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2
doc/Manual.html
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@ -179,7 +179,7 @@ it gives quick access to documentation for all LAMMPS commands.
<BR>
6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A>
<BR>
6.14 <A HREF = "Section_howto.html#howto_14">Extended spherical and aspherical particles</A>
6.14 <A HREF = "Section_howto.html#howto_14">Finite-size spherical and aspherical particles</A>
<BR>
6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A>
<BR>

2
doc/Manual.txt
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@ -126,7 +126,7 @@ it gives quick access to documentation for all LAMMPS commands.
6.11 "Visualizing LAMMPS snapshots"_howto_11 :b
6.12 "Triclinic (non-orthogonal) simulation boxes"_howto_12 :b
6.13 "NEMD simulations"_howto_13 :b
6.14 "Extended spherical and aspherical particles"_howto_14 :b
6.14 "Finite-size spherical and aspherical particles"_howto_14 :b
6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_howto_15 :b
6.16 "Thermostatting, barostatting, and compute temperature"_howto_16 :b
6.17 "Walls"_howto_17 :b

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doc/Section_example.html
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@ -31,15 +31,21 @@ Site</A>.
<P>These are the sample problems in the examples sub-directories:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >body</TD><TD > body particles, 2d system</TD></TR>
<TR><TD >colloid</TD><TD > big colloid particles in a small particle solvent, 2d system</TD></TR>
<TR><TD >comb</TD><TD > models using the COMB potential</TD></TR>
<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
<TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR>
<TR><TD >dreiding</TD><TD > methanol via Dreiding FF</TD></TR>
<TR><TD >eim</TD><TD > NaCl using the EIM potential</TD></TR>
<TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR>
<TR><TD >flow</TD><TD > Couette and Poiseuille flow in a 2d channel</TD></TR>
<TR><TD >friction</TD><TD > frictional contact of spherical asperities between 2d surfaces</TD></TR>
<TR><TD >gpu</TD><TD > use of the GPU package for GPU acceleration</TD></TR>
<TR><TD >hugoniostat</TD><TD > Hugoniostat shock dynamics</TD></TR>
<TR><TD >indent</TD><TD > spherical indenter into a 2d solid</TD></TR>
<TR><TD >kim</TD><TD > use of potentials in Knowledge Base for Interatomic Models (KIM)</TD></TR>
<TR><TD >line</TD><TD > line segment particles in 2d rigid bodies</TD></TR>
<TR><TD >meam</TD><TD > MEAM test for SiC and shear (same as shear examples)</TD></TR>
<TR><TD >melt</TD><TD > rapid melt of 3d LJ system</TD></TR>
<TR><TD >micelle</TD><TD > self-assembly of small lipid-like molecules into 2d bilayers</TD></TR>
@ -51,11 +57,13 @@ Site</A>.
<TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR>
<TR><TD >peri</TD><TD > Peridynamic model of cylinder impacted by indenter</TD></TR>
<TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR>
<TR><TD >prd</TD><TD > parallel replica dynamics of a vacancy diffusion in bulk Si</TD></TR>
<TR><TD >prd</TD><TD > parallel replica dynamics of vacancy diffusion in bulk Si</TD></TR>
<TR><TD >reax</TD><TD > RDX and TATB models using the ReaxFF</TD></TR>
<TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR>
<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void</TD></TR>
<TR><TD >srd</TD><TD > stochastic rotation dynamics (SRD) particles as solvent
<TR><TD >srd</TD><TD > stochastic rotation dynamics (SRD) particles as solvent</TD></TR>
<TR><TD >tad</TD><TD > temperature-accelerated dynamics of vacancy diffusion in bulk Si</TD></TR>
<TR><TD >tri</TD><TD > triangular particles in rigid bodies
</TD></TR></TABLE></DIV>
<P>Here is how you might run and visualize one of the sample problems:

