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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14864 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2016-04-22 17:40:22 +00:00
parent cc0049dce5
commit af63793e71
21 changed files with 190 additions and 66 deletions
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4
doc/Eqs/improper_umbrella.tex
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@ -1,9 +1,9 @@
\documentstyle[12pt]{article}
\documentclass[12pt]{article}
\begin{document}
$$
E=\frac{1}{2}K\left( \frac{1+cos\omega_0}{sin\omega_0}\right) ^2 \left( cos\omega - cos\omega_0\right) \qquad \omega_0 \neq 0^o
E=\frac{1}{2}K\left( \frac{1}{\sin\omega_0}\right) ^2 \left( \cos\omega - \cos\omega_0\right) ^2 \qquad \omega_0 \neq 0^o
$$
$$

12
doc/_sources/angle_zero.txt
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@ -8,7 +8,7 @@ Syntax
.. parsed-literal::
angle_style zero
angle_style zero *nocoeff*
Examples
""""""""
@ -16,7 +16,9 @@ Examples
.. parsed-literal::
angle_style zero
angle_style zero nocoeff
angle_coeff *
angle_coeff * 120.0
Description
"""""""""""
@ -31,8 +33,14 @@ triplets of angle atoms listed in the data file read by the
:doc:`read_data <read_data>` command. If no angle style is defined,
this command cannot be used.
The optional *nocoeff* flag allows to read data files with AngleCoeff
section for any angle style. Similarly, any angle_coeff commands
will only be checked for the angle type number and the rest ignored.
Note that the :doc:`angle_coeff <angle_coeff>` command must be used for
all angle types, though no additional values are specified.
all angle types. If specified, there can be only one value, which is
going to be used to assign an equilibrium angle, e.g. for use with
:doc:`fix shake <fix_shake>`.
Restrictions
""""""""""""

12
doc/_sources/bond_zero.txt
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@ -8,7 +8,7 @@ Syntax
.. parsed-literal::
bond_style zero
bond_style zero *nocoeff*
Examples
""""""""
@ -16,7 +16,9 @@ Examples
.. parsed-literal::
bond_style zero
bond_style zero nocoeff
bond_coeff *
bond_coeff * 2.14
Description
"""""""""""
@ -30,8 +32,14 @@ command can be used to compute distances for the list of pairs of bond
atoms listed in the data file read by the :doc:`read_data <read_data>`
command. If no bond style is defined, this command cannot be used.
The optional *nocoeff* flag allows to read data files with a BondCoeff
section for any bond style. Similarly, any bond_coeff commands
will only be checked for the bond type number and the rest ignored.
Note that the :doc:`bond_coeff <bond_coeff>` command must be used for
all bond types, though no additional values are specified.
all bond types. If specified, there can be only one value, which is
going to be used to assign an equilibrium distance, e.g. for use with
:doc:`fix shake <fix_shake>`.
Restrictions
""""""""""""

7
doc/_sources/dihedral_zero.txt
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@ -8,7 +8,7 @@ Syntax
.. parsed-literal::
dihedral_style zero
dihedral_style zero *nocoeff*
Examples
""""""""
@ -16,6 +16,7 @@ Examples
.. parsed-literal::
dihedral_style zero
dihedral_style zero nocoeff
dihedral_coeff *
Description
@ -31,6 +32,10 @@ listed in the data file read by the :doc:`read_data <read_data>`
command. If no dihedral style is defined, this command cannot be
used.
The optional *nocoeff* flag allows to read data files with a DihedralCoeff
section for any dihedral style. Similarly, any dihedral_coeff commands
will only be checked for the dihedral type number and the rest ignored.
Note that the :doc:`dihedral_coeff <dihedral_coeff>` command must be
used for all dihedral types, though no additional values are
specified.

7
doc/_sources/improper_zero.txt
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@ -8,7 +8,7 @@ Syntax
.. parsed-literal::
improper_style zero
improper_style zero *nocoeff*
Examples
""""""""
@ -16,6 +16,7 @@ Examples
.. parsed-literal::
improper_style zero
improper_style zero nocoeff
improper_coeff *
Description
@ -31,6 +32,10 @@ listed in the data file read by the :doc:`read_data <read_data>`
command. If no improper style is defined, this command cannot be
used.
The optional *nocoeff* flag allows to read data files with a ImproperCoeff
section for any improper style. Similarly, any improper_coeff commands
will only be checked for the improper type number and the rest ignored.
Note that the :doc:`improper_coeff <improper_coeff>` command must be
used for all improper types, though no additional values are
specified.

