git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1295 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/compute_ackland_atom.html

@@ -25,14 +25,14 @@
 <P><B>Description:</B>
 </P>
 <P>Defines a computation that calculates the local lattice structure
-according to <A HREF = "#Ackland">(Ackland)</A>.
+according to the formulation given in <A HREF = "#Ackland">(Ackland)</A>.
 </P>
 <P>In contrast to the <A HREF = "compute_centro_atom.html">centro-symmetry
 parameter</A> this method is stable against
 temperature boost, because it is based not on the distance between
 particles but the angles.  Therefore statistical fluctuations are
 averaged out a little more.  A comparison with the Common Neighbor
-Analysis metric is made in the paper..
+Analysis metric is made in the paper.
 </P>
 <P>The result is a number which is mapped to the following different
 lattice structures:
@@ -49,6 +49,13 @@ is dumped).  Thus it can be inefficient to compute/dump this quantity
 too frequently or to have multiple compute/dump commands, each of
 which computes this quantity.-
 </P>
+<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
+<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
+output options.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>

doc/compute_ackland_atom.txt

@@ -22,14 +22,14 @@ compute 1 all ackland/atom :pre
 [Description:]
 
 Defines a computation that calculates the local lattice structure
-according to "(Ackland)"_#Ackland.
+according to the formulation given in "(Ackland)"_#Ackland.
 
 In contrast to the "centro-symmetry
 parameter"_compute_centro_atom.html this method is stable against
 temperature boost, because it is based not on the distance between
 particles but the angles.  Therefore statistical fluctuations are
 averaged out a little more.  A comparison with the Common Neighbor
-Analysis metric is made in the paper..
+Analysis metric is made in the paper.
 
 The result is a number which is mapped to the following different
 lattice structures:
@@ -46,6 +46,13 @@ is dumped).  Thus it can be inefficient to compute/dump this quantity
 too frequently or to have multiple compute/dump commands, each of
 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
+"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+output options.
+
 [Restrictions:] none
 
 [Related commands:]

doc/compute_centro_atom.html

@@ -50,6 +50,13 @@ is dumped).  Thus it can be inefficient to compute/dump this quantity
 too frequently or to have multiple compute/dump commands, each of a
 <I>centro/atom</I> style.
 </P>
+<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
+<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
+output options.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B> none

doc/compute_centro_atom.txt

@@ -47,6 +47,13 @@ is dumped).  Thus it can be inefficient to compute/dump this quantity
 too frequently or to have multiple compute/dump commands, each of a
 {centro/atom} style.
 
+[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
+"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+output options.
+
 [Restrictions:] none
 
 [Related commands:] none

doc/compute_coord_atom.html

@@ -42,6 +42,13 @@ is dumped).  Thus it can be inefficient to compute/dump this quantity
 too frequently or to have multiple compute/dump commands, each of a
 <I>coord/atom</I> style.
 </P>
+<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
+<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
+output options.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B> none

doc/compute_coord_atom.txt

@@ -39,6 +39,13 @@ is dumped).  Thus it can be inefficient to compute/dump this quantity
 too frequently or to have multiple compute/dump commands, each of a
 {coord/atom} style.
 
+[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
+"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+output options.
+
 [Restrictions:] none
 
 [Related commands:] none

doc/compute_displace_atom.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 displace/atom command 
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID displace/atom fix-ID 
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>displace/atom = style name of this compute command
+<LI>fix-ID = ID of a fix of style <A HREF = "fix_coord_original.html">coord/original</A> 
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all displace/atom myCoords 
+</PRE>
+<P><B>Description:</B>
+</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.  The original
+coordinates are stored by a <A HREF = "fix_coord_original.html">fix
+coord/original</A> command, whose ID must be
+specified with this compute.  They are the coordinates at the time the
+fix command was issued.  The displacement can be output directly via
+the <A HREF = "dump.html">dump custom</A> command.  It could also be used to
+calculate a diffusion coefficient for a group of atoms, as is done by
+the <A HREF = "fix_msd.html">fix msd</A> command.
+</P>
+<P>The value of the displacement will be 0.0 for atoms not in the
+specified compute group.  Note that the fix defines its own group and
+stores (0.0,0.0,0.0) for the original coordinates of any atom not in
+the fix group.
+</P>
+<P><B>Output info:</B>
+</P>
+<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
+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>
+<P><B>Default:</B> none
+</P>
+</HTML>

doc/compute_displace_atom.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 displace/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID displace/atom fix-ID :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+displace/atom = style name of this compute command
+fix-ID = ID of a fix of style "coord/original"_fix_coord_original.html :ul
+
+[Examples:]
+
+compute 1 all displace/atom myCoords :pre
+
+[Description:]
+
+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.  The original
+coordinates are stored by a "fix
+coord/original"_fix_coord_original.html command, whose ID must be
+specified with this compute.  They are the coordinates at the time the
+fix command was issued.  The displacement can be output directly via
+the "dump custom"_dump.html command.  It could also be used to
+calculate a diffusion coefficient for a group of atoms, as is done by
+the "fix msd"_fix_msd.html command.
+
+The value of the displacement will be 0.0 for atoms not in the
+specified compute group.  Note that the fix defines its own group and
+stores (0.0,0.0,0.0) for the original coordinates of any atom not in
+the fix group.
+
+[Output info:]
+
+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
+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
+
+[Default:] none

