git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11330 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/atom_style.html

@@ -147,6 +147,18 @@ molecule and which atom-within-the-molecule they represent.  Using the
 can save memory for systems comprised of a large number of small
 molecules, all of a single type (or small number of types).
 </P>
+<P>IMPORTANT NOTE: When using the <I>template</I> style with a <A HREF = "molecule.html">molecule
+template</A> that contains multiple molecules, you should
+insure the atom types, bond types, angle_types, etc in all the
+molecules are consistent.  E.g. if one molecule represents H2O and
+another CO2, then you probably do not want each molecule file to
+define 2 atom types and a single bond type, because they will conflict
+with each other when a mixture system of H2O and CO2 molecules is
+defined, e.g. by the <A HREF = "read_data.html">read_data</A> command.  Rather the
+H2O molecule should define atom types 1 and 2, and bond type 1.  And
+the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
+2 if a single oxygen type is desired), and bond type 2.
+</P>
 <P>For the <I>body</I> style, the particles are arbitrary bodies with internal
 attributes defined by the "style" of the bodies, which is specified by
 the <I>bstyle</I> argument.  Body particles can represent complex entities,

doc/atom_style.txt

@@ -143,6 +143,18 @@ molecule and which atom-within-the-molecule they represent.  Using the
 can save memory for systems comprised of a large number of small
 molecules, all of a single type (or small number of types).
 
+IMPORTANT NOTE: When using the {template} style with a "molecule
+template"_molecule.html that contains multiple molecules, you should
+insure the atom types, bond types, angle_types, etc in all the
+molecules are consistent.  E.g. if one molecule represents H2O and
+another CO2, then you probably do not want each molecule file to
+define 2 atom types and a single bond type, because they will conflict
+with each other when a mixture system of H2O and CO2 molecules is
+defined, e.g. by the "read_data"_read_data.html command.  Rather the
+H2O molecule should define atom types 1 and 2, and bond type 1.  And
+the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
+2 if a single oxygen type is desired), and bond type 2.
+
 For the {body} style, the particles are arbitrary bodies with internal
 attributes defined by the "style" of the bodies, which is specified by
 the {bstyle} argument.  Body particles can represent complex entities,

doc/molecule.html

@@ -49,6 +49,18 @@ contains multiple molecules.  The <A HREF = "atom_style.html">atom_style
 template</A> command allows multiple-molecule templates
 to define a system with more than one templated molecule.
 </P>
+<P>IMPORTANT NOTE: When using the <A HREF = "atom_style.html">atom_style template</A>
+command with a molecule template that contains multiple molecules, you
+should insure the atom types, bond types, angle_types, etc in all the
+molecules are consistent.  E.g. if one molecule represents H2O and
+another CO2, then you probably do not want each molecule file to
+define 2 atom types and a single bond type, because they will conflict
+with each other when a mixture system of H2O and CO2 molecules is
+defined, e.g.  by the <A HREF = "read_data.html">read_data</A> command.  Rather the
+H2O molecule should define atom types 1 and 2, and bond type 1.  And
+the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
+2 if a single oxygen type is desired), and bond type 2.
+</P>
 <P>The format of an individual molecule file is similar to the data file
 read by the <A HREF = "read_data.html">read_data</A> commands, and is as follows.
 </P>

doc/molecule.txt

@@ -46,6 +46,18 @@ contains multiple molecules.  The "atom_style
 template"_atom_style.html command allows multiple-molecule templates
 to define a system with more than one templated molecule.
 
+IMPORTANT NOTE: When using the "atom_style template"_atom_style.html
+command with a molecule template that contains multiple molecules, you
+should insure the atom types, bond types, angle_types, etc in all the
+molecules are consistent.  E.g. if one molecule represents H2O and
+another CO2, then you probably do not want each molecule file to
+define 2 atom types and a single bond type, because they will conflict
+with each other when a mixture system of H2O and CO2 molecules is
+defined, e.g.  by the "read_data"_read_data.html command.  Rather the
+H2O molecule should define atom types 1 and 2, and bond type 1.  And
+the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
+2 if a single oxygen type is desired), and bond type 2.
+
 The format of an individual molecule file is similar to the data file
 read by the "read_data"_read_data.html commands, and is as follows.
 

doc/read_data.html

@@ -208,6 +208,15 @@ are point particles.  See the discussion of ellipsoidflag and the
 <I>Triangles</I> section below.  See the discussion of bodyflag and the
 <I>Bodies</I> section below.
 </P>
+<P>IMPORTANT NOTE: For <A HREF = "atom_style.html">atom_style template</A>, the
+molecular topology (bonds,angles,etc) is contained in the molecule
+templates read-in by the <A HREF = "molecule.html">molecule</A> command.  This means
+you cannot set the <I>bonds</I>, <I>angles</I>, etc header keywords in the data
+file, nor can you define <I>Bonds</I>, <I>Angles</I>, etc sections as discussed
+below.  You can set the <I>bond types</I>, <I>angle types</I>, etc header
+keywords, though it is not necessary.  If specified, they must match
+the maximum values defined in any of the template molecules.
+</P>
 <HR>
 
 <P>These are the section keywords for the body of the file.

doc/read_data.txt

@@ -202,6 +202,15 @@ are point particles.  See the discussion of ellipsoidflag and the
 {Triangles} section below.  See the discussion of bodyflag and the
 {Bodies} section below.
 
+IMPORTANT NOTE: For "atom_style template"_atom_style.html, the
+molecular topology (bonds,angles,etc) is contained in the molecule
+templates read-in by the "molecule"_molecule.html command.  This means
+you cannot set the {bonds}, {angles}, etc header keywords in the data
+file, nor can you define {Bonds}, {Angles}, etc sections as discussed
+below.  You can set the {bond types}, {angle types}, etc header
+keywords, though it is not necessary.  If specified, they must match
+the maximum values defined in any of the template molecules.
+
 :line
 
 These are the section keywords for the body of the file.