23
doc/_sources/pair_zero.txt
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@ -8,25 +8,27 @@ Syntax
.. parsed-literal::
pair_style zero cutoff
pair_style zero cutoff *nocoeff*
* zero = style name of this pair style
cutoff = global cutoff (distance units)
nocoeff = ignore all pair_coeff parameters (optional)
Examples
""""""""
.. parsed-literal::
pair_style zero
pair_style zero 10.0
pair_style zero 5.0 nocoeff
pair_coeff * *
pair_coeff 1 2 3.0
pair_coeff 1 2*4 3.0
Description
"""""""""""
Define a global cutoff length for the purpose of building a neighbor
list and acquiring ghost atoms, but do not compute any pairwise forces
or energies.
Define a global or per-type cutoff length for the purpose of
building a neighbor list and acquiring ghost atoms, but do
not compute any pairwise forces or energies.
This can be useful for fixes or computes which require a neighbor list
to enumerate pairs of atoms within some cutoff distance, but when
@ -37,6 +39,11 @@ Note that the :doc:`comm_modify cutoff <comm_modify>` command can be
used to insure communication of ghost atoms even when a pair style is
not defined, but it will not trigger neighbor list generation.
The optional *nocoeff* flag allows to read data files with a PairCoeff
section for any pair style. Similarly, any pair_coeff commands
will only be checked for the atom type numbers and the rest ignored.
In this case, only the global cutoff will be used.
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
above, or in the data file or restart files read by the
@ -46,7 +53,9 @@ commands, or by mixing as described below:
* cutoff (distance units)
This coefficient is optional. If not specified, the global cutoff
specified in the pair_style command is used.
specified in the pair_style command is used. If the pair_style has
been specified with the optional *nocoeff* flag, then a cutoff
pair coefficient is ignored.
----------

11
doc/_sources/read_data.txt
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@ -12,7 +12,7 @@ Syntax
* file = name of data file to read in
* zero or more keyword/arg pairs may be appended
* keyword = *add* or *offset* or *shift* or *extra/atom/types* or *extra/bond/types* or *extra/angle/types* or *extra/dihedral/types* or *extra/improper/types* or *group* or *fix*
* keyword = *add* or *offset* or *shift* or *extra/atom/types* or *extra/bond/types* or *extra/angle/types* or *extra/dihedral/types* or *extra/improper/types* or *group* or *nocoeff* or *fix*
.. parsed-literal::
*add* arg = *append* or *Nstart* or *merge*
@ -34,6 +34,7 @@ Syntax
*extra/improper/types* arg = # of extra improper types
*group* args = groupID
groupID = add atoms in data file to this group
*nocoeff* = ignore force field parameters
*fix* args = fix-ID header-string section-string
fix-ID = ID of fix to process header lines and sections of data file
header-string = header lines containing this string will be passed to fix
@ -48,7 +49,7 @@ Examples
read_data data.lj
read_data ../run7/data.polymer.gz
read_data data.protein fix mycmap crossterm CMAP
read_data data.protein fix mycmap crossterm CMAP
read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
read_data data.water add merge 1 group solvent
@ -77,6 +78,12 @@ the :doc:`displace_atoms <displace_atoms>` command. Note that atoms
read from the data file are also always added to the "all" group. The
:doc:`group <group>` command discusses atom groups, as used in LAMMPS.
The *nocoeff* keyword tells read_data to ignore force field parameters.
The various Coeff sections are still read and have to have the correct
number of lines, but they are not applied. This also allows to read a
data file without having any pair, bond, angle, dihedral or improper
styles defined, or to read a data file for a different force field.
The use of the *fix* keyword is discussed below.

