git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15460 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/html/_sources/fix_ave_atom.txt

@@ -77,7 +77,7 @@ means all indices from m to n (inclusive).
 
 Using a wildcard is the same as if the individual columns of the array
 had been listed one by one.  E.g. these 2 fix ave/atom commands are
-equivalent, since the :doc:`compute stress/atom <compute_stress/atom>`
+equivalent, since the :doc:`compute stress/atom <compute_stress_atom>`
 command creates a per-atom array with 6 columns:
 
 .. parsed-literal::

doc/html/_sources/thermo_style.txt

@@ -147,34 +147,6 @@ atoms in the system), and the numeric precision of each printed value.
 ----------
 
 
-Note that for values from a compute or fix, the bracketed index I used
-to index a vector, as in *c_ID[I]* or *f_ID[I]*\ , can be specified
-using a wildcard asterisk with the index to effectively specify
-multiple values.  This takes the form "*" or "*n" or "n*" or "m*n".
-If N = the size of the vector (for *mode* = scalar) or the number of
-columns in the array (for *mode* = vector), then an asterisk with no
-numeric values means all indices from 1 to N.  A leading asterisk
-means all indices from 1 to n (inclusive).  A trailing asterisk means
-all indices from n to N (inclusive).  A middle asterisk means all
-indices from m to n (inclusive).
-
-Using a wildcard is the same as if the individual elements of the
-vector had been listed one by one.  E.g. these 2 thermo_style commands
-are equivalent, since the :doc:`compute temp <compute_temp>` command
-creates a global vector with 6 values.
-
-.. parsed-literal::
-
-   compute myTemp all temp
-   thermo_style custom step temp etotal c_myTemp[*]
-   thermo_style custom step temp etotal &
-                c_myTemp[1] c_myTemp[2] c_myTemp[3] &
-                c_myTemp[4] c_myTemp[5] c_myTemp[6]
-
-
-----------
-
-
 Several of the thermodynamic quantities require a temperature to be
 computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx", etc.  By
 default this is done by using a *temperature* compute which is created
@@ -341,6 +313,34 @@ of these quantities in terms of the internal LAMMPS cell dimensions
 ----------
 
 
+For output values from a compute or fix, the bracketed index I used to
+index a vector, as in *c_ID[I]* or *f_ID[I]*\ , can be specified
+using a wildcard asterisk with the index to effectively specify
+multiple values.  This takes the form "*" or "*n" or "n*" or "m*n".
+If N = the size of the vector (for *mode* = scalar) or the number of
+columns in the array (for *mode* = vector), then an asterisk with no
+numeric values means all indices from 1 to N.  A leading asterisk
+means all indices from 1 to n (inclusive).  A trailing asterisk means
+all indices from n to N (inclusive).  A middle asterisk means all
+indices from m to n (inclusive).
+
+Using a wildcard is the same as if the individual elements of the
+vector had been listed one by one.  E.g. these 2 thermo_style commands
+are equivalent, since the :doc:`compute temp <compute_temp>` command
+creates a global vector with 6 values.
+
+.. parsed-literal::
+
+   compute myTemp all temp
+   thermo_style custom step temp etotal c_myTemp[*]
+   thermo_style custom step temp etotal &
+                c_myTemp[1] c_myTemp[2] c_myTemp[3] &
+                c_myTemp[4] c_myTemp[5] c_myTemp[6]
+
+
+----------
+
+
 The *c_ID* and *c_ID[I]* and *c_ID[I][J]* keywords allow global
 values calculated by a compute to be output.  As discussed on the
 :doc:`compute <compute>` doc page, computes can calculate global,

doc/html/fix_ave_atom.html

@@ -190,7 +190,7 @@ asterisk means all indices from n to N (inclusive).  A middle asterisk
 means all indices from m to n (inclusive).</p>
 <p>Using a wildcard is the same as if the individual columns of the array
 had been listed one by one.  E.g. these 2 fix ave/atom commands are
-equivalent, since the <span class="xref doc">compute stress/atom</span>
+equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
 command creates a per-atom array with 6 columns:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">my_stress</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
 <span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>

