forked from lijiext/lammps
pair vashishta/table
This commit is contained in:
Steve Plimpton
commit
ed52f9ea5e
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@ -129,30 +129,49 @@
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|||
</div>
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<div class="section" id="pair-style-vashishta-omp-command">
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<h1>pair_style vashishta/omp command</h1>
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</div>
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<div class="section" id="pair-style-vashishta-table-command">
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||||
<h1>pair_style vashishta/table command</h1>
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</div>
|
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<div class="section" id="pair-style-vashishta-table-omp-command">
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<h1>pair_style vashishta/table/omp command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">vashishta</span>
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</pre></div>
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</div>
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<pre class="literal-block">
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pair_style style args
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</pre>
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<ul class="simple">
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<li>style = <em>vashishta</em> or <em>vashishta/table</em> or <em>vashishta/omp</em> or <em>vashishta/table/omp</em></li>
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<li>args = list of arguments for a particular style</li>
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</ul>
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<pre class="literal-block">
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<em>vashishta</em> or <em>vashishta/omp</em> args = none
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<em>vashishta/table</em> or <em>vashishta/table/omp</em> args = Ntable cutinner
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Ntable = # of tabulation points
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cutinner = tablulate from cutinner to cutoff
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">vashishta</span>
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<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">vashishta</span> <span class="n">Si</span> <span class="n">C</span>
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</pre></div>
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</div>
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<pre class="literal-block">
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pair_style vashishta
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pair_coeff * * SiC.vashishta Si C
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</pre>
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<pre class="literal-block">
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pair_style vashishta/table 100000 0.2
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pair_coeff * * SiC.vashishta Si C
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</pre>
|
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</div>
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<div class="section" id="description">
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<h2>Description</h2>
|
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<p>The <em>vashishta</em> style computes the combined 2-body and 3-body
|
||||
family of potentials developed in the group of Vashishta and
|
||||
co-workers. By combining repulsive, screened Coulombic,
|
||||
screened charge-dipole, and dispersion interactions with a
|
||||
bond-angle energy based on the Stillinger-Weber potential,
|
||||
this potential has been used to describe a variety of inorganic
|
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compounds, including SiO2 <a class="reference internal" href="#vashishta1990"><span class="std std-ref">Vashishta1990</span></a>,
|
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SiC <a class="reference internal" href="#vashishta2007"><span class="std std-ref">Vashishta2007</span></a>,
|
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and InP <a class="reference internal" href="#branicio2009"><span class="std std-ref">Branicio2009</span></a>.</p>
|
||||
<p>The <em>vashishta</em> and <em>vashishta/table</em> styles compute the combined
|
||||
2-body and 3-body family of potentials developed in the group of Priya
|
||||
Vashishta and collaborators. By combining repulsive, screened
|
||||
Coulombic, screened charge-dipole, and dispersion interactions with a
|
||||
bond-angle energy based on the Stillinger-Weber potential, this
|
||||
potential has been used to describe a variety of inorganic compounds,
|
||||
including SiO2 <a class="reference internal" href="#vashishta1990"><span class="std std-ref">Vashishta1990</span></a>, SiC
|
||||
<a class="reference internal" href="#vashishta2007"><span class="std std-ref">Vashishta2007</span></a>, and InP <a class="reference internal" href="#branicio2009"><span class="std std-ref">Branicio2009</span></a>.</p>
|
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<p>The potential for the energy U of a system of atoms is</p>
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<img alt="_images/pair_vashishta.jpg" class="align-center" src="_images/pair_vashishta.jpg" />
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<p>where we follow the notation used in <a class="reference internal" href="#branicio2009"><span class="std std-ref">Branicio2009</span></a>.