15
doc/angle_zero.html
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@ -128,14 +128,16 @@
<span id="index-0"></span><h1>angle_style zero command<a class="headerlink" href="#angle-style-zero-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>angle_style zero
</pre></div>
</div>
<pre class="literal-block">
angle_style zero <em>nocoeff</em>
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>angle_style zero
angle_style zero nocoeff
angle_coeff *
angle_coeff * 120.0
</pre></div>
</div>
</div>
@ -149,8 +151,13 @@ command can be used to compute the theta values for the list of
triplets of angle atoms listed in the data file read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command. If no angle style is defined,
this command cannot be used.</p>
<p>The optional <em>nocoeff</em> flag allows to read data files with AngleCoeff
section for any angle style. Similarly, any angle_coeff commands
will only be checked for the angle type number and the rest ignored.</p>
<p>Note that the <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command must be used for
all angle types, though no additional values are specified.</p>
all angle types. If specified, there can be only one value, which is
going to be used to assign an equilibrium angle, e.g. for use with
<a class="reference internal" href="fix_shake.html"><em>fix shake</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>

14
doc/angle_zero.txt
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@ -10,12 +10,14 @@ angle_style zero command :h3
[Syntax:]
angle_style zero :pre
angle_style zero {nocoeff} :pre
[Examples:]
angle_style zero
angle_coeff * :pre
angle_style zero nocoeff
angle_coeff *
angle_coeff * 120.0 :pre
[Description:]
@ -29,8 +31,14 @@ triplets of angle atoms listed in the data file read by the
"read_data"_read_data.html command. If no angle style is defined,
this command cannot be used.
The optional {nocoeff} flag allows to read data files with AngleCoeff
section for any angle style. Similarly, any angle_coeff commands
will only be checked for the angle type number and the rest ignored.
Note that the "angle_coeff"_angle_coeff.html command must be used for
all angle types, though no additional values are specified.
all angle types. If specified, there can be only one value, which is
going to be used to assign an equilibrium angle, e.g. for use with
"fix shake"_fix_shake.html.
[Restrictions:] none

15
doc/bond_zero.html
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@ -128,14 +128,16 @@
<span id="index-0"></span><h1>bond_style zero command<a class="headerlink" href="#bond-style-zero-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>bond_style zero
</pre></div>
</div>
<pre class="literal-block">
bond_style zero <em>nocoeff</em>
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>bond_style zero
bond_style zero nocoeff
bond_coeff *
bond_coeff * 2.14
</pre></div>
</div>
</div>
@ -148,8 +150,13 @@ commands.</p>
command can be used to compute distances for the list of pairs of bond
atoms listed in the data file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
command. If no bond style is defined, this command cannot be used.</p>
<p>The optional <em>nocoeff</em> flag allows to read data files with a BondCoeff
section for any bond style. Similarly, any bond_coeff commands
will only be checked for the bond type number and the rest ignored.</p>
<p>Note that the <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command must be used for
all bond types, though no additional values are specified.</p>
all bond types. If specified, there can be only one value, which is
going to be used to assign an equilibrium distance, e.g. for use with
<a class="reference internal" href="fix_shake.html"><em>fix shake</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>

14
doc/bond_zero.txt
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@ -10,12 +10,14 @@ bond_style zero command :h3
[Syntax:]
bond_style zero :pre
bond_style zero {nocoeff} :pre
[Examples:]
bond_style zero
bond_coeff * :pre
bond_style zero nocoeff
bond_coeff *
bond_coeff * 2.14 :pre
[Description:]
@ -28,8 +30,14 @@ command can be used to compute distances for the list of pairs of bond
atoms listed in the data file read by the "read_data"_read_data.html
command. If no bond style is defined, this command cannot be used.
The optional {nocoeff} flag allows to read data files with a BondCoeff
section for any bond style. Similarly, any bond_coeff commands
will only be checked for the bond type number and the rest ignored.
Note that the "bond_coeff"_bond_coeff.html command must be used for
all bond types, though no additional values are specified.
all bond types. If specified, there can be only one value, which is
going to be used to assign an equilibrium distance, e.g. for use with
"fix shake"_fix_shake.html.
[Restrictions:] none

