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 +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. +
4.3 CHARMM and AMBER force fields
@@ -315,15 +320,26 @@
4.6 Granular models
+
Granular system are composed of spherical particles with a diameter, +as opposed to point particles. This means they have an angular +velocity and torque can be imparted to them to cause them to rotate. +
To run a simulation of a granular model, you will want to use the following commands:
- atom_style granular -
- fix nve/gran -
- fix gravity -
- thermo_style gran +
- fix nve/sphere +
- fix gravity +
This compute +
+ -Use one of these 3 pair potentials: +
calculates rotational kinetic energy which can be output with +thermodynamic info. +
+Use one of these 3 pair potentials, which compute forces and torques +between interacting pairs of particles:
- pair_style gran/history
- pair_style gran/no_history
@@ -332,7 +348,6 @@
These commands implement fix options specific to granular systems:
- fix freeze -
- fix gran/diag
- fix pour
- fix viscous
- fix wall/gran
@@ -795,6 +810,10 @@
interactions computed by another pair potential, such as pair_style
lj/cut.
+
IMPORTANT NOTE: In 2d, aspherical particles will still be ellipsoids, +not ellipses, meaning their moments of inertia will be the same as in +3d. +
4.15 Output from LAMMPS diff -Naur lammps-18Mar08/doc/Section_howto.txt lammps-19Mar08/doc/Section_howto.txt --- lammps-18Mar08/doc/Section_howto.txt 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/Section_howto.txt 2008-03-18 15:07:29.000000000 -0600 @@ -153,6 +153,11 @@ 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 +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. + :line 4.3 CHARMM and AMBER force fields :link(4_3),h4 @@ -311,15 +316,26 @@ 4.6 Granular models :link(4_6),h4 +Granular system are composed of spherical particles with a diameter, +as opposed to point particles. This means they have an angular +velocity and torque can be imparted to them to cause them to rotate. + To run a simulation of a granular model, you will want to use the following commands: "atom_style"_atom_style.html granular -"fix nve/gran"_fix_nve_gran.html -"fix gravity"_fix_gravity.html -"thermo_style"_thermo_style.html gran :ul +"fix nve/sphere"_fix_nve_sphere.html +"fix gravity"_fix_gravity.html :ul + +This compute -Use one of these 3 pair potentials: +"compute erotate/sphere"_compute_erotate_sphere.html :ul + +calculates rotational kinetic energy which can be "output with +thermodynamic info"_Section_howto.html#4_15. + +Use one of these 3 pair potentials, which compute forces and torques +between interacting pairs of particles: "pair_style"_pair_style.html gran/history "pair_style"_pair_style.html gran/no_history @@ -328,7 +344,6 @@ These commands implement fix options specific to granular systems: "fix freeze"_fix_freeze.html -"fix gran/diag"_fix_gran_diag.html "fix pour"_fix_pour.html "fix viscous"_fix_viscous.html "fix wall/gran"_fix_wall_gran.html :ul @@ -788,6 +803,10 @@ interactions computed by another pair potential, such as "pair_style lj/cut"_pair_lj.html. +IMPORTANT NOTE: In 2d, aspherical particles will still be ellipsoids, +not ellipses, meaning their moments of inertia will be the same as in +3d. + :line 4.15 Output from LAMMPS :link(4_15),h4 diff -Naur lammps-18Mar08/doc/Section_intro.html lammps-19Mar08/doc/Section_intro.html --- lammps-18Mar08/doc/Section_intro.html 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/Section_intro.html 2008-03-18 14:18:54.000000000 -0600 @@ -128,8 +128,8 @@
- angle potentials: harmonic, CHARMM, cosine, cosine/squared, class 2 (COMPASS)
- dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS
- improper potentials: harmonic, cvff, class 2 (COMPASS) -
- hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simlulation -
- overlayed potentials: superposition of multiple pair potentials +
- hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation +
- overlaid potentials: superposition of multiple pair potentials
- polymer potentials: all-atom, united-atom, bead-spring, breakable
- water potentials: TIP3P, TIP4P, SPC
- implicit solvent potentials: hydrodynamic lubrication, Debye
diff -Naur lammps-18Mar08/doc/Section_intro.txt lammps-19Mar08/doc/Section_intro.txt
--- lammps-18Mar08/doc/Section_intro.txt 2008-02-29 18:13:20.000000000 -0700
+++ lammps-19Mar08/doc/Section_intro.txt 2008-03-18 14:18:54.000000000 -0600
@@ -129,8 +129,8 @@
class 2 (COMPASS), OPLS
improper potentials: harmonic, cvff, class 2 (COMPASS)
hybrid potentials: multiple pair, bond, angle, dihedral, improper \
- potentials can be used in one simlulation
- overlayed potentials: superposition of multiple pair potentials
+ potentials can be used in one simulation
+ overlaid potentials: superposition of multiple pair potentials
polymer potentials: all-atom, united-atom, bead-spring, breakable
water potentials: TIP3P, TIP4P, SPC
implicit solvent potentials: hydrodynamic lubrication, Debye
diff -Naur lammps-18Mar08/doc/Section_modify.html lammps-19Mar08/doc/Section_modify.html
--- lammps-18Mar08/doc/Section_modify.html 2008-02-29 18:13:20.000000000 -0700
+++ lammps-19Mar08/doc/Section_modify.html 2008-03-18 14:18:54.000000000 -0600
@@ -14,7 +14,7 @@
8. Modifying & extending LAMMPS
LAMMPS is designed in a modular fashion so as to be easy to modify and -extend with new functionality. In fact, about 75% if its source code +extend with new functionality. In fact, about 75% of its source code is files added in this fashion.
In this section, changes and additions users can make are listed along diff -Naur lammps-18Mar08/doc/Section_modify.txt lammps-19Mar08/doc/Section_modify.txt --- lammps-18Mar08/doc/Section_modify.txt 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/Section_modify.txt 2008-03-18 14:18:54.000000000 -0600 @@ -11,7 +11,7 @@ 8. Modifying & extending LAMMPS :h3 LAMMPS is designed in a modular fashion so as to be easy to modify and -extend with new functionality. In fact, about 75% if its source code +extend with new functionality. In fact, about 75% of its source code is files added in this fashion. In this section, changes and additions users can make are listed along diff -Naur lammps-18Mar08/doc/Section_start.html lammps-19Mar08/doc/Section_start.html --- lammps-18Mar08/doc/Section_start.html 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/Section_start.html 2008-03-18 15:09:15.000000000 -0600 @@ -219,8 +219,8 @@
(1) Building LAMMPS for multiple platforms.
You can make LAMMPS for multiple platforms from the same src -directory. Each target creates its own object sub-dir called Obj_name -where it stores the system-specific *.o files. +directory. Each target creates its own object sub-directory called +Obj_name where it stores the system-specific *.o files.
