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first commit: added SDPD

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This commit is contained in:
Morteza Jalalvand
2018-10-30 17:40:00 +03:30
parent fb4df86d3d
commit ba6f6f73f1
39 changed files with 4281 additions and 8 deletions
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2
doc/src/Commands_fix.txt
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@ -94,6 +94,7 @@ OPT.
"lineforce"_fix_lineforce.html,
"manifoldforce"_fix_manifoldforce.html,
"meso"_fix_meso.html,
"meso/move"_fix_meso_move.html,
"meso/stationary"_fix_meso_stationary.html,
"momentum (k)"_fix_momentum.html,
"move"_fix_move.html,
@ -172,6 +173,7 @@ OPT.
"restrain"_fix_restrain.html,
"rhok"_fix_rhok.html,
"rigid (o)"_fix_rigid.html,
"rigid/meso"_fix_rigid_meso.html,
"rigid/nph (o)"_fix_rigid.html,
"rigid/nph/small"_fix_rigid.html,
"rigid/npt (o)"_fix_rigid.html,

1
doc/src/Commands_pair.txt
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@ -198,6 +198,7 @@ OPT.
"reax/c (ko)"_pair_reaxc.html,
"rebo (io)"_pair_airebo.html,
"resquared (go)"_pair_resquared.html,
"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html,
"smd/hertz"_pair_smd_hertz.html,
"smd/tlsph"_pair_smd_tlsph.html,
"smd/tri_surface"_pair_smd_triangulated_surface.html,

26
doc/src/Packages_details.txt
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@ -95,6 +95,7 @@ as contained in the file name.
"USER-QUIP"_#PKG-USER-QUIP,
"USER-REAXC"_#PKG-USER-REAXC,
"USER-SCAFACOS"_#PKG-USER-SCAFACOS,
"USER-SDPD"_#PKG-USER-SDPD,
"USER-SMD"_#PKG-USER-SMD,
"USER-SMTBQ"_#PKG-USER-SMTBQ,
"USER-SPH"_#PKG-USER-SPH,
@ -1916,6 +1917,31 @@ examples/USER/scafacos :ul
:line
USER-SDPD package :link(PKG-USER-SDPD),h4
[Contents:]
A pair style for smoothed dissipative particle dynamics (SDPD), which
is an extension of smoothed particle hydrodynamics (SPH) to mesoscale
where thermal fluctuations are important (see the
"USER-SPH package"_#PKG-USER-SPH).
Also two fixes for moving and rigid body integration of SPH/SDPD particles
(particles of atom_style meso).
[Author:] Morteza Jalalvand (Institute for Advanced Studies in Basic
Sciences, Iran).
[Supporting info:]
src/USER-SDPD: filenames -> commands
src/USER-SDPD/README
"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html
"fix meso/move"_fix_meso_move.html
"fix rigid/meso"_fix_rigid_meso.html
examples/USER/sdpd :ul
:line
USER-SMD package :link(PKG-USER-SMD),h4
[Contents:]

1
doc/src/Packages_user.txt
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@ -68,6 +68,7 @@ Package, Description, Doc page, Example, Library
"USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
"USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no
"USER-SCAFACOS"_Packages_details.html#PKG-USER-SCAFACOS, wrapper on ScaFaCoS solver,"kspace_style scafacos"_kspace_style.html, USER/scafacos, ext
"USER-SDPD"_Packages_details.html#PKG-USER-SDPD, smoothed dissipative particle dynamics,"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal, USER/sdpd, no
"USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
"USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, no
"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no

2
doc/src/fix.txt
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@ -237,6 +237,7 @@ accelerated styles exist.
"lineforce"_fix_lineforce.html - constrain atoms to move in a line
"manifoldforce"_fix_manifoldforce.html -
"meso"_fix_meso.html -
"meso"_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
@ -331,6 +332,7 @@ accelerated styles exist.
"rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration
"rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration
"rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
"rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
"rx"_fix_rx.html -
"saed/vtk"_fix_saed_vtk.html -
"setforce"_fix_setforce.html - set the force on each atom