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@ -163,10 +182,20 @@ tilted by a linear function so that the energy and force are
|
|||
both zero at <em>rc</em>. The summation over three-body terms
|
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is over all neighbors J and K within a cut-off distance = <em>r0</em>,
|
||||
where the exponential screening function becomes zero.</p>
|
||||
<p>Only a single pair_coeff command is used with the <em>vashishta</em> style which
|
||||
specifies a Vashishta potential file with parameters for all
|
||||
needed elements. These are mapped to LAMMPS atom types by specifying
|
||||
N additional arguments after the filename in the pair_coeff command,
|
||||
<p>The <em>vashishta</em> style computes these formulas analytically. The
|
||||
<em>vashishta/table</em> style tabulates the analytic values for <em>Ntable</em>
|
||||
points from cutinner to the cutoff of the potential. The points are
|
||||
equally spaced in R^2 space from cutinner^2 to cutoff^2. For the
|
||||
two-body term in the above equation, a linear interpolation for each
|
||||
pairwise distance between adjacent points in the table. In practice
|
||||
the tabulated version can run 3-5x faster than the analytic version
|
||||
with with moderate to little loss of accuracy for Ntable values
|
||||
between 10000 and 1000000. It is not recommended to use less than
|
||||
5000 tabulation points.</p>
|
||||
<p>Only a single pair_coeff command is used with either style which
|
||||
specifies a Vashishta potential file with parameters for all needed
|
||||
elements. These are mapped to LAMMPS atom types by specifying N
|
||||
additional arguments after the filename in the pair_coeff command,
|
||||
where N is the number of LAMMPS atom types:</p>
|
||||
<ul class="simple">
|
||||
<li>filename</li>
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||||
|
|
@ -178,9 +207,9 @@ to specify the path for the potential file.</p>
|
|||
Si and C. If your LAMMPS simulation has 4 atoms types and you want
|
||||
the 1st 3 to be Si, and the 4th to be C, you would use the following
|
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pair_coeff command:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">vashishta</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">C</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
pair_coeff * * SiC.vashishta Si Si Si C
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||||
</pre>
|
||||
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
|
||||
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
|
||||
element in the file. The final C argument maps LAMMPS atom type 4
|
||||
|
|
@ -213,56 +242,49 @@ and three-body coefficients in the formulae above:</p>
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|||
<li>C</li>
|
||||
<li>costheta0</li>
|
||||
</ul>
|
||||
<p>The non-annotated parameters are unitless.
|
||||
The Vashishta potential file must contain entries for all the
|
||||
elements listed in the pair_coeff command. It can also contain
|
||||
entries for additional elements not being used in a particular
|
||||
simulation; LAMMPS ignores those entries.
|
||||
For a single-element simulation, only a single entry is required
|
||||
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
|
||||
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
|
||||
specify parameters for all permutations of the two elements
|
||||
interacting in three-body configurations. Thus for 3 elements, 27
|
||||
entries would be required, etc.</p>
|
||||
<p>Depending on the particular version of the Vashishta potential,
|
||||
the values of these parameters may be keyed to the identities of
|
||||
zero, one, two, or three elements.
|
||||
In order to make the input file format unambiguous, general,
|
||||
and simple to code,
|
||||
LAMMPS uses a slightly confusing method for specifying parameters.
|
||||
All parameters are divided into two classes: two-body and three-body.
|
||||
Two-body and three-body parameters are handled differently,
|
||||
as described below.
|
||||
The two-body parameters are H, eta, lambda1, D, lambda4, W, rc, gamma, and r0.
|
||||
They appear in the above formulae with two subscripts.
|
||||
The parameters Zi and Zj are also classified as two-body parameters,
|
||||
even though they only have 1 subscript.
|
||||
The three-body parameters are B, C, costheta0.
|
||||
They appear in the above formulae with three subscripts.
|
||||
Two-body and three-body parameters are handled differently,
|
||||
as described below.</p>
|
||||
<p>The first element in each entry is the center atom
|
||||
in a three-body interaction, while the second and third elements
|
||||
are two neighbor atoms. Three-body parameters for a central atom I
|
||||
and two neighbors J and K are taken from the IJK entry.
|
||||
Note that even though three-body parameters do not depend on the order of
|
||||
J and K, LAMMPS stores three-body parameters for both IJK and IKJ.
|
||||
The user must ensure that these values are equal.
|
||||
Two-body parameters for an atom I interacting with atom J are taken from
|
||||
the IJJ entry, where the 2nd and 3rd
|
||||
elements are the same. Thus the two-body parameters
|
||||
for Si interacting with C come from the SiCC entry. Note that even
|
||||
though two-body parameters (except possibly gamma and r0 in U3)
|
||||
do not depend on the order of the two elements,
|
||||
LAMMPS will get the Si-C value from the SiCC entry
|
||||
and the C-Si value from the CSiSi entry. The user must ensure
|
||||
that these values are equal. Two-body parameters appearing
|
||||
in entries where the 2nd and 3rd elements are different are
|
||||
stored but never used. It is good practice to enter zero for
|
||||
these values. Note that the three-body function U3 above
|
||||
contains the two-body parameters gamma and r0. So U3 for a
|
||||
central C atom bonded to an Si atom and a second C atom
|
||||
will take three-body parameters from the CSiC entry, but
|
||||
<p>The non-annotated parameters are unitless. The Vashishta potential
|
||||
file must contain entries for all the elements listed in the
|
||||
pair_coeff command. It can also contain entries for additional
|
||||
elements not being used in a particular simulation; LAMMPS ignores
|
||||
those entries. For a single-element simulation, only a single entry
|
||||
is required (e.g. SiSiSi). For a two-element simulation, the file
|
||||
must contain 8 entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC,
|
||||
CCSi, CCC), that specify parameters for all permutations of the two
|
||||
elements interacting in three-body configurations. Thus for 3
|
||||
elements, 27 entries would be required, etc.</p>
|
||||
<p>Depending on the particular version of the Vashishta potential, the
|
||||
values of these parameters may be keyed to the identities of zero,
|
||||
one, two, or three elements. In order to make the input file format
|
||||
unambiguous, general, and simple to code, LAMMPS uses a slightly
|
||||
confusing method for specifying parameters. All parameters are
|
||||
divided into two classes: two-body and three-body. Two-body and
|
||||
three-body parameters are handled differently, as described below.