(2) Cleaning up.
diff -Naur lammps-18Mar08/doc/Section_start.txt lammps-19Mar08/doc/Section_start.txt --- lammps-18Mar08/doc/Section_start.txt 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/Section_start.txt 2008-03-18 15:09:15.000000000 -0600 @@ -214,8 +214,8 @@ (1) Building LAMMPS for multiple platforms. You can make LAMMPS for multiple platforms from the same src -directory. Each target creates its own object sub-dir called Obj_name -where it stores the system-specific *.o files. +directory. Each target creates its own object sub-directory called +Obj_name where it stores the system-specific *.o files. (2) Cleaning up. diff -Naur lammps-18Mar08/doc/Section_tools.html lammps-19Mar08/doc/Section_tools.html --- lammps-18Mar08/doc/Section_tools.html 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/Section_tools.html 2008-03-18 14:18:54.000000000 -0600 @@ -65,7 +65,7 @@amber2lmp tool
-The amber2lmp sub-directory contain two Python scripts for converting +
The amber2lmp sub-directory contains two Python scripts for converting files back-and-forth between the AMBER MD code and LAMMPS. See the README file in amber2lmp for more information.
diff -Naur lammps-18Mar08/doc/Section_tools.txt lammps-19Mar08/doc/Section_tools.txt --- lammps-18Mar08/doc/Section_tools.txt 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/Section_tools.txt 2008-03-18 14:18:54.000000000 -0600 @@ -61,7 +61,7 @@ amber2lmp tool :h4,link(amber) -The amber2lmp sub-directory contain two Python scripts for converting +The amber2lmp sub-directory contains two Python scripts for converting files back-and-forth between the AMBER MD code and LAMMPS. See the README file in amber2lmp for more information. diff -Naur lammps-18Mar08/doc/angle_coeff.html lammps-19Mar08/doc/angle_coeff.html --- lammps-18Mar08/doc/angle_coeff.html 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/angle_coeff.html 2008-03-18 14:18:54.000000000 -0600 @@ -32,7 +32,7 @@ read_data command or in a restart file.N can be specified in one of two ways. An explicit numeric value can -be used, as in the 1st example above. Or a wild-card asterik can be +be used, as in the 1st example above. Or a wild-card asterisk can be used to set the coefficients for multiple angle types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of angle types, then an asterisk with no numeric values means all types from 1 to N. A diff -Naur lammps-18Mar08/doc/angle_coeff.txt lammps-19Mar08/doc/angle_coeff.txt --- lammps-18Mar08/doc/angle_coeff.txt 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/angle_coeff.txt 2008-03-18 14:18:54.000000000 -0600 @@ -29,7 +29,7 @@ "read_data"_read_data.html command or in a restart file. N can be specified in one of two ways. An explicit numeric value can -be used, as in the 1st example above. Or a wild-card asterik can be +be used, as in the 1st example above. Or a wild-card asterisk can be used to set the coefficients for multiple angle types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of angle types, then an asterisk with no numeric values means all types from 1 to N. A diff -Naur lammps-18Mar08/doc/compute.html lammps-19Mar08/doc/compute.html --- lammps-18Mar08/doc/compute.html 2008-03-11 10:37:01.000000000 -0600 +++ lammps-19Mar08/doc/compute.html 2008-03-17 18:23:39.000000000 -0600 @@ -112,14 +112,13 @@
- centro/atom - centro-symmetry parameter for each atom
- coord/atom - coordination number for each atom
- displace/atom - displacement of each atom +
- erotate/sphere - rotational energy of spherical particles
- group/group - energy/force between two groups of atoms
- ke/atom - kinetic energy for each atom
- pe - potential energy
- pe/atom - potential energy for each atom
- pressure - total pressure and pressure tensor
- reduce - combine per-atom quantities into a single global value -
- rotate/dipole - rotational energy of dipolar atoms -
- rotate/gran - rotational energy of granular atoms
- stress/atom - stress tensor for each atom
- temp - temperature of group of atoms
- temp/asphere - temperature of aspherical particles @@ -128,7 +127,8 @@
- temp/dipole - temperature of point dipolar particles
- temp/partial - temperature excluding one or more dimensions of velocity
- temp/ramp - temperature excluding ramped velocity component -
- temp/region - temperature of a region of atoms +
- temp/region - temperature of a region of atoms +
- temp/sphere - temperature of spherical particles
There are also additional compute styles submitted by users which are included in the LAMMPS distribution. The list of these with links to diff -Naur lammps-18Mar08/doc/compute.txt lammps-19Mar08/doc/compute.txt --- lammps-18Mar08/doc/compute.txt 2008-03-11 10:37:01.000000000 -0600 +++ lammps-19Mar08/doc/compute.txt 2008-03-17 18:23:39.000000000 -0600 @@ -109,14 +109,13 @@ "centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom "coord/atom"_compute_coord_atom.html - coordination number for each atom "displace/atom"_compute_displace_atom.html - displacement of each atom +"erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles "group/group"_compute_group_group.html - energy/force between two groups of atoms "ke/atom"_compute_ke_atom.html - kinetic energy for each atom "pe"_compute_pe.html - potential energy "pe/atom"_compute_pe_atom.html - potential energy for each atom "pressure"_compute_pressure.html - total pressure and pressure tensor "reduce"_compute_reduce.html - combine per-atom quantities into a single global value -"rotate/dipole"_compute_rotate_dipole.html - rotational energy of dipolar atoms -"rotate/gran"_compute_rotate_gran.html - rotational energy of granular atoms "stress/atom"_compute_stress_atom.html - stress tensor for each atom "temp"_compute_temp.html - temperature of group of atoms "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles @@ -125,7 +124,8 @@ "temp/dipole"_compute_temp_dipole.html - temperature of point dipolar particles "temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component -"temp/region"_compute_temp_region.html - temperature of a region of atoms :ul +"temp/region"_compute_temp_region.html - temperature of a region of atoms +"temp/sphere"_compute_temp_sphere.html - temperature of spherical particles :ul There are also additional compute styles submitted by users which are included in the LAMMPS distribution. The list of these with links to diff -Naur lammps-18Mar08/doc/compute_erotate_sphere.html lammps-19Mar08/doc/compute_erotate_sphere.html --- lammps-18Mar08/doc/compute_erotate_sphere.html 1969-12-31 17:00:00.000000000 -0700 +++ lammps-19Mar08/doc/compute_erotate_sphere.html 2008-03-18 15:02:30.000000000 -0600 @@ -0,0 +1,54 @@ + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands + + + + + + + +
+ +compute erotate/sphere command +
+Syntax: +
+compute ID group-ID erotate/sphere +
+- ID, group-ID are documented in compute command +
- erotate/sphere = style name of this compute command +
Examples: +
+compute 1 all erotate/sphere +
+Description: +
+Define a computation that calculates the rotational kinetic energy of +a group of spherical particles. +
+The rotational energy is computed as 1/2 I w^2, where I is the moment +of inertia for a sphere and w is the particle's angular velocity. +
+IMPORTANT NOTE: For 2d models, particles are treated +as spheres, not disks, meaning their moment of inertia will be the +same as in 3d. +
+Output info: +
+The scalar value calculated by this compute is "extensive", meaning it +it scales with the number of atoms in the simulation. +
+Restrictions: +
+This compute requires that particles be represented as extended +spheres and not point particles. This means they will have an angular +velocity and a diameter which is determined either by the +shape command or by each particle being assigned an +individual radius, e.g. for atom_style granular. +
+Related commands: none +
+Default: none +
