git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10723 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_commands.html

@@ -427,13 +427,14 @@ each style or click on the style itself for a full description:
 <DIV ALIGN=center><TABLE  BORDER=1 >
 <TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_atom_molecule.html">atom/molecule</A></TD><TD ><A HREF = "compute_body_local.html">body/local</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cluster_atom.html">cluster/atom</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_com_molecule.html">com/molecule</A></TD><TD ><A HREF = "compute_contact_atom.html">contact/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_erotate_sphere_atom.html">erotate/sphere/atom</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_rigid.html">erotate/rigid</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_erotate_sphere_atom.html">erotate/sphere/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_molecule.html">gyration/molecule</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_inertia_molecule.html">inertia/molecule</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_molecule.html">gyration/molecule</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_molecule.html">msd/molecule</A></TD><TD ><A HREF = "compute_msd_nongauss.html">msd/nongauss</A></TD><TD ><A HREF = "compute_pair.html">pair</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_inertia_molecule.html">inertia/molecule</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_ke_rigid.html">ke/rigid</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_molecule.html">msd/molecule</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD><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_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_msd_nongauss.html">msd/nongauss</A></TD><TD ><A HREF = "compute_pair.html">pair</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD><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></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_property_molecule.html">property/molecule</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_molecule.html">property/molecule</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</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_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_slice.html">slice</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><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></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></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A></TD><TD ><A HREF = "compute_voronoi_atom.html">voronoi/atom</A> 
+<TR ALIGN="center"><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_voronoi_atom.html">voronoi/atom</A> 
 </TD></TR></TABLE></DIV>
 
 <P>These are compute styles contributed by users, which can be used if

doc/Section_commands.txt

@@ -625,6 +625,7 @@ each style or click on the style itself for a full description:
 "dihedral/local"_compute_dihedral_local.html,
 "displace/atom"_compute_displace_atom.html,
 "erotate/asphere"_compute_erotate_asphere.html,
+"erotate/rigid"_compute_erotate_rigid.html,
 "erotate/sphere"_compute_erotate_sphere.html,
 "erotate/sphere/atom"_compute_erotate_sphere_atom.html,
 "event/displace"_compute_event_displace.html,
@@ -636,6 +637,7 @@ each style or click on the style itself for a full description:
 "inertia/molecule"_compute_inertia_molecule.html,
 "ke"_compute_ke.html,
 "ke/atom"_compute_ke_atom.html,
+"ke/rigid"_compute_ke_rigid.html,
 "msd"_compute_msd.html,
 "msd/molecule"_compute_msd_molecule.html,
 "msd/nongauss"_compute_msd_nongauss.html,

doc/compute.html

@@ -182,6 +182,7 @@ available in LAMMPS:
 <LI><A HREF = "compute_dihedral_local.html">dihedral/local</A> - angle of each dihedral
 <LI><A HREF = "compute_displace_atom.html">displace/atom</A> - displacement of each atom
 <LI><A HREF = "compute_erotate_asphere.html">erotate/asphere</A> - rotational energy of aspherical particles
+<LI><A HREF = "compute_erotate_rigid.html">erotate/rigid</A> - rotational energy of rigid bodies
 <LI><A HREF = "compute_erotate_sphere.html">erotate/sphere</A> - rotational energy of spherical particles
 <LI><A HREF = "compute_erotate_sphere.html">erotate/sphere/atom</A> - rotational energy for each spherical particle
 <LI><A HREF = "compute_event_displace.html">event/displace</A> - detect event on atom displacement
@@ -193,6 +194,7 @@ available in LAMMPS:
 <LI><A HREF = "compute_inertia_molecule.html">inertia/molecule</A> - inertia tensor for each molecule
 <LI><A HREF = "compute_ke.html">ke</A> - translational kinetic energy
 <LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
+<LI><A HREF = "compute_ke_rigid.html">ke/rigid</A> - translational kinetic energy of rigid bodies
 <LI><A HREF = "compute_msd.html">msd</A> - mean-squared displacement of group of atoms
 <LI><A HREF = "compute_msd_molecule.html">msd/molecule</A> - mean-squared displacement for each molecule
 <LI><A HREF = "compute_pair.html">pair</A> - values computed by a pair style