10
doc/dihedral_zero.html
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@ -128,13 +128,14 @@
<span id="index-0"></span><h1>dihedral_style zero command<a class="headerlink" href="#dihedral-style-zero-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>dihedral_style zero
</pre></div>
</div>
<pre class="literal-block">
dihedral_style zero <em>nocoeff</em>
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>dihedral_style zero
dihedral_style zero nocoeff
dihedral_coeff *
</pre></div>
</div>
@ -149,6 +150,9 @@ compute the theta values for the list of quadruplets of dihedral atoms
listed in the data file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
command. If no dihedral style is defined, this command cannot be
used.</p>
<p>The optional <em>nocoeff</em> flag allows to read data files with a DihedralCoeff
section for any dihedral style. Similarly, any dihedral_coeff commands
will only be checked for the dihedral type number and the rest ignored.</p>
<p>Note that the <a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a> command must be
used for all dihedral types, though no additional values are
specified.</p>

7
doc/dihedral_zero.txt
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@ -10,11 +10,12 @@ dihedral_style zero command :h3
[Syntax:]
dihedral_style zero :pre
dihedral_style zero {nocoeff} :pre
[Examples:]
dihedral_style zero
dihedral_style zero nocoeff
dihedral_coeff * :pre
[Description:]
@ -30,6 +31,10 @@ listed in the data file read by the "read_data"_read_data.html
command. If no dihedral style is defined, this command cannot be
used.
The optional {nocoeff} flag allows to read data files with a DihedralCoeff
section for any dihedral style. Similarly, any dihedral_coeff commands
will only be checked for the dihedral type number and the rest ignored.
Note that the "dihedral_coeff"_dihedral_coeff.html command must be
used for all dihedral types, though no additional values are
specified.

8
doc/genindex.html
View File

@ -436,6 +436,10 @@
</dt>
<dt><a href="compute_dipole_chunk.html#index-0">compute dipole/chunk</a>
</dt>
<dt><a href="compute_displace_atom.html#index-0">compute displace/atom</a>
</dt>
@ -567,12 +571,12 @@
<dt><a href="compute_pair_local.html#index-0">compute pair/local</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="compute_pe.html#index-0">compute pe</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="compute_pe_atom.html#index-0">compute pe/atom</a>
</dt>

10
doc/improper_zero.html
View File

@ -128,13 +128,14 @@
<span id="index-0"></span><h1>improper_style zero command<a class="headerlink" href="#improper-style-zero-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>improper_style zero
</pre></div>
</div>
<pre class="literal-block">
improper_style zero <em>nocoeff</em>
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>improper_style zero
improper_style zero nocoeff
improper_coeff *
</pre></div>
</div>
@ -149,6 +150,9 @@ compute the chi values for the list of quadruplets of improper atoms
listed in the data file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
command. If no improper style is defined, this command cannot be
used.</p>
<p>The optional <em>nocoeff</em> flag allows to read data files with a ImproperCoeff
section for any improper style. Similarly, any improper_coeff commands
will only be checked for the improper type number and the rest ignored.</p>
<p>Note that the <a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a> command must be
used for all improper types, though no additional values are
specified.</p>

7
doc/improper_zero.txt
View File

@ -10,11 +10,12 @@ improper_style zero command :h3
[Syntax:]
improper_style zero :pre
improper_style zero {nocoeff} :pre
[Examples:]
improper_style zero
improper_style zero nocoeff
improper_coeff * :pre
[Description:]
@ -30,6 +31,10 @@ listed in the data file read by the "read_data"_read_data.html
command. If no improper style is defined, this command cannot be
used.
The optional {nocoeff} flag allows to read data files with a ImproperCoeff
section for any improper style. Similarly, any improper_coeff commands
will only be checked for the improper type number and the rest ignored.
Note that the "improper_coeff"_improper_coeff.html command must be
used for all improper types, though no additional values are
specified.

