git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1613 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_errors.html

@@ -374,7 +374,7 @@ are too far apart to make a valid bond.
 
 <DT><I>Bond atoms %d %d missing on proc %d at step %d</I> 
 
-<DD>One or more of 2 atoms needed to compute a particular bond are
+<DD>One or both of 2 atoms needed to compute a particular bond are
 missing on this processor.  Typically this is because the pairwise
 cutoff is set too short or the bond has blown apart and an atom is
 too far away. 
@@ -514,7 +514,7 @@ or create_box command.
 
 <DT><I>Cannot fix deform on a non-periodic boundary</I> 
 
-<DD>Only a periodiic boundary can be modified. 
+<DD>Only a periodic boundary can be modified. 
 
 <DT><I>Cannot have both pair_modify shift and tail set to yes</I> 
 
@@ -1036,6 +1036,10 @@ does not exist.
 
 <DD>A group ID used in the dump command does not exist. 
 
+<DT><I>Could not find dump_modify ID</I> 
+
+<DD>Self-explanatory. 
+
 <DT><I>Could not find fix ID to delete</I> 
 
 <DD>Self-explanatory. 
@@ -1136,10 +1140,6 @@ does not exist.
 <DD>If using a Kspace solver, all Coulomb cutoffs of long pair styles must
 be the same. 
 
-<DT><I>Cound not find dump_modify ID</I> 
-
-<DD>Self-explanatory. 
-
 <DT><I>Create_atoms command before simulation box is defined</I> 
 
 <DD>The create_atoms command cannot be used before a read_data,
@@ -1187,7 +1187,7 @@ read_restart, or create_box command.
 
 <DT><I>Deposition region extends outside simulation box</I> 
 
-<DD>Self-explatory. 
+<DD>Self-explanatory. 
 
 <DT><I>Did not assign all atoms correctly</I> 
 
@@ -2387,7 +2387,7 @@ orthogonal.
 <DD>The three specified lattice orientation vectors must create a
 right-handed coordinate system such that a1 cross a2 = a3. 
 
-<DT><I>Lattice primitive vectors are colinear</I> 
+<DT><I>Lattice primitive vectors are collinear</I> 
 
 <DD>The specified lattice primitive vectors do not for a unit cell with
 non-zero volume. 
@@ -3104,7 +3104,7 @@ outside a non-periodic simulation box.
 
 <DD>Fix poems will only work with bodies (collections of atoms) that have
 non-zero principal moments of inertia.  This means they must be 3 or
-more non-colinear atoms, even with joint atoms removed. 
+more non-collinear atoms, even with joint atoms removed. 
 
 <DT><I>Rigid fix must come before NPT/NPH fix</I> 
 

doc/Section_errors.txt

@@ -371,7 +371,7 @@ are too far apart to make a valid bond. :dd
 
 {Bond atoms %d %d missing on proc %d at step %d} :dt
 
-One or more of 2 atoms needed to compute a particular bond are
+One or both of 2 atoms needed to compute a particular bond are
 missing on this processor.  Typically this is because the pairwise
 cutoff is set too short or the bond has blown apart and an atom is
 too far away. :dd
@@ -511,7 +511,7 @@ Group ID used in the delete_bonds command does not exist. :dd
 
 {Cannot fix deform on a non-periodic boundary} :dt
 
-Only a periodiic boundary can be modified. :dd
+Only a periodic boundary can be modified. :dd
 
 {Cannot have both pair_modify shift and tail set to yes} :dt
 
@@ -1033,6 +1033,10 @@ Self-explanatory. :dd
 
 A group ID used in the dump command does not exist. :dd
 
+{Could not find dump_modify ID} :dt
+
+Self-explanatory. :dd
+
 {Could not find fix ID to delete} :dt
 
 Self-explanatory. :dd
@@ -1133,10 +1137,6 @@ does not exist. :dd
 If using a Kspace solver, all Coulomb cutoffs of long pair styles must
 be the same. :dd
 
-{Cound not find dump_modify ID} :dt
-
-Self-explanatory. :dd
-
 {Create_atoms command before simulation box is defined} :dt
 
 The create_atoms command cannot be used before a read_data,
@@ -1184,7 +1184,7 @@ No atoms are yet defined so the delete_bonds command cannot be used. :dd
 
 {Deposition region extends outside simulation box} :dt
 
-Self-explatory. :dd
+Self-explanatory. :dd
 
 {Did not assign all atoms correctly} :dt
 
@@ -2384,7 +2384,7 @@ orthogonal. :dd
 The three specified lattice orientation vectors must create a
 right-handed coordinate system such that a1 cross a2 = a3. :dd
 
