git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3495 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_commands.html

@@ -348,9 +348,9 @@ 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_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/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><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><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_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_ke.html">ke</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_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_msd.html">msd</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_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_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><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></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A> 
+<TR ALIGN="center"><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></TR></TABLE></DIV>
 
 <P>These are compute styles contributed by users, which can be used if

doc/Section_commands.txt

@@ -474,6 +474,7 @@ each style or click on the style itself for a full description:
 "heat/flux"_compute_heat_flux.html,
 "ke"_compute_ke.html,
 "ke/atom"_compute_ke_atom.html,
+"msd"_compute_msd.html,
 "pe"_compute_pe.html,
 "pe/atom"_compute_pe_atom.html,
 "pressure"_compute_pressure.html,

doc/compute.html

@@ -121,6 +121,7 @@ available in LAMMPS:
 <LI><A HREF = "compute_heat_flux.html">heat/flux</A> - heat flux through a group of atoms
 <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_msd.html">msd</A> - mean-squared displacement of group of atoms
 <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

doc/compute.txt

@@ -118,6 +118,7 @@ available in LAMMPS:
 "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
 "ke"_compute_ke.html - translational kinetic energy
 "ke/atom"_compute_ke_atom.html - kinetic energy for each atom
+"msd"_compute_msd.html - mean-squared displacement of group of atoms
 "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

doc/compute_ackland_atom.html

@@ -52,9 +52,9 @@ which computes this quantity.-
 <P><B>Output info:</B>
 </P>
 <P>This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom computes as input.  See
+accessed by any command that uses per-atom values from a compute as
-<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
+input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P><B>Restrictions:</B>
 </P>

doc/compute_ackland_atom.txt

@@ -49,9 +49,9 @@ which computes this quantity.-
 [Output info:]
 
 This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom computes as input.  See
+accessed by any command that uses per-atom values from a compute as
-"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+input.  See "this section"_Section_howto.html#4_15 for an overview of
-output options.
+LAMMPS output options.
 
 [Restrictions:]
 

doc/compute_centro_atom.html

@@ -53,9 +53,9 @@ too frequently or to have multiple compute/dump commands, each with a
 <P><B>Output info:</B>
 </P>
 <P>This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom computes as input.  See
+accessed by any command that uses per-atom values from a compute as
-<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
+input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/compute_centro_atom.txt

@@ -50,9 +50,9 @@ too frequently or to have multiple compute/dump commands, each with a
 [Output info:]
 
 This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom computes as input.  See
+accessed by any command that uses per-atom values from a compute as
-"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+input.  See "this section"_Section_howto.html#4_15 for an overview of
-output options.
+LAMMPS output options.
 
 [Restrictions:] none
 

doc/compute_cna_atom.html

@@ -76,9 +76,9 @@ too frequently or to have multiple compute/dump commands, each with a
 <P><B>Output info:</B>
 </P>
 <P>This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom computes as input.  See
+accessed by any command that uses per-atom values from a compute as
-<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
+input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/compute_cna_atom.txt

@@ -73,9 +73,9 @@ too frequently or to have multiple compute/dump commands, each with a
 [Output info:]
 
 This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom computes as input.  See
+accessed by any command that uses per-atom values from a compute as
-"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+input.  See "this section"_Section_howto.html#4_15 for an overview of
-output options.
+LAMMPS output options.
 
 [Restrictions:] none
 

doc/compute_coord_atom.html

@@ -45,9 +45,9 @@ too frequently or to have multiple compute/dump commands, each of a
 <P><B>Output info:</B>
 </P>
 <P>This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom computes as input.  See
+accessed by any command that uses per-atom values from a compute as
-<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
+input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/compute_coord_atom.txt

@@ -42,9 +42,9 @@ too frequently or to have multiple compute/dump commands, each of a
 [Output info:]
 
 This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom computes as input.  See
+accessed by any command that uses per-atom values from a compute as
-"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+input.  See "this section"_Section_howto.html#4_15 for an overview of
-output options.
+LAMMPS output options.
 
 [Restrictions:] none
 

doc/compute_damage_atom.html

@@ -36,9 +36,9 @@ compute group.
 <P><B>Output info:</B>
 </P>
 <P>This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom computes as input.  See
+accessed by any command that uses per-atom values from a compute as
-<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
+input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P><B>Restrictions:</B>
 </P>

doc/compute_damage_atom.txt

@@ -33,9 +33,9 @@ compute group.
 [Output info:]
 
 This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom computes as input.  See
+accessed by any command that uses per-atom values from a compute as
-"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+input.  See "this section"_Section_howto.html#4_15 for an overview of
-output options.
+LAMMPS output options.
 
 [Restrictions:]
 

doc/compute_displace_atom.html

@@ -26,9 +26,12 @@
 </P>
 <P>Define a computation that calculates the current displacement of each
 atom in the group from its original coordinates, including all effects
-due to atoms passing thru periodic boundaries.  Four quantites per
+due to atoms passing thru periodic boundaries.
-atom are computed: the x,y,z displacements and the total displacement.
+</P>
-See below for details.
+<P>A vector of four quantites per atom are calculated by this compute.
+The first 3 elements of the cector are the dx,dy,dz displacements.
+The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
+dz*dz).
 </P>
 <P>To store the original coordinates at the time this compute is issued,
 the compute creates its own fix of style "coord/original", as if this
@@ -41,6 +44,9 @@ details.  Note that the ID of the new fix is the compute-ID +
 underscore + "coord_original", and the group for the new fix is
 the same as the compute group.
 </P>
+<P>The value of the displacement will be 0.0 for atoms not in the
+specified compute group.
+</P>
 <P>IMPORTANT NOTE: Fix coord/original stores the initial coordinates in
 "unwrapped" form, by using the image flags associated with each atom.
 See the <A HREF = "dump.html">dump custom</A> command for a discussion of
@@ -50,11 +56,13 @@ how they are set for each atom.  You can reset the image flags
 (e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
 image</A> command.
 </P>
-<P>The displacements can be output directly via the <A HREF = "dump.html">dump
+<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix
-custom</A> command.
+rigid</A> command), it's periodic image flags are altered,
-</P>
+and the computed MSD will not reflect its true displacement.  See the
-<P>The value of the displacement will be 0.0 for atoms not in the
+<A HREF = "fix_rigid.html">fix rigid</A> command for details.  Thus, to compute the
-specified compute group.
+MSD of rigid bodies as they cross periodic boundaries, you will need
+to post-process a <A HREF = "dump.html">dump file</A> containing coordinates of the
+atoms in the bodies.
 </P>
 <P>IMPORTANT NOTE: If you want the quantities calculated by this compute
 to be continuous when running from a <A HREF = "read_restart.html">restart file</A>,
@@ -68,15 +76,14 @@ file.
 <P>This compute calculates a vector of length 4 for each atom, which can
 be accessed by indices 1-4 by any command that uses per-atom computes
 as input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview
-of LAMMPS output options.  The first 3 components of the vector are
+of LAMMPS output options.
-the x,y,z displacements.  The 4th component is the total displacement,
-i.e. sqrt(dx*dx + dy*dy + dz*dz).
 </P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "dump.html">dump custom</A>, <A HREF = "fix_msd.html">fix msd</A>
+<P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "dump.html">dump custom</A>, <A HREF = "fix_coord_original.html">fix
+coord/original</A>
 </P>
 <P><B>Default:</B> none
 </P>