+ diff -Naur lammps-18Mar08/doc/compute_erotate_sphere.txt lammps-19Mar08/doc/compute_erotate_sphere.txt --- lammps-18Mar08/doc/compute_erotate_sphere.txt 1969-12-31 17:00:00.000000000 -0700 +++ lammps-19Mar08/doc/compute_erotate_sphere.txt 2008-03-18 15:02:30.000000000 -0600 @@ -0,0 +1,49 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute erotate/sphere command :h3 + +[Syntax:] + +compute ID group-ID erotate/sphere :pre + +ID, group-ID are documented in "compute"_compute.html command +erotate/sphere = style name of this compute command :ul + +[Examples:] + +compute 1 all erotate/sphere :pre + +[Description:] + +Define a computation that calculates the rotational kinetic energy of +a group of spherical particles. + +The rotational energy is computed as 1/2 I w^2, where I is the moment +of inertia for a sphere and w is the particle's angular velocity. + +IMPORTANT NOTE: For "2d models"_dimension.html, particles are treated +as spheres, not disks, meaning their moment of inertia will be the +same as in 3d. + +[Output info:] + +The scalar value calculated by this compute is "extensive", meaning it +it scales with the number of atoms in the simulation. + +[Restrictions:] + +This compute requires that particles be represented as extended +spheres and not point particles. This means they will have an angular +velocity and a diameter which is determined either by the +"shape"_shape.html command or by each particle being assigned an +individual radius, e.g. for "atom_style granular"_atom_style.html. + +[Related commands:] none + +[Default:] none diff -Naur lammps-18Mar08/doc/compute_rotate_dipole.html lammps-19Mar08/doc/compute_rotate_dipole.html --- lammps-18Mar08/doc/compute_rotate_dipole.html 2008-01-02 12:25:15.000000000 -0700 +++ lammps-19Mar08/doc/compute_rotate_dipole.html 1969-12-31 17:00:00.000000000 -0700 @@ -1,45 +0,0 @@ - -LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands - - - - - - - -
- -compute rotate/dipole command -
-Syntax: -
-compute ID group-ID rotate/dipole -
-- ID, group-ID are documented in compute command -
- rotate/dipole = style name of this compute command -
Examples: -
-compute 1 all rotate/dipole -
-Description: -
-Define a computation that calculates the total rotational energy of a -group of atoms with point dipole moments. -
-The rotational energy is calculated as the sum of 1/2 I w^2 over all -the atoms in the group, where I is the moment of inertia of a -disk/spherical (2d/3d) particle, and w is its angular velocity. -
-Output info: -
-The scalar value calculated by this compute is "extensive", meaning it -it scales with the number of atoms in the simulation. -
-Restrictions: none -
-Related commands: none -
-Default: none -
- diff -Naur lammps-18Mar08/doc/compute_rotate_dipole.txt lammps-19Mar08/doc/compute_rotate_dipole.txt --- lammps-18Mar08/doc/compute_rotate_dipole.txt 2008-01-02 12:25:15.000000000 -0700 +++ lammps-19Mar08/doc/compute_rotate_dipole.txt 1969-12-31 17:00:00.000000000 -0700 @@ -1,40 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -compute rotate/dipole command :h3 - -[Syntax:] - -compute ID group-ID rotate/dipole :pre - -ID, group-ID are documented in "compute"_compute.html command -rotate/dipole = style name of this compute command :ul - -[Examples:] - -compute 1 all rotate/dipole :pre - -[Description:] - -Define a computation that calculates the total rotational energy of a -group of atoms with point dipole moments. - -The rotational energy is calculated as the sum of 1/2 I w^2 over all -the atoms in the group, where I is the moment of inertia of a -disk/spherical (2d/3d) particle, and w is its angular velocity. - -[Output info:] - -The scalar value calculated by this compute is "extensive", meaning it -it scales with the number of atoms in the simulation. - -[Restrictions:] none - -[Related commands:] none - -[Default:] none diff -Naur lammps-18Mar08/doc/compute_rotate_gran.html lammps-19Mar08/doc/compute_rotate_gran.html --- lammps-18Mar08/doc/compute_rotate_gran.html 2008-01-02 12:25:15.000000000 -0700 +++ lammps-19Mar08/doc/compute_rotate_gran.html 1969-12-31 17:00:00.000000000 -0700 @@ -1,45 +0,0 @@ - -LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands - - - - - - - -
- -compute rotate/gran command -
-Syntax: -
-compute ID group-ID rotate/gran -
-- ID, group-ID are documented in compute command -
- rotate/gran = style name of this compute command -
Examples: -
-compute 1 all rotate/gran -
-Description: -
-Define a computation that calculates the total rotational energy of a -group of granular atoms. -
-The rotational energy is calculated as the sum of 1/2 I w^2 over all -the atoms in the group, where I is the moment of inertia of a -disk/spherical (2d/3d) particle, and w is its angular velocity. -
-Output info: -
-The scalar value calculated by this compute is "extensive", meaning it -it scales with the number of atoms in the simulation. -
-Restrictions: none -
-Related commands: none -
-Default: none -
- diff -Naur lammps-18Mar08/doc/compute_rotate_gran.txt lammps-19Mar08/doc/compute_rotate_gran.txt --- lammps-18Mar08/doc/compute_rotate_gran.txt 2008-01-02 12:25:15.000000000 -0700 +++ lammps-19Mar08/doc/compute_rotate_gran.txt 1969-12-31 17:00:00.000000000 -0700 @@ -1,40 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -compute rotate/gran command :h3 - -[Syntax:] - -compute ID group-ID rotate/gran :pre - -ID, group-ID are documented in "compute"_compute.html command -rotate/gran = style name of this compute command :ul - -[Examples:] - -compute 1 all rotate/gran :pre - -[Description:] - -Define a computation that calculates the total rotational energy of a -group of granular atoms. - -The rotational energy is calculated as the sum of 1/2 I w^2 over all -the atoms in the group, where I is the moment of inertia of a -disk/spherical (2d/3d) particle, and w is its angular velocity. - -[Output info:] - -The scalar value calculated by this compute is "extensive", meaning it -it scales with the number of atoms in the simulation. - -[Restrictions:] none - -[Related commands:] none - -[Default:] none diff -Naur lammps-18Mar08/doc/compute_temp_asphere.html lammps-19Mar08/doc/compute_temp_asphere.html --- lammps-18Mar08/doc/compute_temp_asphere.html 2008-01-02 12:25:15.000000000 -0700 +++ lammps-19Mar08/doc/compute_temp_asphere.html 2008-03-18 15:02:30.000000000 -0600 @@ -26,12 +26,54 @@Description:
Define a computation that calculates the temperature of a group of -aspherical or ellipsoidal particles. The computation is similar to -compute_temp, however, additional degrees of -freedom (2 or 3) are incorporated for particles where the principal -moments of inertia are unequal. The associated kinetic energy thus -includes a rotational term KE_rotational = 1/2 I w^2, where I is the -moment of inertia and w is the angular velocity. +aspherical particles, including a contribution from both their +translational and rotational kinetic energy. This differs from the +usual compute temp command, which assumes point +particles with only translational kinetic energy. +
+For 3d aspherical particles, each has 3, 5, or 6 degrees of freedom (3 +translational, remainder rotational), depending on whether the +particle is spherical, uniaxial, or biaxial. This is determined by +the shape command. Uniaxial means two of its three shape +parameters are equal. Biaxial means all 3 shape parameters are +different. +
+For 2d aspherical particles, each has 3 or 4 degrees of freedom (3 +translational, remainder rotational), depending on whether the +particle is spherical, or biaxial. Biaxial means the x,y shape +parameters are unequal. +
+IMPORTANT NOTE: These degrees of freedom assume that the interaction +potential between degenerate aspherical particles does not impart +rotational motion to the extra degrees of freedom. E.g. the GayBerne +pair potential does not impart torque to spherical +particles, so they do not rotate. +
+The rotational kinetic energy is computed as 1/2 I w^2, where I is the +inertia tensor for the aspherical particle and w is its angular +velocity, which is computed from its angular momentum. +
+IMPORTANT NOTE: For 2d models, particles are treated +as ellipsoids, not ellipses, meaning their moments of inertia will be +the same as in 3d. +
+A 6-component kinetic energy tensor is also calculated by this +compute. The formula for the components of the tensor is the same as +the above formula, except that v^2 and w^2 are replaced by vx*vy and +wx*wy for the xy component, and the appropriate elements of the +inertia tensor are used. +
+The number of atoms contributing to the temperature is assumed to be +constant for the duration of the run; use the dynamic option of the +compute_modify command if this is not the case. +
+This compute subtracts out translational degrees-of-freedom due to +fixes that constrain molecular motion, such as fix +shake and fix rigid. This means the +temperature of groups of atoms that include these constraints will be +computed correctly. If needed, the subtracted degrees-of-freedom can +be altered using the extra option of the +compute_modify command.
Output info:
@@ -42,7 +84,10 @@Restrictions:
-Can only be used if LAMMPS was built with the "asphere" package. +
This compute requires that particles be represented as extended +ellipsoids and not point particles. This means they will have an +angular momentum and a shape which is determined by the +shape command.
