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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15042 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2016-05-12 14:02:27 +00:00
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10
doc/html/Section_howto.html
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@ -1344,9 +1344,9 @@ to output and the kind of data they operate on and produce:</p>
<li><a class="reference internal" href="#scalar"><span class="std std-ref">Scalar/vector/array data</span></a></li>
<li><a class="reference internal" href="#thermo"><span class="std std-ref">Thermodynamic output</span></a></li>
<li><a class="reference internal" href="#dump"><span class="std std-ref">Dump file output</span></a></li>
<li><span class="xref std std-ref">Fixes that write output files</span></li>
<li><a class="reference internal" href="#fixoutput"><span class="std std-ref">Fixes that write output files</span></a></li>
<li><a class="reference internal" href="#computeoutput"><span class="std std-ref">Computes that process output quantities</span></a></li>
<li><span class="xref std std-ref">Fixes that process output quantities</span></li>
<li><a class="reference internal" href="#fixprocoutput"><span class="std std-ref">Fixes that process output quantities</span></a></li>
<li><a class="reference internal" href="#compute"><span class="std std-ref">Computes that generate values to output</span></a></li>
<li><a class="reference internal" href="#fix"><span class="std std-ref">Fixes that generate values to output</span></a></li>
<li><a class="reference internal" href="#variable"><span class="std std-ref">Variables that generate values to output</span></a></li>
@ -1372,7 +1372,7 @@ per-atom vector.</p>
<p>When a quantity is accessed, as in many of the output commands
discussed below, it can be referenced via the following bracket
notation, where ID in this case is the ID of a compute. The leading
&#8220;<a href="#id75"><span class="problematic" id="id76">c_</span></a>&#8221; would be replaced by &#8220;<a href="#id77"><span class="problematic" id="id78">f_</span></a>&#8221; for a fix, or &#8220;<a href="#id79"><span class="problematic" id="id80">v_</span></a>&#8221; for a variable:</p>
&#8220;<a href="#id74"><span class="problematic" id="id75">c_</span></a>&#8221; would be replaced by &#8220;<a href="#id76"><span class="problematic" id="id77">f_</span></a>&#8221; for a fix, or &#8220;<a href="#id78"><span class="problematic" id="id79">v_</span></a>&#8221; for a variable:</p>
<table border="1" class="docutils">
<colgroup>
<col width="21%" />
@ -1509,7 +1509,7 @@ are produced as output values which can be used as input to other
output commands.</p>
</div>
<div class="section" id="fixes-that-process-output-quantities">
<span id="id5"></span><h3>6.15.7. Fixes that process output quantities</h3>
<span id="fixprocoutput"></span><h3>6.15.7. Fixes that process output quantities</h3>
<p>The <a class="reference internal" href="fix_vector.html"><span class="doc">fix vector</span></a> command can create global vectors as
output from global scalars as input, accumulating them one element at
a time.</p>
@ -2274,7 +2274,7 @@ fix produces a global array as output with one row of values per
chunk.</p>
</div>
<div class="section" id="compute-chunk-commands">
<h3>6.23.3. Compute <a href="#id72"><span class="problematic" id="id73">*</span></a>/chunk commands:</h3>
<h3>6.23.3. Compute <a href="#id71"><span class="problematic" id="id72">*</span></a>/chunk commands:</h3>
<p>Currently the following computes operate on chunks of atoms to produce
per-chunk values.</p>
<ul class="simple">

6
doc/html/_sources/Section_howto.txt
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@ -1429,7 +1429,7 @@ to output and the kind of data they operate on and produce:
* :ref:`Dump file output <dump>`
* :ref:`Fixes that write output files <fixoutput>`
* :ref:`Computes that process output quantities <computeoutput>`
* :ref:`Fixes that process output quantities <fixoutput>`
* :ref:`Fixes that process output quantities <fixprocoutput>`
* :ref:`Computes that generate values to output <compute>`
* :ref:`Fixes that generate values to output <fix>`
* :ref:`Variables that generate values to output <variable>`
@ -1613,10 +1613,10 @@ info, etc) and stores the values in a local vector or array. These
are produced as output values which can be used as input to other
output commands.
.. _fixoutput:
.. _fixprocoutput:
Fixes that process output quantities
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The :doc:`fix vector <fix_vector>` command can create global vectors as
output from global scalars as input, accumulating them one element at