|
||||
The two-body parameters are H, eta, lambda1, D, lambda4, W, rc, gamma,
|
||||
and r0. They appear in the above formulae with two subscripts. The
|
||||
parameters Zi and Zj are also classified as two-body parameters, even
|
||||
though they only have 1 subscript. The three-body parameters are B,
|
||||
C, costheta0. They appear in the above formulae with three
|
||||
subscripts. Two-body and three-body parameters are handled
|
||||
differently, as described below.</p>
|
||||
<p>The first element in each entry is the center atom in a three-body
|
||||
interaction, while the second and third elements are two neighbor
|
||||
atoms. Three-body parameters for a central atom I and two neighbors J
|
||||
and K are taken from the IJK entry. Note that even though three-body
|
||||
parameters do not depend on the order of J and K, LAMMPS stores
|
||||
three-body parameters for both IJK and IKJ. The user must ensure that
|
||||
these values are equal. Two-body parameters for an atom I interacting
|
||||
with atom J are taken from the IJJ entry, where the 2nd and 3rd
|
||||
elements are the same. Thus the two-body parameters for Si interacting
|
||||
with C come from the SiCC entry. Note that even though two-body
|
||||
parameters (except possibly gamma and r0 in U3) do not depend on the
|
||||
order of the two elements, LAMMPS will get the Si-C value from the
|
||||
SiCC entry and the C-Si value from the CSiSi entry. The user must
|
||||
ensure that these values are equal. Two-body parameters appearing in
|
||||
entries where the 2nd and 3rd elements are different are stored but
|
||||
never used. It is good practice to enter zero for these values. Note
|
||||
that the three-body function U3 above contains the two-body parameters
|
||||
gamma and r0. So U3 for a central C atom bonded to an Si atom and a
|
||||
second C atom will take three-body parameters from the CSiC entry, but
|
||||
two-body parameters from the CCC and CSiSi entries.</p>
|
||||
<hr class="docutils" />
|
||||
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
|
||||
|
|
@ -297,15 +319,16 @@ script that reads a restart file.</p>
|
|||
<hr class="docutils" />
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
<p>This pair style is part of the MANYBODY package. It is only enabled
|
||||
if LAMMPS was built with that package (which it is by default). See
|
||||
the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
||||
<p>This pair style requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be “on”
|
||||
<p>These pair style are part of the MANYBODY package. They is only
|
||||
enabled if LAMMPS was built with that package (which it is by
|
||||
default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section
|
||||
for more info.</p>
|
||||
<p>These pair styles requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be “on”
|
||||
for pair interactions.</p>
|
||||
<p>The Vashishta potential files provided with LAMMPS (see the
|
||||
potentials directory) are parameterized for metal <a class="reference internal" href="units.html"><span class="doc">units</span></a>.