12
doc/Section_example.txt
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@ -27,15 +27,21 @@ Site"_lws.
These are the sample problems in the examples sub-directories:
body: body particles, 2d system
colloid: big colloid particles in a small particle solvent, 2d system
comb: models using the COMB potential
crack: crack propagation in a 2d solid
dipole: point dipolar particles, 2d system
dreiding: methanol via Dreiding FF
eim: NaCl using the EIM potential
ellipse: ellipsoidal particles in spherical solvent, 2d system
flow: Couette and Poiseuille flow in a 2d channel
friction: frictional contact of spherical asperities between 2d surfaces
gpu: use of the GPU package for GPU acceleration
hugoniostat: Hugoniostat shock dynamics
indent: spherical indenter into a 2d solid
kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
line: line segment particles in 2d rigid bodies
meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system
micelle: self-assembly of small lipid-like molecules into 2d bilayers
@ -47,11 +53,13 @@ obstacle: flow around two voids in a 2d channel
peptide: dynamics of a small solvated peptide chain (5-mer)
peri: Peridynamic model of cylinder impacted by indenter
pour: pouring of granular particles into a 3d box, then chute flow
prd: parallel replica dynamics of a vacancy diffusion in bulk Si
prd: parallel replica dynamics of vacancy diffusion in bulk Si
reax: RDX and TATB models using the ReaxFF
rigid: rigid bodies modeled as independent or coupled
shear: sideways shear applied to 2d solid, with and without a void
srd: stochastic rotation dynamics (SRD) particles as solvent :tb(s=:)
srd: stochastic rotation dynamics (SRD) particles as solvent
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
tri: triangular particles in rigid bodies :tb(s=:)
Here is how you might run and visualize one of the sample problems:

92
doc/Section_howto.html
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@ -26,7 +26,7 @@
6.11 <A HREF = "#howto_11">Visualizing LAMMPS snapshots</A><BR>
6.12 <A HREF = "#howto_12">Triclinic (non-orthogonal) simulation boxes</A><BR>
6.13 <A HREF = "#howto_13">NEMD simulations</A><BR>
6.14 <A HREF = "#howto_14">Extended spherical and aspherical particles</A><BR>
6.14 <A HREF = "#howto_14">Finite-size spherical and aspherical particles</A><BR>
6.15 <A HREF = "#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A><BR>
6.16 <A HREF = "#howto_16">Thermostatting, barostatting and computing temperature</A><BR>
6.17 <A HREF = "#howto_17">Walls</A><BR>
@ -163,7 +163,7 @@ so that any forces induced by other fixes will be zeroed out.
<P>Many of the example input scripts included in the LAMMPS distribution
are for 2d models.
</P>
<P>IMPORTANT NOTE: Some models in LAMMPS treat particles as extended
<P>IMPORTANT NOTE: Some models in LAMMPS treat particles as finite-size
spheres, as opposed to point particles. In 2d, the particles will
still be spheres, not disks, meaning their moment of inertia will be
the same as in 3d.
@ -1012,7 +1012,7 @@ profile consistent with the applied shear strain rate.
</P>
<HR>
<A NAME = "howto_14"></A><H4>6.14 Extended spherical and aspherical particles
<A NAME = "howto_14"></A><H4>6.14 Finite-size spherical and aspherical particles
</H4>
<P>Typical MD models treat atoms or particles as point masses. Sometimes
it is desirable to have a model with finite-size particles such as
@ -1028,8 +1028,12 @@ particles. The following aspects are discussed in turn:
<LI>pair potentials
<LI>time integration
<LI>computes, thermodynamics, and dump output
<LI>rigid bodies composed of extended particles
<LI>rigid bodies composed of finite-size particles
</UL>
<P>Example input scripts for these kinds of models are in the body,
colloid, dipole, ellipse, line, peri, pour, and tri directories of the
<A HREF = "Section_examples.html">examples directory</A> in the LAMMPS distribution.
</P>
<H5>Atom styles
</H5>
<P>There are several <A HREF = "atom_style.html">atom styles</A> that allow for
@ -1042,13 +1046,14 @@ particles store an angular velocity (omega) and can be acted upon by
torque. The "set" command can be used to modify the diameter and mass
of individual particles, after then are created.
</P>
<P>The dipole style does not actually define extended particles, but is
often used in conjunction with spherical particles, via a command like
<P>The dipole style does not actually define finite-size particles, but
is often used in conjunction with spherical particles, via a command
like
</P>
<PRE>atom_style hybrid sphere dipole
</PRE>
<P>This is because when dipoles interact with each other, they induce
torques, and a particle must be extended (i.e. have a moment of
torques, and a particle must be finite-size (i.e. have a moment of
inertia) in order to respond and rotate. See the <A HREF = "atom_style.html">atom_style
dipole</A> command for details. The "set" command can be
used to modify the orientation and length of the dipole moment of
@ -1094,30 +1099,29 @@ diameter is set to 0.0, it will be a point particle. In the line or
tri style, if the lineflag or triflag is specified as 0, then it
will be a point particle.
</P>
<P>Many of the pair styles used to compute pairwise interactions between
extended particles typically compute the correct interaction in these
simplified (cheaper) cases. e.g. the interaction between a point
particle and an extended particle or between two point particles. If
necessary, <A HREF = "pair_hybrid.html">pair_style hybrid</A> can be used to insure
the correct interactions are computed for the appropriate style of
interactions. Likewise, using groups to partition particles
(ellipsoids versus spheres versus point particles) will allow you to
use the appropriate time integrators and temperature computations for
each class of particles. See the doc pages for various commands for
details.
<P>Some of the pair styles used to compute pairwise interactions between
finite-size particles also compute the correct interaction with point
particles as well, e.g. the interaction between a point particle and a
finite-size particle or between two point particles. If necessary,
<A HREF = "pair_hybrid.html">pair_style hybrid</A> can be used to insure the correct
interactions are computed for the appropriate style of interactions.
Likewise, using groups to partition particles (ellipsoids versus
spheres versus point particles) will allow you to use the appropriate
time integrators and temperature computations for each class of
particles. See the doc pages for various commands for details.
</P>
<P>Also note that for <A HREF = "dimension.html">2d simulations</A>, atom styles sphere
and ellipsoid still use 3d particles, rather than as circular disks or
ellipses. This means they have the same moment of inertia as a 3d
extended object. When temperature is computed, the correct degrees of
freedom are used for rotation in a 2d versus 3d system.
ellipses. This means they have the same moment of inertia as the 3d
object. When temperature is computed, the correct degrees of freedom
are used for rotation in a 2d versus 3d system.
</P>
<H5>Pair potentials
</H5>
<P>When a system with extended particles is defined, the particles will
only rotate and experience torque if the force field computes such
interactions. These are the various <A HREF = "pair_style.html">pair styles</A>