2
doc/html/_sources/angle_cosine_shift.txt
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@ -80,7 +80,7 @@ Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`,
:doc:`angle_cosineshiftexp <angle_cosineshiftexp>`
:doc:`angle_cosine_shift_exp <angle_cosine_shift_exp>`
**Default:** none

4
doc/html/_sources/angle_cosine_shift_exp.txt
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@ -92,8 +92,8 @@ Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`,
:doc:`angle_cosineshift <angle_cosineshift>`,
:doc:`dihedral_cosineshift <dihedral_cosineshift>`
:doc:`angle_cosine_shift <angle_cosine_shift>`,
:doc:`dihedral_cosine_shift_exp <dihedral_cosine_shift_exp>`
**Default:** none

2
doc/html/_sources/angle_dipole.txt
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@ -102,7 +102,7 @@ Restrictions
This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the :ref:`Making LAMMPS <2_3>`
USER-MISC package. See the :ref:`Making LAMMPS <start_2_3>`
section for more info on packages.
.. note::

2
doc/html/_sources/bond_harmonic_shift_cut.txt
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@ -83,7 +83,7 @@ Related commands
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`,
:doc:`bond_harmonic <bond_harmonic>`,
:doc:`bond_harmonicshift <bond_harmonicshift>`
:doc:`bond_harmonic_shift <bond_harmonic_shift>`
**Default:** none

2
doc/html/_sources/dihedral_cosine_shift_exp.txt
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@ -91,7 +91,7 @@ Related commands
""""""""""""""""
:doc:`dihedral_coeff <dihedral_coeff>`,
:doc:`angle_cosineshiftexp <angle_cosineshiftexp>`
:doc:`angle_cosine_shift_exp <angle_cosine_shift_exp>`
**Default:** none

4
doc/html/_sources/fix_lb_fluid.txt
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@ -266,7 +266,7 @@ N timesteps.
If the keyword *trilinear* is used, the trilinear stencil is used to
interpolate the particle nodes onto the fluid mesh. By default, the
immersed boundary method, Peskin stencil is used. Both of these
interpolation methods are described in :ref:`Mackay et al. <Mfluid-ackay>`.
interpolation methods are described in :ref:`Mackay et al. <fluid-Mackay>`.
If the keyword *D3Q19* is used, the 19 velocity (D3Q19) lattice is
used by the lattice-Boltzmann algorithm. By default, the 15 velocity
@ -324,7 +324,7 @@ is written to the main LAMMPS :doc:`binary restart files <restart>`.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
access by various :ref:`output commands <4_15>`. No
access by various :ref:`output commands <howto_15>`. No
parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.

2
doc/html/_sources/fix_ti_rs.txt
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@ -34,7 +34,7 @@ Description
This fix allows you to compute the free energy temperature dependence
by performing a thermodynamic integration procedure known as
Reversible Scaling :ref:`(de Koning99, <deKoning99>` :ref:`de Koning00a) <deKoning00a">`. The thermodynamic integration is performed
Reversible Scaling :ref:`(de Koning99, <deKoning99>` :ref:`de Koning00a) <deKoning00a>`. The thermodynamic integration is performed
using the nonequilibrium method of Adiabatic Switching
:ref:`(Watanabe, <Watanabe>` :ref:`de Koning96) <deKoning96>`.