|
||||
You can use the Vashishta potential with any LAMMPS units, but you would need
|
||||
to create your own Vashishta potential file with coefficients listed in the
|
||||
<p>The Vashishta potential files provided with LAMMPS (see the potentials
|
||||
directory) are parameterized for metal <a class="reference internal" href="units.html"><span class="doc">units</span></a>. You can
|
||||
use the Vashishta potential with any LAMMPS units, but you would need
|
||||
to create your own potential file with coefficients listed in the
|
||||
appropriate units if your simulation doesn’t use “metal” units.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
|
|
@ -313,9 +336,12 @@ appropriate units if your simulation doesn’t use “metal” units
|
|||
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
<hr class="docutils" />
|
||||
<p id="vashishta1990"><strong>(Vashishta1990)</strong> P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B 41, 12197 (1990).</p>
|
||||
<p id="vashishta2007"><strong>(Vashishta2007)</strong> P. Vashishta, R. K. Kalia, A. Nakano, J. P. Rino. J. Appl. Phys. 101, 103515 (2007).</p>
|
||||
<p id="branicio2009"><strong>(Branicio2009)</strong> Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002</p>
|
||||
<p id="vashishta1990"><strong>(Vashishta1990)</strong> P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B
|
||||
41, 12197 (1990).</p>
|
||||
<p id="vashishta2007"><strong>(Vashishta2007)</strong> P. Vashishta, R. K. Kalia, A. Nakano,
|
||||
J. P. Rino. J. Appl. Phys. 101, 103515 (2007).</p>
|
||||
<p id="branicio2009"><strong>(Branicio2009)</strong> Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed
|
||||
Matter 21 (2009) 095002</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -8,27 +8,38 @@
|
|||
|
||||
pair_style vashishta command :h3
|
||||
pair_style vashishta/omp command :h3
|
||||
pair_style vashishta/table command :h3
|
||||
pair_style vashishta/table/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style vashishta :pre
|
||||
pair_style style args :pre
|
||||
|
||||
style = {vashishta} or {vashishta/table} or {vashishta/omp} or {vashishta/table/omp}
|
||||
args = list of arguments for a particular style :ul
|
||||
{vashishta} or {vashishta/omp} args = none
|
||||
{vashishta/table} or {vashishta/table/omp} args = Ntable cutinner
|
||||
Ntable = # of tabulation points
|
||||
cutinner = tablulate from cutinner to cutoff :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style vashishta
|
||||
pair_coeff * * SiC.vashishta Si C :pre
|
||||
|
||||
pair_style vashishta/table 100000 0.2
|
||||
pair_coeff * * SiC.vashishta Si C :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {vashishta} style computes the combined 2-body and 3-body
|
||||
family of potentials developed in the group of Vashishta and
|
||||
co-workers. By combining repulsive, screened Coulombic,
|
||||
screened charge-dipole, and dispersion interactions with a
|
||||
bond-angle energy based on the Stillinger-Weber potential,
|
||||
this potential has been used to describe a variety of inorganic
|
||||
compounds, including SiO2 "Vashishta1990"_#Vashishta1990,
|
||||
SiC "Vashishta2007"_#Vashishta2007,
|
||||
and InP "Branicio2009"_#Branicio2009.
|
||||
The {vashishta} and {vashishta/table} styles compute the combined
|
||||
2-body and 3-body family of potentials developed in the group of Priya
|
||||
Vashishta and collaborators. By combining repulsive, screened
|
||||
Coulombic, screened charge-dipole, and dispersion interactions with a
|
||||
bond-angle energy based on the Stillinger-Weber potential, this
|
||||
potential has been used to describe a variety of inorganic compounds,
|
||||
including SiO2 "Vashishta1990"_#Vashishta1990, SiC
|
||||
"Vashishta2007"_#Vashishta2007, and InP "Branicio2009"_#Branicio2009.
|
||||
|
||||
The potential for the energy U of a system of atoms is
|
||||
|
||||
|
|
@ -43,10 +54,21 @@ both zero at {rc}. The summation over three-body terms
|
|||
is over all neighbors J and K within a cut-off distance = {r0},
|
||||
where the exponential screening function becomes zero.
|
||||
|
||||
Only a single pair_coeff command is used with the {vashishta} style which
|
||||
specifies a Vashishta potential file with parameters for all
|
||||
needed elements. These are mapped to LAMMPS atom types by specifying
|
||||
N additional arguments after the filename in the pair_coeff command,
|
||||
The {vashishta} style computes these formulas analytically. The
|
||||
{vashishta/table} style tabulates the analytic values for {Ntable}
|
||||
points from cutinner to the cutoff of the potential. The points are
|
||||
equally spaced in R^2 space from cutinner^2 to cutoff^2. For the
|
||||
two-body term in the above equation, a linear interpolation for each
|
||||
pairwise distance between adjacent points in the table. In practice
|
||||
the tabulated version can run 3-5x faster than the analytic version
|
||||
with with moderate to little loss of accuracy for Ntable values
|
||||
between 10000 and 1000000. It is not recommended to use less than
|
||||
5000 tabulation points.
|
||||
|
||||
Only a single pair_coeff command is used with either style which
|
||||
specifies a Vashishta potential file with parameters for all needed
|
||||
elements. These are mapped to LAMMPS atom types by specifying N
|
||||
additional arguments after the filename in the pair_coeff command,
|
||||
where N is the number of LAMMPS atom types:
|
||||
|
||||
filename
|
||||
|
|
@ -95,59 +117,52 @@ r0 (distance units)
|
|||
C
|
||||
costheta0 :ul
|
||||
|
||||
The non-annotated parameters are unitless.