28
doc/pair_zero.html
View File

@ -128,27 +128,29 @@
<span id="index-0"></span><h1>pair_style zero command<a class="headerlink" href="#pair-style-zero-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style zero cutoff
</pre></div>
</div>
<pre class="literal-block">
pair_style zero cutoff <em>nocoeff</em>
</pre>
<ul class="simple">
<li>zero = style name of this pair style
cutoff = global cutoff (distance units)</li>
cutoff = global cutoff (distance units)
nocoeff = ignore all pair_coeff parameters (optional)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style zero
<div class="highlight-python"><div class="highlight"><pre>pair_style zero 10.0
pair_style zero 5.0 nocoeff
pair_coeff * *
pair_coeff 1 2 3.0
pair_coeff 1 2*4 3.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a global cutoff length for the purpose of building a neighbor
list and acquiring ghost atoms, but do not compute any pairwise forces
or energies.</p>
<p>Define a global or per-type cutoff length for the purpose of
building a neighbor list and acquiring ghost atoms, but do
not compute any pairwise forces or energies.</p>
<p>This can be useful for fixes or computes which require a neighbor list
to enumerate pairs of atoms within some cutoff distance, but when
pairwise forces are not otherwise needed. Examples are the <a class="reference internal" href="fix_bond_create.html"><em>fix bond/create</em></a>, <a class="reference internal" href="compute_rdf.html"><em>compute rdf</em></a>,
@ -156,6 +158,10 @@ pairwise forces are not otherwise needed. Examples are the <a class="reference
<p>Note that the <a class="reference internal" href="comm_modify.html"><em>comm_modify cutoff</em></a> command can be
used to insure communication of ghost atoms even when a pair style is
not defined, but it will not trigger neighbor list generation.</p>
<p>The optional <em>nocoeff</em> flag allows to read data files with a PairCoeff
section for any pair style. Similarly, any pair_coeff commands
will only be checked for the atom type numbers and the rest ignored.
In this case, only the global cutoff will be used.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
@ -165,7 +171,9 @@ commands, or by mixing as described below:</p>
<li>cutoff (distance units)</li>
</ul>
<p>This coefficient is optional. If not specified, the global cutoff
specified in the pair_style command is used.</p>
specified in the pair_style command is used. If the pair_style has
been specified with the optional <em>nocoeff</em> flag, then a cutoff
pair coefficient is ignored.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>The cutoff distance for this pair style can be mixed. The default mix

25
doc/pair_zero.txt
View File

@ -10,22 +10,24 @@ pair_style zero command :h3
[Syntax:]
pair_style zero cutoff :pre
pair_style zero cutoff {nocoeff} :pre
zero = style name of this pair style
cutoff = global cutoff (distance units) :l
cutoff = global cutoff (distance units)
nocoeff = ignore all pair_coeff parameters (optional) :l
[Examples:]
pair_style zero
pair_style zero 10.0
pair_style zero 5.0 nocoeff
pair_coeff * *
pair_coeff 1 2 3.0 :pre
pair_coeff 1 2*4 3.0 :pre
[Description:]
Define a global cutoff length for the purpose of building a neighbor
list and acquiring ghost atoms, but do not compute any pairwise forces
or energies.
Define a global or per-type cutoff length for the purpose of
building a neighbor list and acquiring ghost atoms, but do
not compute any pairwise forces or energies.
This can be useful for fixes or computes which require a neighbor list
to enumerate pairs of atoms within some cutoff distance, but when
@ -37,6 +39,11 @@ Note that the "comm_modify cutoff"_comm_modify.html command can be
used to insure communication of ghost atoms even when a pair style is
not defined, but it will not trigger neighbor list generation.
The optional {nocoeff} flag allows to read data files with a PairCoeff
section for any pair style. Similarly, any pair_coeff commands
will only be checked for the atom type numbers and the rest ignored.
In this case, only the global cutoff will be used.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
@ -46,7 +53,9 @@ commands, or by mixing as described below:
cutoff (distance units) :ul
This coefficient is optional. If not specified, the global cutoff
specified in the pair_style command is used.
specified in the pair_style command is used. If the pair_style has
been specified with the optional {nocoeff} flag, then a cutoff
pair coefficient is ignored.
:line

