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

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sjplimp 2016-08-08 13:48:22 +00:00
parent 056ff192c6
commit 17e8e9a9c9
8 changed files with 89 additions and 95 deletions
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2
doc/html/_sources/fix_ave_atom.txt
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@ -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::

56
doc/html/_sources/thermo_style.txt
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@ -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,

2
doc/html/fix_ave_atom.html
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@ -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>

2
doc/html/searchindex.js
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File diff suppressed because one or more lines are too long

44
doc/html/thermo_style.html
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@ -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,

28
doc/src/dump_modify.txt
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@ -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
more than one field. The {int} and {float} keywords take a single
format argument and are applied to all integer or floating-point
quantities output. The setting for {M string} also takes a single
format argument which is used for the Mth value output in each line,
e.g. the 5th column is output in high precision for "format 5
%20.15g".
each atom (do not include a trailing "\n"), with N fields, which you
must enclose in quotes if it is more than one field. The {int} and
{float} keywords take a single format argument and are applied to all
integer or floating-point quantities output. The setting for {M
string} also takes a single format argument which is used for the Mth
value output in each line, e.g. the 5th column is output in high
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

2
doc/src/fix_ave_atom.txt
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@ -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

48
doc/src/thermo_style.txt
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@ -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,