doc/html/thermo_style.html

@@ -256,28 +256,6 @@ if your input script specifies a thermo_style command, you should use
 the thermo_modify command after it.</p>
 </div>
 <hr class="docutils" />
-<p>Note that for values from a compute or fix, the bracketed index I used
-to index a vector, as in <em>c_ID[I]</em> or <em>f_ID[I]</em>, can be specified
-using a wildcard asterisk with the index to effectively specify
-multiple values.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.
-If N = the size of the vector (for <em>mode</em> = scalar) or the number of
-columns in the array (for <em>mode</em> = vector), then an asterisk with no
-numeric values means all indices from 1 to N.  A leading asterisk
-means all indices from 1 to n (inclusive).  A trailing asterisk means
-all indices from n to N (inclusive).  A middle asterisk means all
-indices from m to n (inclusive).</p>
-<p>Using a wildcard is the same as if the individual elements of the
-vector had been listed one by one.  E.g. these 2 thermo_style commands
-are equivalent, since the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command
-creates a global vector with 6 values.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myTemp</span> <span class="nb">all</span> <span class="n">temp</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="o">&amp;</span>
-             <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&amp;</span>
-             <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
-</pre></div>
-</div>
-<hr class="docutils" />
 <p>Several of the thermodynamic quantities require a temperature to be
 computed: &#8220;temp&#8221;, &#8220;press&#8221;, &#8220;ke&#8221;, &#8220;etotal&#8221;, &#8220;enthalpy&#8221;, &#8220;pxx&#8221;, etc.  By
 default this is done by using a <em>temperature</em> compute which is created
@@ -413,6 +391,28 @@ description of triclinic periodic cells, including a precise defintion
 of these quantities in terms of the internal LAMMPS cell dimensions
 <em>lx</em>, <em>ly</em>, <em>lz</em>, <em>yz</em>, <em>xz</em>, <em>xy</em>.</p>
 <hr class="docutils" />
+<p>For output values from a compute or fix, the bracketed index I used to
+index a vector, as in <em>c_ID[I]</em> or <em>f_ID[I]</em>, can be specified
+using a wildcard asterisk with the index to effectively specify
+multiple values.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.
+If N = the size of the vector (for <em>mode</em> = scalar) or the number of
+columns in the array (for <em>mode</em> = vector), then an asterisk with no
+numeric values means all indices from 1 to N.  A leading asterisk
+means all indices from 1 to n (inclusive).  A trailing asterisk means
+all indices from n to N (inclusive).  A middle asterisk means all
+indices from m to n (inclusive).</p>
+<p>Using a wildcard is the same as if the individual elements of the
+vector had been listed one by one.  E.g. these 2 thermo_style commands
+are equivalent, since the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command
+creates a global vector with 6 values.</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myTemp</span> <span class="nb">all</span> <span class="n">temp</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="o">&amp;</span>
+             <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&amp;</span>
+             <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
+</pre></div>
+</div>
+<hr class="docutils" />
 <p>The <em>c_ID</em> and <em>c_ID[I]</em> and <em>c_ID[I][J]</em> keywords allow global
 values calculated by a compute to be output.  As discussed on the
 <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> doc page, computes can calculate global,

doc/src/dump_modify.txt

@@ -265,13 +265,17 @@ options can be used with the {atom} and {xyz} styles.
 All the specified format strings are C-style formats, e.g. as used by
 the C/C++ printf() command.  The {line} keyword takes a single
 argument which is the format string for an entire line of output for
-each atoms, with N fields, which you must enclose in quotes if it is
+each atom (do not include a trailing "\n"), with N fields, which you
-more than one field.  The {int} and {float} keywords take a single
+must enclose in quotes if it is more than one field.  The {int} and
-format argument and are applied to all integer or floating-point
+{float} keywords take a single format argument and are applied to all
-quantities output.  The setting for {M string} also takes a single
+integer or floating-point quantities output.  The setting for {M
-format argument which is used for the Mth value output in each line,
+string} also takes a single format argument which is used for the Mth
-e.g. the 5th column is output in high precision for "format 5
+value output in each line, e.g. the 5th column is output in high
-%20.15g".
+precision for "format 5 %20.15g".
+
+NOTE: When using the {line} keyword for the {cfg} style, the first two
+fields (atom ID and type) are not actually written into the CFG file,
+however you must include formats for them in the format string.
 
 The {format} keyword can be used multiple times.  The precedence is
 that for each value in a line of output, the {M} format (if specified)
@@ -290,16 +294,6 @@ string} option for those values, you should specify a format string
 appropriate for an 8-byte signed integer, e.g. one with "%ld", if
 LAMMPS was compiled with the -DLAMMPS_BIGBIG option for 8-byte IDs.
 