|
||||
The Vashishta potential file must contain entries for all the
|
||||
elements listed in the pair_coeff command. It can also contain
|
||||
entries for additional elements not being used in a particular
|
||||
simulation; LAMMPS ignores those entries.
|
||||
For a single-element simulation, only a single entry is required
|
||||
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
|
||||
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
|
||||
specify parameters for all permutations of the two elements
|
||||
interacting in three-body configurations. Thus for 3 elements, 27
|
||||
entries would be required, etc.
|
||||
The non-annotated parameters are unitless. The Vashishta potential
|
||||
file must contain entries for all the elements listed in the
|
||||
pair_coeff command. It can also contain entries for additional
|
||||
elements not being used in a particular simulation; LAMMPS ignores
|
||||
those entries. For a single-element simulation, only a single entry
|
||||
is required (e.g. SiSiSi). For a two-element simulation, the file
|
||||
must contain 8 entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC,
|
||||
CCSi, CCC), that specify parameters for all permutations of the two
|
||||
elements interacting in three-body configurations. Thus for 3
|
||||
elements, 27 entries would be required, etc.
|
||||
|
||||
Depending on the particular version of the Vashishta potential,
|
||||
the values of these parameters may be keyed to the identities of
|
||||
zero, one, two, or three elements.
|
||||
In order to make the input file format unambiguous, general,
|
||||
and simple to code,
|
||||
LAMMPS uses a slightly confusing method for specifying parameters.
|
||||
All parameters are divided into two classes: two-body and three-body.
|
||||
Two-body and three-body parameters are handled differently,
|
||||
as described below.
|
||||
The two-body parameters are H, eta, lambda1, D, lambda4, W, rc, gamma, and r0.
|
||||
They appear in the above formulae with two subscripts.
|
||||
The parameters Zi and Zj are also classified as two-body parameters,
|
||||
even though they only have 1 subscript.
|
||||
The three-body parameters are B, C, costheta0.
|
||||
They appear in the above formulae with three subscripts.
|
||||
Two-body and three-body parameters are handled differently,
|
||||
as described below.
|
||||
Depending on the particular version of the Vashishta potential, the
|
||||
values of these parameters may be keyed to the identities of zero,
|
||||
one, two, or three elements. In order to make the input file format
|
||||
unambiguous, general, and simple to code, LAMMPS uses a slightly
|
||||
confusing method for specifying parameters. All parameters are
|
||||
divided into two classes: two-body and three-body. Two-body and
|
||||
three-body parameters are handled differently, as described below.
|
||||
The two-body parameters are H, eta, lambda1, D, lambda4, W, rc, gamma,
|
||||
and r0. They appear in the above formulae with two subscripts. The
|
||||
parameters Zi and Zj are also classified as two-body parameters, even
|
||||
though they only have 1 subscript. The three-body parameters are B,
|
||||
C, costheta0. They appear in the above formulae with three
|
||||
subscripts. Two-body and three-body parameters are handled
|
||||
differently, as described below.
|
||||
|
||||
The first element in each entry is the center atom
|
||||
in a three-body interaction, while the second and third elements
|
||||
are two neighbor atoms. Three-body parameters for a central atom I
|
||||
and two neighbors J and K are taken from the IJK entry.
|
||||
Note that even though three-body parameters do not depend on the order of
|
||||
J and K, LAMMPS stores three-body parameters for both IJK and IKJ.
|
||||
The user must ensure that these values are equal.
|
||||
Two-body parameters for an atom I interacting with atom J are taken from
|
||||
the IJJ entry, where the 2nd and 3rd
|
||||
elements are the same. Thus the two-body parameters
|
||||
for Si interacting with C come from the SiCC entry. Note that even
|
||||
though two-body parameters (except possibly gamma and r0 in U3)
|
||||
do not depend on the order of the two elements,
|
||||
LAMMPS will get the Si-C value from the SiCC entry
|
||||
and the C-Si value from the CSiSi entry. The user must ensure
|
||||
that these values are equal. Two-body parameters appearing
|
||||
in entries where the 2nd and 3rd elements are different are
|
||||
stored but never used. It is good practice to enter zero for
|
||||
these values. Note that the three-body function U3 above
|
||||
contains the two-body parameters gamma and r0. So U3 for a
|
||||
central C atom bonded to an Si atom and a second C atom
|
||||
will take three-body parameters from the CSiC entry, but
|
||||
two-body parameters from the CCC and CSiSi entries.