Related commands:
diff -Naur lammps-18Mar08/doc/compute_temp_asphere.txt lammps-19Mar08/doc/compute_temp_asphere.txt --- lammps-18Mar08/doc/compute_temp_asphere.txt 2008-01-02 12:25:15.000000000 -0700 +++ lammps-19Mar08/doc/compute_temp_asphere.txt 2008-03-18 15:02:30.000000000 -0600 @@ -23,12 +23,54 @@ [Description:] Define a computation that calculates the temperature of a group of -aspherical or ellipsoidal particles. The computation is similar to -"compute_temp"_compute_temp.html, however, additional degrees of -freedom (2 or 3) are incorporated for particles where the principal -moments of inertia are unequal. The associated kinetic energy thus -includes a rotational term KE_rotational = 1/2 I w^2, where I is the -moment of inertia and w is the angular velocity. +aspherical particles, including a contribution from both their +translational and rotational kinetic energy. This differs from the +usual "compute temp"_compute_temp.html command, which assumes point +particles with only translational kinetic energy. + +For 3d aspherical particles, each has 3, 5, or 6 degrees of freedom (3 +translational, remainder rotational), depending on whether the +particle is spherical, uniaxial, or biaxial. This is determined by +the "shape"_shape.html command. Uniaxial means two of its three shape +parameters are equal. Biaxial means all 3 shape parameters are +different. + +For 2d aspherical particles, each has 3 or 4 degrees of freedom (3 +translational, remainder rotational), depending on whether the +particle is spherical, or biaxial. Biaxial means the x,y shape +parameters are unequal. + +IMPORTANT NOTE: These degrees of freedom assume that the interaction +potential between degenerate aspherical particles does not impart +rotational motion to the extra degrees of freedom. E.g. the "GayBerne +pair potential"_pair_gayberne.html does not impart torque to spherical +particles, so they do not rotate. + +The rotational kinetic energy is computed as 1/2 I w^2, where I is the +inertia tensor for the aspherical particle and w is its angular +velocity, which is computed from its angular momentum. + +IMPORTANT NOTE: For "2d models"_dimension.html, particles are treated +as ellipsoids, not ellipses, meaning their moments of inertia will be +the same as in 3d. + +A 6-component kinetic energy tensor is also calculated by this +compute. The formula for the components of the tensor is the same as +the above formula, except that v^2 and w^2 are replaced by vx*vy and +wx*wy for the xy component, and the appropriate elements of the +inertia tensor are used. + +The number of atoms contributing to the temperature is assumed to be +constant for the duration of the run; use the {dynamic} option of the +"compute_modify"_compute_modify.html command if this is not the case. + +This compute subtracts out translational degrees-of-freedom due to +fixes that constrain molecular motion, such as "fix +shake"_fix_shake.html and "fix rigid"_fix_rigid.html. This means the +temperature of groups of atoms that include these constraints will be +computed correctly. If needed, the subtracted degrees-of-freedom can +be altered using the {extra} option of the +"compute_modify"_compute_modify.html command. [Output info:] @@ -39,7 +81,10 @@ [Restrictions:] -Can only be used if LAMMPS was built with the "asphere" package. +This compute requires that particles be represented as extended +ellipsoids and not point particles. This means they will have an +angular momentum and a shape which is determined by the +"shape"_shape.html command. [Related commands:] diff -Naur lammps-18Mar08/doc/compute_temp_dipole.html lammps-19Mar08/doc/compute_temp_dipole.html --- lammps-18Mar08/doc/compute_temp_dipole.html 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/compute_temp_dipole.html 1969-12-31 17:00:00.000000000 -0700 @@ -1,53 +0,0 @@ - -LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands - - - - - - - -
- -compute temp/dipole command -
-Syntax: -
-compute ID group-ID temp/dipole -
-- ID, group-ID are documented in compute command -
- temp/dipole = style name of this compute command -
Examples: -
-compute 1 all temp/dipole -compute myTemp mobile temp/dipole -
-Description: -
-Define a computation that calculates the temperature of a group of -particles that include a point dipole. The computation is similar to -compute_temp, however, additional degrees of -freedom are included to account for the rotational state of the -particles. The associated kinetic energy includes a rotational term -KE_rotational = 1/2 I w^2, where I is the moment of inertia and w is -the angular velocity. -
-Output info: -
-The scalar value calculated by this compute is "intensive", meaning it -is independent of the number of atoms in the simulation. The vector -values are "extensive", meaning they scale with the number of atoms in -the simulation. -
-Restrictions: -
-Can only be used if LAMMPS was built with the "dipole" package. -
-Related commands: -
- -Default: none -
- diff -Naur lammps-18Mar08/doc/compute_temp_dipole.txt lammps-19Mar08/doc/compute_temp_dipole.txt --- lammps-18Mar08/doc/compute_temp_dipole.txt 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/compute_temp_dipole.txt 1969-12-31 17:00:00.000000000 -0700 @@ -1,48 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -compute temp/dipole command :h3 - -[Syntax:] - -compute ID group-ID temp/dipole :pre - -ID, group-ID are documented in "compute"_compute.html command -temp/dipole = style name of this compute command :ul - -[Examples:] - -compute 1 all temp/dipole -compute myTemp mobile temp/dipole :pre - -[Description:] - -Define a computation that calculates the temperature of a group of -particles that include a point dipole. The computation is similar to -"compute_temp"_compute_temp.html, however, additional degrees of -freedom are included to account for the rotational state of the -particles. The associated kinetic energy includes a rotational term -KE_rotational = 1/2 I w^2, where I is the moment of inertia and w is -the angular velocity. - -[Output info:] - -The scalar value calculated by this compute is "intensive", meaning it -is independent of the number of atoms in the simulation. The vector -values are "extensive", meaning they scale with the number of atoms in -the simulation. - -[Restrictions:] - -Can only be used if LAMMPS was built with the "dipole" package. - -[Related commands:] - -"compute temp"_compute_temp.html - -[Default:] none diff -Naur lammps-18Mar08/doc/compute_temp_sphere.html lammps-19Mar08/doc/compute_temp_sphere.html --- lammps-18Mar08/doc/compute_temp_sphere.html 1969-12-31 17:00:00.000000000 -0700 +++ lammps-19Mar08/doc/compute_temp_sphere.html 2008-03-18 15:02:30.000000000 -0600 @@ -0,0 +1,85 @@ + +LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands + + + + + + + +
+ +compute temp/sphere command +
+Syntax: +
+compute ID group-ID temp/sphere +
+- ID, group-ID are documented in compute command +
- temp/sphere = style name of this compute command +
Examples: +
+compute 1 all temp/sphere +compute myTemp mobile temp/sphere +
+Description: +
+Define a computation that calculates the temperature of a group of +spherical particles, including a contribution from both their +translational and rotational kinetic energy. This differs from the +usual compute temp command, which assumes point +particles with only translational kinetic energy. +
+For 3d spherical particles, each has 6 degrees of freedom (3 +translational, 3 rotational). For 2d spherical particles, each has 3 +degrees of freedom (2 translational, 1 rotational). +
+The rotational kinetic energy is computed as 1/2 I w^2, where I is the +moment of inertia for a sphere and w is the particle's angular +velocity. +
+IMPORTANT NOTE: For 2d models, particles are treated +as spheres, not disks, meaning their moment of inertia will be the +same as in 3d. +
+A 6-component kinetic energy tensor is also calculated by this +compute. The formula for the components of the tensor is the same as +the above formula, except that v^2 and w^2 are replaced by vx*vy and +wx*wy for the xy component. +
+The number of atoms contributing to the temperature is assumed to be +constant for the duration of the run; use the dynamic option of the +compute_modify command if this is not the case. +
+This compute subtracts out translational degrees-of-freedom due to +fixes that constrain molecular motion, such as fix +shake and fix rigid. This means the +temperature of groups of atoms that include these constraints will be +computed correctly. If needed, the subtracted degrees-of-freedom can +be altered using the extra option of the +compute_modify command. +
+Output info: +