233
doc/src/fix_meso_move.txt Normal file
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@ -0,0 +1,233 @@
"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 meso/move command :h3
[Syntax:]
fix ID group-ID meso/move style args keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
meso/move = style name of this fix command :l
style = {linear} or {wiggle} or {rotate} or {variable} :l
{linear} args = Vx Vy Vz
Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
{wiggle} args = Ax Ay Az period
Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
period = period of oscillation (time units)
{rotate} args = Px Py Pz Rx Ry Rz period
Px,Py,Pz = origin point of axis of rotation (distance units)
Rx,Ry,Rz = axis of rotation vector
period = period of rotation (time units)
{variable} args = v_dx v_dy v_dz v_vx v_vy v_vz
v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL :pre
zero or more keyword/value pairs may be appended :l
keyword = {units} :l
{units} value = {box} or {lattice} :pre
:ule
[Examples:]
fix 1 boundary meso/move wiggle 3.0 0.0 0.0 1.0 units box
fix 2 boundary meso/move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
fix 2 boundary meso/move variable v_myx v_myy NULL v_VX v_VY NULL :pre
[Description:]
Perform updates of position, velocity, internal energy and local
density for mesoscopic particles in the group each timestep using the
specified settings or formulas, without regard to forces on the
particles. This can be useful for boundary, solid bodies or other
particles, whose movement can influence nearby particles.
The operation of this fix is exactly like that described by the
"fix move"_fix_move.html command, except that particles' density,
internal energy and extrapolated velocity are also updated.
NOTE: The particles affected by this fix should not be time integrated
by other fixes (e.g. "fix meso"_fix_meso.html, "fix
meso/stationary"_fix_meso_stationary.html), since that will change their
positions and velocities twice.
NOTE: As particles move due to this fix, they will pass thru periodic
boundaries and be remapped to the other side of the simulation box,
just as they would during normal time integration (e.g. via the "fix
meso"_fix_meso.html command). It is up to you to decide whether periodic
boundaries are appropriate with the kind of particle motion you are
prescribing with this fix.
NOTE: As dicsussed below, particles are moved relative to their initial
position at the time the fix is specified. These initial coordinates
are stored by the fix in "unwrapped" form, by using the image flags
associated with each particle. See the "dump custom"_dump.html command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the "read_data"_read_data.html command for a discussion of image flags
and how they are set for each particle. You can reset the image flags
(e.g. to 0) before invoking this fix by using the "set image"_set.html
command.
:line
The {linear} style moves particles at a constant velocity, so that their
position {X} = (x,y,z) as a function of time is given in vector
notation as
X(t) = X0 + V * delta :pre
where {X0} = (x0,y0,z0) is their position at the time the fix is
specified, {V} is the specified velocity vector with components
(Vx,Vy,Vz), and {delta} is the time elapsed since the fix was
specified. This style also sets the velocity of each particle to V =
(Vx,Vy,Vz). If any of the velocity components is specified as NULL,
then the position and velocity of that component is time integrated
the same as the "fix meso"_fix_meso.html command would perform, using
the corresponding force component on the particle.
Note that the {linear} style is identical to using the {variable}
style with an "equal-style variable"_variable.html that uses the
vdisplace() function. E.g.
variable V equal 10.0
variable x equal vdisplace(0.0,$V)
fix 1 boundary move variable v_x NULL NULL v_V NULL NULL :pre
The {wiggle} style moves particles in an oscillatory fashion, so that
their position {X} = (x,y,z) as a function of time is given in vector
notation as
X(t) = X0 + A sin(omega*delta) :pre
where {X0} = (x0,y0,z0) is their position at the time the fix is
specified, {A} is the specified amplitude vector with components
(Ax,Ay,Az), {omega} is 2 PI / {period}, and {delta} is the time
elapsed since the fix was specified. This style also sets the
velocity of each particle to the time derivative of this expression.
If any of the amplitude components is specified as NULL, then the
position and velocity of that component is time integrated the same as
the "fix meso"_fix_meso.html command would perform, using the
corresponding force component on the particle.
Note that the {wiggle} style is identical to using the {variable}
style with "equal-style variables"_variable.html that use the
swiggle() and cwiggle() functions. E.g.
variable A equal 10.0