doc/compute_displace_atom.txt

@@ -23,9 +23,12 @@ compute 1 all displace/atom :pre
 
 Define a computation that calculates the current displacement of each
 atom in the group from its original coordinates, including all effects
-due to atoms passing thru periodic boundaries.  Four quantites per
+due to atoms passing thru periodic boundaries.
-atom are computed: the x,y,z displacements and the total displacement.
+
-See below for details.
+A vector of four quantites per atom are calculated by this compute.
+The first 3 elements of the cector are the dx,dy,dz displacements.
+The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
+dz*dz).
 
 To store the original coordinates at the time this compute is issued,
 the compute creates its own fix of style "coord/original", as if this
@@ -38,6 +41,9 @@ details.  Note that the ID of the new fix is the compute-ID +
 underscore + "coord_original", and the group for the new fix is
 the same as the compute group.
 
+The value of the displacement will be 0.0 for atoms not in the
+specified compute group.
+
 IMPORTANT NOTE: Fix coord/original stores the initial coordinates in
 "unwrapped" form, by using the image flags associated with each atom.
 See the "dump custom"_dump.html command for a discussion of
@@ -47,11 +53,13 @@ how they are set for each atom.  You can reset the image flags
 (e.g. to 0) before invoking this compute by using the "set
 image"_set.html command.
 
-The displacements can be output directly via the "dump
+IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix
-custom"_dump.html command.
+rigid"_fix_rigid.html command), it's periodic image flags are altered,
-
+and the computed MSD will not reflect its true displacement.  See the
-The value of the displacement will be 0.0 for atoms not in the
+"fix rigid"_fix_rigid.html command for details.  Thus, to compute the
-specified compute group.
+MSD of rigid bodies as they cross periodic boundaries, you will need
+to post-process a "dump file"_dump.html containing coordinates of the
+atoms in the bodies.
 
 IMPORTANT NOTE: If you want the quantities calculated by this compute
 to be continuous when running from a "restart file"_read_restart.html,
@@ -65,14 +73,13 @@ file.
 This compute calculates a vector of length 4 for each atom, which can
 be accessed by indices 1-4 by any command that uses per-atom computes
 as input.  See "this section"_Section_howto.html#4_15 for an overview
-of LAMMPS output options.  The first 3 components of the vector are
+of LAMMPS output options.
-the x,y,z displacements.  The 4th component is the total displacement,
-i.e. sqrt(dx*dx + dy*dy + dz*dz).
 
 [Restrictions:] none
 
 [Related commands:]
 
-"dump custom"_dump.html, "fix msd"_fix_msd.html
+"compute msd"_compute_msd.html, "dump custom"_dump.html, "fix
+coord/original"_fix_coord_original.html
 
 [Default:] none

doc/compute_erotate_asphere.html

@@ -37,6 +37,11 @@ the same as in 3d.
 </P>
 <P><B>Output info:</B>
 </P>
+<P>This compute calculates a global scalar (the KE).  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#4_15">this section</A> for an overview of
+LAMMPS output options.
+</P>
 <P>The scalar value calculated by this compute is "extensive", meaning it
 it scales with the number of atoms in the simulation.
 </P>

doc/compute_erotate_asphere.txt

@@ -34,6 +34,11 @@ the same as in 3d.
 
 [Output info:]
 
+This compute calculates a global scalar (the KE).  This value can be
+used by any command that uses a global scalar value from a compute as
+input.  See "this section"_Section_howto.html#4_15 for an overview of
+LAMMPS output options.
+
 The scalar value calculated by this compute is "extensive", meaning it
 it scales with the number of atoms in the simulation.
 

doc/compute_erotate_sphere.html

@@ -36,6 +36,11 @@ same as in 3d.
 </P>
 <P><B>Output info:</B>
 </P>
+<P>This compute calculates a global scalar (the KE).  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#4_15">this section</A> for an overview of
+LAMMPS output options.
+</P>
 <P>The scalar value calculated by this compute is "extensive", meaning it
 it scales with the number of atoms in the simulation.
 </P>

doc/compute_erotate_sphere.txt

@@ -33,6 +33,11 @@ same as in 3d.
 
 [Output info:]
 
+This compute calculates a global scalar (the KE).  This value can be
+used by any command that uses a global scalar value from a compute as
+input.  See "this section"_Section_howto.html#4_15 for an overview of
+LAMMPS output options.
+
 The scalar value calculated by this compute is "extensive", meaning it
 it scales with the number of atoms in the simulation.
 

doc/compute_event_displace.html

@@ -38,6 +38,11 @@ further than the threshold distance.
 </P>
 <P><B>Output info:</B>
 </P>
+<P>This compute calculates a global scalar (the flag).  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#4_15">this section</A> for an overview of
+LAMMPS output options.
+</P>
 <P>The scalar value calculated by this compute is "intensive", meaning it
 is independent of the number of atoms in the simulation.
 </P>

doc/compute_event_displace.txt

@@ -35,6 +35,11 @@ further than the threshold distance.
 