-The text-based dump styles have a default C-style format string which
-simply specifies %d for integers and %g for floating-point values.
-The {format} keyword can be used to override the default with a new
-C-style format string.  Do not include a trailing "\\n" newline
-character in the format string.  This option has no effect on the
-{dcd} and {xtc} dump styles since they write binary files.  Note that
-for the {cfg} style, the first two fields (atom id and type) are not
-actually written into the CFG file, though you must include formats
-for them in the format string.
-
 NOTE: Any value written to a text-based dump file that is a per-atom
 quantity calculated by a "compute"_compute.html or "fix"_fix.html is
 stored internally as a floating-point value.  If the value is actually

doc/src/fix_ave_atom.txt

@@ -75,7 +75,7 @@ means all indices from m to n (inclusive).
 
 Using a wildcard is the same as if the individual columns of the array
 had been listed one by one.  E.g. these 2 fix ave/atom commands are
-equivalent, since the "compute stress/atom"_compute_stress/atom.html
+equivalent, since the "compute stress/atom"_compute_stress_atom.html
 command creates a per-atom array with 6 columns:
 
 compute my_stress all stress/atom NULL

doc/src/thermo_style.txt

@@ -138,30 +138,6 @@ the thermo_modify command after it.
 
 :line
 
-Note that for values from a compute or fix, the bracketed index I used
-to index a vector, as in {c_ID\[I\]} or {f_ID\[I\]}, can be specified
-using a wildcard asterisk with the index to effectively specify
-multiple values.  This takes the form "*" or "*n" or "n*" or "m*n".
-If N = the size of the vector (for {mode} = scalar) or the number of
-columns in the array (for {mode} = vector), then an asterisk with no
-numeric values means all indices from 1 to N.  A leading asterisk
-means all indices from 1 to n (inclusive).  A trailing asterisk means
-all indices from n to N (inclusive).  A middle asterisk means all
-indices from m to n (inclusive).
-
-Using a wildcard is the same as if the individual elements of the
-vector had been listed one by one.  E.g. these 2 thermo_style commands
-are equivalent, since the "compute temp"_compute_temp.html command
-creates a global vector with 6 values.
-
-compute myTemp all temp
-thermo_style custom step temp etotal c_myTemp\[*\]
-thermo_style custom step temp etotal &
-             c_myTemp\[1\] c_myTemp\[2\] c_myTemp\[3\] &
-             c_myTemp\[4\] c_myTemp\[5\] c_myTemp\[6\] :pre
-
-:line
-
 Several of the thermodynamic quantities require a temperature to be
 computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx", etc.  By
 default this is done by using a {temperature} compute which is created
@@ -319,6 +295,30 @@ of these quantities in terms of the internal LAMMPS cell dimensions
 
 :line
 
+For output values from a compute or fix, the bracketed index I used to
+index a vector, as in {c_ID\[I\]} or {f_ID\[I\]}, can be specified
+using a wildcard asterisk with the index to effectively specify
+multiple values.  This takes the form "*" or "*n" or "n*" or "m*n".
+If N = the size of the vector (for {mode} = scalar) or the number of
+columns in the array (for {mode} = vector), then an asterisk with no
+numeric values means all indices from 1 to N.  A leading asterisk
+means all indices from 1 to n (inclusive).  A trailing asterisk means
+all indices from n to N (inclusive).  A middle asterisk means all
+indices from m to n (inclusive).
+
+Using a wildcard is the same as if the individual elements of the
+vector had been listed one by one.  E.g. these 2 thermo_style commands
+are equivalent, since the "compute temp"_compute_temp.html command
+creates a global vector with 6 values.
+
+compute myTemp all temp
+thermo_style custom step temp etotal c_myTemp\[*\]
+thermo_style custom step temp etotal &
+             c_myTemp\[1\] c_myTemp\[2\] c_myTemp\[3\] &
+             c_myTemp\[4\] c_myTemp\[5\] c_myTemp\[6\] :pre
+
+:line
+
 The {c_ID} and {c_ID\[I\]} and {c_ID\[I\]\[J\]} keywords allow global
 values calculated by a compute to be output.  As discussed on the
 "compute"_compute.html doc page, computes can calculate global,