git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4191 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_ave_histo.html

@@ -94,14 +94,24 @@ component) or can be the result of a <A HREF = "compute.html">compute</A> or
 <A HREF = "fix.html">fix</A> or the evaluation of an equal-style or atom-style
 <A HREF = "variable.html">variable</A>.  The set of input values can be either all
 global, all per-atom, or all local quantities.  Inputs of different
-kinds (e.g. global and per-atom) cannot be mixed.  The input values
-must also be either all scalar or all vector values, depending on the
-setting of the <I>mode</I> keyword.
+kinds (e.g. global and per-atom) cannot be mixed.  Atom attributes are
+per-atom vector values.  See the doc page for individual "compute" and
+"fix" commands to see what kinds of quantities they generate.
 </P>
-<P>Atom attributes are per-atom vector values.  See the doc page for
-individual "compute" and "fix" commands to see what kinds of
-quantities they generate.
+<P>The input values must either be all scalars or all vectors (or
+arrays), depending on the setting of the <I>mode</I> keyword.
 </P>
+<P>If <I>mode</I> = vector, then the input values may either be vectors or
+arrays.  If a global array is listed, then it is the same as if the
+individual columns of the array had been listed one by one.
+E.g. these 2 fix ave/histo commands are equivalent, since the <A HREF = "compute_com_molecule.html">compute
+com/molecule</A> command creates a global array
+with 3 columns:
+</P>
+<PRE>compute myCOM all com/molecule
+fix 1 all ave/histo 100 1 100 c_myCOM file tmp1.com mode vector
+fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector 
+</PRE>
 <P>The output of this command is a single histogram for all input values
 combined together, not one histogram per input value.  See below for
 details on the format of the output of this fix.
@@ -138,9 +148,11 @@ no bracketed term is appended, the global scalar calculated by the
 compute is used.  If a bracketed term is appended, the Ith element of
 the global vector calculated by the compute is used.  If <I>mode</I> =
 vector, then if no bracketed term is appended, the global or per-atom
-or local vector calculated by the compute is used.  If a bracketed
-term is appended, the Ith column of the global or per-atom or local
-array calculated by the compute is used.
+or local vector calculated by the compute is used.  Or if the compute
+calculates an array, all of the columns of the array are used as if
+they had been specified as individual vectors (see description above).
+If a bracketed term is appended, the Ith column of the global or
+per-atom or local array calculated by the compute is used.
 </P>
 <P>Note that there is a <A HREF = "compute_reduce.html">compute reduce</A> command
 which can sum per-atom quantities into a global scalar or vector which
@@ -158,9 +170,11 @@ no bracketed term is appended, the global scalar calculated by the fix
 is used.  If a bracketed term is appended, the Ith element of the
 global vector calculated by the fix is used.  If <I>mode</I> = vector, then
 if no bracketed term is appended, the global or per-atom or local
-vector calculated by the fix is used.  If a bracketed term is
-appended, the Ith column of the global or per-atom or local array
-calculated by the fix is used.
+vector calculated by the fix is used.  Or if the fix calculates an
+array, all of the columns of the array are used as if they had been
+specified as individual vectors (see description above).  If a
+bracketed term is appended, the Ith column of the global or per-atom
+or local array calculated by the fix is used.
 </P>
 <P>Note that some fixes only produce their values on certain timesteps,
 which must be compatible with <I>Nevery</I>, else an error will result.

doc/fix_ave_histo.txt

@@ -82,13 +82,23 @@ component) or can be the result of a "compute"_compute.html or
 "fix"_fix.html or the evaluation of an equal-style or atom-style
 "variable"_variable.html.  The set of input values can be either all
 global, all per-atom, or all local quantities.  Inputs of different
-kinds (e.g. global and per-atom) cannot be mixed.  The input values
-must also be either all scalar or all vector values, depending on the
-setting of the {mode} keyword.
+kinds (e.g. global and per-atom) cannot be mixed.  Atom attributes are
+per-atom vector values.  See the doc page for individual "compute" and
+"fix" commands to see what kinds of quantities they generate.
 