 [Output info:]
 
+This compute calculates a global scalar (the flag).  This value can be
+used by any command that uses a global scalar value from a compute as
+input.  See "this section"_Section_howto.html#4_15 for an overview of
+LAMMPS output options.
+
 The scalar value calculated by this compute is "intensive", meaning it
 is independent of the number of atoms in the simulation.
 

doc/compute_group_group.html

@@ -41,10 +41,16 @@ quantity too frequently.
 </P>
 <P><B>Output info:</B>
 </P>
-<P>The interaction energy calculated by this compute is a scalar
+<P>This compute calculates a global scalar (the energy) and a global
-quantity.  The interaction force is a vector of length 3.  Both the
+vector of length 3 (force), which can be accessed by indices 1-3.
-scalar and vector values calculated by this compute are "extensive",
+These values can be used by any command that uses global scalar or
-meaning they scale with the number of atoms in the simulation.
+vector values from a compute as input.  See <A HREF = "Section_howto.html#4_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>Both the scalar and vector values calculated by this compute are
+"extensive", meaning they scale with the number of atoms in the
+simulation.
 </P>
 <P><B>Restrictions:</B>
 </P>

doc/compute_group_group.txt

@@ -38,10 +38,16 @@ quantity too frequently.
 
 [Output info:]
 
-The interaction energy calculated by this compute is a scalar
+This compute calculates a global scalar (the energy) and a global
-quantity.  The interaction force is a vector of length 3.  Both the
+vector of length 3 (force), which can be accessed by indices 1-3.
-scalar and vector values calculated by this compute are "extensive",
+These values can be used by any command that uses global scalar or
-meaning they scale with the number of atoms in the simulation.
+vector values from a compute as input.  See "this
+section"_Section_howto.html#4_15 for an overview of LAMMPS output
+options.
+
+Both the scalar and vector values calculated by this compute are
+"extensive", meaning they scale with the number of atoms in the
+simulation.
 
 [Restrictions:]
 

doc/compute_heat_flux.html

@@ -84,12 +84,19 @@ interval and the appropriate unit conversion factors.  For real
 <A HREF = "units.html">units</A> in LAMMPS, this is 2917703220.0 in this case.  The
 final thermal conductivity value obtained is 0.25 W/mK.
 </P>
+<P>The 6 components of the vector calculated by this compute are as
+follows.  The first 3 components are the x, y, z components of the
+full heat flux.  The next 3 components are the x, y, z components of
+just the convective portion of the flux, which is the energy per atom
+times the velocity of the atom.
+</P>
 <P><B>Output info:</B>
 </P>
-<P>This compute calculates a vector of length 6.  The 6 components are
+<P>This compute calculates a global vector of length 6 (heat flux
-the x, y, z components of the full heat flux, followed by the x, y, z
+vector), which can be accessed by indices 1-6.  These values can be
-components of just the convective portion of the flux, which is the
+used by any command that uses global vector values from a compute as
-energy per atom times the velocity of the atom.
+input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
+LAMMPS output options.
 </P>
 <P>The vector values calculated by this compute are "extensive", meaning
 they scale with the number of atoms in the simulation.  They should be

doc/compute_heat_flux.txt

@@ -81,12 +81,19 @@ interval and the appropriate unit conversion factors.  For real
 "units"_units.html in LAMMPS, this is 2917703220.0 in this case.  The
 final thermal conductivity value obtained is 0.25 W/mK.
 
+The 6 components of the vector calculated by this compute are as
+follows.  The first 3 components are the x, y, z components of the
+full heat flux.  The next 3 components are the x, y, z components of
+just the convective portion of the flux, which is the energy per atom
+times the velocity of the atom.
+
 [Output info:]
 
-This compute calculates a vector of length 6.  The 6 components are
+This compute calculates a global vector of length 6 (heat flux
-the x, y, z components of the full heat flux, followed by the x, y, z
+vector), which can be accessed by indices 1-6.  These values can be
-components of just the convective portion of the flux, which is the
+used by any command that uses global vector values from a compute as
-energy per atom times the velocity of the atom.
+input.  See "this section"_Section_howto.html#4_15 for an overview of
+LAMMPS output options.
 
 The vector values calculated by this compute are "extensive", meaning
 they scale with the number of atoms in the simulation.  They should be

doc/compute_ke.html

@@ -45,6 +45,11 @@ include different degrees of freedom (translational, rotational, etc).
 </P>
 <P><B>Output info:</B>
 </P>
+<P>This compute calculates a global scalar (the KE).  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#4_15">this section</A> for an overview of
+LAMMPS output options.
+</P>
 <P>The scalar value calculated by this compute is "extensive", meaning it
 it scales with the number of atoms in the simulation.
 </P>

doc/compute_ke.txt

@@ -42,6 +42,11 @@ include different degrees of freedom (translational, rotational, etc).
 
 [Output info:]
 
+This compute calculates a global scalar (the KE).  This value can be
+used by any command that uses a global scalar value from a compute as
+input.  See "this section"_Section_howto.html#4_15 for an overview of
+LAMMPS output options.
+
 The scalar value calculated by this compute is "extensive", meaning it
 it scales with the number of atoms in the simulation.
 

doc/compute_ke_atom.html

@@ -36,9 +36,9 @@ specified compute group.
 <P><B>Output info:</B>
 </P>
 <P>This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom computes as input.  See
+accessed by any command that uses per-atom values from a compute as
-<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
+input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/compute_ke_atom.txt

@@ -33,9 +33,9 @@ specified compute group.
 [Output info:]
 
 This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom computes as input.  See
+accessed by any command that uses per-atom values from a compute as
-"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+input.  See "this section"_Section_howto.html#4_15 for an overview of
-output options.
+LAMMPS output options.
 
 [Restrictions:] none
 

doc/compute_pe.html

@@ -56,6 +56,11 @@ LAMMPS starts up, as if this command were in the input script:
 </P>
 <P><B>Output info:</B>
 </P>
+<P>This compute calculates a global scalar (the potential energy).  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#4_15">this section</A> for an
+overview of LAMMPS output options.
+</P>
 <P>The scalar value calculated by this compute is "extensive", meaning it
 it scales with the number of atoms in the simulation.
 </P>

doc/compute_pe.txt

@@ -53,6 +53,11 @@ See the "thermo_style" command for more details.
 