that generate torque:
<P>When a system with finite-size particles is defined, the particles
will only rotate and experience torque if the force field computes
such interactions. These are the various <A HREF = "pair_style.html">pair
styles</A> that generate torque:
</P>
<UL><LI><A HREF = "pair_gran.html">pair_style gran/history</A>
<LI><A HREF = "pair_gran.html">pair_style gran/hertzian</A>
@ -1142,7 +1146,7 @@ triangular, and body particles respectively.
</P>
<H5>Time integration
</H5>
<P>There are several fixes that perform time integration on extended
<P>There are several fixes that perform time integration on finite-size
spherical particles, meaning the integrators update the rotational
orientation and angular velocity or angular momentum of the particles:
</P>
@ -1163,7 +1167,7 @@ calculation and thermostatting. The <A HREF = "fix_langevin">fix langevin</A>
command can also be used with its <I>omgea</I> or <I>angmom</I> options to
thermostat the rotational degrees of freedom for spherical or
ellipsoidal particles. Other thermostatting fixes only operate on the
translational kinetic energy of extended particles.
translational kinetic energy of finite-size particles.
</P>
<P>These fixes perform constant NVE time integration on line segment,
triangular, and body particles:
@ -1172,9 +1176,9 @@ triangular, and body particles:
<LI><A HREF = "fix_nve_tri.html">fix nve/tri</A>
<LI><A HREF = "fix_nve_body.html">fix nve/body</A>
</UL>
<P>Note that for mixtures of point and extended particles, these
<P>Note that for mixtures of point and finite-size particles, these
integration fixes can only be used with <A HREF = "group.html">groups</A> which
contain extended particles.
contain finite-size particles.
</P>
<H5>Computes, thermodynamics, and dump output
</H5>
@ -1188,15 +1192,15 @@ rotational energy of spherical or ellipsoidal particles:
</UL>
<P>These include rotational degrees of freedom in their computation. If
you wish the thermodynamic output of temperature or pressure to use
one of these computes (e.g. for a system entirely composed of extended
particles), then the compute can be defined and the
one of these computes (e.g. for a system entirely composed of
finite-size particles), then the compute can be defined and the
<A HREF = "thermo_modify.html">thermo_modify</A> command used. Note that by default
thermodynamic quantities will be calculated with a temperature that
only includes translational degrees of freedom. See the
<A HREF = "thermo_style.html">thermo_style</A> command for details.
</P>
<P>These commands can be used to output various attributes
of extended particles:
<P>These commands can be used to output various attributes of finite-size
particles:
</P>
<UL><LI><A HREF = "dump.html">dump custom</A>
<LI><A HREF = "compute_property_atom.html">compute property/atom</A>
@ -1207,23 +1211,23 @@ angular momentum, the quaternion, the torque, the end-point and
corner-point coordinates (for line and tri particles), and
sub-particle attributes of body particles.
</P>
<H5>Rigid bodies composed of extended particles
<H5>Rigid bodies composed of finite-size particles
</H5>
<P>The <A HREF = "fix_rigid.html">fix rigid</A> command treats a collection of
particles as a rigid body, computes its inertia tensor, sums the total
force and torque on the rigid body each timestep due to forces on its
constituent particles, and integrates the motion of the rigid body.
</P>
<P>If any of the constituent particles of a rigid body are extended
<P>If any of the constituent particles of a rigid body are finite-size
particles (spheres or ellipsoids or line segments or triangles), then
their contribution to the inertia tensor of the body is different than
if they were point particles. This means the rotational dynamics of
the rigid body will be different. Thus a model of a dimer is
different if the dimer consists of two point masses versus two
extended sphereoids, even if the two particles have the same mass.
Extended particles that experience torque due to their interaction
with other particles will also impart that torque to a rigid body they
are part of.
spheroids, even if the two particles have the same mass. Finite-size
particles that experience torque due to their interaction with other
particles will also impart that torque to a rigid body they are part
of.
</P>
<P>See the "fix rigid" command for example of complex rigid-body models
it is possible to define in LAMMPS.
@ -1574,11 +1578,11 @@ pressure</A> command calculates pressure.
velocities) that are removed when computing the thermal temperature.
<A HREF = "compute_temp_sphere.html">Compute temp/sphere</A> and <A HREF = "compute_temp_asphere.html">compute
temp/asphere</A> compute kinetic energy for
extended particles that includes rotational degrees of freedom. They
both allow, as an extra argument, which is another temperature compute
that subtracts a velocity bias. This allows the translational
velocity of extended spherical or aspherical particles to be adjusted
in prescribed ways.
finite-size particles that includes rotational degrees of freedom.
They both allow, as an extra argument, which is another temperature
compute that subtracts a velocity bias. This allows the translational
velocity of spherical or aspherical particles to be adjusted in
prescribed ways.
</P>
<P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>, or in one
case by a pair style. Four thermostatting fixes are currently