doc/compute_ke_atom.html

@@ -33,6 +33,13 @@ specified compute group.
 <P>The kinetic energy is simply 1/2 m v^2, where m is the mass and v is
 the velocity of each atom.
 </P>
+<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
+<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
+output options.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>

doc/compute_ke_atom.txt

@@ -30,6 +30,13 @@ specified compute group.
 The kinetic energy is simply 1/2 m v^2, where m is the mass and v is
 the velocity of each atom.
 
+[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
+"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+output options.
+
 [Restrictions:] none
 
 [Related commands:]

doc/compute_pe_atom.html

@@ -55,6 +55,13 @@ E.g. 1/4 of the dihedral energy to each of the 4 atoms.
 pairwise interactions between 1-4 atoms.  The energy contribution of
 these terms is included in the pair energy, not the dihedral energy.
 </P>
+<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
+<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
+output options.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>

doc/compute_pe_atom.txt

@@ -52,6 +52,13 @@ The "dihedral_style charmm"_dihedral_charmm.html style calculates
 pairwise interactions between 1-4 atoms.  The energy contribution of
 these terms is included in the pair energy, not the dihedral energy.
 
+[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
+"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+output options.
+
 [Restrictions:] none
 
 [Related commands:]

doc/compute_stress_atom.html

@@ -33,9 +33,10 @@ 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
 pressure</A> command if you want the stress tensor
 (pressure) of the entire system.  The 6 components can be accessed by
-indices 1-6 by any command that uses per-atom computes, e.g. the <A HREF = "dump.html">dump
+indices 1-6 by any command that uses per-atom computes as input,
-custom</A> command or <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>
+e.g. the <A HREF = "dump.html">dump custom</A> command or <A HREF = "fix_ave_spatial.html">fix
-command or <A HREF = "fix_ave_atom.html">fix ave/atom</A> command.  See <A HREF = "Section_howto.html#4_15">this
+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,
@@ -97,6 +98,14 @@ possible to compute.  There are also a few pair styles for manybody
 potentials that are not yet instrumented to yield per-atom stress.
 See the Restrictions below.
 </P>
+<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
+as input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview
+of LAMMPS output options.  The 6 components of the vector are ordered
+xx, yy, zz, xy, xz, yz.
+</P>
 <P><B>Restrictions:</B>
 </P>
 <P>These pair styles do not yet tabulate per-atom virial information to

doc/compute_stress_atom.txt

@@ -29,9 +29,10 @@ tensor for each atom in a group.  The tensor for each atom has 6
 components: 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
-indices 1-6 by any command that uses per-atom computes, e.g. the "dump
+indices 1-6 by any command that uses per-atom computes as input,
-custom"_dump.html command or "fix ave/spatial"_fix_ave_spatial.html
+e.g. the "dump custom"_dump.html command or "fix
-command or "fix ave/atom"_fix_ave_atom.html command.  See "this
+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,
@@ -93,6 +94,14 @@ possible to compute.  There are also a few pair styles for manybody
 potentials that are not yet instrumented to yield per-atom stress.
 See the Restrictions below.
 
+[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
+as input.  See "this section"_Section_howto.html#4_15 for an overview
+of LAMMPS output options.  The 6 components of the vector are ordered
+xx, yy, zz, xy, xz, yz.
+
 [Restrictions:]
 
 These pair styles do not yet tabulate per-atom virial information to

doc/fix_ave_atom.html

@@ -53,7 +53,7 @@ ave/spatial</A> or <A HREF = "dump.html">dump custom</A> commands.
 </P>
 <P>Each listed value is averaged independently.  The group specified with
 the command means only atoms within the group have their averages
-computed.  Atoms not in the group have their result set to 0.0.
+computed.  Atoms not in the group have their result(s) set to 0.0.
 </P>
 <P>Each listed value can be an atom attribute (position, velocity, force
 component) or can be the result of a <A HREF = "compute.html">compute</A> or

doc/fix_ave_atom.txt

@@ -42,7 +42,7 @@ ave/spatial"_fix_ave_spatial.html or "dump custom"_dump.html commands.
 
 Each listed value is averaged independently.  The group specified with
 the command means only atoms within the group have their averages
-computed.  Atoms not in the group have their result set to 0.0.
+computed.  Atoms not in the group have their result(s) set to 0.0.
 
 Each listed value can be an atom attribute (position, velocity, force
 component) or can be the result of a "compute"_compute.html or