 [Output info:]
 
+This compute calculates a global scalar (the potential energy).  This
+value can be used by any command that uses a global scalar value from
+a compute as input.  See "this section"_Section_howto.html#4_15 for an
+overview of LAMMPS output options.
+
 The scalar value calculated by this compute is "extensive", meaning it
 it scales with the number of atoms in the simulation.
 

doc/compute_pe_atom.html

@@ -30,12 +30,7 @@ compute 1 all pe/atom pair bond
 </P>
 <P>Define a computation that computes the per-atom potential energy for
 each atom in a group.  See the <A HREF = "compute_pe.html">compute pe</A> command if
-you want the potential energy of the entire system.  The per-atom
+you want the potential energy of the entire system.
-energies can be accessed as scalar values by any command that uses
-per-atom computes, e.g. the <A HREF = "dump.html">dump custom</A> command or <A HREF = "fix_ave_spatial.html">fix
-ave/spatial</A> command or <A HREF = "fix_ave_atom.html">fix
-ave/atom</A> command.  See <A HREF = "Section_howto.html#4_15">this
-section</A> for an overview.
 </P>
 <P>The per-atom energy is calculated by the various pair, bond, etc
 potentials defined for the simulation.  If no extra keywords are
@@ -71,9 +66,9 @@ contribution can easily be computed.
 <P><B>Output info:</B>
 </P>
 <P>This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom computes as input.  See
+accessed by any command that uses per-atom values from a compute as
-<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
+input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P><B>Restrictions:</B>
 </P>

doc/compute_pe_atom.txt

@@ -27,12 +27,7 @@ compute 1 all pe/atom pair bond :pre
 
 Define a computation that computes the per-atom potential energy for
 each atom in a group.  See the "compute pe"_compute_pe.html command if
-you want the potential energy of the entire system.  The per-atom
+you want the potential energy of the entire system.
-energies can be accessed as scalar values by any command that uses
-per-atom computes, e.g. the "dump custom"_dump.html command or "fix
-ave/spatial"_fix_ave_spatial.html command or "fix
-ave/atom"_fix_ave_atom.html command.  See "this
-section"_Section_howto.html#4_15 for an overview.
 
 The per-atom energy is calculated by the various pair, bond, etc
 potentials defined for the simulation.  If no extra keywords are
@@ -68,9 +63,9 @@ contribution can easily be computed.
 [Output info:]
 
 This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom computes as input.  See
+accessed by any command that uses per-atom values from a compute as
-"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+input.  See "this section"_Section_howto.html#4_15 for an overview of
-output options.
+LAMMPS output options.
 
 [Restrictions:]
 

doc/compute_pressure.html

@@ -47,14 +47,12 @@ and long-range interactions.  <A HREF = "fix.html">Fixes</A> that impose constra
 (e.g. the <A HREF = "fix_shake.html">fix shake</A> command) also contribute to the
 virial term.
 </P>
-<P>A 6-component symmetric pressure tensor is also calculated by this
+<P>A symmetric pressure tensor, stored as a 6-element vector, is also
-compute whose components can be output by the <A HREF = "thermo_style.html">thermo_style
+calculated by this compute.  The 6 components of the vector are
-custom</A> command or accessed by other
+ordered xx, yy, zz, xy, xz, yz.  The equation for the I,J components
-<A HREF = "compute.html">compute</A> and <A HREF = "fix.html">fix</A> commands.  The equation for
+(where I and J = x,y,z) is similar to the above formula, except that
-the I,J components (where I and J = x,y,z) is similar to the above
+the first term uses components of the kinetic energy tensor and the
-formula, except that the first term uses components of the kinetic
+second term uses components of the virial tensor:
-energy tensor and the second term uses components of the virial
-tensor:
 </P>
 <CENTER><IMG SRC = "Eqs/pressure_tensor.jpg">
 </CENTER>
@@ -88,10 +86,16 @@ LAMMPS starts up, as if this command were in the input script:
 </P>
 <P><B>Output info:</B>
 </P>
+<P>This compute calculates a global scalar (the pressure) and a global
+vector of length 6 (pressure tensor), which can be accessed by indices
+1-6.  These values can be used by any command that uses global scalar
+or vector values from a compute as input.  See <A HREF = "Section_howto.html#4_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
 <P>The scalar and vector values calculated by this compute are
 "intensive", meaning they are independent of the number of atoms in
-the simulation.  The 6 components of the vector are ordered xx, yy,
+the simulation.
-zz, xy, xz, yz.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/compute_pressure.txt

@@ -44,14 +44,12 @@ and long-range interactions.  "Fixes"_fix.html that impose constraints
 (e.g. the "fix shake"_fix_shake.html command) also contribute to the
 virial term.
 
-A 6-component symmetric pressure tensor is also calculated by this
+A symmetric pressure tensor, stored as a 6-element vector, is also
-compute whose components can be output by the "thermo_style
+calculated by this compute.  The 6 components of the vector are
-custom"_thermo_style.html command or accessed by other
+ordered xx, yy, zz, xy, xz, yz.  The equation for the I,J components
-"compute"_compute.html and "fix"_fix.html commands.  The equation for
+(where I and J = x,y,z) is similar to the above formula, except that
-the I,J components (where I and J = x,y,z) is similar to the above
+the first term uses components of the kinetic energy tensor and the
-formula, except that the first term uses components of the kinetic
+second term uses components of the virial tensor:
-energy tensor and the second term uses components of the virial
-tensor:
 
 :c,image(Eqs/pressure_tensor.jpg)
 
@@ -85,10 +83,16 @@ where "thermo_temp" is the ID of a similarly defined compute of style
 
 [Output info:]
 
+This compute calculates a global scalar (the pressure) and a global
+vector of length 6 (pressure tensor), which can be accessed by indices
+1-6.  These values can be used by any command that uses global scalar
+or vector values from a compute as input.  See "this
+section"_Section_howto.html#4_15 for an overview of LAMMPS output
+options.
+
 The scalar and vector values calculated by this compute are
 "intensive", meaning they are independent of the number of atoms in
-the simulation.  The 6 components of the vector are ordered xx, yy,
+the simulation.
-zz, xy, xz, yz.
 