92
doc/Section_howto.txt
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@ -23,7 +23,7 @@ This section describes how to perform common tasks using LAMMPS.
6.11 "Visualizing LAMMPS snapshots"_#howto_11
6.12 "Triclinic (non-orthogonal) simulation boxes"_#howto_12
6.13 "NEMD simulations"_#howto_13
6.14 "Extended spherical and aspherical particles"_#howto_14
6.14 "Finite-size spherical and aspherical particles"_#howto_14
6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#howto_15
6.16 "Thermostatting, barostatting and computing temperature"_#howto_16
6.17 "Walls"_#howto_17
@ -159,7 +159,7 @@ so that any forces induced by other fixes will be zeroed out.
Many of the example input scripts included in the LAMMPS distribution
are for 2d models.
IMPORTANT NOTE: Some models in LAMMPS treat particles as extended
IMPORTANT NOTE: Some models in LAMMPS treat particles as finite-size
spheres, as opposed to point particles. In 2d, the particles will
still be spheres, not disks, meaning their moment of inertia will be
the same as in 3d.
@ -1003,7 +1003,7 @@ An alternative method for calculating viscosities is provided via the
:line
6.14 Extended spherical and aspherical particles :link(howto_14),h4
6.14 Finite-size spherical and aspherical particles :link(howto_14),h4
Typical MD models treat atoms or particles as point masses. Sometimes
it is desirable to have a model with finite-size particles such as
@ -1019,7 +1019,11 @@ atom styles
pair potentials
time integration
computes, thermodynamics, and dump output
rigid bodies composed of extended particles :ul
rigid bodies composed of finite-size particles :ul
Example input scripts for these kinds of models are in the body,
colloid, dipole, ellipse, line, peri, pour, and tri directories of the
"examples directory"_Section_examples.html in the LAMMPS distribution.
Atom styles :h5
@ -1033,13 +1037,14 @@ particles store an angular velocity (omega) and can be acted upon by
torque. The "set" command can be used to modify the diameter and mass
of individual particles, after then are created.
The dipole style does not actually define extended particles, but is
often used in conjunction with spherical particles, via a command like
The dipole style does not actually define finite-size particles, but
is often used in conjunction with spherical particles, via a command
like
atom_style hybrid sphere dipole :pre
This is because when dipoles interact with each other, they induce
torques, and a particle must be extended (i.e. have a moment of
torques, and a particle must be finite-size (i.e. have a moment of
inertia) in order to respond and rotate. See the "atom_style
dipole"_atom_style.html command for details. The "set" command can be
used to modify the orientation and length of the dipole moment of
@ -1085,30 +1090,29 @@ diameter is set to 0.0, it will be a point particle. In the line or
tri style, if the lineflag or triflag is specified as 0, then it
will be a point particle.
Many of the pair styles used to compute pairwise interactions between
extended particles typically compute the correct interaction in these
simplified (cheaper) cases. e.g. the interaction between a point
particle and an extended particle or between two point particles. If
necessary, "pair_style hybrid"_pair_hybrid.html can be used to insure
the correct interactions are computed for the appropriate style of
interactions. Likewise, using groups to partition particles
(ellipsoids versus spheres versus point particles) will allow you to
use the appropriate time integrators and temperature computations for
each class of particles. See the doc pages for various commands for
details.
Some of the pair styles used to compute pairwise interactions between
finite-size particles also compute the correct interaction with point
particles as well, e.g. the interaction between a point particle and a
finite-size particle or between two point particles. If necessary,
"pair_style hybrid"_pair_hybrid.html can be used to insure the correct
interactions are computed for the appropriate style of interactions.
Likewise, using groups to partition particles (ellipsoids versus
spheres versus point particles) will allow you to use the appropriate
time integrators and temperature computations for each class of
particles. See the doc pages for various commands for details.
Also note that for "2d simulations"_dimension.html, atom styles sphere
and ellipsoid still use 3d particles, rather than as circular disks or
ellipses. This means they have the same moment of inertia as a 3d
extended object. When temperature is computed, the correct degrees of
freedom are used for rotation in a 2d versus 3d system.
ellipses. This means they have the same moment of inertia as the 3d
object. When temperature is computed, the correct degrees of freedom
are used for rotation in a 2d versus 3d system.
Pair potentials :h5
When a system with extended particles is defined, the particles will
only rotate and experience torque if the force field computes such
interactions. These are the various "pair styles"_pair_style.html
that generate torque:
When a system with finite-size particles is defined, the particles
will only rotate and experience torque if the force field computes
such interactions. These are the various "pair
styles"_pair_style.html that generate torque:
"pair_style gran/history"_pair_gran.html
"pair_style gran/hertzian"_pair_gran.html
@ -1133,7 +1137,7 @@ triangular, and body particles respectively.
Time integration :h5
There are several fixes that perform time integration on extended
There are several fixes that perform time integration on finite-size
spherical particles, meaning the integrators update the rotational
orientation and angular velocity or angular momentum of the particles:
@ -1154,7 +1158,7 @@ calculation and thermostatting. The "fix langevin"_fix_langevin
command can also be used with its {omgea} or {angmom} options to
thermostat the rotational degrees of freedom for spherical or
ellipsoidal particles. Other thermostatting fixes only operate on the
translational kinetic energy of extended particles.
translational kinetic energy of finite-size particles.
These fixes perform constant NVE time integration on line segment,
triangular, and body particles:
@ -1163,9 +1167,9 @@ triangular, and body particles:
"fix nve/tri"_fix_nve_tri.html
"fix nve/body"_fix_nve_body.html :ul
Note that for mixtures of point and extended particles, these
Note that for mixtures of point and finite-size particles, these
integration fixes can only be used with "groups"_group.html which
contain extended particles.
contain finite-size particles.
Computes, thermodynamics, and dump output :h5
@ -1179,15 +1183,15 @@ rotational energy of spherical or ellipsoidal particles:
These include rotational degrees of freedom in their computation. If
you wish the thermodynamic output of temperature or pressure to use
one of these computes (e.g. for a system entirely composed of extended
particles), then the compute can be defined and the
one of these computes (e.g. for a system entirely composed of
finite-size particles), then the compute can be defined and the
"thermo_modify"_thermo_modify.html command used. Note that by default
thermodynamic quantities will be calculated with a temperature that
only includes translational degrees of freedom. See the
"thermo_style"_thermo_style.html command for details.
These commands can be used to output various attributes
of extended particles:
These commands can be used to output various attributes of finite-size
particles:
"dump custom"_dump.html
"compute property/atom"_compute_property_atom.html
@ -1198,23 +1202,23 @@ angular momentum, the quaternion, the torque, the end-point and
corner-point coordinates (for line and tri particles), and
sub-particle attributes of body particles.
Rigid bodies composed of extended particles :h5
Rigid bodies composed of finite-size particles :h5
The "fix rigid"_fix_rigid.html command treats a collection of
particles as a rigid body, computes its inertia tensor, sums the total
force and torque on the rigid body each timestep due to forces on its
constituent particles, and integrates the motion of the rigid body.
If any of the constituent particles of a rigid body are extended
If any of the constituent particles of a rigid body are finite-size
particles (spheres or ellipsoids or line segments or triangles), then
their contribution to the inertia tensor of the body is different than
if they were point particles. This means the rotational dynamics of
the rigid body will be different. Thus a model of a dimer is
different if the dimer consists of two point masses versus two
extended sphereoids, even if the two particles have the same mass.
Extended particles that experience torque due to their interaction
with other particles will also impart that torque to a rigid body they
are part of.
spheroids, even if the two particles have the same mass. Finite-size
particles that experience torque due to their interaction with other
particles will also impart that torque to a rigid body they are part
of.
See the "fix rigid" command for example of complex rigid-body models
it is possible to define in LAMMPS.
@ -1561,11 +1565,11 @@ All but the first 3 calculate velocity biases (i.e. advection
velocities) that are removed when computing the thermal temperature.
"Compute temp/sphere"_compute_temp_sphere.html and "compute
temp/asphere"_compute_temp_asphere.html compute kinetic energy for
extended particles that includes rotational degrees of freedom. They
both allow, as an extra argument, which is another temperature compute
that subtracts a velocity bias. This allows the translational
velocity of extended spherical or aspherical particles to be adjusted
in prescribed ways.
finite-size particles that includes rotational degrees of freedom.
They both allow, as an extra argument, which is another temperature
compute that subtracts a velocity bias. This allows the translational
velocity of spherical or aspherical particles to be adjusted in
prescribed ways.
Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one
case by a pair style. Four thermostatting fixes are currently