+The scalar value calculated by this compute is "intensive", meaning it +is independent of the number of atoms in the simulation. The vector +values are "extensive", meaning they scale with the number of atoms in +the simulation. +
+Restrictions: +
+This compute requires that particles be represented as extended +spheres and not point particles. This means they will have an angular +velocity and a diameter which is determined either by the +shape command or by each particle being assigned an +individual radius, e.g. for atom_style granular. +
+Related commands: +
+compute temp, compute +temp/asphere +
+Default: none +
+ diff -Naur lammps-18Mar08/doc/compute_temp_sphere.txt lammps-19Mar08/doc/compute_temp_sphere.txt --- lammps-18Mar08/doc/compute_temp_sphere.txt 1969-12-31 17:00:00.000000000 -0700 +++ lammps-19Mar08/doc/compute_temp_sphere.txt 2008-03-18 15:02:30.000000000 -0600 @@ -0,0 +1,80 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute temp/sphere command :h3 + +[Syntax:] + +compute ID group-ID temp/sphere :pre + +ID, group-ID are documented in "compute"_compute.html command +temp/sphere = style name of this compute command :ul + +[Examples:] + +compute 1 all temp/sphere +compute myTemp mobile temp/sphere :pre + +[Description:] + +Define a computation that calculates the temperature of a group of +spherical particles, including a contribution from both their +translational and rotational kinetic energy. This differs from the +usual "compute temp"_compute_temp.html command, which assumes point +particles with only translational kinetic energy. + +For 3d spherical particles, each has 6 degrees of freedom (3 +translational, 3 rotational). For 2d spherical particles, each has 3 +degrees of freedom (2 translational, 1 rotational). + +The rotational kinetic energy is computed as 1/2 I w^2, where I is the +moment of inertia for a sphere and w is the particle's angular +velocity. + +IMPORTANT NOTE: For "2d models"_dimension.html, particles are treated +as spheres, not disks, meaning their moment of inertia will be the +same as in 3d. + +A 6-component kinetic energy tensor is also calculated by this +compute. The formula for the components of the tensor is the same as +the above formula, except that v^2 and w^2 are replaced by vx*vy and +wx*wy for the xy component. + +The number of atoms contributing to the temperature is assumed to be +constant for the duration of the run; use the {dynamic} option of the +"compute_modify"_compute_modify.html command if this is not the case. + +This compute subtracts out translational degrees-of-freedom due to +fixes that constrain molecular motion, such as "fix +shake"_fix_shake.html and "fix rigid"_fix_rigid.html. This means the +temperature of groups of atoms that include these constraints will be +computed correctly. If needed, the subtracted degrees-of-freedom can +be altered using the {extra} option of the +"compute_modify"_compute_modify.html command. + +[Output info:] + +The scalar value calculated by this compute is "intensive", meaning it +is independent of the number of atoms in the simulation. The vector +values are "extensive", meaning they scale with the number of atoms in +the simulation. + +[Restrictions:] + +This compute requires that particles be represented as extended +spheres and not point particles. This means they will have an angular +velocity and a diameter which is determined either by the +"shape"_shape.html command or by each particle being assigned an +individual radius, e.g. for "atom_style granular"_atom_style.html. + +[Related commands:] + +"compute temp"_compute_temp.html, "compute +temp/asphere"_compute_temp.html + +[Default:] none diff -Naur lammps-18Mar08/doc/dimension.html lammps-19Mar08/doc/dimension.html --- lammps-18Mar08/doc/dimension.html 2006-09-21 10:22:34.000000000 -0600 +++ lammps-19Mar08/doc/dimension.html 2008-03-18 15:09:15.000000000 -0600 @@ -32,6 +32,11 @@See the discussion in this section for additional instructions on how to run 2d simulations.
+IMPORTANT NOTE: Some models in LAMMPS treat particles as extended +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. +
Restrictions:
This command must be used before the simulation box is defined by a diff -Naur lammps-18Mar08/doc/dimension.txt lammps-19Mar08/doc/dimension.txt --- lammps-18Mar08/doc/dimension.txt 2006-09-21 10:22:34.000000000 -0600 +++ lammps-19Mar08/doc/dimension.txt 2008-03-18 15:09:15.000000000 -0600 @@ -29,6 +29,11 @@ See the discussion in "this section"_Section_howto.html for additional instructions on how to run 2d simulations. +IMPORTANT NOTE: Some models in LAMMPS treat particles as extended +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. + [Restrictions:] This command must be used before the simulation box is defined by a diff -Naur lammps-18Mar08/doc/fix.html lammps-19Mar08/doc/fix.html --- lammps-18Mar08/doc/fix.html 2008-03-11 10:37:01.000000000 -0600 +++ lammps-19Mar08/doc/fix.html 2008-03-17 18:23:39.000000000 -0600 @@ -130,10 +130,9 @@
- npt/asphere - NPT for aspherical particles
- nve - constant NVE time integration
- nve/asphere - NVT for aspherical particles -
- nve/dipole - NVE for point dipolar particles -
- nve/gran - NVE for granular particles
- nve/limit - NVE with limited step length
- nve/noforce - NVE without forces (v only) +
- nve/sphere - NVT for spherical particles
- nvt - constant NVT time integration via Nose/Hoover
- nvt/asphere - NVT for aspherical particles
- nvt/sllod - NVT for NEMD with SLLOD equations
diff -Naur lammps-18Mar08/doc/fix.txt lammps-19Mar08/doc/fix.txt
--- lammps-18Mar08/doc/fix.txt 2008-03-11 10:37:01.000000000 -0600
+++ lammps-19Mar08/doc/fix.txt 2008-03-17 18:23:39.000000000 -0600
@@ -129,10 +129,9 @@
"npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
"nve"_fix_nve.html - constant NVE time integration
"nve/asphere"_fix_nve_asphere.html - NVT for aspherical particles
-"nve/dipole"_fix_nve_dipole.html - NVE for point dipolar particles
-"nve/gran"_fix_nve_gran.html - NVE for granular particles
"nve/limit"_fix_nve_limit.html - NVE with limited step length
"nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
+"nve/sphere"_fix_nve_asphere.html - NVT for spherical particles
"nvt"_fix_nvt.html - constant NVT time integration via Nose/Hoover
"nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
"nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
diff -Naur lammps-18Mar08/doc/fix_langevin.html lammps-19Mar08/doc/fix_langevin.html
--- lammps-18Mar08/doc/fix_langevin.html 2008-03-17 14:49:34.000000000 -0600
+++ lammps-19Mar08/doc/fix_langevin.html 2008-03-18 14:18:54.000000000 -0600
@@ -119,7 +119,7 @@
the specified factor for atoms of that type. This can be useful when
different atom types have different sizes or masses. It can be used
multiple times to adjust damp for several atom types. Note that
-specifying a ratio of 2 increase the relaxation time which is
+specifying a ratio of 2 increases the relaxation time which is
equivalent to the the solvent's viscosity acting on particles with 1/2
the diameter. This is the opposite effect of scale factors used by
the fix viscous command, since the damp factor in
diff -Naur lammps-18Mar08/doc/fix_langevin.txt lammps-19Mar08/doc/fix_langevin.txt
--- lammps-18Mar08/doc/fix_langevin.txt 2008-03-17 14:49:34.000000000 -0600
+++ lammps-19Mar08/doc/fix_langevin.txt 2008-03-18 14:18:54.000000000 -0600
@@ -109,7 +109,7 @@
the specified factor for atoms of that type. This can be useful when
different atom types have different sizes or masses. It can be used
multiple times to adjust damp for several atom types. Note that
-specifying a ratio of 2 increase the relaxation time which is
+specifying a ratio of 2 increases the relaxation time which is
equivalent to the the solvent's viscosity acting on particles with 1/2
the diameter. This is the opposite effect of scale factors used by
the "fix viscous"_fix_viscous.html command, since the damp factor in
diff -Naur lammps-18Mar08/doc/fix_nve_asphere.html lammps-19Mar08/doc/fix_nve_asphere.html
--- lammps-18Mar08/doc/fix_nve_asphere.html 2007-10-10 16:28:11.000000000 -0600
+++ lammps-19Mar08/doc/fix_nve_asphere.html 2008-03-18 15:09:15.000000000 -0600
@@ -25,9 +25,12 @@
Description:
Perform constant NVE updates of position, velocity, orientation, and -angular velocity for aspherical or ellipsoidal particles in the group -each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. +angular velocity for aspherical particles in the group each timestep. +V is volume; E is energy. This creates a system trajectory consistent +with the microcanonical ensemble. +
+This fix differs from the fix nve command, which +assumes point particles and only updates their position and velocity.