 [Restrictions:] none
 

doc/compute_reduce.html

@@ -51,12 +51,7 @@ compute 2 all reduce min c_press<B>2</B> f_ave v_myKE
 <P>Define a calculation that "reduces" one or more per-atom inputs across
 all atoms in the group to yield a single global scalar for each listed
 input.  If the compute reduce/region command is used, the selection of
-atoms is limited to atoms in the region as well as in the group.  The
+atoms is limited to atoms in the region as well as in the group.
-resulting value(s) can be accessed by any command that uses global
-computes, e.g. the <A HREF = "therml_style.html">thermo custom</A> command or <A HREF = "fix_ave_time.html">fix
-ave/time</A> command or by a <A HREF = "variable.html">variable</A>
-command.  See <A HREF = "Section_howto.html#4_15">this section</A> of the
-documentation for an overview of output options.
 </P>
 <P>The reduction operation is specified by the <I>mode</I> setting.  The <I>sum</I>
 option adds the per-atom quantities into a global total.  The <I>min</I> or
@@ -100,6 +95,13 @@ divides by the appropriate atom count.
 </P>
 <P><B>Output info:</B>
 </P>
+<P>This compute calculates a global scalar or global vector of length N
+where N is the number of inputs, and which can be accessed by indices
+1-6.  These values can be used by any command that uses global scalar
+or vector values from a compute as input.  See <A HREF = "Section_howto.html#4_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
 <P>For <I>sum</I> mode, the scalar and vector values calculated by this
 compute are "extensive", meaning they scale with the number of atoms
 in the simulation.  For <I>min</I> and <I>max</I> modes, the value(s) are

doc/compute_reduce.txt

@@ -40,12 +40,7 @@ compute 2 all reduce min c_press[2] f_ave v_myKE :pre
 Define a calculation that "reduces" one or more per-atom inputs across
 all atoms in the group to yield a single global scalar for each listed
 input.  If the compute reduce/region command is used, the selection of
-atoms is limited to atoms in the region as well as in the group.  The
+atoms is limited to atoms in the region as well as in the group.
-resulting value(s) can be accessed by any command that uses global
-computes, e.g. the "thermo custom"_therml_style.html command or "fix
-ave/time"_fix_ave_time.html command or by a "variable"_variable.html
-command.  See "this section"_Section_howto.html#4_15 of the
-documentation for an overview of output options.
 
 The reduction operation is specified by the {mode} setting.  The {sum}
 option adds the per-atom quantities into a global total.  The {min} or
@@ -89,6 +84,13 @@ divides by the appropriate atom count.
 
 [Output info:]
 
+This compute calculates a global scalar or global vector of length N
+where N is the number of inputs, and which can be accessed by indices
+1-6.  These values can be used by any command that uses global scalar
+or vector values from a compute as input.  See "this
+section"_Section_howto.html#4_15 for an overview of LAMMPS output
+options.
+
 For {sum} mode, the scalar and vector values calculated by this
 compute are "extensive", meaning they scale with the number of atoms
 in the simulation.  For {min} and {max} modes, the value(s) are

doc/compute_stress_atom.html

@@ -29,14 +29,10 @@ compute 1 all stress/atom pair bond
 </P>
 <P>Define a computation that computes the symmetric per-atom stress
 tensor for each atom in a group.  The tensor for each atom has 6
-components: xx, yy, zz, xy, xz, yz.  See the <A HREF = "compute_pressure.html">compute
+components and is stored as a 6-element vector in the following order:
+xx, yy, zz, xy, xz, yz.  See the <A HREF = "compute_pressure.html">compute
 pressure</A> command if you want the stress tensor
-(pressure) of the entire system.  The 6 components can be accessed by
+(pressure) of the entire system.
-indices 1-6 by any command that uses per-atom computes as input,
-e.g. the <A HREF = "dump.html">dump custom</A> command or <A HREF = "fix_ave_spatial.html">fix
-ave/spatial</A> command or <A HREF = "fix_ave_atom.html">fix
-ave/atom</A> command.  See <A HREF = "Section_howto.html#4_15">this
-section</A> for an overview.
 </P>
 <P>The stress tensor for atom <I>I</I> is given by the following formula,
 where <I>a</I> and <I>b</I> take on values x,y,z to generate the 6 components of
@@ -105,10 +101,9 @@ contribution can easily be computed.
 <P><B>Output info:</B>
 </P>
 <P>This compute calculates a vector of length 6 for each atom, which can
-be accessed by indices 1-6 by any command that uses per-atom computes
+be accessed by indices 1-6 by any command that uses per-atom values
-as input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview
+from a compute as input.  See <A HREF = "Section_howto.html#4_15">this section</A>
-of LAMMPS output options.  The 6 components of the vector are ordered
+for an overview of LAMMPS output options.
-xx, yy, zz, xy, xz, yz.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/compute_stress_atom.txt

@@ -26,14 +26,10 @@ compute 1 all stress/atom pair bond :pre
 
 Define a computation that computes the symmetric per-atom stress
 tensor for each atom in a group.  The tensor for each atom has 6
-components: xx, yy, zz, xy, xz, yz.  See the "compute
+components and is stored as a 6-element vector in the following order:
+xx, yy, zz, xy, xz, yz.  See the "compute
 pressure"_compute_pressure.html command if you want the stress tensor
-(pressure) of the entire system.  The 6 components can be accessed by
+(pressure) of the entire system.
-indices 1-6 by any command that uses per-atom computes as input,
-e.g. the "dump custom"_dump.html command or "fix
-ave/spatial"_fix_ave_spatial.html command or "fix
-ave/atom"_fix_ave_atom.html command.  See "this
-section"_Section_howto.html#4_15 for an overview.
 
 The stress tensor for atom {I} is given by the following formula,
 where {a} and {b} take on values x,y,z to generate the 6 components of
@@ -102,10 +98,9 @@ contribution can easily be computed.
 [Output info:]
 
 This compute calculates a vector of length 6 for each atom, which can
-be accessed by indices 1-6 by any command that uses per-atom computes
+be accessed by indices 1-6 by any command that uses per-atom values
-as input.  See "this section"_Section_howto.html#4_15 for an overview
+from a compute as input.  See "this section"_Section_howto.html#4_15
-of LAMMPS output options.  The 6 components of the vector are ordered
+for an overview of LAMMPS output options.
-xx, yy, zz, xy, xz, yz.
 
