git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7388 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/boundary.html

@@ -65,6 +65,8 @@ atoms becomes less than 50.0.
 <P>This command cannot be used after the simulation box is defined by a
 <A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
 </P>
+<P>For 2d simulations, the z dimension must be periodic.
+</P>
 <P><B>Related commands:</B>
 </P>
 <P>See the <A HREF = "thermo_modify.html">thermo_modify</A> command for a discussion

doc/boundary.txt

@@ -60,6 +60,8 @@ atoms becomes less than 50.0.
 This command cannot be used after the simulation box is defined by a
 "read_data"_read_data.html or "create_box"_create_box.html command.
 
+For 2d simulations, the z dimension must be periodic.
+
 [Related commands:]
 
 See the "thermo_modify"_thermo_modify.html command for a discussion

doc/compute_bond_local.html

@@ -58,6 +58,12 @@ property/local</A> command can be combined
 with data from this command and output by the <A HREF = "dump.html">dump local</A>
 command in a consistent way.
 </P>
+<P>Here is an example of how to do this:
+</P>
+<PRE>compute 1 all property/local batom1 batom2 btype 
+compute 2 all bond/local dist eng
+dump 1 all local 1000 tmp.dump index c_1<B>1</B> c_1<B>2</B> c_1<B>3</B> c_2<B>1</B> c_2<B>2</B> 
+</PRE>
 <P><B>Output info:</B>
 </P>
 <P>This compute calculates a local vector or local array depending on the

doc/compute_bond_local.txt

@@ -50,6 +50,12 @@ property/local"_compute_property_local.html command can be combined
 with data from this command and output by the "dump local"_dump.html
 command in a consistent way.
 
+Here is an example of how to do this:
+
+compute 1 all property/local batom1 batom2 btype 
+compute 2 all bond/local dist eng
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2] :pre
+
 [Output info:]
 
 This compute calculates a local vector or local array depending on the

doc/dump.html

@@ -386,6 +386,13 @@ the fix is printed.  If <I>f_ID[N]</I> is used, then N must be in the
 range from 1-M, which will print the Nth column of the M-length local
 array calculated by the fix.
 </P>
+<P>Here is an example of how to dump bond info for a system,
+including the distance and energy of each bond:
+</P>
+<PRE>compute 1 all property/local batom1 batom2 btype 
+compute 2 all bond/local dist eng
+dump 1 all local 1000 tmp.dump index c_1<B>1</B> c_1<B>2</B> c_1<B>3</B> c_2<B>1</B> c_2<B>2</B> 
+</PRE>
 <HR>
 
 <P>This section explains the atom attributes that can be specified as

doc/dump.txt

@@ -375,6 +375,13 @@ the fix is printed.  If {f_ID\[N\]} is used, then N must be in the
 range from 1-M, which will print the Nth column of the M-length local
 array calculated by the fix.
 
+Here is an example of how to dump bond info for a system,
+including the distance and energy of each bond:
+
+compute 1 all property/local batom1 batom2 btype 
+compute 2 all bond/local dist eng
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2] :pre
+
 :line
 
 This section explains the atom attributes that can be specified as

doc/partition.html

@@ -69,7 +69,7 @@ command lays out a 3d grid of processors in each of 2 partitions.
 </P>
 <P><B>Restrictions:</B> none
 </P>
-<P><B>Related commands:</B> none
+<P><B>Related commands:</B>
 </P>
 <P><A HREF = "run_style.html">run_style verlet/split</A>
 </P>

doc/partition.txt

@@ -66,7 +66,7 @@ command lays out a 3d grid of processors in each of 2 partitions.
 
 [Restrictions:] none
 
-[Related commands:] none
+[Related commands:]
 
 "run_style verlet/split"_run_style.html
 

doc/thermo_modify.html

@@ -106,13 +106,13 @@ this case.  If the format for a specific column has been set, it will
 take precedent over the <I>int</I> or <I>float</I> setting.
 </P>
 <P>IMPORTANT NOTE: The thermo output values <I>step</I> and <I>atoms</I> are stored
-internally as 8-byte unsigned integers, rather than the usual 4-byte
+internally as 8-byte signed integers, rather than the usual 4-byte
 signed integers.  When specifying the "format int" keyword you can use
 a "%d"-style format identifier in the format string and LAMMPS will
 convert this to the corresponding "%lu" form when it is applied to
 those keywords.  However, when specifying the "format M string"
 keyword for <I>step</I> and <I>natoms</I>, you should specify a string
-appropriate for an 8-byte unsigned integer, e.g. one with "%lu".
+appropriate for an 8-byte signed integer, e.g. one with "%ld".
 </P>
 <P>The <I>temp</I> keyword is used to determine how thermodynamic temperature
 is calculated, which is used by all thermo quantities that require a

doc/thermo_modify.txt

@@ -100,13 +100,13 @@ this case.  If the format for a specific column has been set, it will
 take precedent over the {int} or {float} setting.
 
 IMPORTANT NOTE: The thermo output values {step} and {atoms} are stored
-internally as 8-byte unsigned integers, rather than the usual 4-byte
+internally as 8-byte signed integers, rather than the usual 4-byte
 signed integers.  When specifying the "format int" keyword you can use
 a "%d"-style format identifier in the format string and LAMMPS will
 convert this to the corresponding "%lu" form when it is applied to
 those keywords.  However, when specifying the "format M string"
 keyword for {step} and {natoms}, you should specify a string
-appropriate for an 8-byte unsigned integer, e.g. one with "%lu".
+appropriate for an 8-byte signed integer, e.g. one with "%ld".
 
 The {temp} keyword is used to determine how thermodynamic temperature
 is calculated, which is used by all thermo quantities that require a