8
doc/read_data.html
View File

@ -134,7 +134,7 @@
<ul class="simple">
<li>file = name of data file to read in</li>
<li>zero or more keyword/arg pairs may be appended</li>
<li>keyword = <em>add</em> or <em>offset</em> or <em>shift</em> or <em>extra/atom/types</em> or <em>extra/bond/types</em> or <em>extra/angle/types</em> or <em>extra/dihedral/types</em> or <em>extra/improper/types</em> or <em>group</em> or <em>fix</em></li>
<li>keyword = <em>add</em> or <em>offset</em> or <em>shift</em> or <em>extra/atom/types</em> or <em>extra/bond/types</em> or <em>extra/angle/types</em> or <em>extra/dihedral/types</em> or <em>extra/improper/types</em> or <em>group</em> or <em>nocoeff</em> or <em>fix</em></li>
</ul>
<pre class="literal-block">
<em>add</em> arg = <em>append</em> or <em>Nstart</em> or <em>merge</em>
@ -156,6 +156,7 @@
<em>extra/improper/types</em> arg = # of extra improper types
<em>group</em> args = groupID
groupID = add atoms in data file to this group
<em>nocoeff</em> = ignore force field parameters
<em>fix</em> args = fix-ID header-string section-string
fix-ID = ID of fix to process header lines and sections of data file
header-string = header lines containing this string will be passed to fix
@ -193,6 +194,11 @@ later. E.g. a group of added atoms can be moved to new positions via
the <a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a> command. Note that atoms
read from the data file are also always added to the &#8220;all&#8221; group. The
<a class="reference internal" href="group.html"><em>group</em></a> command discusses atom groups, as used in LAMMPS.</p>
<p>The <em>nocoeff</em> keyword tells read_data to ignore force field parameters.
The various Coeff sections are still read and have to have the correct
number of lines, but they are not applied. This also allows to read a
data file without having any pair, bond, angle, dihedral or improper
styles defined, or to read a data file for a different force field.</p>
<p>The use of the <em>fix</em> keyword is discussed below.</p>
<hr class="docutils" />
<p><strong>Reading multiple data files</strong></p>

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@ -14,7 +14,7 @@ read_data file keyword args ... :pre
file = name of data file to read in :ulb,l
zero or more keyword/arg pairs may be appended :l
keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/types} or {extra/angle/types} or {extra/dihedral/types} or {extra/improper/types} or {group} or {fix} :l
keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/types} or {extra/angle/types} or {extra/dihedral/types} or {extra/improper/types} or {group} or {nocoeff} or {fix} :l
{add} arg = {append} or {Nstart} or {merge}
append = add new atoms with IDs appended to current IDs
Nstart = add new atoms with IDs starting with Nstart
@ -34,6 +34,7 @@ keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/type
{extra/improper/types} arg = # of extra improper types
{group} args = groupID
groupID = add atoms in data file to this group
{nocoeff} = ignore force field parameters
{fix} args = fix-ID header-string section-string
fix-ID = ID of fix to process header lines and sections of data file
header-string = header lines containing this string will be passed to fix
@ -44,7 +45,7 @@ keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/type
read_data data.lj
read_data ../run7/data.polymer.gz
read_data data.protein fix mycmap crossterm CMAP
read_data data.protein fix mycmap crossterm CMAP
read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
read_data data.water add merge 1 group solvent :pre
@ -73,6 +74,12 @@ the "displace_atoms"_displace_atoms.html command. Note that atoms
read from the data file are also always added to the "all" group. The
"group"_group.html command discusses atom groups, as used in LAMMPS.
The {nocoeff} keyword tells read_data to ignore force field parameters.
The various Coeff sections are still read and have to have the correct
number of lines, but they are not applied. This also allows to read a
data file without having any pair, bond, angle, dihedral or improper
styles defined, or to read a data file for a different force field.
The use of the {fix} keyword is discussed below.
:line
@ -405,8 +412,8 @@ the maximum values defined in any of the template molecules.
These are the section keywords for the body of the file.
{Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies} = atom-property sections
{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections
{Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies} = atom-property sections
{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections
{Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, \
Improper Coeffs} = force field sections
{BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, \
@ -548,7 +555,7 @@ atom-ID = integer ID of atom
atom-type = type of atom (1-Ntype)
bodyflag = 1 for body particles, 0 for point particles
contact-radius = ??? (distance units)
cs_re,cs_im = real/imaginary parts of wavepacket coefficients
cs_re,cs_im = real/imaginary parts of wavepacket coefficients
cv = heat capacity (need units) for SPH particles
density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
diameter = diameter of spherical atom (distance units)

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