2
doc/html/_sources/neb.txt
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@ -253,7 +253,7 @@ In the second stage of NEB, the replica with the highest energy
is selected and the inter-replica forces on it are converted to a
force that drives its atom coordinates to the top or saddle point of
the barrier, via the barrier-climbing calculation described in
:ref:`(Henkelman2) <Hinkelman2>`. As before, the other replicas rearrange
:ref:`(Henkelman2) <Henkelman2>`. As before, the other replicas rearrange
themselves along the MEP so as to be roughly equally spaced.
When both stages are complete, if the NEB calculation was successful,

2
doc/html/_sources/pair_body.txt
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@ -114,7 +114,7 @@ Restrictions
This style is part of the BODY package. It is only enabled if LAMMPS
was built with that package. See the :ref:`Making LAMMPS <2_3>` section for more info.
was built with that package. See the :ref:`Making LAMMPS <start_2_3>` section for more info.
Defining particles to be bodies so they participate in body/body or
body/particle interactions requires the use of the :doc:`atom_style body <atom_style>` command.

8
doc/html/_sources/pair_bop.txt
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@ -102,7 +102,7 @@ incorporation of dihedral angles effects.
potentials with hydrogen, you will likely want to set the mass of H
atoms to be 10x or 20x larger to avoid having to use a tiny timestep.
You can do this by using the :doc:`mass <mass>` command after using the
:doc:`pair_coeff <doc/pair_coeff>` command to read the BOP potential
:doc:`pair_coeff <pair_coeff>` command to read the BOP potential
file.
One option can be specified as a keyword with the pair_style command.
@ -405,21 +405,21 @@ non-tabulated potential file, a_0 is non-zero.
----------
.. _Pettofor_1:
.. _Pettifor_1:
**(Pettifor_1)** D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487
(1999).
.. _Pettofor_2:
.. _Pettifor_2:
**(Pettifor_2)** D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84,
4124 (2000).
.. _Pettofor_3:
.. _Pettifor_3:

2
doc/html/_sources/pair_coul_diel.txt
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@ -95,7 +95,7 @@ Restrictions
This style is part of the "user-misc" package. It is only enabled
if LAMMPS was built with that package. See the :ref:`Making LAMMPS <2_3>` section for more info.
if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_2_3>` section for more info.
Related commands
""""""""""""""""

2
doc/html/_sources/pair_gauss.txt
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@ -163,7 +163,7 @@ Restrictions
The *gauss/cut* style is part of the "user-misc" package. It is only
enabled if LAMMPS is build with that package. See the :ref:`Making of LAMMPS <3>` section for more info.
enabled if LAMMPS is build with that package. See the :ref:`Making of LAMMPS <start_3>` section for more info.
Related commands
""""""""""""""""

2
doc/html/_sources/pair_list.txt
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@ -149,7 +149,7 @@ atom J (assuming the images are within the cutoff distance), but only
with the nearest image.
This style is part of the USER-MISC package. It is only enabled if
LAMMPS is build with that package. See the :ref:`Making of LAMMPS <3>` section for more info.
LAMMPS is build with that package. See the :ref:`Making of LAMMPS <start_3>` section for more info.
Related commands
""""""""""""""""

2
doc/html/_sources/pair_lubricate.txt
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@ -208,7 +208,7 @@ Restrictions
These styles are part of the COLLOID package. They are only enabled
if LAMMPS was built with that package. See the :ref:`Making LAMMPS <2_3>` section for more info.
if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_2_3>` section for more info.
Only spherical monodisperse particles are allowed for pair_style
lubricate.

2
doc/html/_sources/pair_lubricateU.txt
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@ -189,7 +189,7 @@ Restrictions
These styles are part of the COLLOID package. They are only enabled
if LAMMPS was built with that package. See the :ref:`Making LAMMPS <2_3>` section for more info.
if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_2_3>` section for more info.
Currently, these pair styles assume that all other types of
forces/torques on the particles have been already been computed when

2
doc/html/_sources/pair_meam.txt
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@ -315,7 +315,7 @@ this function is:
Most published MEAM parameter sets use the default values attrac=repulse=0.
Setting repuls=attrac=delta corresponds to the form used in several
recent published MEAM parameter sets, such as :ref:`(Vallone) <Vallone>`
recent published MEAM parameter sets, such as :ref:`(Valone) <Valone>`
.. note::

