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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1611 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2008-03-18 00:23:39 +00:00
parent 8f133431b8
commit 12cba76c74
16 changed files with 114 additions and 416 deletions
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17
doc/Section_commands.html
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@ -320,11 +320,10 @@ of each style or click on the style itself for a full description:
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_coord_original.html">coord/original</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_dipole.html">nve/dipole</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wiggle.html">wiggle</A>
<TR ALIGN="center"><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
</TD></TR></TABLE></DIV>
<HR>
@ -334,10 +333,10 @@ descriptions of each style or click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A>
<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
</TD></TR></TABLE></DIV>
<P>These are compute styles contributed by users, which can be used if

9
doc/Section_commands.txt
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@ -402,10 +402,9 @@ of each style or click on the style itself for a full description:
"npt/asphere"_fix_npt_asphere.html,
"nve"_fix_nve.html,
"nve/asphere"_fix_nve_asphere.html,
"nve/dipole"_fix_nve_dipole.html,
"nve/gran"_fix_nve_gran.html,
"nve/limit"_fix_nve_limit.html,
"nve/noforce"_fix_nve_noforce.html,
"nve/sphere"_fix_nve_sphere.html,
"nvt"_fix_nvt.html,
"nvt/asphere"_fix_nvt_asphere.html,
"nvt/sllod"_fix_nvt_sllod.html,
@ -442,14 +441,13 @@ description:
"centro/atom"_compute_centro_atom.html,
"coord/atom"_compute_coord_atom.html,
"displace/atom"_compute_displace_atom.html,
"erotate/sphere"_compute_erotate_sphere.html,
"group/group"_compute_group_group.html,
"ke/atom"_compute_ke_atom.html,
"pe"_compute_pe.html,
"pe/atom"_compute_pe_atom.html,
"pressure"_compute_pressure.html,
"reduce"_compute_reduce.html,
"rotate/dipole"_compute_rotate_dipole.html,
"rotate/gran"_compute_rotate_gran.html,
"stress/atom"_compute_stress_atom.html,
"temp"_compute_temp.html,
"temp/asphere"_compute_temp_asphere.html,
@ -458,7 +456,8 @@ description:
"temp/dipole"_compute_temp_dipole.html,
"temp/partial"_compute_temp_partial.html,
"temp/ramp"_compute_temp_ramp.html,
"temp/region"_compute_temp_region.html :tb(c=6,ea=c)
"temp/region"_compute_temp_region.html,
"temp/sphere"_compute_temp_sphere.html :tb(c=6,ea=c)
These are compute styles contributed by users, which can be used if
"LAMMPS is built with the appropriate package"_Section_start.html#2_3.

6
doc/compute.html
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@ -112,14 +112,13 @@ available in LAMMPS:
<UL><LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
<LI><A HREF = "compute_coord_atom.html">coord/atom</A> - coordination number for each atom
<LI><A HREF = "compute_displace_atom.html">displace/atom</A> - displacement of each atom
<LI><A HREF = "compute_erotate_sphere.html">erotate/sphere</A> - rotational energy of spherical particles
<LI><A HREF = "compute_group_group.html">group/group</A> - energy/force between two groups of atoms
<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
<LI><A HREF = "compute_pe.html">pe</A> - potential energy
<LI><A HREF = "compute_pe_atom.html">pe/atom</A> - potential energy for each atom
<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor
<LI><A HREF = "compute_reduce.html">reduce</A> - combine per-atom quantities into a single global value
<LI><A HREF = "compute_rotate_dipole.html">rotate/dipole</A> - rotational energy of dipolar atoms
<LI><A HREF = "compute_rotate_gran.html">rotate/gran</A> - rotational energy of granular atoms
<LI><A HREF = "compute_stress_atom.html">stress/atom</A> - stress tensor for each atom
<LI><A HREF = "compute_temp.html">temp</A> - temperature of group of atoms
<LI><A HREF = "compute_temp_asphere.html">temp/asphere</A> - temperature of aspherical particles
@ -128,7 +127,8 @@ available in LAMMPS:
<LI><A HREF = "compute_temp_dipole.html">temp/dipole</A> - temperature of point dipolar particles
<LI><A HREF = "compute_temp_partial.html">temp/partial</A> - temperature excluding one or more dimensions of velocity
<LI><A HREF = "compute_temp_ramp.html">temp/ramp</A> - temperature excluding ramped velocity component
<LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
<LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
<LI><A HREF = "compute_temp_sphere.html">temp/sphere</A> - temperature of spherical particles
</UL>
<P>There are also additional compute styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to

6
doc/compute.txt
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@ -109,14 +109,13 @@ available in LAMMPS:
"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 @@ available in LAMMPS:
"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

45
doc/compute_rotate_dipole.html
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@ -1,45 +0,0 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute rotate/dipole command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID rotate/dipole
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>rotate/dipole = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all rotate/dipole
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the total rotational energy of a
group of atoms with point dipole moments.
</P>
<P>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.
</P>
<P><B>Output info:</B>
</P>
<P>The scalar value calculated by this compute is "extensive", meaning it
it scales with the number of atoms in the simulation.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>