variable T equal 5.0
variable omega equal 2.0*PI/$T
variable x equal swiggle(0.0,$A,$T)
variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre
The {rotate} style rotates particles around a rotation axis {R} =
(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz). The {period} of
the rotation is also specified. The direction of rotation for the
particles around the rotation axis is consistent with the right-hand
rule: if your right-hand thumb points along {R}, then your fingers wrap
around the axis in the direction of rotation.
This style also sets the velocity of each particle to (omega cross
Rperp) where omega is its angular velocity around the rotation axis and
Rperp is a perpendicular vector from the rotation axis to the particle.
The {variable} style allows the position and velocity components of
each particle to be set by formulas specified via the
"variable"_variable.html command. Each of the 6 variables is
specified as an argument to the fix as v_name, where name is the
variable name that is defined elsewhere in the input script.
Each variable must be of either the {equal} or {atom} style.
{Equal}-style variables compute a single numeric quantity, that can be
a function of the timestep as well as of other simulation values.
{Atom}-style variables compute a numeric quantity for each particle, that
can be a function per-atom quantities, such as the particle's position, as
well as of the timestep and other simulation values. Note that this
fix stores the original coordinates of each particle (see note below) so
that per-atom quantity can be used in an atom-style variable formula.
See the "variable"_variable.html command for details.
The first 3 variables (v_dx,v_dy,v_dz) specified for the {variable}
style are used to calculate a displacement from the particle's original
position at the time the fix was specified. The second 3 variables
(v_vx,v_vy,v_vz) specified are used to compute a velocity for each
particle.
Any of the 6 variables can be specified as NULL. If both the
displacement and velocity variables for a particular x,y,z component
are specified as NULL, then the position and velocity of that
component is time integrated the same as the "fix meso"_fix_meso.html
command would perform, using the corresponding force component on the
particle. If only the velocity variable for a component is specified as
NULL, then the displacement variable will be used to set the position
of the particle, and its velocity component will not be changed. If only
the displacement variable for a component is specified as NULL, then
the velocity variable will be used to set the velocity of the particle,
and the position of the particle will be time integrated using that
velocity.
The {units} keyword determines the meaning of the distance units used
to define the {linear} velocity and {wiggle} amplitude and {rotate}
origin. This setting is ignored for the {variable} style. A {box}
value selects standard units as defined by the "units"_units.html
command, e.g. velocity in Angstroms/fmsec and amplitude and position
in Angstroms for units = real. A {lattice} value means the velocity
units are in lattice spacings per time and the amplitude and position
are in lattice spacings. The "lattice"_lattice.html command must have
been previously used to define the lattice spacing. Each of these 3
quantities may be dependent on the x,y,z dimension, since the lattice
spacings can be different in x,y,z.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the original coordinates of moving particles to "binary
restart files"_restart.html, as well as the initial timestep, so that
the motion can be continuous 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, so that the
operation of the fix continues in an uninterrupted fashion.
NOTE: Because the move positions are a function of the current
timestep and the initial timestep, you cannot reset the timestep to a
different value after reading a restart file, if you expect a fix move
command to work in an uninterrupted fashion.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix.
This fix produces a per-atom array which can be accessed by various
"output commands"_Howto_output.html. The number of columns for each
atom is 3, and the columns store the original unwrapped x,y,z coords
of each particle. The per-atom values can be accessed on any timestep.
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 USER-SDPD package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
This fix requires that atoms store density and internal energy as
defined by the "atom_style meso"_atom_style.html command.
All particles in the group must be mesoscopic SPH/SDPD particles.
[Related commands:]
"fix move"_fix_move.html, "fix meso"_fix_meso.html,
"displace_atoms"_displace_atoms.html
[Default:]
The option default is units = lattice.