-{Lattice primitive vectors are colinear} :dt
+{Lattice primitive vectors are collinear} :dt
 
 The specified lattice primitive vectors do not for a unit cell with
 non-zero volume. :dd
@@ -3101,7 +3101,7 @@ A region ID cannot be used twice. :dd
 
 Fix poems will only work with bodies (collections of atoms) that have
 non-zero principal moments of inertia.  This means they must be 3 or
-more non-colinear atoms, even with joint atoms removed. :dd
+more non-collinear atoms, even with joint atoms removed. :dd
 
 {Rigid fix must come before NPT/NPH fix} :dt
 

doc/Section_howto.html

@@ -319,10 +319,16 @@ place:
 the following commands:
 </P>
 <UL><LI><A HREF = "atom_style.html">atom_style</A> granular
-<LI><A HREF = "fix_nve_gran.html">fix nve/gran</A>
+<LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
 <LI><A HREF = "fix_gravity.html">fix gravity</A> 
-<LI><A HREF = "thermo_style.html">thermo_style</A> gran 
 </UL>
+<P>This compute
+</P>
+<UL><LI><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A> 
+</UL>
+<P>will calculate rotational kinetic energy which can then be <A HREF = "">output
+with thermodynamic info</A>.
+</P>
 <P>Use one of these 3 pair potentials:
 </P>
 <UL><LI><A HREF = "pair_style.html">pair_style</A> gran/history

doc/Section_howto.txt

@@ -315,9 +315,15 @@ To run a simulation of a granular model, you will want to use
 the following commands:
 
 "atom_style"_atom_style.html granular
-"fix nve/gran"_fix_nve_gran.html
+"fix nve/sphere"_fix_nve_sphere.html
-"fix gravity"_fix_gravity.html
+"fix gravity"_fix_gravity.html :ul
-"thermo_style"_thermo_style.html gran :ul
+
+This compute
+
+"compute erotate/sphere"_compute_erotate_sphere.html :ul
+
+will calculate rotational kinetic energy which can then be "output
+with thermodynamic info"_.
 
 Use one of these 3 pair potentials:
 

doc/Section_intro.html

@@ -128,8 +128,8 @@ commands)
 <LI>  angle potentials: harmonic, CHARMM, cosine, cosine/squared,     class 2 (COMPASS)
 <LI>  dihedral potentials: harmonic, CHARMM, multi-harmonic, helix,     class 2 (COMPASS), OPLS
 <LI>  improper potentials: harmonic, cvff, class 2 (COMPASS)
-<LI>  hybrid potentials: multiple pair, bond, angle, dihedral, improper     potentials can be used in one simlulation
+<LI>  hybrid potentials: multiple pair, bond, angle, dihedral, improper     potentials can be used in one simulation
-<LI>  overlayed potentials: superposition of multiple pair potentials
+<LI>  overlaid potentials: superposition of multiple pair potentials
 <LI>  polymer potentials: all-atom, united-atom, bead-spring, breakable
 <LI>  water potentials: TIP3P, TIP4P, SPC
 <LI>  implicit solvent potentials: hydrodynamic lubrication, Debye

doc/Section_intro.txt

@@ -129,8 +129,8 @@ commands)
     class 2 (COMPASS), OPLS
   improper potentials: harmonic, cvff, class 2 (COMPASS)
   hybrid potentials: multiple pair, bond, angle, dihedral, improper \
-    potentials can be used in one simlulation
+    potentials can be used in one simulation
-  overlayed potentials: superposition of multiple pair potentials
+  overlaid potentials: superposition of multiple pair potentials
   polymer potentials: all-atom, united-atom, bead-spring, breakable
   water potentials: TIP3P, TIP4P, SPC
   implicit solvent potentials: hydrodynamic lubrication, Debye

doc/Section_modify.html

@@ -14,7 +14,7 @@ Section</A>
 <H3>8. Modifying & extending LAMMPS 
 </H3>
 <P>LAMMPS is designed in a modular fashion so as to be easy to modify and
-extend with new functionality.  In fact, about 75% if its source code
+extend with new functionality.  In fact, about 75% of its source code
 is files added in this fashion.
 </P>
 <P>In this section, changes and additions users can make are listed along

doc/Section_modify.txt

@@ -11,7 +11,7 @@ Section"_Section_errors.html :c
 8. Modifying & extending LAMMPS :h3
 
 LAMMPS is designed in a modular fashion so as to be easy to modify and
-extend with new functionality.  In fact, about 75% if its source code
+extend with new functionality.  In fact, about 75% of its source code
 is files added in this fashion.
 