|
||||
The first element in each entry is the center atom in a three-body
|
||||
interaction, while the second and third elements are two neighbor
|
||||
atoms. Three-body parameters for a central atom I and two neighbors J
|
||||
and K are taken from the IJK entry. Note that even though three-body
|
||||
parameters do not depend on the order of J and K, LAMMPS stores
|
||||
three-body parameters for both IJK and IKJ. The user must ensure that
|
||||
these values are equal. Two-body parameters for an atom I interacting
|
||||
with atom J are taken from the IJJ entry, where the 2nd and 3rd
|
||||
elements are the same. Thus the two-body parameters for Si interacting
|
||||
with C come from the SiCC entry. Note that even though two-body
|
||||
parameters (except possibly gamma and r0 in U3) do not depend on the
|
||||
order of the two elements, LAMMPS will get the Si-C value from the
|
||||
SiCC entry and the C-Si value from the CSiSi entry. The user must
|
||||
ensure that these values are equal. Two-body parameters appearing in
|
||||
entries where the 2nd and 3rd elements are different are stored but
|
||||
never used. It is good practice to enter zero for these values. Note
|
||||
that the three-body function U3 above contains the two-body parameters
|
||||
gamma and r0. So U3 for a central C atom bonded to an Si atom and a
|
||||
second C atom will take three-body parameters from the CSiC entry, but
|
||||
two-body parameters from the CCC and CSiSi entries.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -196,17 +211,18 @@ This pair style can only be used via the {pair} keyword of the
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
This pair style is part of the MANYBODY package. It is only enabled
|
||||
if LAMMPS was built with that package (which it is by default). See
|
||||
the "Making LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
These pair style are part of the MANYBODY package. They is only
|
||||
enabled if LAMMPS was built with that package (which it is by
|
||||
default). See the "Making LAMMPS"_Section_start.html#start_3 section
|
||||
for more info.
|
||||
|
||||
This pair style requires the "newton"_newton.html setting to be "on"
|
||||
These pair styles requires the "newton"_newton.html setting to be "on"
|
||||
for pair interactions.
|
||||
|
||||
The Vashishta potential files provided with LAMMPS (see the
|
||||
potentials directory) are parameterized for metal "units"_units.html.
|
||||
You can use the Vashishta potential with any LAMMPS units, but you would need
|
||||
to create your own Vashishta potential file with coefficients listed in the
|
||||
The Vashishta potential files provided with LAMMPS (see the potentials
|
||||
directory) are parameterized for metal "units"_units.html. You can
|
||||
use the Vashishta potential with any LAMMPS units, but you would need
|
||||
to create your own potential file with coefficients listed in the
|
||||
appropriate units if your simulation doesn't use "metal" units.
|
||||
|
||||
[Related commands:]
|
||||
|
|
@ -218,11 +234,13 @@ appropriate units if your simulation doesn't use "metal" units.
|
|||
:line
|
||||
|
||||
:link(Vashishta1990)
|
||||
[(Vashishta1990)] P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B 41, 12197 (1990).
|
||||
[(Vashishta1990)] P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B
|
||||
41, 12197 (1990).
|
||||
|
||||
:link(Vashishta2007)
|
||||
[(Vashishta2007)] P. Vashishta, R. K. Kalia, A. Nakano, J. P. Rino. J. Appl. Phys. 101, 103515 (2007).