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@ -0,0 +1,349 @@
"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 rigid/meso command :h3
[Syntax:]
fix ID group-ID rigid/meso bodystyle args keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
rigid/meso = style name of this fix command :l
bodystyle = {single} or {molecule} or {group} :l
{single} args = none
{molecule} args = none
{custom} args = {i_propname} or {v_varname}
i_propname = an integer property defined via fix property/atom
v_varname = an atom-style or atomfile-style variable
{group} args = N groupID1 groupID2 ...
N = # of groups
groupID1, groupID2, ... = list of N group IDs :pre
zero or more keyword/value pairs may be appended :l
keyword = {reinit} or {force} or {torque} or {infile} :l
{reinit} = {yes} or {no}
{force} values = M xflag yflag zflag
M = which rigid body from 1-Nbody (see asterisk form below)
xflag,yflag,zflag = off/on if component of center-of-mass force is active
{torque} values = M xflag yflag zflag
M = which rigid body from 1-Nbody (see asterisk form below)
xflag,yflag,zflag = off/on if component of center-of-mass torque is active
{infile} filename
filename = file with per-body values of mass, center-of-mass, moments of inertia :pre
:ule
[Examples:]
fix 1 ellipsoid rigid/meso single
fix 1 rods rigid/meso molecule
fix 1 spheres rigid/meso single force 1 off off on
fix 1 particles rigid/meso molecule force 1*5 off off off force 6*10 off off on
fix 2 spheres rigid/meso group 3 sphere1 sphere2 sphere3 torque * off off off :pre
[Description:]
Treat one or more sets of mesoscopic SPH/SDPD particles as independent
rigid bodies. This means that each timestep the total force and torque
on each rigid body is computed as the sum of the forces and torques on
its constituent particles. The coordinates and velocities of the
particles in each body are then updated so that the body moves and
rotates as a single entity using the methods described in the paper by
"(Miller)"_#Miller. Density and internal energy of the particles will
also be updated. This is implemented by creating internal data structures
for each rigid body and performing time integration on these data
structures. Positions and velocities of the constituent particles are
regenerated from the rigid body data structures in every time step. This
restricts which operations and fixes can be applied to rigid bodies. See
below for a detailed discussion.
The operation of this fix is exactly like that described by the
"fix rigid/nve"_fix_rigid.html command, except that particles' density,
internal energy and extrapolated velocity are also updated.
NOTE: You should not update the particles in rigid bodies via other
time-integration fixes (e.g. "fix meso"_fix_meso.html,
"fix meso/stationary"_fix_meso_stationary.html), or you will have conflicting
updates to positions and velocities resulting in unphysical behavior in most
cases. When performing a hybrid simulation with some atoms in rigid bodies,
and some not, a separate time integration fix like "fix meso"_fix_meso.html
should be used for the non-rigid particles.
NOTE: These fixes are overkill if you simply want to hold a collection
of particles stationary or have them move with a constant velocity. To
hold particles stationary use "fix
meso/stationary"_fix_meso_stationary.html instead. If you would like to
move particles with a constant velocity use "fix
meso/move"_fix_meso_move.html.
IMPORTANT NOTE: The aggregate properties of each rigid body are
calculated at the start of a simulation run and are maintained in
internal data structures. The properties include the position and
velocity of the center-of-mass of the body, its moments of inertia, and
its angular momentum. This is done using the properties of the
constituent particles of the body at that point in time (or see the {infile}
keyword option). Thereafter, changing these properties of individual
particles in the body will have no effect on a rigid body's dynamics, unless
they effect any computation of per-particle forces or torques. If the
keyword {reinit} is set to {yes} (the default), the rigid body data
structures will be recreated at the beginning of each {run} command;
if the keyword {reinit} is set to {no}, the rigid body data structures
will be built only at the very first {run} command and maintained for
as long as the rigid fix is defined. For example, you might think you
could displace the particles in a body or add a large velocity to each particle
in a body to make it move in a desired direction before a 2nd run is
performed, using the "set"_set.html or
"displace_atoms"_displace_atoms.html or "velocity"_velocity.html
commands. But these commands will not affect the internal attributes
of the body unless {reinit} is set to {yes}. With {reinit} set to {no}
(or using the {infile} option, which implies {reinit} {no}) the position
and velocity of individual particles in the body will be reset when time
integration starts again.
:line
Each rigid body must have two or more particles. A particle can belong
to at most one rigid body. Which particles are in which bodies can be
defined via several options.
For bodystyle {single} the entire fix group of particles is treated as
one rigid body.
For bodystyle {molecule}, particles are grouped into rigid bodies by their
respective molecule IDs: each set of particles in the fix group with the
same molecule ID is treated as a different rigid body. Note that particles
with a molecule ID = 0 will be treated as a single rigid body. For a