6
doc/atom_style.html
View File

@ -64,7 +64,7 @@ quantities.
<TR><TD ><I>charge</I> </TD><TD > charge </TD><TD > atomic system with charges </TD></TR>
<TR><TD ><I>dipole</I> </TD><TD > charge and dipole moment </TD><TD > system with dipolar particles </TD></TR>
<TR><TD ><I>electron</I> </TD><TD > charge and spin and eradius </TD><TD > electronic force field </TD></TR>
<TR><TD ><I>ellipsoid</I> </TD><TD > shape, quaternion, angular momentum </TD><TD > extended aspherical particles </TD></TR>
<TR><TD ><I>ellipsoid</I> </TD><TD > shape, quaternion, angular momentum </TD><TD > aspherical particles </TD></TR>
<TR><TD ><I>full</I> </TD><TD > molecular + charge </TD><TD > bio-molecules </TD></TR>
<TR><TD ><I>line</I> </TD><TD > end points, angular velocity </TD><TD > rigid bodies </TD></TR>
<TR><TD ><I>meso</I> </TD><TD > rho, e, cv </TD><TD > SPH particles </TD></TR>
@ -77,7 +77,9 @@ quantities.
<P>All of the styles define point particles, except the <I>sphere</I>,
<I>ellipsoid</I>, <I>electron</I>, <I>peri</I>, <I>wavepacket</I>, <I>line</I>, <I>tri</I>, and
<I>body</I> styles, which define finite-size particles.
<I>body</I> styles, which define finite-size particles. See <A HREF = "Section_howto.html#howto_14">Section_howto
14</A> for an overview of using finite-size
particle models with LAMMPS.
</P>
<P>All of the styles assign mass to particles on a per-type basis, using
the <A HREF = "mass.html">mass</A> command, except for the finite-size particle

6
doc/atom_style.txt
View File

@ -61,7 +61,7 @@ quantities.
{charge} | charge | atomic system with charges |
{dipole} | charge and dipole moment | system with dipolar particles |
{electron} | charge and spin and eradius | electronic force field |
{ellipsoid} | shape, quaternion, angular momentum | extended aspherical particles |
{ellipsoid} | shape, quaternion, angular momentum | aspherical particles |
{full} | molecular + charge | bio-molecules |
{line} | end points, angular velocity | rigid bodies |
{meso} | rho, e, cv | SPH particles |
@ -73,7 +73,9 @@ quantities.
All of the styles define point particles, except the {sphere},
{ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, {tri}, and
{body} styles, which define finite-size particles.
{body} styles, which define finite-size particles. See "Section_howto
14"_Section_howto.html#howto_14 for an overview of using finite-size
particle models with LAMMPS.
All of the styles assign mass to particles on a per-type basis, using
the "mass"_mass.html command, except for the finite-size particle

6
doc/compute_property_atom.html
View File

@ -49,11 +49,11 @@
mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom
radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
shapex,shapey,shapez = 3 diameters of aspherical particle
quatw,quati,quatj,quatk = quaternion components for aspherical or body particles
tqx,tqy,tqz = torque on extended particles
tqx,tqy,tqz = torque on finite-size particles
spin = electron spin
eradius = electron radius
ervel = electron radial velocity