4
doc/html/_sources/pair_smtbq.txt
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@ -188,7 +188,7 @@ For each cations (metal):
7) Charge initialization mode:
* Keyword (\ *QInitMode*\ ) and initial oxygen charge (\ *Q<sub>init</sub>*\ ). If keyword = 'true', all oxygen charges are initially set equal to *Q<sub>init</sub>*\ . The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create_atom"#create_atom command or the charge specified in the file structure using :ref:`read_data <read_data.html>` command.
* Keyword (\ *QInitMode*\ ) and initial oxygen charge (\ *Q<sub>init</sub>*\ ). If keyword = 'true', all oxygen charges are initially set equal to *Q<sub>init</sub>*\ . The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create_atom"#create_atom command or the charge specified in the file structure using :doc:`read_data <read_data>` command.
* Divided line
8) Mode for the electronegativity equalization (Qeq)
@ -241,7 +241,7 @@ This pair style requires the :doc:`newton <newton>` setting to be "on"
for pair interactions.
The SMTB-Q potential files provided with LAMMPS (see the potentials
directory) are parameterized for metal :doc:`units <unit>`.
directory) are parameterized for metal :doc:`units <units>`.
----------

2
doc/html/_sources/pair_sph_taitwater.txt
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@ -81,7 +81,7 @@ Related commands
----------
.. _Monoghan:
.. _Monaghan:

2
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@ -184,7 +184,7 @@ section for more info on packages.</p>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a>,
<span class="xref doc">angle_cosineshiftexp</span></p>
<a class="reference internal" href="angle_cosine_shift_exp.html"><span class="doc">angle_cosine_shift_exp</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

4
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@ -194,8 +194,8 @@ section for more info on packages.</p>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a>,
<span class="xref doc">angle_cosineshift</span>,
<span class="xref doc">dihedral_cosineshift</span></p>
<a class="reference internal" href="angle_cosine_shift.html"><span class="doc">angle_cosine_shift</span></a>,
<a class="reference internal" href="dihedral_cosine_shift_exp.html"><span class="doc">dihedral_cosine_shift_exp</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

2
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@ -198,7 +198,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the <span class="xref std std-ref">Making LAMMPS</span>
USER-MISC package. See the <a class="reference internal" href="Section_start.html#start-2-3"><span class="std std-ref">Making LAMMPS</span></a>
section for more info on packages.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>

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@ -187,7 +187,7 @@ section for more info on packages.</p>
<h2>Related commands</h2>
<p><a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a>,
<a class="reference internal" href="bond_harmonic.html"><span class="doc">bond_harmonic</span></a>,
<span class="xref doc">bond_harmonicshift</span></p>
<a class="reference internal" href="bond_harmonic_shift.html"><span class="doc">bond_harmonic_shift</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

2
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@ -193,7 +193,7 @@ section for more info on packages.</p>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a>,
<span class="xref doc">angle_cosineshiftexp</span></p>
<a class="reference internal" href="angle_cosine_shift_exp.html"><span class="doc">angle_cosine_shift_exp</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

4
doc/html/fix_lb_fluid.html
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@ -341,7 +341,7 @@ N timesteps.</p>
<p>If the keyword <em>trilinear</em> is used, the trilinear stencil is used to
interpolate the particle nodes onto the fluid mesh. By default, the
immersed boundary method, Peskin stencil is used. Both of these
interpolation methods are described in <span class="xref std std-ref">Mackay et al.</span>.</p>
interpolation methods are described in <a class="reference internal" href="#fluid-mackay"><span class="std std-ref">Mackay et al.</span></a>.</p>
<p>If the keyword <em>D3Q19</em> is used, the 19 velocity (D3Q19) lattice is
used by the lattice-Boltzmann algorithm. By default, the 15 velocity
(D3Q15) lattice is used.</p>
@ -384,7 +384,7 @@ binary restart files, if requested, independent of the main LAMMPS
is written to the main LAMMPS <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
access by various <span class="xref std std-ref">output commands</span>. No
access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No
parameter of this fix can be used with the <em>start/stop</em> keywords of
the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
</div>