Restart, fix_modify, output, run start/stop, minimize info:
@@ -45,9 +48,14 @@ LAMMPS was built with that package. See the Making LAMMPS section for more info. +This fix requires that particles be represented as extended ellipsoids +and not point particles. This means they will have an angular +momentum and a shape which is determined by the shape +command. +
Related commands:
-fix nve +
Default: none
diff -Naur lammps-18Mar08/doc/fix_nve_asphere.txt lammps-19Mar08/doc/fix_nve_asphere.txt --- lammps-18Mar08/doc/fix_nve_asphere.txt 2007-10-10 16:28:11.000000000 -0600 +++ lammps-19Mar08/doc/fix_nve_asphere.txt 2008-03-18 15:09:15.000000000 -0600 @@ -22,9 +22,12 @@ [Description:] Perform constant NVE updates of position, velocity, orientation, and -angular velocity for aspherical or ellipsoidal particles in the group -each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. +angular velocity for aspherical particles in the group each timestep. +V is volume; E is energy. This creates a system trajectory consistent +with the microcanonical ensemble. + +This fix differs from the "fix nve"_fix_nve.html command, which +assumes point particles and only updates their position and velocity. [Restart, fix_modify, output, run start/stop, minimize info:] @@ -42,8 +45,13 @@ LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. +This fix requires that particles be represented as extended ellipsoids +and not point particles. This means they will have an angular +momentum and a shape which is determined by the "shape"_shape.html +command. + [Related commands:] -"fix nve"_fix_nve.html +"fix nve"_fix_nve.html, "fix nve/sphere"_fix_nve_sphere.html [Default:] none diff -Naur lammps-18Mar08/doc/fix_nve_dipole.html lammps-19Mar08/doc/fix_nve_dipole.html --- lammps-18Mar08/doc/fix_nve_dipole.html 2007-10-10 16:28:11.000000000 -0600 +++ lammps-19Mar08/doc/fix_nve_dipole.html 1969-12-31 17:00:00.000000000 -0700 @@ -1,54 +0,0 @@ - -LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands - - - - - - - -
- -fix nve/dipole command -
-Syntax: -
-fix ID group-ID nve/dipole -
-- ID, group-ID are documented in fix command -
- nve/dipole = style name of this fix command -
Examples: -
-fix 1 all nve/dipole -
-Description: -
-Perform constant NVE updates of position, velocity, orientation, and -angular velocity for particles with point dipole moments in the group -each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. -
-Restart, fix_modify, output, run start/stop, minimize info: -
-No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global scalar or vector or per-atom -quantities are stored by this fix for access by various output -commands. No parameter of this fix can be -used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -
-Restrictions: -
-This fix is part of the "dipole" package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -
-Related commands: -
-fix nve -
-Default: none -
- diff -Naur lammps-18Mar08/doc/fix_nve_dipole.txt lammps-19Mar08/doc/fix_nve_dipole.txt --- lammps-18Mar08/doc/fix_nve_dipole.txt 2007-10-10 16:28:11.000000000 -0600 +++ lammps-19Mar08/doc/fix_nve_dipole.txt 1969-12-31 17:00:00.000000000 -0700 @@ -1,49 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -fix nve/dipole command :h3 - -[Syntax:] - -fix ID group-ID nve/dipole :pre - -ID, group-ID are documented in "fix"_fix.html command -nve/dipole = style name of this fix command :ul - -[Examples:] - -fix 1 all nve/dipole :pre - -[Description:] - -Perform constant NVE updates of position, velocity, orientation, and -angular velocity for particles with point dipole moments in the group -each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global scalar or vector or per-atom -quantities are stored by this fix for access by various "output -commands"_Section_howto.html#4_15. 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 "dipole" package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_3 section for more info. - -[Related commands:] - -"fix nve"_fix_nve.html - -[Default:] none diff -Naur lammps-18Mar08/doc/fix_nve_gran.html lammps-19Mar08/doc/fix_nve_gran.html --- lammps-18Mar08/doc/fix_nve_gran.html 2007-10-10 16:28:11.000000000 -0600 +++ lammps-19Mar08/doc/fix_nve_gran.html 1969-12-31 17:00:00.000000000 -0700 @@ -1,55 +0,0 @@ - -LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands - - - - - - - -
- -fix nve/gran command -
-Syntax: -
-fix ID group-ID nve/gran -
-- ID, group-ID are documented in fix command -
- nve/gran = style name of this fix command -
Examples: -
-fix 1 all nve/gran -
-Description: -
-Perform constant NVE updates each timestep on a group of atoms of atom -style granular. V is volume; E is energy. Granular atoms store -rotational information as well as position and velocity, so this -integrator updates translational and rotational degrees of freedom due -to forces and torques. -
-Restart, fix_modify, output, run start/stop, minimize info: -
-No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global scalar or vector or per-atom -quantities are stored by this fix for access by various output -commands. No parameter of this fix can be -used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -
-Restrictions: none -
-This fix is part of the "granular" package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -
-Related commands: -
- -Default: none -
- diff -Naur lammps-18Mar08/doc/fix_nve_gran.txt lammps-19Mar08/doc/fix_nve_gran.txt --- lammps-18Mar08/doc/fix_nve_gran.txt 2007-10-10 16:28:11.000000000 -0600 +++ lammps-19Mar08/doc/fix_nve_gran.txt 1969-12-31 17:00:00.000000000 -0700 @@ -1,50 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -fix nve/gran command :h3 - -[Syntax:] - -fix ID group-ID nve/gran :pre - -ID, group-ID are documented in "fix"_fix.html command -nve/gran = style name of this fix command :ul - -[Examples:] - -fix 1 all nve/gran :pre - -[Description:] - -Perform constant NVE updates each timestep on a group of atoms of atom -style granular. V is volume; E is energy. Granular atoms store -rotational information as well as position and velocity, so this -integrator updates translational and rotational degrees of freedom due -to forces and torques. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global scalar or vector or per-atom -quantities are stored by this fix for access by various "output -commands"_Section_howto.html#4_15. 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:] none - -This fix is part of the "granular" package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_3 section for more info. - -[Related commands:] - -"atom_style granular"_atom_style.html - -[Default:] none diff -Naur lammps-18Mar08/doc/fix_nve_sphere.html lammps-19Mar08/doc/fix_nve_sphere.html --- lammps-18Mar08/doc/fix_nve_sphere.html 1969-12-31 17:00:00.000000000 -0700 +++ lammps-19Mar08/doc/fix_nve_sphere.html 2008-03-18 14:56:15.000000000 -0600 @@ -0,0 +1,76 @@ + +LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands + + + + + + + +
+ +fix nve/sphere command +
+Syntax: +
+fix ID group-ID nve/sphere +
+- ID, group-ID are documented in fix command + +
- nve/sphere = style name of this fix command + +
- zero or more keyword/value pairs may be appended + +
- keyword = update
+
+
update value = dipole + dipole = update orientation of dipole moment during integration +
+ +
Examples: +
+fix 1 all nve/sphere +fix 1 all nve/sphere update dipole +
+Description: +
+Perform constant NVE updates of position, velocity, and angular +velocity for spherical particles in the group each timestep. V is +volume; E is energy. This creates a system trajectory consistent with +the microcanonical ensemble. +
+This fix differs from the fix nve command, which +assumes point particles and only updates their position and velocity. +
+If the update keyword is used with the dipole value, then the +orientation of the dipole moment of each particle is also updated +during the time integration. This option should be used for models +where a dipole moment is assigned to particles via the +dipole command. +
+Restart, fix_modify, output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various output +commands. No parameter of this fix can be +used with the start/stop keywords of the run command. +This fix is not invoked during energy minimization. +
+Restrictions: +
+This fix requires that particles be represented as extended spheres +and not point particles. This means they will have an angular +velocity and a diameter which is determined either by the +shape command or by each particle being assigned an +individual radius, e.g. for atom_style granular. +
+Related commands: +
+ +Default: none +