|
||||
[(Vashishta2007)] P. Vashishta, R. K. Kalia, A. Nakano,
|
||||
J. P. Rino. J. Appl. Phys. 101, 103515 (2007).
|
||||
|
||||
:link(Branicio2009)
|
||||
[(Branicio2009)] Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002
|
||||
|
||||
[(Branicio2009)] Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed
|
||||
Matter 21 (2009) 095002
|
||||
|
|
|
|||
|
|
@ -0,0 +1,75 @@
|
|||
# calculate the energy volume curve for InP zincblende
|
||||
|
||||
# define volume range and filename
|
||||
|
||||
variable ndelta equal 100
|
||||
variable volatom_min equal 20.0
|
||||
variable volatom_max equal 29.0
|
||||
variable evsvolfile string evsvol.dat
|
||||
|
||||
# set up cell
|
||||
|
||||
units metal
|
||||
|
||||
boundary p p p
|
||||
|
||||
# setup loop variables for box volume
|
||||
|
||||
variable amin equal ${volatom_min}^(1/3)*2
|
||||
variable delta equal (${volatom_max}-${volatom_min})/${ndelta}
|
||||
variable scale equal (${delta}/v_volatom+1)^(1/3)
|
||||
|
||||
# set up 8 atom InP zincblende unit cell
|
||||
|
||||
lattice diamond ${amin}
|
||||
|
||||
region box prism &
|
||||
0 1 &
|
||||
0 1 &
|
||||
0 1 &
|
||||
0 0 0
|
||||
|
||||
create_box 2 box
|
||||
|
||||
create_atoms 1 box &
|
||||
basis 5 2 &
|
||||
basis 6 2 &
|
||||
basis 7 2 &
|
||||
basis 8 2
|
||||
|
||||
mass 1 114.76
|
||||
mass 2 30.98
|
||||
|
||||
# choose potential
|
||||
|
||||
pair_style vashishta/table 100000 0.2
|
||||
pair_coeff * * InP.vashishta In P
|
||||
|
||||
# setup neighbor style
|
||||
|
||||
neighbor 1.0 nsq
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# setup output
|
||||
|
||||
thermo_style custom step temp pe press vol
|
||||
thermo_modify norm no
|
||||
variable volatom equal vol/atoms
|
||||
variable eatom equal pe/atoms
|
||||
print "# Volume [A^3/atom] Energy [eV/atom]" file ${evsvolfile}
|
||||
|
||||
# loop over range of volumes
|
||||
|
||||
label loop
|
||||
variable i loop ${ndelta}
|
||||
|
||||
change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap
|
||||
|
||||
# calculate energy
|
||||
# no energy minimization needed for zincblende
|
||||
|
||||
run 0
|
||||
print "${volatom} ${eatom}" append ${evsvolfile}
|
||||
|
||||
next i
|
||||
jump SELF loop
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
# test Vashishta potential for quartz
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
variable ntable index 100000
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.quartz
|
||||
|
||||
replicate 4 4 4
|
||||
velocity all create 2000.0 277387 mom yes
|
||||
displace_atoms all move 0.05 0.9 0.4 units box
|
||||
|
||||
pair_style vashishta/table ${ntable} 0.2
|
||||
pair_coeff * * SiO.1990.vashishta Si O
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz
|
||||
#dump_modify 1 element Si O
|
||||
|
||||
run 100
|
||||
|
||||
|
|
@ -0,0 +1,75 @@
|
|||
# calculate the energy volume curve for InP zincblende
|
||||
|
||||
# define volume range and filename
|
||||
|
||||
variable ndelta equal 100
|
||||
variable volatom_min equal 20.0
|
||||
variable volatom_max equal 29.0
|
||||
variable evsvolfile string evsvol.dat
|
||||
|
||||
# set up cell
|
||||
|
||||
units metal
|
||||
|
||||
boundary p p p
|
||||
|
||||
# setup loop variables for box volume
|
||||
|
||||
variable amin equal ${volatom_min}^(1/3)*2
|
||||
variable delta equal (${volatom_max}-${volatom_min})/${ndelta}
|
||||
variable scale equal (${delta}/v_volatom+1)^(1/3)
|
||||
|
||||
# set up 8 atom InP zincblende unit cell
|
||||
|
||||
lattice diamond ${amin}
|
||||
|
||||
region box prism &
|
||||
0 1 &
|
||||
0 1 &
|
||||
0 1 &
|
||||
0 0 0
|
||||
|
||||
create_box 2 box
|
||||
|
||||
create_atoms 1 box &
|
||||
basis 5 2 &
|
||||
basis 6 2 &
|
||||
basis 7 2 &
|
||||
basis 8 2
|
||||
|
||||
mass 1 114.76
|
||||
mass 2 30.98
|
||||
|
||||
# choose potential
|
||||
|
||||
pair_style vashishta
|
||||
pair_coeff * * InP.vashishta In P
|
||||
|
||||
# setup neighbor style
|
||||
|
||||
neighbor 1.0 nsq
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# setup output
|
||||
|
||||
thermo_style custom step temp pe press vol
|
||||
thermo_modify norm no
|
||||
variable volatom equal vol/atoms
|
||||
variable eatom equal pe/atoms
|
||||
print "# Volume [A^3/atom] Energy [eV/atom]" file ${evsvolfile}
|
||||
|
||||
# loop over range of volumes
|
||||
|
||||
label loop
|
||||
variable i loop ${ndelta}
|
||||
|
||||
change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap
|