system with solvent (typically this is particles with molecule ID = 0)
surrounding rigid bodies, this may not be what you want. Thus you
should be careful to use a fix group that only includes particles you
want to be part of rigid bodies.
Bodystyle {custom} is similar to bodystyle {molecule} except that it
is more flexible in using other per-atom properties to define the sets
of particles that form rigid bodies. An integer vector defined by the
"fix property/atom"_fix_property_atom.html command can be used. Or an
"atom-style or atomfile-style variable"_variable.html can be used; the
floating-point value produced by the variable is rounded to an
integer. As with bondstyle {molecule}, each set of particles in the fix
groups with the same integer value is treated as a different rigid
body. Since fix property/atom vectors and atom-style variables
produce values for all particles, you should be careful to use a fix group
that only includes particles you want to be part of rigid bodies.
For bodystyle {group}, each of the listed groups is treated as a
separate rigid body. Only particles that are also in the fix group are
included in each rigid body.
NOTE: To compute the initial center-of-mass position and other
properties of each rigid body, the image flags for each particle in the
body are used to "unwrap" the particle coordinates. Thus you must
insure that these image flags are consistent so that the unwrapping
creates a valid rigid body (one where the particles are close together)
, particularly if the particles in a single rigid body straddle a
periodic boundary. This means the input data file or restart file must
define the image flags for each particle consistently or that you have
used the "set"_set.html command to specify them correctly. If a
dimension is non-periodic then the image flag of each particle must be
0 in that dimension, else an error is generated.
By default, each rigid body is acted on by other particles which induce
an external force and torque on its center of mass, causing it to
translate and rotate. Components of the external center-of-mass force
and torque can be turned off by the {force} and {torque} keywords.
This may be useful if you wish a body to rotate but not translate, or
vice versa, or if you wish it to rotate or translate continuously
unaffected by interactions with other particles. Note that if you
expect a rigid body not to move or rotate by using these keywords, you
must insure its initial center-of-mass translational or angular
velocity is 0.0. Otherwise the initial translational or angular
momentum the body has will persist.
An xflag, yflag, or zflag set to {off} means turn off the component of
force or torque in that dimension. A setting of {on} means turn on
the component, which is the default. Which rigid body(s) the settings
apply to is determined by the first argument of the {force} and
{torque} keywords. It can be an integer M from 1 to Nbody, where
Nbody is the number of rigid bodies defined. A wild-card asterisk can
be used in place of, or in conjunction with, the M argument to set the
flags for multiple rigid bodies. This takes the form "*" or "*n" or
"n*" or "m*n". If N = the number of rigid bodies, then an asterisk
with no numeric values means all bodies from 1 to N. A leading
asterisk means all bodies from 1 to n (inclusive). A trailing
asterisk means all bodies from n to N (inclusive). A middle asterisk
means all bodies from m to n (inclusive). Note that you can use the
{force} or {torque} keywords as many times as you like. If a
particular rigid body has its component flags set multiple times, the
settings from the final keyword are used.
For computational efficiency, you should typically define one fix
rigid/meso command which includes all the desired rigid bodies. LAMMPS
will allow multiple rigid/meso fixes to be defined, but it is more
expensive.
:line
The keyword/value option pairs are used in the following ways.
The {reinit} keyword determines, whether the rigid body properties
are re-initialized between run commands. With the option {yes} (the
default) this is done, with the option {no} this is not done. Turning
off the re-initialization can be helpful to protect rigid bodies against
unphysical manipulations between runs or when properties cannot be
easily re-computed (e.g. when read from a file). When using the {infile}
keyword, the {reinit} option is automatically set to {no}.
:line
The {infile} keyword allows a file of rigid body attributes to be read
in from a file, rather then having LAMMPS compute them. There are 5
such attributes: the total mass of the rigid body, its center-of-mass
position, its 6 moments of inertia, its center-of-mass velocity, and
the 3 image flags of the center-of-mass position. For rigid bodies
consisting of point particles or non-overlapping finite-size
particles, LAMMPS can compute these values accurately. However, for
rigid bodies consisting of finite-size particles which overlap each
other, LAMMPS will ignore the overlaps when computing these 4
attributes. The amount of error this induces depends on the amount of
overlap. To avoid this issue, the values can be pre-computed
(e.g. using Monte Carlo integration).
The format of the file is as follows. Note that the file does not
have to list attributes for every rigid body integrated by fix rigid.
Only bodies which the file specifies will have their computed
attributes overridden. The file can contain initial blank lines or
comment lines starting with "#" which are ignored. The first