 In this section, changes and additions users can make are listed along

doc/Section_tools.html

@@ -65,7 +65,7 @@ own sub-directories with their own Makefiles.
 
 <H4><A NAME = "amber"></A>amber2lmp tool 
 </H4>
-<P>The amber2lmp sub-directory contain two Python scripts for converting
+<P>The amber2lmp sub-directory contains two Python scripts for converting
 files back-and-forth between the AMBER MD code and LAMMPS.  See the
 README file in amber2lmp for more information.
 </P>

doc/Section_tools.txt

@@ -61,7 +61,7 @@ own sub-directories with their own Makefiles.
 
 amber2lmp tool :h4,link(amber)
 
-The amber2lmp sub-directory contain two Python scripts for converting
+The amber2lmp sub-directory contains two Python scripts for converting
 files back-and-forth between the AMBER MD code and LAMMPS.  See the
 README file in amber2lmp for more information.
 

doc/angle_coeff.html

@@ -32,7 +32,7 @@ Angle coefficients can also be set in the data file read by the
 <A HREF = "read_data.html">read_data</A> command or in a restart file.
 </P>
 <P>N can be specified in one of two ways.  An explicit numeric value can
-be used, as in the 1st example above.  Or a wild-card asterik can be
+be used, as in the 1st example above.  Or a wild-card asterisk can be
 used to set the coefficients for multiple angle types.  This takes the
 form "*" or "*n" or "n*" or "m*n".  If N = the number of angle types,
 then an asterisk with no numeric values means all types from 1 to N.  A

doc/angle_coeff.txt

@@ -29,7 +29,7 @@ Angle coefficients can also be set in the data file read by the
 "read_data"_read_data.html command or in a restart file.
 
 N can be specified in one of two ways.  An explicit numeric value can
-be used, as in the 1st example above.  Or a wild-card asterik can be
+be used, as in the 1st example above.  Or a wild-card asterisk can be
 used to set the coefficients for multiple angle types.  This takes the
 form "*" or "*n" or "n*" or "m*n".  If N = the number of angle types,
 then an asterisk with no numeric values means all types from 1 to N.  A

doc/fix_langevin.html

@@ -119,7 +119,7 @@ include that dimension.  The default is 1 for all 3 dimensions.
 the specified factor for atoms of that type.  This can be useful when
 different atom types have different sizes or masses.  It can be used
 multiple times to adjust damp for several atom types.  Note that
-specifying a ratio of 2 increase the relaxation time which is
+specifying a ratio of 2 increases the relaxation time which is
 equivalent to the the solvent's viscosity acting on particles with 1/2
 the diameter.  This is the opposite effect of scale factors used by
 the <A HREF = "fix_viscous.html">fix viscous</A> command, since the damp factor in

doc/fix_langevin.txt

@@ -109,7 +109,7 @@ The keyword {scale} allows the damp factor to be scaled up or down by
 the specified factor for atoms of that type.  This can be useful when
 different atom types have different sizes or masses.  It can be used
 multiple times to adjust damp for several atom types.  Note that
-specifying a ratio of 2 increase the relaxation time which is
+specifying a ratio of 2 increases the relaxation time which is
 equivalent to the the solvent's viscosity acting on particles with 1/2
 the diameter.  This is the opposite effect of scale factors used by
 the "fix viscous"_fix_viscous.html command, since the damp factor in

doc/fix_poems.html

@@ -59,7 +59,7 @@ a constant-energy time integration, so you should not update the same
 atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
 </P>
 <P>Each body must have a non-degenerate inertia tensor, which means if
-must contain at least 3 non-colinear atoms.  Which atoms are in which
+must contain at least 3 non-collinear atoms.  Which atoms are in which
 bodies can be defined via several options.
 </P>
 <P>For option <I>group</I>, each of the listed groups is treated as a rigid

doc/fix_poems.txt

@@ -52,7 +52,7 @@ a constant-energy time integration, so you should not update the same
 atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
 
 Each body must have a non-degenerate inertia tensor, which means if
-must contain at least 3 non-colinear atoms.  Which atoms are in which
+must contain at least 3 non-collinear atoms.  Which atoms are in which
 bodies can be defined via several options.
 
