git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5069 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/compute_atom_molecute.html

@@ -34,8 +34,7 @@
 <P><B>Examples:</B>
 </P>
 <PRE>compute 1 all atom/molecule c_ke c_pe
-</PRE>
-<PRE>compute 1 top atom/molecule v_myFormula c_stress<B>3</B> 
+compute 1 top atom/molecule v_myFormula c_stress<B>3</B> 
 </PRE>
 <P><B>Description:</B>
 </P>
@@ -54,13 +53,11 @@ they return.  For example, if a compute is used as an input which
 generates a per-atom vector, it will generate values of 0.0 for atoms
 that are not in the group specified for that compute.
 </P>
-<P>The ordering of per-molecule quantities produced by this compute are
+<P>The ordering of per-molecule quantities produced by this compute is
 consistent with the ordering produced by other compute commands that
-generate per-molecule datums.  Let Nmolecules be the number of
-molecules for which a result is calculated.  If not all molecules have
-atoms in the group, then the molecule with the lowest ID is the first
-of the Nmolecules.  The next lowest ID is the second, etc, up to
-Nmolecules.
+generate per-molecule datums.  Conceptually, them molecule IDs will be
+in ascending order for any molecule with one or more of its atoms in
+the specified group.
 </P>
 <P>If an input begins with "c_", a compute ID must follow which has been
 previously defined in the input script and which generates per-atom

doc/compute_atom_molecute.txt

@@ -45,13 +45,11 @@ they return.  For example, if a compute is used as an input which
 generates a per-atom vector, it will generate values of 0.0 for atoms
 that are not in the group specified for that compute.
 
-The ordering of per-molecule quantities produced by this compute are
+The ordering of per-molecule quantities produced by this compute is
 consistent with the ordering produced by other compute commands that
-generate per-molecule datums.  Let Nmolecules be the number of
-molecules for which a result is calculated.  If not all molecules have
-atoms in the group, then the molecule with the lowest ID is the first
-of the Nmolecules.  The next lowest ID is the second, etc, up to
-Nmolecules.
+generate per-molecule datums.  Conceptually, them molecule IDs will be
+in ascending order for any molecule with one or more of its atoms in
+the specified group.
 
 If an input begins with "c_", a compute ID must follow which has been
 previously defined in the input script and which generates per-atom

doc/compute_com_molecule.html

@@ -35,10 +35,11 @@ however this is not required.  LAMMPS will warn you if this is not the
 case.  Only atoms in the group contribute to the center-of-mass
 calculation for the molecule.
 </P>
-<P>Let Nmolecules be the number of molecules for which the center-of-mass
-is calculated.  If not all molecules have atoms in the group, then the
-molecule with the lowest ID is the first of the Nmolecules.  The next
-lowest ID is the second, etc, up to Nmolecules.
+<P>The ordering of per-molecule quantities produced by this compute is
+consistent with the ordering produced by other compute commands that
+generate per-molecule datums.  Conceptually, them molecule IDs will be
+in ascending order for any molecule with one or more of its atoms in
+the specified group.
 </P>
 <P>IMPORTANT NOTE: The coordinates of an atom contribute to the
 molecule's center-of-mass in "unwrapped" form, by using the image

doc/compute_com_molecule.txt

@@ -32,10 +32,11 @@ however this is not required.  LAMMPS will warn you if this is not the
 case.  Only atoms in the group contribute to the center-of-mass
 calculation for the molecule.
 
-Let Nmolecules be the number of molecules for which the center-of-mass
-is calculated.  If not all molecules have atoms in the group, then the
-molecule with the lowest ID is the first of the Nmolecules.  The next
-lowest ID is the second, etc, up to Nmolecules.
+The ordering of per-molecule quantities produced by this compute is
+consistent with the ordering produced by other compute commands that
+generate per-molecule datums.  Conceptually, them molecule IDs will be
+in ascending order for any molecule with one or more of its atoms in
+the specified group.
 
 IMPORTANT NOTE: The coordinates of an atom contribute to the
 molecule's center-of-mass in "unwrapped" form, by using the image

doc/compute_gyration_molecule.html

@@ -43,10 +43,11 @@ should be in the group, however this is not required.  LAMMPS will
 warn you if this is not the case.  Only atoms in the group contribute
 to the Rg calculation for the molecule.
 </P>
-<P>Let Nmolecules be the number of molecules for which Rg is calculated.
-If not all molecules have atoms in the group, then the molecule with
-the lowest ID is the first of the Nmolecules.  The next lowest ID is
-the second, etc, up to Nmolecules.
+<P>The ordering of per-molecule quantities produced by this compute is
+consistent with the ordering produced by other compute commands that
+generate per-molecule datums.  Conceptually, them molecule IDs will be
+in ascending order for any molecule with one or more of its atoms in
+the specified group.
 </P>
 <P>IMPORTANT NOTE: The coordinates of an atom contribute to Rg in
 "unwrapped" form, by using the image flags associated with each atom.

doc/compute_gyration_molecule.txt

@@ -40,10 +40,11 @@ should be in the group, however this is not required.  LAMMPS will
 warn you if this is not the case.  Only atoms in the group contribute
 to the Rg calculation for the molecule.
 