2
doc/html/fix_ti_rs.html
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@ -152,7 +152,7 @@
<h2>Description</h2>
<p>This fix allows you to compute the free energy temperature dependence
by performing a thermodynamic integration procedure known as
Reversible Scaling <a class="reference internal" href="#dekoning99"><span class="std std-ref">(de Koning99,</span></a> <span class="xref std std-ref">de Koning00a)</span>. The thermodynamic integration is performed
Reversible Scaling <a class="reference internal" href="#dekoning99"><span class="std std-ref">(de Koning99,</span></a> <a class="reference internal" href="#dekoning00a"><span class="std std-ref">de Koning00a)</span></a>. The thermodynamic integration is performed
using the nonequilibrium method of Adiabatic Switching
<a class="reference internal" href="fix_ti_spring.html#watanabe"><span class="std std-ref">(Watanabe,</span></a> <a class="reference internal" href="fix_ti_spring.html#dekoning96"><span class="std std-ref">de Koning96)</span></a>.</p>
<p>The forces on the atoms are dynamically scaled during the simulation,

2
doc/html/neb.html
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@ -346,7 +346,7 @@ due to the inter-replica spring force added by the <a class="reference internal"
is selected and the inter-replica forces on it are converted to a
force that drives its atom coordinates to the top or saddle point of
the barrier, via the barrier-climbing calculation described in
<span class="xref std std-ref">(Henkelman2)</span>. As before, the other replicas rearrange
<a class="reference internal" href="#henkelman2"><span class="std std-ref">(Henkelman2)</span></a>. As before, the other replicas rearrange
themselves along the MEP so as to be roughly equally spaced.</p>
<p>When both stages are complete, if the NEB calculation was successful,
one of the replicas should be an atomic configuration at the top or

2
doc/html/pair_body.html
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@ -212,7 +212,7 @@ shift, table, and tail options.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This style is part of the BODY package. It is only enabled if LAMMPS
was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
was built with that package. See the <a class="reference internal" href="Section_start.html#start-2-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>Defining particles to be bodies so they participate in body/body or
body/particle interactions requires the use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style body</span></a> command.</p>
</div>