 For option {group}, each of the listed groups is treated as a rigid

doc/jump.html

@@ -52,7 +52,7 @@ jump in.lj loop
 <P>If the jump <I>file</I> argument is a variable, the jump command can be
 used to cause different processor partitions to run different input
 scripts.  In this example, LAMMPS is run on 40 processors, with 4
-partions of 10 procs each.  An in.file containing the example variable
+partitions of 10 procs each.  An in.file containing the example variable
 and jump command will cause each partition to run a different
 simulation.
 </P>

doc/jump.txt

@@ -49,7 +49,7 @@ jump in.lj loop :pre
 If the jump {file} argument is a variable, the jump command can be
 used to cause different processor partitions to run different input
 scripts.  In this example, LAMMPS is run on 40 processors, with 4
-partions of 10 procs each.  An in.file containing the example variable
+partitions of 10 procs each.  An in.file containing the example variable
 and jump command will cause each partition to run a different
 simulation.
 

doc/mass.html

@@ -36,7 +36,7 @@ individual atoms, not types.  <A HREF = "pair_eam.html">Pair_style eam</A> defin
 the masses of atom types in the EAM potential file.
 </P>
 <P>I can be specified in one of two ways.  An explicit numeric value can
-be used, as in the 1st example above.  Or a wild-card asterik can be
+be used, as in the 1st example above.  Or a wild-card asterisk can be
 used to set the mass for multiple atom types.  This takes the form "*"
 or "*n" or "n*" or "m*n".  If N = the number of atom types, then an
 asterisk with no numeric values means all types from 1 to N.  A leading
@@ -46,7 +46,7 @@ types from m to n (inclusive).
 </P>
 <P>A line in a data file that specifies mass uses the same format as the
 arguments of the mass command in an input script, except that no
-wild-card asterik can be used.  For example, under the "Masses"
+wild-card asterisk can be used.  For example, under the "Masses"
 section of a data file, the line that corresponds to the 1st example
 above would be listed as
 </P>

doc/mass.txt

@@ -33,7 +33,7 @@ individual atoms, not types.  "Pair_style eam"_pair_eam.html defines
 the masses of atom types in the EAM potential file.
 
 I can be specified in one of two ways.  An explicit numeric value can
-be used, as in the 1st example above.  Or a wild-card asterik can be
+be used, as in the 1st example above.  Or a wild-card asterisk can be
 used to set the mass for multiple atom types.  This takes the form "*"
 or "*n" or "n*" or "m*n".  If N = the number of atom types, then an
 asterisk with no numeric values means all types from 1 to N.  A leading
@@ -43,7 +43,7 @@ types from m to n (inclusive).
 
 A line in a data file that specifies mass uses the same format as the
 arguments of the mass command in an input script, except that no
-wild-card asterik can be used.  For example, under the "Masses"
+wild-card asterisk can be used.  For example, under the "Masses"
 section of a data file, the line that corresponds to the 1st example
 above would be listed as
 

doc/pair_airebo.html

@@ -80,9 +80,9 @@ LAMMPS atom types:
 <UL><LI>filename
 <LI>N element names = mapping of AIREBO elements to atom types 
 </UL>
-<P>As an example, if your LAMMPS simulation has 4 atoms types and you
+<P>As an example, if your LAMMPS simulation has 4 atom types and you want
-want the 1st 3 to be C, and the 4th to be H, you would use the
+the 1st 3 to be C, and the 4th to be H, you would use the following
-following pair_coeff command:
+pair_coeff command:
 </P>
 <PRE>pair_coeff * * CH.airebo C C C H 
 </PRE>

doc/pair_airebo.txt

@@ -77,9 +77,9 @@ LAMMPS atom types:
 filename
 N element names = mapping of AIREBO elements to atom types :ul
 
-As an example, if your LAMMPS simulation has 4 atoms types and you
+As an example, if your LAMMPS simulation has 4 atom types and you want
-want the 1st 3 to be C, and the 4th to be H, you would use the
+the 1st 3 to be C, and the 4th to be H, you would use the following
-following pair_coeff command:
+pair_coeff command:
 
 pair_coeff * * CH.airebo C C C H :pre
 

doc/pair_gran.html

@@ -44,7 +44,7 @@ apart when r is less than the contact distance d.
 <CENTER><IMG SRC = "Eqs/pair_granular.jpg">
 </CENTER>
 <P>The 1st term is a normal force and the 2nd term is a tangential force.
-The other quantites are as follows:
+The other quantities are as follows:
 </P>
 <UL><LI>delta = d - r
 <LI>f(x) = 1 for Hookean contacts used in pair styles <I>history</I> and <I>no_history</I>

doc/pair_gran.txt

@@ -34,7 +34,7 @@ apart when r is less than the contact distance d.
 :c,image(Eqs/pair_granular.jpg)
 