non-blank, non-comment line should list N = the number of lines to
follow. The N successive lines contain the following information:
ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
...
IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm :pre
The rigid body IDs are all positive integers. For the {single}
bodystyle, only an ID of 1 can be used. For the {group} bodystyle,
IDs from 1 to Ng can be used where Ng is the number of specified
groups. For the {molecule} bodystyle, use the molecule ID for the
atoms in a specific rigid body as the rigid body ID.
The masstotal and center-of-mass coordinates (xcm,ycm,zcm) are
self-explanatory. The center-of-mass should be consistent with what
is calculated for the position of the rigid body with all its atoms
unwrapped by their respective image flags. If this produces a
center-of-mass that is outside the simulation box, LAMMPS wraps it
back into the box.
The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
values consistent with the current orientation of the rigid body
around its center of mass. The values are with respect to the
simulation box XYZ axes, not with respect to the principal axes of the
rigid body itself. LAMMPS performs the latter calculation internally.
The (vxcm,vycm,vzcm) values are the velocity of the center of mass.
The (lx,ly,lz) values are the angular momentum of the body. The
(vxcm,vycm,vzcm) and (lx,ly,lz) values can simply be set to 0 if you
wish the body to have no initial motion.
The (ixcm,iycm,izcm) values are the image flags of the center of mass
of the body. For periodic dimensions, they specify which image of the
simulation box the body is considered to be in. An image of 0 means
it is inside the box as defined. A value of 2 means add 2 box lengths
to get the true value. A value of -1 means subtract 1 box length to
get the true value. LAMMPS updates these flags as the rigid bodies
cross periodic boundaries during the simulation.
NOTE: If you use the {infile} keyword and write restart
files during a simulation, then each time a restart file is written,
the fix also write an auxiliary restart file with the name
rfile.rigid, where "rfile" is the name of the restart file,
e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary
file is in the same format described above. Thus it can be used in a
new input script that restarts the run and re-specifies a rigid fix
using an {infile} keyword and the appropriate filename. Note that the
auxiliary file will contain one line for every rigid body, even if the
original file only listed a subset of the rigid bodies.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information is written to "binary restart files"_restart.html.
If the {infile} keyword is used, an auxiliary file is written out
with rigid body information each time a restart file is written, as
explained above for the {infile} keyword.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix.
This fix computes a global array of values which can be accessed by
various "output commands"_Howto_output.html.
The number of rows in the array is equal to the number of rigid
bodies. The number of columns is 28. Thus for each rigid body, 28
values are stored: the xyz coords of the center of mass (COM), the xyz
components of the COM velocity, the xyz components of the force acting
on the COM, the components of the 4-vector quaternion representing the
orientation of the rigid body, the xyz components of the angular momentum
of the body around its COM, the xyz components of the torque acting on the
COM, the 3 principal components of the moment of inertia and the xyz image
flags of the COM.
The center of mass (COM) for each body is similar to unwrapped
coordinates written to a dump file. It will always be inside (or
slightly outside) the simulation box. The image flags have the same
meaning as image flags for particle positions (see the "dump" command).
This means you can calculate the unwrapped COM by applying the image
flags to the COM, the same as when unwrapped coordinates are written
to a dump file.
The force and torque values in the array are not affected by the
{force} and {torque} keywords in the fix rigid command; they reflect
values before any changes are made by those keywords.
The ordering of the rigid bodies (by row in the array) is as follows.
For the {single} keyword there is just one rigid body. For the
{molecule} keyword, the bodies are ordered by ascending molecule ID.
For the {group} keyword, the list of group IDs determines the ordering
of bodies.
The array values calculated by this fix are "intensive", meaning they
are independent of the number of particles in the simulation.
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.
:line
[Restrictions:]
This fix is part of the USER-SDPD package and also depends on the RIGID
package. It is only enabled if LAMMPS was built with both packages. See
the "Build package"_Build_package.html doc page for more info.
This fix requires that atoms store density and internal energy as
defined by the "atom_style meso"_atom_style.html command.
All particles in the group must be mesoscopic SPH/SDPD particles.
[Related commands:]
"fix meso/move"_fix_meso_move.html, "fix rigid"_fix_rigid.html,
"neigh_modify exclude"_neigh_modify.html
[Default:]
The option defaults are force * on on on and torque * on on on,
meaning all rigid bodies are acted on by center-of-mass force and
torque. Also reinit = yes.
:line
:link(Miller)
[(Miller)] Miller, Eleftheriou, Pattnaik, Ndirango, and Newns,
J Chem Phys, 116, 8649 (2002).