-Atom attributes are per-atom vector values.  See the doc page for
-individual "compute" and "fix" commands to see what kinds of
-quantities they generate.
+The input values must either be all scalars or all vectors (or
+arrays), depending on the setting of the {mode} keyword.
+
+If {mode} = vector, then the input values may either be vectors or
+arrays.  If a global array is listed, then it is the same as if the
+individual columns of the array had been listed one by one.
+E.g. these 2 fix ave/histo commands are equivalent, since the "compute
+com/molecule"_compute_com_molecule.html command creates a global array
+with 3 columns:
+
+compute myCOM all com/molecule
+fix 1 all ave/histo 100 1 100 c_myCOM file tmp1.com mode vector
+fix 2 all ave/histo 100 1 100 c_myCOM\[1\] c_myCOM\[2\] c_myCOM\[3\] file tmp2.com mode vector :pre
 
 The output of this command is a single histogram for all input values
 combined together, not one histogram per input value.  See below for
@@ -126,9 +136,11 @@ no bracketed term is appended, the global scalar calculated by the
 compute is used.  If a bracketed term is appended, the Ith element of
 the global vector calculated by the compute is used.  If {mode} =
 vector, then if no bracketed term is appended, the global or per-atom
-or local vector calculated by the compute is used.  If a bracketed
-term is appended, the Ith column of the global or per-atom or local
-array calculated by the compute is used.
+or local vector calculated by the compute is used.  Or if the compute
+calculates an array, all of the columns of the array are used as if
+they had been specified as individual vectors (see description above).
+If a bracketed term is appended, the Ith column of the global or
+per-atom or local array calculated by the compute is used.
 
 Note that there is a "compute reduce"_compute_reduce.html command
 which can sum per-atom quantities into a global scalar or vector which
@@ -146,9 +158,11 @@ no bracketed term is appended, the global scalar calculated by the fix
 is used.  If a bracketed term is appended, the Ith element of the
 global vector calculated by the fix is used.  If {mode} = vector, then
 if no bracketed term is appended, the global or per-atom or local
-vector calculated by the fix is used.  If a bracketed term is
-appended, the Ith column of the global or per-atom or local array
-calculated by the fix is used.
+vector calculated by the fix is used.  Or if the fix calculates an
+array, all of the columns of the array are used as if they had been
+specified as individual vectors (see description above).  If a
+bracketed term is appended, the Ith column of the global or per-atom
+or local array calculated by the fix is used.
 
 Note that some fixes only produce their values on certain timesteps,
 which must be compatible with {Nevery}, else an error will result.

doc/fix_ave_time.html

@@ -100,19 +100,19 @@ individual fixes for info on which ones produce such values.
 be used with this fix.  Variables of style <I>atom</I> cannot be used,
 since they produce per-atom values.
 </P>
-<P>The listed values must either be all scalars or all vectors (or
-arrays), depending on the setting of the <I>mode</I> option.  In both
+<P>The input values must either be all scalars or all vectors (or
+arrays), depending on the setting of the <I>mode</I> keyword.  In both
 cases, the averaging is performed independently on each input value.
 I.e. each input scalar is averaged independently and each element of
 each input vector (or array) is averaged independently.
 </P>
-<P>If <I>mode</I> = vector, then the listed values may either be vectors or
+<P>If <I>mode</I> = vector, then the input values may either be vectors or
 arrays and all must be the same "length", which is the length of the
 vector or number of rows in the array.  If a global array is listed,
 then it is the same as if the individual columns of the array had been
 listed one by one.  E.g. these 2 fix ave/time commands are equivalent,
-since the <A HREF = "compute.rdf.html">compute rdf</A> command creates (in this
-case) a global array with 3 columns, each of length 50.
+since the <A HREF = "compute_rdf.html">compute rdf</A> command creates, in this
+case, a global array with 3 columns, each of length 50:
 </P>
 <PRE>compute myRDF all rdf 50 1 2
 fix 1 all ave/time 100 1 100 c_myRDF file tmp1.rdf mode vector
@@ -144,10 +144,10 @@ no bracketed term is appended, the global scalar calculated by the
 compute is used.  If a bracketed term is appended, the Ith element of
 the global vector calculated by the compute is used.  If <I>mode</I> =
 vector, then if no bracketed term is appended, the global vector
-calculated by the compute is used.  Or if the compute calculates a
-global array, all of the columns of the global array are used as if
-they had been specified as individual vectors (see description above).
-If a bracketed term is appended, the Ith column of the global array
+calculated by the compute is used.  Or if the compute calculates an
+array, all of the columns of the global array are used as if they had
+been specified as individual vectors (see description above).  If a
+bracketed term is appended, the Ith column of the global array
 calculated by the compute is used.
 </P>
 <P>Note that there is a <A HREF = "compute_reduce.html">compute reduce</A> command
@@ -166,11 +166,10 @@ no bracketed term is appended, the global scalar calculated by the fix
 is used.  If a bracketed term is appended, the Ith element of the
 global vector calculated by the fix is used.  If <I>mode</I> = vector, then
 if no bracketed term is appended, the global vector calculated by the
-fix is used.  Or if the fix calculates a global array, all of the
-columns of the global array are used as if they had been specified as
-individual vectors (see description above).  If a bracketed term is
-appended, the Ith column of the global array calculated by the fix is
-used.
+fix is used.  Or if the fix calculates an array, all of the columns of
+the global array are used as if they had been specified as individual
+vectors (see description above).  If a bracketed term is appended, the
+Ith column of the global array calculated by the fix is used.
 </P>
 <P>Note that some fixes only produce their values on certain timesteps,
 which must be compatible with <I>Nevery</I>, else an error will result.