14
doc/html/pair_bop.html
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@ -156,8 +156,8 @@ quantum mechanical theory incorporating both sigma and pi bondings.
By analytically deriving the BOP from quantum mechanical theory its
transferability to different phases can approach that of quantum
mechanical methods. This potential is similar to the original BOP
developed by Pettifor (<span class="xref std std-ref">Pettifor_1</span>,
<span class="xref std std-ref">Pettifor_2</span>, <span class="xref std std-ref">Pettifor_3</span>) and later updated
developed by Pettifor (<a class="reference internal" href="#pettifor-1"><span class="std std-ref">Pettifor_1</span></a>,
<a class="reference internal" href="#pettifor-2"><span class="std std-ref">Pettifor_2</span></a>, <a class="reference internal" href="#pettifor-3"><span class="std std-ref">Pettifor_3</span></a>) and later updated
by Murdick, Zhou, and Ward (<a class="reference internal" href="#murdick"><span class="std std-ref">Murdick</span></a>, <a class="reference internal" href="#ward"><span class="std std-ref">Ward</span></a>).
Currently, BOP potential files for these systems are provided with
LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A sysstem with
@ -195,7 +195,7 @@ simulations, the derived BOP only takes (and retains) the first two
levels of the recursive representations for both the sigma and the pi
bond-orders. Bond-order terms can be understood in terms of molecular
orbital hopping paths based upon the Cyrot-Lackmann theorem
(<span class="xref std std-ref">Pettifor_1</span>). The sigma bond-order with a half-full
(<a class="reference internal" href="#pettifor-1"><span class="std std-ref">Pettifor_1</span></a>). The sigma bond-order with a half-full
valence shell is used to interpolate the bond-order expressiont that
incorporated explicite valance band filling. This pi bond-order
expression also contains also contains a three-member ring term that
@ -213,7 +213,7 @@ the <a class="reference internal" href="mass.html"><span class="doc">mass</span>
potentials with hydrogen, you will likely want to set the mass of H
atoms to be 10x or 20x larger to avoid having to use a tiny timestep.
You can do this by using the <a class="reference internal" href="mass.html"><span class="doc">mass</span></a> command after using the
<span class="xref doc">pair_coeff</span> command to read the BOP potential
<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command to read the BOP potential
file.</p>
</div>
<p>One option can be specified as a keyword with the pair_style command.</p>
@ -483,11 +483,11 @@ appropriate units if your simulation does not use &#8220;metal&#8221; units.</p>
<h2>Default</h2>
<p>non-tabulated potential file, a_0 is non-zero.</p>
<hr class="docutils" />
<p id="pettofor-1"><strong>(Pettifor_1)</strong> D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487
<p id="pettifor-1"><strong>(Pettifor_1)</strong> D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487
(1999).</p>
<p id="pettofor-2"><strong>(Pettifor_2)</strong> D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84,
<p id="pettifor-2"><strong>(Pettifor_2)</strong> D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84,
4124 (2000).</p>
<p id="pettofor-3"><strong>(Pettifor_3)</strong> D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103
<p id="pettifor-3"><strong>(Pettifor_3)</strong> D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103
(2002).</p>
<p id="murdick"><strong>(Murdick)</strong> D.A. Murdick, X.W. Zhou, H.N.G. Wadley, D. Nguyen-Manh, R.
Drautz, and D.G. Pettifor, Phys. Rev. B, 73, 45206 (2006).</p>

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@ -198,7 +198,7 @@ pressure.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This style is part of the &#8220;user-misc&#8221; package. It is only enabled
if LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-2-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

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@ -249,7 +249,7 @@ heading) the following commands could be included in an input script:</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>The <em>gauss/cut</em> style is part of the &#8220;user-misc&#8221; package. It is only
enabled if LAMMPS is build with that package. See the <span class="xref std std-ref">Making of LAMMPS</span> section for more info.</p>
enabled if LAMMPS is build with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making of LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

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@ -237,7 +237,7 @@ styles in LAMMPS, an atom I will not interact with multiple images of
atom J (assuming the images are within the cutoff distance), but only
with the nearest image.</p>
<p>This style is part of the USER-MISC package. It is only enabled if
LAMMPS is build with that package. See the <span class="xref std std-ref">Making of LAMMPS</span> section for more info.</p>
LAMMPS is build with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making of LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

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@ -286,7 +286,7 @@ to be specified in an input script that reads a restart file.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>These styles are part of the COLLOID package. They are only enabled
if LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-2-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>Only spherical monodisperse particles are allowed for pair_style
lubricate.</p>
<p>Only spherical particles are allowed for pair_style lubricate/poly.</p>

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@ -274,7 +274,7 @@ to be specified in an input script that reads a restart file.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>These styles are part of the COLLOID package. They are only enabled
if LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-2-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>Currently, these pair styles assume that all other types of
forces/torques on the particles have been already been computed when
it is invoked. This requires this style to be defined as the last of

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@ -400,7 +400,7 @@ this function is:</p>
</div>
<p>Most published MEAM parameter sets use the default values attrac=repulse=0.
Setting repuls=attrac=delta corresponds to the form used in several
recent published MEAM parameter sets, such as <span class="xref std std-ref">(Vallone)</span></p>
recent published MEAM parameter sets, such as <a class="reference internal" href="#valone"><span class="std std-ref">(Valone)</span></a></p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The default form of the erose expression in LAMMPS was corrected