-Let Nmolecules be the number of molecules for which Rg is calculated.
-If not all molecules have atoms in the group, then the molecule with
-the lowest ID is the first of the Nmolecules.  The next lowest ID is
-the second, etc, up to Nmolecules.
+The ordering of per-molecule quantities produced by this compute is
+consistent with the ordering produced by other compute commands that
+generate per-molecule datums.  Conceptually, them molecule IDs will be
+in ascending order for any molecule with one or more of its atoms in
+the specified group.
 
 IMPORTANT NOTE: The coordinates of an atom contribute to Rg in
 "unwrapped" form, by using the image flags associated with each atom.

doc/compute_msd_molecule.html

@@ -47,10 +47,11 @@ will warn you if this is not the case.  Only atoms in the group
 contribute to the center-of-mass calculation for the molecule, which
 is used to caculate its initial and current position.
 </P>
-<P>Let Nmolecules be the number of molecules for which the MSD is
-calculated.  If not all molecules have atoms in the group, then the
-molecule with the lowest ID is the first of the Nmolecules.  The next
-lowest ID is the second, etc, up to Nmolecules.
+<P>The ordering of per-molecule quantities produced by this compute is
+consistent with the ordering produced by other compute commands that
+generate per-molecule datums.  Conceptually, them molecule IDs will be
+in ascending order for any molecule with one or more of its atoms in
+the specified group.
 </P>
 <P>IMPORTANT NOTE: The initial coordinates of each molecule are stored in
 "unwrapped" form, by using the image flags associated with each atom.

doc/compute_msd_molecule.txt

@@ -44,10 +44,11 @@ will warn you if this is not the case.  Only atoms in the group
 contribute to the center-of-mass calculation for the molecule, which
 is used to caculate its initial and current position.
 
-Let Nmolecules be the number of molecules for which the MSD is
-calculated.  If not all molecules have atoms in the group, then the
-molecule with the lowest ID is the first of the Nmolecules.  The next
-lowest ID is the second, etc, up to Nmolecules.
+The ordering of per-molecule quantities produced by this compute is
+consistent with the ordering produced by other compute commands that
+generate per-molecule datums.  Conceptually, them molecule IDs will be
+in ascending order for any molecule with one or more of its atoms in
+the specified group.
 
 IMPORTANT NOTE: The initial coordinates of each molecule are stored in
 "unwrapped" form, by using the image flags associated with each atom.

doc/compute_property_molecule.html

@@ -40,13 +40,16 @@ commands that generate per-molecule data, such as <A HREF = "compute_com_molecul
 com/molecule</A> and <A HREF = "compute_msd_molecule.html">compute
 msd/molecule</A>.
 </P>
-<P>The <I>mol</I> attribute generates a list of molecule IDs in ascending
-order for any molecule with one or more of its atoms in the specified
-group.  This list and ordering of molecule IDs will be consistent with
-the ordering produced by other compute commands that generate
-per-molecule datums.  Thus this attribute can be used to produce
-molecule IDs as labels for those datums when they are output to a
-file, e.g. by the <A HREF = "fix_ave_time.html">fix ave/time</A> command.
+<P>The ordering of per-molecule quantities produced by this compute is
+consistent with the ordering produced by other compute commands that
+generate per-molecule datums.  Conceptually, them molecule IDs will be
+in ascending order for any molecule with one or more of its atoms in
+the specified group.
+</P>
+<P>The <I>mol</I> attribute is the molecule ID.  This attribute can be used to
+produce molecule IDs as labels for per-molecule datums generated by
+other computes or fixes when they are output to a file, e.g. by the
+<A HREF = "fix_ave_time.html">fix ave/time</A> command.
 </P>
 <P>The <I>count</I> attribute is the number of atoms in the molecule.
 </P>

doc/compute_property_molecule.txt

@@ -33,13 +33,16 @@ commands that generate per-molecule data, such as "compute
 com/molecule"_compute_com_molecule.html and "compute
 msd/molecule"_compute_msd_molecule.html.
 
-The {mol} attribute generates a list of molecule IDs in ascending
-order for any molecule with one or more of its atoms in the specified
-group.  This list and ordering of molecule IDs will be consistent with
-the ordering produced by other compute commands that generate
-per-molecule datums.  Thus this attribute can be used to produce
-molecule IDs as labels for those datums when they are output to a
-file, e.g. by the "fix ave/time"_fix_ave_time.html command.
+The ordering of per-molecule quantities produced by this compute is
+consistent with the ordering produced by other compute commands that
+generate per-molecule datums.  Conceptually, them molecule IDs will be
+in ascending order for any molecule with one or more of its atoms in
+the specified group.
+
+The {mol} attribute is the molecule ID.  This attribute can be used to
+produce molecule IDs as labels for per-molecule datums generated by
+other computes or fixes when they are output to a file, e.g. by the
+"fix ave/time"_fix_ave_time.html command.
 
 The {count} attribute is the number of atoms in the molecule.