doc/fix_ave_time.txt

@@ -88,19 +88,19 @@ individual fixes for info on which ones produce such values.
 be used with this fix.  Variables of style {atom} cannot be used,
 since they produce per-atom values.
 
-The listed values must either be all scalars or all vectors (or
-arrays), depending on the setting of the {mode} option.  In both
+The input values must either be all scalars or all vectors (or
+arrays), depending on the setting of the {mode} keyword.  In both
 cases, the averaging is performed independently on each input value.
 I.e. each input scalar is averaged independently and each element of
 each input vector (or array) is averaged independently.
 
-If {mode} = vector, then the listed values may either be vectors or
+If {mode} = vector, then the input values may either be vectors or
 arrays and all must be the same "length", which is the length of the
 vector or number of rows in the array.  If a global array is listed,
 then it is the same as if the individual columns of the array had been
 listed one by one.  E.g. these 2 fix ave/time commands are equivalent,
-since the "compute rdf"_compute.rdf.html command creates (in this
-case) a global array with 3 columns, each of length 50.
+since the "compute rdf"_compute_rdf.html command creates, in this
+case, a global array with 3 columns, each of length 50:
 
 compute myRDF all rdf 50 1 2
 fix 1 all ave/time 100 1 100 c_myRDF file tmp1.rdf mode vector
@@ -132,10 +132,10 @@ no bracketed term is appended, the global scalar calculated by the
 compute is used.  If a bracketed term is appended, the Ith element of
 the global vector calculated by the compute is used.  If {mode} =
 vector, then if no bracketed term is appended, the global vector
-calculated by the compute is used.  Or if the compute calculates a
-global array, all of the columns of the global array are used as if
-they had been specified as individual vectors (see description above).
-If a bracketed term is appended, the Ith column of the global array
+calculated by the compute is used.  Or if the compute calculates an
+array, all of the columns of the global array are used as if they had
+been specified as individual vectors (see description above).  If a
+bracketed term is appended, the Ith column of the global array
 calculated by the compute is used.
 
 Note that there is a "compute reduce"_compute_reduce.html command
@@ -154,11 +154,10 @@ no bracketed term is appended, the global scalar calculated by the fix
 is used.  If a bracketed term is appended, the Ith element of the
 global vector calculated by the fix is used.  If {mode} = vector, then
 if no bracketed term is appended, the global vector calculated by the
-fix is used.  Or if the fix calculates a global array, all of the
-columns of the global array are used as if they had been specified as
-individual vectors (see description above).  If a bracketed term is
-appended, the Ith column of the global array calculated by the fix is
-used.
+fix is used.  Or if the fix calculates an array, all of the columns of
+the global array are used as if they had been specified as individual
+vectors (see description above).  If a bracketed term is appended, the
+Ith column of the global array calculated by the fix is used.
 
 Note that some fixes only produce their values on certain timesteps,
 which must be compatible with {Nevery}, else an error will result.