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@ -301,7 +301,7 @@ quotation marks (&#8216;&#8217;).</p>
<li>Charge initialization mode:</li>
</ol>
<ul class="simple">
<li>Keyword (<em>QInitMode</em>) and initial oxygen charge (<em>Q&lt;sub&gt;init&lt;/sub&gt;</em>). If keyword = &#8216;true&#8217;, all oxygen charges are initially set equal to <em>Q&lt;sub&gt;init&lt;/sub&gt;</em>. The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = &#8216;false&#8217;, all atom charges are initially set equal to 0 if you use &#8220;create_atom&#8221;#create_atom command or the charge specified in the file structure using <span class="xref std std-ref">read_data</span> command.</li>
<li>Keyword (<em>QInitMode</em>) and initial oxygen charge (<em>Q&lt;sub&gt;init&lt;/sub&gt;</em>). If keyword = &#8216;true&#8217;, all oxygen charges are initially set equal to <em>Q&lt;sub&gt;init&lt;/sub&gt;</em>. The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = &#8216;false&#8217;, all atom charges are initially set equal to 0 if you use &#8220;create_atom&#8221;#create_atom command or the charge specified in the file structure using <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command.</li>
<li>Divided line</li>
</ul>
<ol class="arabic simple" start="8">
@ -344,7 +344,7 @@ higher than 1 for metal atoms.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be &#8220;on&#8221;
for pair interactions.</p>
<p>The SMTB-Q potential files provided with LAMMPS (see the potentials
directory) are parameterized for metal <span class="xref doc">units</span>.</p>
directory) are parameterized for metal <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
<hr class="docutils" />
<p><strong>Citing this work:</strong></p>
<p>Please cite related publication: N. Salles, O. Politano, E. Amzallag

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@ -147,7 +147,7 @@ according to the ideal gas equation of state:</p>
<p>where gamma = 1.4 is the heat capacity ratio, rho is the local
density, and e is the internal energy per unit mass. This pair style
also computes Monaghan&#8217;s artificial viscosity to prevent particles
from interpentrating <a class="reference internal" href="pair_sph_taitwater.html#monoghan"><span class="std std-ref">(Monaghan)</span></a>.</p>
from interpentrating <a class="reference internal" href="pair_sph_lj.html#monoghan"><span class="std std-ref">(Monaghan)</span></a>.</p>
<p>See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to using SPH in
LAMMPS.</p>
<p>The following coefficients must be defined for each pair of atoms

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@ -146,7 +146,7 @@ to the Lennard-Jones equation of state, which is computed according to
Ree&#8217;s 1980 polynomial fit <a class="reference internal" href="#ree"><span class="std std-ref">(Ree)</span></a>. The Lennard-Jones parameters
epsilon and sigma are set to unity. This pair style also computes
Monaghan&#8217;s artificial viscosity to prevent particles from
interpentrating <a class="reference internal" href="pair_sph_taitwater.html#monoghan"><span class="std std-ref">(Monaghan)</span></a>.</p>
interpentrating <a class="reference internal" href="#monoghan"><span class="std std-ref">(Monaghan)</span></a>.</p>
<p>See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to using SPH in
LAMMPS.</p>
<p>The following coefficients must be defined for each pair of atoms

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@ -147,7 +147,7 @@ according to Tait&#8217;s equation of state:</p>
<p>where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the
reference density and c_0 the reference speed of sound.</p>
<p>This pair style also computes Monaghan&#8217;s artificial viscosity to
prevent particles from interpentrating <span class="xref std std-ref">(Monaghan)</span>.</p>
prevent particles from interpentrating <a class="reference internal" href="#monaghan"><span class="std std-ref">(Monaghan)</span></a>.</p>
<p>See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to using SPH in
LAMMPS.</p>
<p>The following coefficients must be defined for each pair of atoms
@ -180,7 +180,7 @@ if LAMMPS was built with that package. See the <a class="reference internal" hr
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a>, pair_sph/rhosum</p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="monoghan"><strong>(Monaghan)</strong> Monaghan and Gingold, Journal of Computational Physics,
<p id="monaghan"><strong>(Monaghan)</strong> Monaghan and Gingold, Journal of Computational Physics,
52, 374-389 (1983).</p>
</div>
</div>

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