2
doc/src/fixes.txt
View File

@ -73,6 +73,7 @@ Fixes :h1
fix_lineforce
fix_manifoldforce
fix_meso
fix_meso_move
fix_meso_stationary
fix_momentum
fix_move
@ -137,6 +138,7 @@ Fixes :h1
fix_restrain
fix_rhok
fix_rigid
fix_rigid_meso
fix_rx
fix_saed_vtk
fix_setforce

3
doc/src/lammps.book
View File

@ -293,6 +293,7 @@ fix_lb_viscous.html
fix_lineforce.html
fix_manifoldforce.html
fix_meso.html
fix_meso_move.html
fix_meso_stationary.html
fix_momentum.html
fix_move.html
@ -356,6 +357,7 @@ fix_reaxc_species.html
fix_recenter.html
fix_restrain.html
fix_rigid.html
fix_rigid_meso.html
fix_rhok.html
fix_rx.html
fix_saed_vtk.html
@ -615,6 +617,7 @@ pair_reax.html
pair_reaxc.html
pair_resquared.html
pair_sdk.html
pair_sdpd_taitwater_isothermal.html
pair_smd_hertz.html
pair_smd_tlsph.html
pair_smd_triangulated_surface.html

108
doc/src/pair_sdpd_taitwater_isothermal.txt Normal file
View File

@ -0,0 +1,108 @@
"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 sdpd/taitwater/isothermal command :h3
[Syntax:]
pair_style sdpd/taitwater/isothermal temperature viscosity seed
:pre
temperature = temperature of the fluid (temperature units)
viscosity = dynamic viscosity of the fluid (mass*distance/time units)
seed = random number generator seed (positive integer, optional) :ul
[Examples:]
pair_style sdpd/taitwater/isothermal 300. 1. 28681
pair_coeff * * 1000.0 1430.0 2.4 :pre
[Description:]
The sdpd/taitwater/isothermal style computes forces between mesoscopic
particles according to the Smoothed Dissipative Particle Dynamics model
described in this paper by "(Español and Revenga)"_#Español_Revenga under
the following assumptions:
:olb
The temperature is constant and uniform. :l
The shear viscosity is constant and uniform. :l
The volume viscosity is negligible before the shear viscosity. :l
The Boltzmann constant is negligible before the heat capacity of a
single mesoscopic particle of fluid. :ole,l
The third assumption is true for water in nearly incompressible flows.
The fourth holds true for water for any reasonable size one can
imagine for a mesoscopic particle.
The pressure forces between particles will be computed according to
Tait's equation of state:
:c,image(Eqs/pair_sph_tait.jpg)
where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the
reference density and c_0 the reference speed of sound.
The laminar viscosity and the random forces will be computed according
to formulas described in "(Español and Revenga)"_#Español_Revenga.
IMPORTANT NOTE: Similar to "brownian"_pair_brownian.html and
"dpd"_pair_dpd.html styles, the "newton"_newton.html setting for
pairwise interactions needs to be on when running LAMMPS in parallel
if you want to ensure linear momentum conservation. Otherwise random
forces generated for pairs straddling processor boundary will not be
equal and opposite.
NOTE: The actual random seed used will be a mix of what you specify
and other parameters like the MPI ranks. This is to ensure that
different MPI tasks have distinct seeds.
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.
rho0 reference density (mass/volume units)
c0 reference soundspeed (distance/time units)
h kernel function cutoff (distance units) :ul
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
This style does not support the "pair_modify"_pair_modify.html
shift, table, and tail options.
This style does not write information to "binary restart
files"_restart.html. Thus, you need to re-specify the pair_style and
pair_coeff commands in an input script that reads a restart file.
This style can only be used via the {pair} keyword of the "run_style
respa"_run_style.html command. It does not support the {inner},
{middle}, {outer} keywords.
[Restrictions:]
This pair style is part of the USER-SDPD package. It is 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, "pair sph/rhosum"_pair_sph_rhosum.html
[Default:]
The default seed is 0 (before mixing).
:line
:link(Español_Revenga)
[(Español and Revenga)] Español, Revenga, Physical Review E, 67, 026705 (2003).

1
doc/src/pair_style.txt
View File

@ -268,6 +268,7 @@ pair"_Commands_pair.html doc page are followed by one or more of
"reax/c"_pair_reaxc.html - ReaxFF potential in C
"rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner
"resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential
"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html - smoothed dissipative particle dynamics for water at isothermal conditions
"smd/hertz"_pair_smd_hertz.html -
"smd/tlsph"_pair_smd_tlsph.html -
"smd/tri_surface"_pair_smd_triangulated_surface.html -

1
doc/src/pairs.txt
View File

@ -86,6 +86,7 @@ Pair Styles :h1
pair_reaxc
pair_resquared
pair_sdk
pair_sdpd_taitwater_isothermal
pair_smd_hertz
pair_smd_tlsph
pair_smd_triangulated_surface