 [Restrictions:] none
 

doc/compute_temp.html

@@ -35,10 +35,12 @@ KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
 dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
 in the group, k = Boltzmann constant, and T = temperature.
 </P>
-<P>A 6-component kinetic energy tensor is also calculated by this compute
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
-for use in the computation of a pressure tensor.  The formula for the
+calculated by this compute for use in the computation of a pressure
-components of the tensor is the same as the above formula, except that
+tensor.  The formula for the components of the tensor is the same as
-v^2 is replaced by vx * vy for the xy component, etc.
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
 </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
@@ -64,6 +66,13 @@ thermostatting.
 </P>
 <P><B>Output info:</B>
 </P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See <A HREF = "Section_howto.html#4_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
 <P>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

doc/compute_temp.txt

@@ -32,10 +32,12 @@ KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
 dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
 in the group, k = Boltzmann constant, and T = temperature.
 
-A 6-component kinetic energy tensor is also calculated by this compute
+A kinetic energy tensor, stored as a 6-element vector, is also
-for use in the computation of a pressure tensor.  The formula for the
+calculated by this compute for use in the computation of a pressure
-components of the tensor is the same as the above formula, except that
+tensor.  The formula for the components of the tensor is the same as
-v^2 is replaced by vx * vy for the xy component, etc.
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
 
 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
@@ -61,6 +63,13 @@ thermostatting.
 
 [Output info:]
 
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See "this
+section"_Section_howto.html#4_15 for an overview of LAMMPS output
+options.
+
 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

doc/compute_temp_asphere.html

@@ -65,11 +65,12 @@ computed from its angular momentum.
 as ellipsoids, not ellipses, meaning their moments of inertia will be
 the same as in 3d.
 </P>
-<P>A 6-component kinetic energy tensor is also calculated by this
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
-compute.  The formula for the components of the tensor is the same as
+calculated by this compute.  The formula for the components of the
-the above formula, except that v^2 and w^2 are replaced by vx*vy and
+tensor is the same as the above formula, except that v^2 and w^2 are
-wx*wy for the xy component, and the appropriate elements of the
+replaced by vx*vy and wx*wy for the xy component, and the appropriate
-inertia tensor are used.
+elements of the inertia tensor are used.  The 6 components of the
+vector are ordered xx, yy, zz, xy, xz, yz.
 </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
@@ -98,6 +99,13 @@ thermostatting.
 </P>
 <P><B>Output info:</B>
 </P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See <A HREF = "Section_howto.html#4_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
 <P>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

doc/compute_temp_asphere.txt

@@ -62,11 +62,12 @@ 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
+A kinetic energy tensor, stored as a 6-element vector, is also
-compute.  The formula for the components of the tensor is the same as
+calculated by this compute.  The formula for the components of the
-the above formula, except that v^2 and w^2 are replaced by vx*vy and
+tensor is the same as the above formula, except that v^2 and w^2 are
-wx*wy for the xy component, and the appropriate elements of the
+replaced by vx*vy and wx*wy for the xy component, and the appropriate
-inertia tensor are used.
+elements of the inertia tensor are used.  The 6 components of the
+vector are ordered xx, yy, zz, xy, xz, yz.
 
 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
@@ -95,6 +96,13 @@ thermostatting.
 
 [Output info:]
 
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See "this
+section"_Section_howto.html#4_15 for an overview of LAMMPS output
+options.
+
 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

doc/compute_temp_com.html

@@ -39,10 +39,12 @@ KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
 dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
 in the group, k = Boltzmann constant, and T = temperature.
 </P>
-<P>A 6-component kinetic energy tensor is also calculated by this compute
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
-for use in the computation of a pressure tensor.  The formula for the
+calculated by this compute for use in the computation of a pressure
-components of the tensor is the same as the above formula, except that
+tensor.  The formula for the components of the tensor is the same as
-v^2 is replaced by vx * vy for the xy component, etc.
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
 </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
@@ -72,6 +74,13 @@ thermostatting.
 </P>
 <P><B>Output info:</B>
 </P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See <A HREF = "Section_howto.html#4_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
 <P>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

doc/compute_temp_com.txt

@@ -36,10 +36,12 @@ KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
 dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
 in the group, k = Boltzmann constant, and T = temperature.
 
-A 6-component kinetic energy tensor is also calculated by this compute
+A kinetic energy tensor, stored as a 6-element vector, is also
-for use in the computation of a pressure tensor.  The formula for the
+calculated by this compute for use in the computation of a pressure
-components of the tensor is the same as the above formula, except that
+tensor.  The formula for the components of the tensor is the same as
-v^2 is replaced by vx * vy for the xy component, etc.
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
 
 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
@@ -69,6 +71,13 @@ thermostatting.
 
 [Output info:]
 
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See "this
+section"_Section_howto.html#4_15 for an overview of LAMMPS output
+options.
+
 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

doc/compute_temp_deform.html

@@ -63,10 +63,12 @@ or 3 = dimensionality of the simulation, N = number of atoms in the
 group, k = Boltzmann constant, and T = temperature.  Note that v in
 the kinetic energy formula is the atom's thermal velocity.
 </P>
-<P>A 6-component kinetic energy tensor is also calculated by this compute
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
-for use in the computation of a pressure tensor.  The formula for the
+calculated by this compute for use in the computation of a pressure
-components of the tensor is the same as the above formula, except that
+tensor.  The formula for the components of the tensor is the same as
-v^2 is replaced by vx * vy for the xy component, etc.
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
 </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
@@ -96,6 +98,13 @@ thermostatting.
 </P>
 <P><B>Output info:</B>
 </P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See <A HREF = "Section_howto.html#4_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
 <P>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

doc/compute_temp_deform.txt

@@ -60,10 +60,12 @@ or 3 = dimensionality of the simulation, N = number of atoms in the
 group, k = Boltzmann constant, and T = temperature.  Note that v in
 the kinetic energy formula is the atom's thermal velocity.
 
-A 6-component kinetic energy tensor is also calculated by this compute
+A kinetic energy tensor, stored as a 6-element vector, is also
-for use in the computation of a pressure tensor.  The formula for the
+calculated by this compute for use in the computation of a pressure
-components of the tensor is the same as the above formula, except that
+tensor.  The formula for the components of the tensor is the same as
-v^2 is replaced by vx * vy for the xy component, etc.
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
 
 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
@@ -93,6 +95,13 @@ thermostatting.
 
