = 0.0,
attempt = 10, rate = 0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz = 0.0 0.0,
and units = lattice.

86
doc/txt/pair_lj_switch3_coulgauss.txt
View File

@ -1,86 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
pair_style lj/switch3/coulgauss/long command :h3
[Syntax:]
pair_style style args :pre
style = {lj/switch3/coulgauss/long}
args = list of arguments for a particular style :ul
{lj/switch3/coulgauss/long} args = cutoff (cutoff2) width
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
width = width parameter of the smoothing function (distance units) :pre
[Examples:]
pair_style lj/switch3/coulgauss/long 12.0 3.0
pair_coeff 1 0.2 2.5 1.2 :pre
pair_style lj/switch3/coulgauss/long 12.0 10.0 3.0
pair_coeff 1 0.2 2.5 1.2 :pre
[Description:]
The {lj/switch3/coulgauss} style evaluates the LJ
vdW potential
:c,image(Eqs/pair_lj_switch3.jpg)
, which goes smoothly to zero at the cutoff r_c as defined
by the switching function
:c,image(Eqs/pair_switch3.jpg)
where w is the width defined in the arguments. This potential
is combined with Coulomb interaction between Gaussian charge densities:
:c,image(Eqs/pair_coulgauss.jpg)
where qi and qj are the
charges on the 2 atoms, epsilon is the dielectric constant which
can be set by the "dielectric"_dielectric.html command, gamma_i and gamma_j
are the widths of the Gaussian charge distribution and erf() is the error-function.
This style has to be used in conjunction with the "kspace_style"_kspace_style.html command
If one cutoff is specified it is used for both the vdW and Coulomb
terms. If two cutoffs are specified, the first is used as the cutoff
for the vdW terms, and the second is the cutoff for the Coulombic term.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:
epsilon (energy)
sigma (distance)
gamma (distance) :ul
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
Shifting the potential energy is not necessary because the switching
function ensures that the potential is zero at the cut-off.
[Restrictions:]
These styles are part of the USER-YAFF package. They are only
enabled if LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none

3
doc/utils/sphinx-config/false_positives.txt
View File

@ -1141,6 +1141,7 @@ ico
icosahedral
idealgas
IDR
idx
ielement
ieni
ifdefs
@ -2475,6 +2476,8 @@ Runge
runtime
Rutuparna
rx
ry
rz
Ryckaert
Rycroft
Rydbergs

27
src/MISC/fix_deposit.cpp
View File

@ -421,9 +421,15 @@ void FixDeposit::pre_exchange()
while (rng > molfrac[imol]) imol++;
natom = onemols[imol]->natoms;
if (dimension == 3) {
r[0] = random->uniform() - 0.5;
r[1] = random->uniform() - 0.5;
r[2] = random->uniform() - 0.5;
if (orientflag) {
r[0] = rx;
r[1] = ry;
r[2] = rz;
} else {
r[0] = random->uniform() - 0.5;
r[1] = random->uniform() - 0.5;
r[2] = random->uniform() - 0.5;
}
} else {
r[0] = r[1] = 0.0;
r[2] = 1.0;
@ -662,6 +668,10 @@ void FixDeposit::options(int narg, char **arg)
xmid = ymid = zmid = 0.0;
scaleflag = 1;
targetflag = 0;
orientflag = 0;
rx = 0.0;
ry = 0.0;
rz = 0.0;
int iarg = 0;
while (iarg < narg) {
@ -769,6 +779,17 @@ void FixDeposit::options(int narg, char **arg)
vzlo = force->numeric(FLERR,arg[iarg+1]);
vzhi = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"orient") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix deposit command");
orientflag = 1;
rx = force->numeric(FLERR,arg[iarg+1]);
ry = force->numeric(FLERR,arg[iarg+2]);
rz = force->numeric(FLERR,arg[iarg+3]);
if (domain->dimension == 2 && (rx != 0.0 || ry != 0.0))
error->all(FLERR,"Illegal fix deposit orient settings");
if (rx == 0.0 && ry == 0.0 && rz == 0.0)
error->all(FLERR,"Illegal fix deposit orient settings");
iarg += 4;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;

4
src/MISC/fix_deposit.h
View File

@ -38,11 +38,11 @@ class FixDeposit : public Fix {
private:
int ninsert,ntype,nfreq,seed;
int iregion,globalflag,localflag,maxattempt,rateflag,scaleflag,targetflag;
int mode,rigidflag,shakeflag,idnext,distflag;
int mode,rigidflag,shakeflag,idnext,distflag,orientflag;
double lo,hi,deltasq,nearsq,rate,sigma;
double vxlo,vxhi,vylo,vyhi,vzlo,vzhi;
double xlo,xhi,ylo,yhi,zlo,zhi,xmid,ymid,zmid;
double tx,ty,tz;
double rx,ry,rz,tx,ty,tz;
char *idregion;
char *idrigid,*idshake;