doc/compute.txt

@@ -177,6 +177,7 @@ available in LAMMPS:
 "dihedral/local"_compute_dihedral_local.html - angle of each dihedral
 "displace/atom"_compute_displace_atom.html - displacement of each atom
 "erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles
+"erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies
 "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles
 "erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle
 "event/displace"_compute_event_displace.html - detect event on atom displacement
@@ -188,6 +189,7 @@ available in LAMMPS:
 "inertia/molecule"_compute_inertia_molecule.html - inertia tensor for each molecule
 "ke"_compute_ke.html - translational kinetic energy
 "ke/atom"_compute_ke_atom.html - kinetic energy for each atom
+"ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies
 "msd"_compute_msd.html - mean-squared displacement of group of atoms
 "msd/molecule"_compute_msd_molecule.html - mean-squared displacement for each molecule
 "pair"_compute_pair.html - values computed by a pair style

doc/compute_erotate_rigid.html

@@ -0,0 +1,62 @@
+<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 erotate/rigid command 
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID erotate/rigid fix-ID 
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>erotate/rigid = style name of this compute command
+<LI>fix-ID = ID of rigid body fix 
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all erotate/rigid myRigid 
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the rotational kinetic energy of
+a collection of rigid bodies, as defined by one of the <A HREF = "fix_rigid.html">fix
+rigid</A> command variants.
+</P>
+<P>The rotational energy of each rigid body is computed as 1/2 I Wbody^2,
+where I is the inertia tensor for the rigid body, and Wbody is its
+angular velocity vector.  Both I and Wbody are in the frame of
+reference of the rigid body, i.e. I is diagonalized.
+</P>
+<P>The <I>fix-ID</I> should be the ID of one of the <A HREF = "fix_rigid.html">fix rigid</A>
+commands which defines the rigid bodies.  The group specified in the
+compute command is ignored.  The rotational energy of all the rigid
+bodies defined by the fix rigid command in included in the
+calculation.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the summed rotational energy
+of all the rigid bodies).  This value can be used by any command that
+uses a global scalar value from a compute as input.  See
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
+LAMMPS output options.
+</P>
+<P>The scalar value calculated by this compute is "extensive".  The
+scalar value will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_erotate_ke_rigid.html">compute ke/rigid</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>

doc/compute_erotate_rigid.txt

@@ -0,0 +1,57 @@
+"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/rigid command :h3
+
+[Syntax:]
+
+compute ID group-ID erotate/rigid fix-ID :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+erotate/rigid = style name of this compute command
+fix-ID = ID of rigid body fix :ul
+
+[Examples:]
+
+compute 1 all erotate/rigid myRigid :pre
+
+[Description:]
+
+Define a computation that calculates the rotational kinetic energy of
+a collection of rigid bodies, as defined by one of the "fix
+rigid"_fix_rigid.html command variants.
+
+The rotational energy of each rigid body is computed as 1/2 I Wbody^2,
+where I is the inertia tensor for the rigid body, and Wbody is its
+angular velocity vector.  Both I and Wbody are in the frame of
+reference of the rigid body, i.e. I is diagonalized.
+
+The {fix-ID} should be the ID of one of the "fix rigid"_fix_rigid.html
+commands which defines the rigid bodies.  The group specified in the
+compute command is ignored.  The rotational energy of all the rigid
+bodies defined by the fix rigid command in included in the
+calculation.
+
+[Output info:]
+
+This compute calculates a global scalar (the summed rotational energy
+of all the rigid bodies).  This value can be used by any command that
+uses a global scalar value from a compute as input.  See
+"Section_howto 15"_Section_howto.html#howto_15 for an overview of
+LAMMPS output options.
+
+The scalar value calculated by this compute is "extensive".  The
+scalar value will be in energy "units"_units.html.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"compute ke/rigid"_compute_erotate_ke_rigid.html
+
+[Default:] none

doc/compute_ke_rigid.html

@@ -0,0 +1,61 @@
+<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 ke/rigid command 
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID ke/rigid fix-ID 
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>ke = style name of this compute command
+<LI>fix-ID = ID of rigid body fix 
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all ke/rigid myRigid 
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the translational kinetic energy
+of a collection of rigid bodies, as defined by one of the <A HREF = "fix_rigid.html">fix
+rigid</A> command variants.
+</P>
+<P>The kinetic energy of each rigid body is computed as 1/2 M Vcm^2,
+where M is the total mass of the rigid body, and Vcm is its
+center-of-mass velocity.
+</P>
+<P>The <I>fix-ID</I> should be the ID of one of the <A HREF = "fix_rigid.html">fix rigid</A>
+commands which defines the rigid bodies.  The group specified in the
+compute command is ignored.  The kinetic energy of all the rigid
+bodies defined by the fix rigid command in included in the
+calculation.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the summed KE of all the
+rigid bodies).  This value can be used by any command that uses a
+global scalar value from a compute as input.  See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "extensive".  The
+scalar value will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_erotate_rigid.html">compute erotate/rigid</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>