 [Output info:]
 
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See "this
+section"_Section_howto.html#4_15 for an overview of LAMMPS output
+options.
+
 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

doc/compute_temp_partial.html

@@ -25,9 +25,9 @@
 </PRE>
 <P><B>Description:</B>
 </P>
-<P>Define a compute to calculate the temperature of a group of atoms,
+<P>Define a computation that calculates the temperature of a group of
-after excluding one or more velocity components.  A compute of this
+atoms, after excluding one or more velocity components.  A compute of
-style can be used by any command that computes a temperature,
+this style can be used by any command that computes a temperature,
 e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
 temp/rescale</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
 </P>
@@ -39,10 +39,12 @@ of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag =
 0.  The dim parameter is adjusted to give the correct number of
 degrees of freedom.
 </P>
-<P>A 6-component kinetic energy tensor is also calculated by this compute
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
-for use in the calculation of a pressure tensor.  The formula for the
+calculated by this compute for use in the calculation of a pressure
-components of the tensor is the same as the above formula, except that
+tensor.  The formula for the components of the tensor is the same as
-v^2 is replaced by vx * vy for the xy component, etc.
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
 </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
@@ -72,6 +74,13 @@ thermostatting.
 </P>
 <P><B>Output info:</B>
 </P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See <A HREF = "Section_howto.html#4_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
 <P>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

doc/compute_temp_partial.txt

@@ -22,9 +22,9 @@ compute newT flow temp/partial 1 1 0 :pre
 
 [Description:]
 
-Define a compute to calculate the temperature of a group of atoms,
+Define a computation that calculates the temperature of a group of
-after excluding one or more velocity components.  A compute of this
+atoms, after excluding one or more velocity components.  A compute of
-style can be used by any command that computes a temperature,
+this style can be used by any command that computes a temperature,
 e.g. "thermo_modify"_thermo_modify.html, "fix
 temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc.
 
@@ -36,10 +36,12 @@ of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag =
 0.  The dim parameter is adjusted to give the correct number of
 degrees of freedom.
 
-A 6-component kinetic energy tensor is also calculated by this compute
+A kinetic energy tensor, stored as a 6-element vector, is also
-for use in the calculation of a pressure tensor.  The formula for the
+calculated by this compute for use in the calculation of a pressure
-components of the tensor is the same as the above formula, except that
+tensor.  The formula for the components of the tensor is the same as
-v^2 is replaced by vx * vy for the xy component, etc.
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
 
 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
@@ -69,6 +71,13 @@ thermostatting.
 
 [Output info:]
 
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See "this
+section"_Section_howto.html#4_15 for an overview of LAMMPS output
+options.
+
 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

doc/compute_temp_profile.html

@@ -77,10 +77,12 @@ T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m
 v^2), dim = 2 or 3 = dimensionality of the simulation, N = number of
 atoms in the group, k = Boltzmann constant, and T = temperature.
 </P>
-<P>A 6-component kinetic energy tensor is also calculated by this compute
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
-for use in the calculation of a pressure tensor.  The formula for the
+calculated by this compute for use in the computation of a pressure
-components of the tensor is the same as the above formula, except that
+tensor.  The formula for the components of the tensor is the same as
-v^2 is replaced by vx * vy for the xy component, etc.
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
 </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
@@ -112,6 +114,13 @@ profile-unbiased thermostat (PUT), as described in <A HREF = "#Evans">(Evans)</A
 </P>
 <P><B>Output info:</B>
 </P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See <A HREF = "Section_howto.html#4_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
 <P>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

doc/compute_temp_profile.txt

@@ -69,10 +69,12 @@ T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m
 v^2), dim = 2 or 3 = dimensionality of the simulation, N = number of
 atoms in the group, k = Boltzmann constant, and T = temperature.
 
-A 6-component kinetic energy tensor is also calculated by this compute
+A kinetic energy tensor, stored as a 6-element vector, is also
-for use in the calculation of a pressure tensor.  The formula for the
+calculated by this compute for use in the computation of a pressure
-components of the tensor is the same as the above formula, except that
+tensor.  The formula for the components of the tensor is the same as
-v^2 is replaced by vx * vy for the xy component, etc.
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
 
 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
@@ -104,6 +106,13 @@ profile-unbiased thermostat (PUT), as described in "(Evans)"_#Evans.
 
 [Output info:]
 
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See "this
+section"_Section_howto.html#4_15 for an overview of LAMMPS output
+options.
+
 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

doc/compute_temp_ramp.html

@@ -58,10 +58,12 @@ means the distance units are in lattice spacings; e.g. velocity =
 lattice spacings / tau.  The <A HREF = "lattice.html">lattice</A> command must have
 been previously used to define the lattice spacing.
 </P>
-<P>A 6-component kinetic energy tensor is also calculated by this compute
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
-for use in the calculation of a pressure tensor.  The formula for the
+calculated by this compute for use in the computation of a pressure
-components of the tensor is the same as the above formula, except that
+tensor.  The formula for the components of the tensor is the same as
-v^2 is replaced by vx * vy for the xy component, etc.
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
 </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
@@ -91,6 +93,13 @@ thermostatting.
 </P>
 <P><B>Output info:</B>
 </P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See <A HREF = "Section_howto.html#4_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
 <P>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

doc/compute_temp_ramp.txt

@@ -54,10 +54,12 @@ means the distance units are in lattice spacings; e.g. velocity =
 lattice spacings / tau.  The "lattice"_lattice.html command must have
 been previously used to define the lattice spacing.
 
-A 6-component kinetic energy tensor is also calculated by this compute
+A kinetic energy tensor, stored as a 6-element vector, is also
-for use in the calculation of a pressure tensor.  The formula for the
+calculated by this compute for use in the computation of a pressure
-components of the tensor is the same as the above formula, except that
+tensor.  The formula for the components of the tensor is the same as
-v^2 is replaced by vx * vy for the xy component, etc.
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
 
 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
@@ -87,6 +89,13 @@ thermostatting.
 