+ diff -Naur lammps-18Mar08/doc/fix_nve_sphere.txt lammps-19Mar08/doc/fix_nve_sphere.txt --- lammps-18Mar08/doc/fix_nve_sphere.txt 1969-12-31 17:00:00.000000000 -0700 +++ lammps-19Mar08/doc/fix_nve_sphere.txt 2008-03-18 14:56:15.000000000 -0600 @@ -0,0 +1,66 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix nve/sphere command :h3 + +[Syntax:] + +fix ID group-ID nve/sphere :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +nve/sphere = style name of this fix command :l +zero or more keyword/value pairs may be appended :l +keyword = {update} :l + {update} value = {dipole} + dipole = update orientation of dipole moment during integration :pre +:ule + +[Examples:] + +fix 1 all nve/sphere +fix 1 all nve/sphere update dipole :pre + +[Description:] + +Perform constant NVE updates of position, velocity, and angular +velocity for spherical particles in the group each timestep. V is +volume; E is energy. This creates a system trajectory consistent with +the microcanonical ensemble. + +This fix differs from the "fix nve"_fix_nve.html command, which +assumes point particles and only updates their position and velocity. + +If the {update} keyword is used with the {dipole} value, then the +orientation of the dipole moment of each particle is also updated +during the time integration. This option should be used for models +where a dipole moment is assigned to particles via the +"dipole"_dipole.html command. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. 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 requires that particles be represented as extended spheres +and not point particles. This means they will have an angular +velocity and a diameter which is determined either by the +"shape"_shape.html command or by each particle being assigned an +individual radius, e.g. for "atom_style granular"_atom_style.html. + +[Related commands:] + +"fix nve"_fix_nve.html, "fix nve/asphere"_fix_nve_asphere.html + +[Default:] none diff -Naur lammps-18Mar08/doc/fix_poems.html lammps-19Mar08/doc/fix_poems.html --- lammps-18Mar08/doc/fix_poems.html 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/fix_poems.html 2008-03-18 14:18:54.000000000 -0600 @@ -59,7 +59,7 @@ atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).Each body must have a non-degenerate inertia tensor, which means if -must contain at least 3 non-colinear atoms. Which atoms are in which +must contain at least 3 non-collinear atoms. Which atoms are in which bodies can be defined via several options.
For option group, each of the listed groups is treated as a rigid diff -Naur lammps-18Mar08/doc/fix_poems.txt lammps-19Mar08/doc/fix_poems.txt --- lammps-18Mar08/doc/fix_poems.txt 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/fix_poems.txt 2008-03-18 14:18:54.000000000 -0600 @@ -52,7 +52,7 @@ atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin). Each body must have a non-degenerate inertia tensor, which means if -must contain at least 3 non-colinear atoms. Which atoms are in which +must contain at least 3 non-collinear atoms. Which atoms are in which bodies can be defined via several options. For option {group}, each of the listed groups is treated as a rigid diff -Naur lammps-18Mar08/doc/jump.html lammps-19Mar08/doc/jump.html --- lammps-18Mar08/doc/jump.html 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/jump.html 2008-03-18 15:09:15.000000000 -0600 @@ -52,8 +52,8 @@
If the jump file argument is a variable, the jump command can be used to cause different processor partitions to run different input scripts. In this example, LAMMPS is run on 40 processors, with 4 -partions of 10 procs each. An in.file containing the example variable -and jump command will cause each partition to run a different +partitions of 10 procs each. An in.file containing the example +variable and jump command will cause each partition to run a different simulation.
mpirun -np 40 lmp_ibm -partition 4x10 -in in.file diff -Naur lammps-18Mar08/doc/jump.txt lammps-19Mar08/doc/jump.txt --- lammps-18Mar08/doc/jump.txt 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/jump.txt 2008-03-18 15:09:15.000000000 -0600 @@ -49,8 +49,8 @@ If the jump {file} argument is a variable, the jump command can be used to cause different processor partitions to run different input scripts. In this example, LAMMPS is run on 40 processors, with 4 -partions of 10 procs each. An in.file containing the example variable -and jump command will cause each partition to run a different +partitions of 10 procs each. An in.file containing the example +variable and jump command will cause each partition to run a different simulation. mpirun -np 40 lmp_ibm -partition 4x10 -in in.file :pre diff -Naur lammps-18Mar08/doc/mass.html lammps-19Mar08/doc/mass.html --- lammps-18Mar08/doc/mass.html 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/mass.html 2008-03-18 14:18:54.000000000 -0600 @@ -36,7 +36,7 @@ the masses of atom types in the EAM potential file.I can be specified in one of two ways. An explicit numeric value can -be used, as in the 1st example above. Or a wild-card asterik can be +be used, as in the 1st example above. Or a wild-card asterisk can be used to set the mass for multiple atom types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading @@ -46,7 +46,7 @@
A line in a data file that specifies mass uses the same format as the arguments of the mass command in an input script, except that no -wild-card asterik can be used. For example, under the "Masses" +wild-card asterisk can be used. For example, under the "Masses" section of a data file, the line that corresponds to the 1st example above would be listed as
diff -Naur lammps-18Mar08/doc/mass.txt lammps-19Mar08/doc/mass.txt --- lammps-18Mar08/doc/mass.txt 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/mass.txt 2008-03-18 14:18:54.000000000 -0600 @@ -33,7 +33,7 @@ the masses of atom types in the EAM potential file. I can be specified in one of two ways. An explicit numeric value can -be used, as in the 1st example above. Or a wild-card asterik can be +be used, as in the 1st example above. Or a wild-card asterisk can be used to set the mass for multiple atom types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading @@ -43,7 +43,7 @@ A line in a data file that specifies mass uses the same format as the arguments of the mass command in an input script, except that no -wild-card asterik can be used. For example, under the "Masses" +wild-card asterisk can be used. For example, under the "Masses" section of a data file, the line that corresponds to the 1st example above would be listed as diff -Naur lammps-18Mar08/doc/pair_airebo.html lammps-19Mar08/doc/pair_airebo.html --- lammps-18Mar08/doc/pair_airebo.html 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/pair_airebo.html 2008-03-18 14:18:54.000000000 -0600 @@ -80,9 +80,9 @@- filename
- N element names = mapping of AIREBO elements to atom types
As an example, if your LAMMPS simulation has 4 atoms types and you -want the 1st 3 to be C, and the 4th to be H, you would use the -following pair_coeff command: +
As an example, if your LAMMPS simulation has 4 atom types and you want +the 1st 3 to be C, and the 4th to be H, you would use the following +pair_coeff command:
pair_coeff * * CH.airebo C C C H
diff -Naur lammps-18Mar08/doc/pair_airebo.txt lammps-19Mar08/doc/pair_airebo.txt --- lammps-18Mar08/doc/pair_airebo.txt 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/pair_airebo.txt 2008-03-18 14:18:54.000000000 -0600 @@ -77,9 +77,9 @@ filename N element names = mapping of AIREBO elements to atom types :ul -As an example, if your LAMMPS simulation has 4 atoms types and you -want the 1st 3 to be C, and the 4th to be H, you would use the -following pair_coeff command: +As an example, if your LAMMPS simulation has 4 atom types and you want +the 1st 3 to be C, and the 4th to be H, you would use the following +pair_coeff command: pair_coeff * * CH.airebo C C C H :pre diff -Naur lammps-18Mar08/doc/pair_gran.html lammps-19Mar08/doc/pair_gran.html --- lammps-18Mar08/doc/pair_gran.html 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/pair_gran.html 2008-03-18 14:18:54.000000000 -0600 @@ -44,7 +44,7 @@
The 1st term is a normal force and the 2nd term is a tangential force. -The other quantites are as follows: +The other quantities are as follows:
- delta = d - r
- f(x) = 1 for Hookean contacts used in pair styles history and no_history
diff -Naur lammps-18Mar08/doc/pair_gran.txt lammps-19Mar08/doc/pair_gran.txt
--- lammps-18Mar08/doc/pair_gran.txt 2008-02-29 18:13:20.000000000 -0700
+++ lammps-19Mar08/doc/pair_gran.txt 2008-03-18 14:18:54.000000000 -0600
@@ -34,7 +34,7 @@
:c,image(Eqs/pair_granular.jpg)
The 1st term is a normal force and the 2nd term is a tangential force.