doc/compute_ke_rigid.txt

@@ -0,0 +1,56 @@
+"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 ke/rigid command :h3
+
+[Syntax:]
+
+compute ID group-ID ke/rigid fix-ID :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+ke = style name of this compute command
+fix-ID = ID of rigid body fix :ul
+
+[Examples:]
+
+compute 1 all ke/rigid myRigid :pre
+
+[Description:]
+
+Define a computation that calculates the translational kinetic energy
+of a collection of rigid bodies, as defined by one of the "fix
+rigid"_fix_rigid.html command variants.
+
+The kinetic energy of each rigid body is computed as 1/2 M Vcm^2,
+where M is the total mass of the rigid body, and Vcm is its
+center-of-mass velocity.
+
+The {fix-ID} should be the ID of one of the "fix rigid"_fix_rigid.html
+commands which defines the rigid bodies.  The group specified in the
+compute command is ignored.  The kinetic energy of all the rigid
+bodies defined by the fix rigid command in included in the
+calculation.
+
+[Output info:]
+
+This compute calculates a global scalar (the summed KE of all the
+rigid bodies).  This value can be used by any command that uses a
+global scalar value from a compute as input.  See "Section_howto
+15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "extensive".  The
+scalar value will be in energy "units"_units.html.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"compute erotate/rigid"_compute_erotate_rigid.html
+
+[Default:] none

doc/fix.html

@@ -217,6 +217,7 @@ list of fix styles available in LAMMPS:
 <LI><A HREF = "fix_pour.html">pour</A> - pour new atoms into a granular simulation domain
 <LI><A HREF = "fix_press_berendsen.html">press/berendsen</A> - pressure control by      Berendsen barostat
 <LI><A HREF = "fix_print.html">print</A> - print text and variables during a simulation
+<LI><A HREF = "fix_property_atom.html">property/atom</A> - add customized per-atom values
 <LI><A HREF = "fix_reax_bonds.html">reax/bonds</A> - write out ReaxFF bond information <A HREF = "fix_recenter.html">recenter</A> - constrain the center-of-mass position   of a group of atoms
 <LI><A HREF = "fix_restrain.html">restrain</A> - constrain a bond, angle, dihedral
 <LI><A HREF = "fix_rigid.html">rigid</A> - constrain one or more clusters of atoms to      move as a rigid body with NVE integration
@@ -224,6 +225,7 @@ list of fix styles available in LAMMPS:
 <LI><A HREF = "fix_rigid.html">rigid/npt</A> - constrain one or more clusters of atoms to      move as a rigid body with NPT integration
 <LI><A HREF = "fix_rigid.html">rigid/nve</A> - constrain one or more clusters of atoms to      move as a rigid body with alternate NVE integration
 <LI><A HREF = "fix_rigid.html">rigid/nvt</A> - constrain one or more clusters of atoms to      move as a rigid body with NVT integration
+<LI><A HREF = "fix_rigid.html">rigid</A> - constrain many small clusters of atoms to      move as a rigid body with NVE integration
 <LI><A HREF = "fix_setforce.html">setforce</A> - set the force on each atom
 <LI><A HREF = "fix_shake.html">shake</A> - SHAKE constraints on bonds and/or angles
 <LI><A HREF = "fix_spring.html">spring</A> - apply harmonic spring force to group of atoms

doc/fix.txt

@@ -214,6 +214,7 @@ list of fix styles available in LAMMPS:
 "press/berendsen"_fix_press_berendsen.html - pressure control by \
      Berendsen barostat
 "print"_fix_print.html - print text and variables during a simulation
+"property/atom"_fix_property_atom.html - add customized per-atom values
 "reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information \
 "recenter"_fix_recenter.html - constrain the center-of-mass position \
   of a group of atoms
@@ -228,6 +229,8 @@ list of fix styles available in LAMMPS:
      move as a rigid body with alternate NVE integration
 "rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to \
      move as a rigid body with NVT integration
+"rigid"_fix_rigid.html - constrain many small clusters of atoms to \
+     move as a rigid body with NVE integration
 "setforce"_fix_setforce.html - set the force on each atom
 "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
 "spring"_fix_spring.html - apply harmonic spring force to group of atoms