40
doc/compute_rotate_dipole.txt
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@ -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

45
doc/compute_rotate_gran.html
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@ -1,45 +0,0 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute rotate/gran command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID rotate/gran
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>rotate/gran = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all rotate/gran
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the total rotational energy of a
group of granular atoms.
</P>
<P>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.
</P>
<P><B>Output info:</B>
</P>
<P>The scalar value calculated by this compute is "extensive", meaning it
it scales with the number of atoms in the simulation.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>

40
doc/compute_rotate_gran.txt
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@ -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

54
doc/compute_temp_asphere.html
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@ -26,12 +26,49 @@ compute myTemp mobile temp/asphere
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
aspherical or ellipsoidal particles. The computation is similar to
<A HREF = "compute_temp.html">compute_temp</A>, 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.
</P>
<P>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 <A HREF = "shape.html">shape</A> command. Uniaxial means two of its three shape
parameters are equal. Biaxial means they all 3 are different.
</P>
<P>For 2d aspherical particles ...
</P>
<P>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.
</P>
<P>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 <A HREF = "pair_gayberne.html">GayBerne
pair potential</A> does not impart torque to spherical
particles, so they do not rotate.
</P>
<P>IMPORTANT NOTE: For a <A HREF = "dimension.html">2-dimensional system</A>, particles
are treated as ellipsoids, not ellipses.
</P>
<P>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.
</P>
<P>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <I>dynamic</I> option of the
<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
</P>
<P>This compute subtracts out translational degrees-of-freedom due to
fixes that constrain molecular motion, such as <A HREF = "fix_shake.html">fix
shake</A> and <A HREF = "fix_rigid.html">fix rigid</A>. 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 <I>extra</I> option of the
<A HREF = "compute_modify.html">compute_modify</A> command.
</P>
<P><B>Output info:</B>
</P>
@ -42,7 +79,10 @@ the simulation.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "asphere" package.
<P>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
<A HREF = "shape.html">shape</A> command.
</P>
<P><B>Related commands:</B>
</P>

54
doc/compute_temp_asphere.txt
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@ -23,12 +23,49 @@ compute myTemp mobile temp/asphere :pre
[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" 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 they all 3 are different.
For 2d aspherical particles ...
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: 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.
IMPORTANT NOTE: For a "2-dimensional system"_dimension.html, particles
are treated as ellipsoids, not ellipses.
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 +76,10 @@ the simulation.
[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:]

3
doc/fix.html
View File

@ -130,10 +130,9 @@ list of fix styles available in LAMMPS:
<LI><A HREF = "fix_npt_asphere.html">npt/asphere</A> - NPT for aspherical particles
<LI><A HREF = "fix_nve.html">nve</A> - constant NVE time integration
<LI><A HREF = "fix_nve_asphere.html">nve/asphere</A> - NVT for aspherical particles
<LI><A HREF = "fix_nve_dipole.html">nve/dipole</A> - NVE for point dipolar particles
<LI><A HREF = "fix_nve_gran.html">nve/gran</A> - NVE for granular particles
<LI><A HREF = "fix_nve_limit.html">nve/limit</A> - NVE with limited step length
<LI><A HREF = "fix_nve_noforce.html">nve/noforce</A> - NVE without forces (v only)
<LI><A HREF = "fix_nve_asphere.html">nve/sphere</A> - NVT for spherical particles
<LI><A HREF = "fix_nvt.html">nvt</A> - constant NVT time integration via Nose/Hoover
<LI><A HREF = "fix_nvt_asphere.html">nvt/asphere</A> - NVT for aspherical particles
<LI><A HREF = "fix_nvt_sllod.html">nvt/sllod</A> - NVT for NEMD with SLLOD equations

3
doc/fix.txt
View File

@ -129,10 +129,9 @@ list of fix styles available in LAMMPS:
"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

54
doc/fix_nve_dipole.html
View File

@ -1,54 +0,0 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix nve/dipole command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID nve/dipole
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>nve/dipole = style name of this fix command
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nve/dipole
</PRE>
<P><B>Description:</B>
</P>
<P>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.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various <A HREF = "Section_howto.html#4_15">output
commands</A>. No parameter of this fix can be
used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the "dipole" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve.html">fix nve</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

49
doc/fix_nve_dipole.txt
View File

@ -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

55
doc/fix_nve_gran.html
View File

@ -1,55 +0,0 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix nve/gran command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID nve/gran
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>nve/gran = style name of this fix command
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nve/gran
</PRE>
<P><B>Description:</B>
</P>
<P>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.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various <A HREF = "Section_howto.html#4_15">output
commands</A>. No parameter of this fix can be
used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P>This fix is part of the "granular" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "atom_style.html">atom_style granular</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

50
doc/fix_nve_gran.txt
View File

@ -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