6
doc/compute_property_atom.txt
View File

@ -42,11 +42,11 @@ input = one or more atom attributes :l
mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom
radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
shapex,shapey,shapez = 3 diameters of aspherical particle
quatw,quati,quatj,quatk = quaternion components for aspherical or body particles
tqx,tqy,tqz = torque on extended particles
tqx,tqy,tqz = torque on finite-size particles
spin = electron spin
eradius = electron radius
ervel = electron radial velocity

2
doc/dimension.html
View File

@ -32,7 +32,7 @@ Restart files also store this setting.
<P>See the discussion in <A HREF = "Section_howto.html">Section_howto</A> for
additional instructions on how to run 2d simulations.
</P>
<P>IMPORTANT NOTE: Some models in LAMMPS treat particles as extended
<P>IMPORTANT NOTE: Some models in LAMMPS treat particles as finite-size
spheres or ellipsoids, as opposed to point particles. In 2d, the
particles will still be spheres or ellipsoids, not circular disks or
ellipses, meaning their moment of inertia will be the same as in 3d.

2
doc/dimension.txt
View File

@ -29,7 +29,7 @@ Restart files also store this setting.
See the discussion in "Section_howto"_Section_howto.html for
additional instructions on how to run 2d simulations.
IMPORTANT NOTE: Some models in LAMMPS treat particles as extended
IMPORTANT NOTE: Some models in LAMMPS treat particles as finite-size
spheres or ellipsoids, as opposed to point particles. In 2d, the
particles will still be spheres or ellipsoids, not circular disks or
ellipses, meaning their moment of inertia will be the same as in 3d.

6
doc/dump.html
View File

@ -76,9 +76,9 @@
mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom
radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle
tqx,tqy,tqz = torque on extended particles
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
tqx,tqy,tqz = torque on finite-size particles
spin = electron spin
eradius = electron radius
ervel = electron radial velocity

6
doc/dump.txt
View File

@ -65,9 +65,9 @@ args = list of arguments for a particular style :l
mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom
radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle
tqx,tqy,tqz = torque on extended particles
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
tqx,tqy,tqz = torque on finite-size particles
spin = electron spin
eradius = electron radius
ervel = electron radial velocity

10
doc/fix_temp_rescale.html
View File

@ -45,11 +45,11 @@ fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
their velocities.
</P>
<P>The rescaling is applied to only the translational degrees of freedom
for the particles, which is an important consideration if extended
spherical or aspherical particles which have rotational degrees of
freedom are being thermostatted with this fix. The translational
degrees of freedom can also have a bias velocity removed from them
before thermostatting takes place; see the description below.
for the particles, which is an important consideration if finite-size
particles which have rotational degrees of freedom are being
thermostatted with this fix. The translational degrees of freedom can
also have a bias velocity removed from them before thermostatting
takes place; see the description below.
</P>
<P>Rescaling is performed every N timesteps. The target temperature is a
ramped value between the <I>Tstart</I> and <I>Tstop</I> temperatures at the

10
doc/fix_temp_rescale.txt
View File

@ -34,11 +34,11 @@ Reset the temperature of a group of atoms by explicitly rescaling
their velocities.
The rescaling is applied to only the translational degrees of freedom
for the particles, which is an important consideration if extended
spherical or aspherical particles which have rotational degrees of
freedom are being thermostatted with this fix. The translational
degrees of freedom can also have a bias velocity removed from them
before thermostatting takes place; see the description below.
for the particles, which is an important consideration if finite-size
particles which have rotational degrees of freedom are being
thermostatted with this fix. The translational degrees of freedom can
also have a bias velocity removed from them before thermostatting
takes place; see the description below.
Rescaling is performed every N timesteps. The target temperature is a
ramped value between the {Tstart} and {Tstop} temperatures at the