 The 1st term is a normal force and the 2nd term is a tangential force.
-The other quantites are as follows:
+The other quantities are as follows:
 
 delta = d - r
 f(x) = 1 for Hookean contacts used in pair styles {history} and {no_history}

doc/pair_soft.html

@@ -65,7 +65,7 @@ always mixed via a <I>geometric</I> rule.  The cutoff is mixed according to
 the pair_modify mix value.  The default mix value is <I>geometric</I>.  See
 the "pair_modify" command for details.
 </P>
-<P>This pair styles does not support the <A HREF = "pair_modify.html">pair_modify</A>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
 shift option, since the pair interaction goes to 0.0 at the cutoff.
 </P>
 <P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not

doc/pair_soft.txt

@@ -62,7 +62,7 @@ always mixed via a {geometric} rule.  The cutoff is mixed according to
 the pair_modify mix value.  The default mix value is {geometric}.  See
 the "pair_modify" command for details.
 
-This pair styles does not support the "pair_modify"_pair_modify.html
+This pair style does not support the "pair_modify"_pair_modify.html
 shift option, since the pair interaction goes to 0.0 at the cutoff.
 
 The "pair_modify"_pair_modify.html table and tail options are not

doc/pair_sw.html

@@ -85,19 +85,17 @@ for both two-body and three-body interactions. gamma is used only in the
 three-body interactions, but is defined for pairs of atoms.   
 The non-annotated parameters are unitless.
 </P>
-<P>LAMMPS introduces an additional performance-optimization parameter 
+<P>LAMMPS introduces an additional performance-optimization parameter tol
-tol that is used for
+that is used for both two-body and three-body interactions.  In the
-both two-body and three-body interactions.
+Stillinger-Weber potential, the interaction energies become negligibly
-In the Stillinger-Weber potential, the
+small at atomic separations substantially less than the theoretical
-interaction energies become negligibly small at atomic separations 
+cutoff distances.  LAMMPS therefore defines a virtual cutoff distance
-substantially less than the theoretical cutoff
+based on a user defined tolerance tol.  The use of the virtual cutoff
-distances.  LAMMPS therefore defines a virtual cutoff distance 
+distance in constructing atom neighbor lists can significantly reduce
-based on a user defined tolerance tol.  
+the neighbor list sizes and therefore the computational cost.  LAMMPS
-The use of the virtual cutoff distance in constructing atom neighbor
+provides a <I>tol</I> value for each of the three-body entries so that they
-lists can significantly reduce the neighbor list sizes and therefore the
+can be separately controlled. If tol = 0.0, then the standard
-computational cost.  LAMMPS provide a tol value for each of the three-body
+Stillinger-Weber cutoff is used.
-entries so that they can be separately controlled. If tol = 0.0, then 
-the standard Stillinger-Weber cutoff is used.
 </P>
 <P>The Stillinger-Weber potential file must contain entries for all the
 elements listed in the pair_coeff command.  It can also contain

doc/pair_sw.txt

@@ -82,19 +82,17 @@ for both two-body and three-body interactions. gamma is used only in the
 three-body interactions, but is defined for pairs of atoms.   
 The non-annotated parameters are unitless.
 
-LAMMPS introduces an additional performance-optimization parameter 
+LAMMPS introduces an additional performance-optimization parameter tol
-tol that is used for
+that is used for both two-body and three-body interactions.  In the
-both two-body and three-body interactions.
+Stillinger-Weber potential, the interaction energies become negligibly
-In the Stillinger-Weber potential, the
+small at atomic separations substantially less than the theoretical
-interaction energies become negligibly small at atomic separations 
+cutoff distances.  LAMMPS therefore defines a virtual cutoff distance
-substantially less than the theoretical cutoff
+based on a user defined tolerance tol.  The use of the virtual cutoff
-distances.  LAMMPS therefore defines a virtual cutoff distance 
+distance in constructing atom neighbor lists can significantly reduce
-based on a user defined tolerance tol.  
+the neighbor list sizes and therefore the computational cost.  LAMMPS
-The use of the virtual cutoff distance in constructing atom neighbor
+provides a {tol} value for each of the three-body entries so that they
-lists can significantly reduce the neighbor list sizes and therefore the
+can be separately controlled. If tol = 0.0, then the standard
-computational cost.  LAMMPS provide a tol value for each of the three-body
+Stillinger-Weber cutoff is used.
-entries so that they can be separately controlled. If tol = 0.0, then 
-the standard Stillinger-Weber cutoff is used.
 
 The Stillinger-Weber potential file must contain entries for all the
 elements listed in the pair_coeff command.  It can also contain