 [Output info:]
 
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See "this
+section"_Section_howto.html#4_15 for an overview of LAMMPS output
+options.
+
 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

doc/compute_temp_region.html

@@ -46,10 +46,12 @@ dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
 in both the group and region, k = Boltzmann constant, and T =
 temperature.
 </P>
-<P>A 6-component kinetic energy tensor is also calculated by this compute
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
-for use in the computation of a pressure tensor.  The formula for the
+calculated by this compute for use in the computation of a pressure
-components of the tensor is the same as the above formula, except that
+tensor.  The formula for the components of the tensor is the same as
-v^2 is replaced by vx * vy for the xy component, etc.
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
 </P>
 <P>The number of atoms contributing to the temperature is compute each
 time the temperature is evaluated since it is assumed atoms can
@@ -83,6 +85,13 @@ thermostatting.
 </P>
 <P><B>Output info:</B>
 </P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See <A HREF = "Section_howto.html#4_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
 <P>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

doc/compute_temp_region.txt

@@ -43,10 +43,12 @@ dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
 in both the group and region, k = Boltzmann constant, and T =
 temperature.
 
-A 6-component kinetic energy tensor is also calculated by this compute
+A kinetic energy tensor, stored as a 6-element vector, is also
-for use in the computation of a pressure tensor.  The formula for the
+calculated by this compute for use in the computation of a pressure
-components of the tensor is the same as the above formula, except that
+tensor.  The formula for the components of the tensor is the same as
-v^2 is replaced by vx * vy for the xy component, etc.
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc.  The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
 
 The number of atoms contributing to the temperature is compute each
 time the temperature is evaluated since it is assumed atoms can
@@ -80,6 +82,13 @@ thermostatting.
 
 [Output info:]
 
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See "this
+section"_Section_howto.html#4_15 for an overview of LAMMPS output
+options.
+
 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

doc/compute_temp_sphere.html

@@ -56,10 +56,11 @@ inertia for a sphere and w is the particle's angular velocity.
 as spheres, not disks, meaning their moment of inertia will be the
 same as in 3d.
 </P>
-<P>A 6-component kinetic energy tensor is also calculated by this
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
-compute.  The formula for the components of the tensor is the same as
+calculated by this compute.  The formula for the components of the
-the above formulas, except that v^2 and w^2 are replaced by vx*vy and
+tensor is the same as the above formulas, except that v^2 and w^2 are
-wx*wy for the xy component.
+replaced by vx*vy and wx*wy for the xy component.  The 6 components of
+the vector are ordered xx, yy, zz, xy, xz, yz.
 </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
@@ -88,6 +89,13 @@ thermostatting.
 </P>
 <P><B>Output info:</B>
 </P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See <A HREF = "Section_howto.html#4_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
 <P>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

doc/compute_temp_sphere.txt

@@ -53,10 +53,11 @@ 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
+A kinetic energy tensor, stored as a 6-element vector, is also
-compute.  The formula for the components of the tensor is the same as
+calculated by this compute.  The formula for the components of the
-the above formulas, except that v^2 and w^2 are replaced by vx*vy and
+tensor is the same as the above formulas, except that v^2 and w^2 are
-wx*wy for the xy component.
+replaced by vx*vy and wx*wy for the xy component.  The 6 components of
+the vector are ordered xx, yy, zz, xy, xz, yz.
 
 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
@@ -85,6 +86,13 @@ thermostatting.
 
 [Output info:]
 
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See "this
+section"_Section_howto.html#4_15 for an overview of LAMMPS output
+options.
+
 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

doc/fix_coord_original.html

@@ -13,14 +13,24 @@
 </H3>
 <P><B>Syntax:</B>
 </P>
-<PRE>fix ID group-ID coord/original 
+<PRE>fix ID group-ID coord/original keyword values ... 
 </PRE>
 <UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command 
+
 <LI>coord/original = style name of this fix command 
+
+<LI>zero or more keyword/value pairs may be appended 
+
+<LI>keyword = <I>com</I> 
+
+<PRE>  <I>com</I> value = <I>yes</I> or <I>no</I> 
+</PRE>
+
 </UL>
 <P><B>Examples:</B>
 </P>
 <PRE>fix 1 all coord/original
+fix 1 upper coord/original com yes 
 </PRE>
 <P><B>Description:</B>
 </P>
@@ -45,6 +55,11 @@ rigid</A> command), it's periodic image flags are altered,
 and its original coordinates may not be what you expect.  See the
 <A HREF = "fix_rigid.html">fix rigid</A> command for details.
 </P>
+<P>If the <I>com</I> keyword is set to <I>yes</I> then the position
+of each atom relative to the center-of-mass of the group of
+atoms is stored, instead of the absolute position.  This option
+is used by the <A HREF = "compute_msd.html">compute msd</A> command.
+</P>
 <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
 </P>
 <P>This fix writes the original coordinates of the atoms to <A HREF = "restart.html">binary
@@ -71,9 +86,11 @@ minimization</A>.
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "fix_msd.html">fix msd</A>, <A HREF = "compute_displace_atom.html">compute
+<P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "compute_displace_atom.html">compute
 displace/atom</A>
 </P>
-<P><B>Default:</B> none
+<P><B>Default:</B>
+</P>
+<P>The option default is com = no.
 </P>
 </HTML>

doc/fix_coord_original.txt

@@ -10,14 +10,19 @@ fix coord/original command :h3
 
 [Syntax:]
 
-fix ID group-ID coord/original :pre
+fix ID group-ID coord/original keyword values ... :pre
 
-ID, group-ID are documented in "fix"_fix.html command
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
-coord/original = style name of this fix command :ul
+coord/original = style name of this fix command :l
+zero or more keyword/value pairs may be appended :l
+keyword = {com} :l
+  {com} value = {yes} or {no} :pre
+:ule
 
 [Examples:]
 
-fix 1 all coord/original :pre
+fix 1 all coord/original
+fix 1 upper coord/original com yes :pre
 
 [Description:]
 
@@ -42,6 +47,11 @@ rigid"_fix_rigid.html command), it's periodic image flags are altered,
 and its original coordinates may not be what you expect.  See the
 "fix rigid"_fix_rigid.html command for details.
 
+If the {com} keyword is set to {yes} then the position
+of each atom relative to the center-of-mass of the group of
+atoms is stored, instead of the absolute position.  This option
+is used by the "compute msd"_compute_msd.html command.
+
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 This fix writes the original coordinates of the atoms to "binary
@@ -68,7 +78,9 @@ minimization"_minimize.html.
 
 [Related commands:]
 
-"fix msd"_fix_msd.html, "compute
+"compute msd"_compute_msd.html, "compute
 displace/atom"_compute_displace_atom.html
 
-[Default:] none
+[Default:]
+
+The option default is com = no.