git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2335 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/thermo_modify.html

@@ -55,10 +55,26 @@ If the value is <I>error</I> or <I>warn</I>, LAMMPS checks and either issues an
 error or warning.  The code will exit with an error and continue with
 a warning.  This can be a useful debugging option.
 </P>
-<P>The <I>norm</I> keyword determines whether the thermodynamic print-out is
-normalized by the number of atoms or is the total summed across all
-atoms.  Different unit styles have different defaults for this
-setting.
+<P>The <I>norm</I> keyword determines whether various thermodynamic output
+values are normalized by the number of atoms or not, depending on
+whether it is set to <I>yes</I> or <I>no</I>.  Different unit styles have
+different defaults for this setting (see below).  Even if <I>norm</I> is
+set to <I>yes</I>, a value is only normalized if it is an "extensive"
+quantity, meaning that it scales with the number of atoms in the
+system.  For the thermo keywords described by the doc page for the
+<A HREF = "thermo_style.html">thermo_style</A> command, all energy-related keywords
+are extensive, such as <I>pe</I> or <I>ebond</I> or <I>enthalpy</I>.  Other keywords
+such as <I>temp</I> or <I>press</I> are "intensive" meaning their value is
+independent (in a statistical sense) of the number of atoms in the
+system and thus are never normalized.  For thermodynamic output values
+extracted from fixes and computes in a <A HREF = "thermo_style.html">thermo_style
+custom</A> command, the doc page for the individual
+<A HREF = "fix.html">fix</A> or <A HREF = "compute.html">compute</A> lists whether the value is
+"extensive" or "intensive" and thus whether it is normalized.
+Thermodynamic output values calculated by a variable formula are
+assumed to be "intensive" and thus are never normalized.  You can
+always include a divide by the number of atoms in the variable formula
+if this is not the case.
 </P>
 <P>The <I>flush</I> keyword invokes a flush operation after thermodynamic info
 is written to the log file.  This insures the output in that file is

doc/thermo_modify.txt

@@ -50,10 +50,26 @@ If the value is {error} or {warn}, LAMMPS checks and either issues an
 error or warning.  The code will exit with an error and continue with
 a warning.  This can be a useful debugging option.
 
-The {norm} keyword determines whether the thermodynamic print-out is
-normalized by the number of atoms or is the total summed across all
-atoms.  Different unit styles have different defaults for this
-setting.
+The {norm} keyword determines whether various thermodynamic output
+values are normalized by the number of atoms or not, depending on
+whether it is set to {yes} or {no}.  Different unit styles have
+different defaults for this setting (see below).  Even if {norm} is
+set to {yes}, a value is only normalized if it is an "extensive"
+quantity, meaning that it scales with the number of atoms in the
+system.  For the thermo keywords described by the doc page for the
+"thermo_style"_thermo_style.html command, all energy-related keywords
+are extensive, such as {pe} or {ebond} or {enthalpy}.  Other keywords
+such as {temp} or {press} are "intensive" meaning their value is
+independent (in a statistical sense) of the number of atoms in the
+system and thus are never normalized.  For thermodynamic output values
+extracted from fixes and computes in a "thermo_style
+custom"_thermo_style.html command, the doc page for the individual
+"fix"_fix.html or "compute"_compute.html lists whether the value is
+"extensive" or "intensive" and thus whether it is normalized.
+Thermodynamic output values calculated by a variable formula are
+assumed to be "intensive" and thus are never normalized.  You can
+always include a divide by the number of atoms in the variable formula
+if this is not the case.
 
 The {flush} keyword invokes a flush operation after thermodynamic info
 is written to the log file.  This insures the output in that file is

doc/thermo_style.html

@@ -102,12 +102,14 @@ f_ID keyword and accessing a fix that does time-averaging such as the
 </P>
 <P>Options invoked by the <A HREF = "thermo_modify.html">thermo_modify</A> command can
 be used to set the one- or multi-line format of the print-out, the
-normalization of energy quantities (total or per-atom), and the
-numeric precision of each printed value.
+normalization of thermodynamic output (total values versus per-atom
+values for "extensive quantities, meaning ones which scale with the
+number of atoms in the system), and the numeric precision of each
+printed value.
 </P>
-<P>IMPORTANT NOTE: When you specify a "thermo_style<A HREF = "thermo_modify.html"> command, all
+<P>IMPORTANT NOTE: When you use a "thermo_style" command, all
 thermodynamic settings are restored to their default values, including
-those previously set by a :thermo_modify</A> command.
+those previously set by a <A HREF = "thermo_modify.html">thermo_modify</A> command.
 Thus if your input script specifies a thermo_style command, you should
 use the thermo_modify command after it.
 </P>

doc/thermo_style.txt

@@ -96,12 +96,14 @@ f_ID keyword and accessing a fix that does time-averaging such as the
 
 Options invoked by the "thermo_modify"_thermo_modify.html command can
 be used to set the one- or multi-line format of the print-out, the
-normalization of energy quantities (total or per-atom), and the
-numeric precision of each printed value.
+normalization of thermodynamic output (total values versus per-atom
+values for "extensive quantities, meaning ones which scale with the
+number of atoms in the system), and the numeric precision of each
+printed value.
 
-IMPORTANT NOTE: When you specify a "thermo_style" command, all
+IMPORTANT NOTE: When you use a "thermo_style" command, all
 thermodynamic settings are restored to their default values, including
-those previously set by a :thermo_modify"_thermo_modify.html command.
+those previously set by a "thermo_modify"_thermo_modify.html command.
 Thus if your input script specifies a thermo_style command, you should
 use the thermo_modify command after it.