-The other quantites are as follows:
+The other quantities are as follows:
delta = d - r
f(x) = 1 for Hookean contacts used in pair styles {history} and {no_history}
diff -Naur lammps-18Mar08/doc/pair_soft.html lammps-19Mar08/doc/pair_soft.html
--- lammps-18Mar08/doc/pair_soft.html 2008-03-10 11:48:22.000000000 -0600
+++ lammps-19Mar08/doc/pair_soft.html 2008-03-18 14:18:54.000000000 -0600
@@ -65,7 +65,7 @@
the pair_modify mix value. The default mix value is geometric. See
the "pair_modify" command for details.
-
This pair styles does not support the pair_modify +
This pair style does not support the pair_modify shift option, since the pair interaction goes to 0.0 at the cutoff.
The pair_modify table and tail options are not diff -Naur lammps-18Mar08/doc/pair_soft.txt lammps-19Mar08/doc/pair_soft.txt --- lammps-18Mar08/doc/pair_soft.txt 2008-03-10 11:48:22.000000000 -0600 +++ lammps-19Mar08/doc/pair_soft.txt 2008-03-18 14:18:54.000000000 -0600 @@ -62,7 +62,7 @@ the pair_modify mix value. The default mix value is {geometric}. See the "pair_modify" command for details. -This pair styles does not support the "pair_modify"_pair_modify.html +This pair style does not support the "pair_modify"_pair_modify.html shift option, since the pair interaction goes to 0.0 at the cutoff. The "pair_modify"_pair_modify.html table and tail options are not diff -Naur lammps-18Mar08/doc/pair_sw.html lammps-19Mar08/doc/pair_sw.html --- lammps-18Mar08/doc/pair_sw.html 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/pair_sw.html 2008-03-18 14:18:54.000000000 -0600 @@ -85,19 +85,17 @@ three-body interactions, but is defined for pairs of atoms. The non-annotated parameters are unitless.
-LAMMPS introduces an additional performance-optimization parameter -tol that is used for -both two-body and three-body interactions. -In the Stillinger-Weber potential, the -interaction energies become negligibly small at atomic separations -substantially less than the theoretical cutoff -distances. LAMMPS therefore defines a virtual cutoff distance -based on a user defined tolerance tol. -The use of the virtual cutoff distance in constructing atom neighbor -lists can significantly reduce the neighbor list sizes and therefore the -computational cost. LAMMPS provide a tol value for each of the three-body -entries so that they can be separately controlled. If tol = 0.0, then -the standard Stillinger-Weber cutoff is used. +
LAMMPS introduces an additional performance-optimization parameter tol +that is used for both two-body and three-body interactions. In the +Stillinger-Weber potential, the interaction energies become negligibly +small at atomic separations substantially less than the theoretical +cutoff distances. LAMMPS therefore defines a virtual cutoff distance +based on a user defined tolerance tol. The use of the virtual cutoff +distance in constructing atom neighbor lists can significantly reduce +the neighbor list sizes and therefore the computational cost. LAMMPS +provides a tol value for each of the three-body entries so that they +can be separately controlled. If tol = 0.0, then the standard +Stillinger-Weber cutoff is used.
The Stillinger-Weber potential file must contain entries for all the elements listed in the pair_coeff command. It can also contain diff -Naur lammps-18Mar08/doc/pair_sw.txt lammps-19Mar08/doc/pair_sw.txt --- lammps-18Mar08/doc/pair_sw.txt 2008-02-29 18:13:20.000000000 -0700 +++ lammps-19Mar08/doc/pair_sw.txt 2008-03-18 14:18:54.000000000 -0600 @@ -82,19 +82,17 @@ three-body interactions, but is defined for pairs of atoms. The non-annotated parameters are unitless. -LAMMPS introduces an additional performance-optimization parameter -tol that is used for -both two-body and three-body interactions. -In the Stillinger-Weber potential, the -interaction energies become negligibly small at atomic separations -substantially less than the theoretical cutoff -distances. LAMMPS therefore defines a virtual cutoff distance -based on a user defined tolerance tol. -The use of the virtual cutoff distance in constructing atom neighbor -lists can significantly reduce the neighbor list sizes and therefore the -computational cost. LAMMPS provide a tol value for each of the three-body -entries so that they can be separately controlled. If tol = 0.0, then -the standard Stillinger-Weber cutoff is used. +LAMMPS introduces an additional performance-optimization parameter tol +that is used for both two-body and three-body interactions. In the +Stillinger-Weber potential, the interaction energies become negligibly +small at atomic separations substantially less than the theoretical +cutoff distances. LAMMPS therefore defines a virtual cutoff distance +based on a user defined tolerance tol. The use of the virtual cutoff +distance in constructing atom neighbor lists can significantly reduce +the neighbor list sizes and therefore the computational cost. LAMMPS +provides a {tol} value for each of the three-body entries so that they +can be separately controlled. If tol = 0.0, then the standard +Stillinger-Weber cutoff is used. The Stillinger-Weber potential file must contain entries for all the elements listed in the pair_coeff command. It can also contain diff -Naur lammps-18Mar08/doc/thermo_modify.html lammps-19Mar08/doc/thermo_modify.html --- lammps-18Mar08/doc/thermo_modify.html 2008-03-11 10:37:01.000000000 -0600 +++ lammps-19Mar08/doc/thermo_modify.html 2008-03-17 17:43:56.000000000 -0600 @@ -17,9 +17,8 @@
- one or more keyword/value pairs may be listed -
- keyword = lost or norm or flush or line or format or temp or press or drot or grot
-
-
lost value = error or warn or ignore +keyword = lost or norm or flush or line or format or temp or press:l + lost value = error or warn or ignore norm value = yes or no flush value = yes or no line value = one or multi @@ -28,9 +27,6 @@ string = C-style format string temp value = compute ID that calculates a temperature press value = compute ID that calculates a pressure - drot value = compute ID that calculates rotational energy for dipolar atoms - grot value = compute ID that calculates rotational energy for granular atoms -
Examples: @@ -113,24 +109,6 @@ pressure compute specified by the press keyword will be unaffected by the temp setting.
-The drot keyword is used to determine how rotational energy is -calculated for dipolar atoms, which is used by the thermo_style -keyword drot. The specified compute ID must have been previously -defined by the user via the compute command. As -described in the thermo_style command, thermo -output has a default compute for this calculation with ID = -thermo_rotate_dipole. This option allows the user to override the -default. -
-The grot keyword is used to determine how rotational energy is -calculated for granular atoms, which is used by the thermo_style -keyword grot. The specified compute ID must have been previously -defined by the user via the compute command. As -described in the thermo_style command, thermo -output has a default compute for this calculation with ID = -thermo_rotate_gran. This option allows the user to override the -default. -
Restrictions: none
Related commands: @@ -141,11 +119,11 @@
The option defaults are lost = error, norm = yes for unit style of lj, norm = no for unit style of real and metal, flush = no, -temp/press/drot/grot = compute IDs defined by thermo_style. +temp/press = compute IDs defined by thermo_style.
The defaults for the line and format options depend on the thermo -style. For styles "one", "granular", and "custom" the line and format -defaults are "one", "%8d", and "%12.8g". For style "multi", the line -and format defaults are "multi", "%8d", and "%14.4f". +style. For styles "one" and and "custom" the line and format defaults +are "one", "%8d", and "%12.8g". For style "multi", the line and +format defaults are "multi", "%8d", and "%14.4f".