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 |
| 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 + |
| srd | stochastic rotation dynamics (SRD) particles as solvent |
| tad | temperature-accelerated dynamics of vacancy diffusion in bulk Si |
| tri | triangular particles in rigid bodies |
Here is how you might run and visualize one of the sample problems:
diff --git a/doc/Section_example.txt b/doc/Section_example.txt
index 947c7957c7..21b5aa8363 100644
--- a/doc/Section_example.txt
+++ b/doc/Section_example.txt
@@ -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:
diff --git a/doc/Section_howto.html b/doc/Section_howto.html
index 04c9dc6812..385c605a0e 100644
--- a/doc/Section_howto.html
+++ b/doc/Section_howto.html
@@ -26,7 +26,7 @@
6.11 Visualizing LAMMPS snapshots
6.12 Triclinic (non-orthogonal) simulation boxes
6.13 NEMD simulations
-6.14 Extended spherical and aspherical particles
+6.14 Finite-size spherical and aspherical particles
6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)
6.16 Thermostatting, barostatting and computing temperature
6.17 Walls
@@ -163,7 +163,7 @@ 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. @@ -1012,7 +1012,7 @@ profile consistent with the applied shear strain rate.
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:
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 in the LAMMPS distribution. +
There are several atom styles 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.
-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
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 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.
-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 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 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, 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.
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 -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 that generate torque:
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:
@@ -1163,7 +1167,7 @@ calculation and thermostatting. The 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: @@ -1172,9 +1176,9 @@ triangular, and body particles:
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 which -contain extended particles. +contain finite-size 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 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 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:
The fix rigid 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. @@ -1574,11 +1578,11 @@ pressure command calculates pressure. velocities) that are removed when computing the thermal temperature. Compute temp/sphere and compute temp/asphere 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, or in one case by a pair style. Four thermostatting fixes are currently diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 7e2f80f235..7b6759d66b 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -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 diff --git a/doc/atom_style.html b/doc/atom_style.html index a1eb01941d..4971ee9233 100644 --- a/doc/atom_style.html +++ b/doc/atom_style.html @@ -64,7 +64,7 @@ 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 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 command, except for the finite-size particle diff --git a/doc/atom_style.txt b/doc/atom_style.txt index 44f2b55cee..d533e3ccf4 100644 --- a/doc/atom_style.txt +++ b/doc/atom_style.txt @@ -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 diff --git a/doc/compute_property_atom.html b/doc/compute_property_atom.html index 76c95b7019..817cccae48 100644 --- a/doc/compute_property_atom.html +++ b/doc/compute_property_atom.html @@ -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 diff --git a/doc/compute_property_atom.txt b/doc/compute_property_atom.txt index f710eb688a..ba80775e45 100644 --- a/doc/compute_property_atom.txt +++ b/doc/compute_property_atom.txt @@ -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 diff --git a/doc/dimension.html b/doc/dimension.html index c4ebeccf73..65099ab255 100644 --- a/doc/dimension.html +++ b/doc/dimension.html @@ -32,7 +32,7 @@ Restart files also store this setting.
See the discussion in Section_howto 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. diff --git a/doc/dimension.txt b/doc/dimension.txt index e8e843c802..b1321d5200 100644 --- a/doc/dimension.txt +++ b/doc/dimension.txt @@ -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. diff --git a/doc/dump.html b/doc/dump.html index 1aa895f460..445f1f82d5 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -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 diff --git a/doc/dump.txt b/doc/dump.txt index d041eae086..7254255601 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -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 diff --git a/doc/fix_temp_rescale.html b/doc/fix_temp_rescale.html index cb748d8439..208a2de9db 100644 --- a/doc/fix_temp_rescale.html +++ b/doc/fix_temp_rescale.html @@ -45,11 +45,11 @@ fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 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 diff --git a/doc/fix_temp_rescale.txt b/doc/fix_temp_rescale.txt index 936bd3957b..e582ccf5cb 100644 --- a/doc/fix_temp_rescale.txt +++ b/doc/fix_temp_rescale.txt @@ -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