||||
|
||||
# calculate energy
|
||||
# no energy minimization needed for zincblende
|
||||
|
||||
run 0
|
||||
print "${volatom} ${eatom}" append ${evsvolfile}
|
||||
|
||||
next i
|
||||
jump SELF loop
|
||||
|
|
@ -0,0 +1,28 @@
|
|||
# test Vashishta potential for quartz
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.quartz
|
||||
|
||||
replicate 4 4 4
|
||||
velocity all create 2000.0 277387 mom yes
|
||||
displace_atoms all move 0.05 0.9 0.4 units box
|
||||
|
||||
pair_style vashishta
|
||||
pair_coeff * * SiO.1990.vashishta Si O
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz
|
||||
#dump_modify 1 element Si O
|
||||
|
||||
run 100
|
||||
|
||||
|
|
@ -0,0 +1,75 @@
|
|||
# calculate the energy volume curve for InP zincblende
|
||||
|
||||
# define volume range and filename
|
||||
|
||||
variable ndelta equal 100
|
||||
variable volatom_min equal 20.0
|
||||
variable volatom_max equal 29.0
|
||||
variable evsvolfile string evsvol.dat
|
||||
|
||||
# set up cell
|
||||
|
||||
units metal
|
||||
|
||||
boundary p p p
|
||||
|
||||
# setup loop variables for box volume
|
||||
|
||||
variable amin equal ${volatom_min}^(1/3)*2
|
||||
variable delta equal (${volatom_max}-${volatom_min})/${ndelta}
|
||||
variable scale equal (${delta}/v_volatom+1)^(1/3)
|
||||
|
||||
# set up 8 atom InP zincblende unit cell
|
||||
|
||||
lattice diamond ${amin}
|
||||
|
||||
region box prism &
|
||||
0 1 &
|
||||
0 1 &
|
||||
0 1 &
|
||||
0 0 0
|
||||
|
||||
create_box 2 box
|
||||
|
||||
create_atoms 1 box &
|
||||
basis 5 2 &
|
||||
basis 6 2 &
|
||||
basis 7 2 &
|
||||
basis 8 2
|
||||
|
||||
mass 1 114.76
|
||||
mass 2 30.98
|
||||
|
||||
# choose potential
|
||||
|
||||
pair_style vashishta/table 100000 0.2
|
||||
pair_coeff * * InP.vashishta In P
|
||||
|
||||
# setup neighbor style
|
||||
|
||||
neighbor 1.0 nsq
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# setup output
|
||||
|
||||
thermo_style custom step temp pe press vol
|
||||
thermo_modify norm no
|
||||
variable volatom equal vol/atoms
|
||||
variable eatom equal pe/atoms
|
||||
print "# Volume [A^3/atom] Energy [eV/atom]" file ${evsvolfile}
|
||||
|
||||
# loop over range of volumes
|
||||
|
||||
label loop
|
||||
variable i loop ${ndelta}
|
||||
|
||||
change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap
|
||||
|
||||
# calculate energy
|
||||
# no energy minimization needed for zincblende
|
||||
|
||||
run 0
|
||||
print "${volatom} ${eatom}" append ${evsvolfile}
|
||||
|
||||
next i
|
||||
jump SELF loop
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
# test Vashishta potential for quartz
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
variable ntable index 100000
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.quartz
|
||||
|
||||
replicate 4 4 4
|
||||
velocity all create 2000.0 277387 mom yes
|
||||
displace_atoms all move 0.05 0.9 0.4 units box
|
||||
|
||||
pair_style vashishta/table ${ntable} 0.2
|
||||
pair_coeff * * SiO.1990.vashishta Si O
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz
|
||||
#dump_modify 1 element Si O
|
||||
|
||||
run 100
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,86 @@
|
|||
LAMMPS (7 Sep 2016)
|
||||
# test Vashishta potential for quartz
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.quartz
|
||||
triclinic box = (0 0 0) to (4.9134 4.25513 5.4052) with tilt (-2.4567 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
9 atoms
|
||||
|
||||
replicate 4 4 4
|
||||
triclinic box = (0 0 0) to (19.6536 17.0205 21.6208) with tilt (-9.8268 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
576 atoms
|
||||
velocity all create 2000.0 277387 mom yes
|
||||
displace_atoms all move 0.05 0.9 0.4 units box
|
||||
|
||||
pair_style vashishta
|
||||
pair_coeff * * SiO.1990.vashishta Si O
|
||||
Reading potential file SiO.1990.vashishta with DATE: 2015-10-14
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz
|
||||
#dump_modify 1 element Si O
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.3
|
||||
ghost atom cutoff = 10.3
|
||||
binsize = 5.15 -> bins = 6 4 5
|
||||
Memory usage per processor = 2.54081 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 2000 -5280.875 0 -5132.2259 -20502.321
|
||||
10 895.65237 -5198.402 0 -5131.833 419.34676
|
||||
20 932.93463 -5201.1569 0 -5131.8169 -21407.961
|
||||
30 936.09591 -5201.3998 0 -5131.8248 -32531.168
|
||||
40 930.05159 -5201.0073 0 -5131.8816 -46445.212
|
||||
50 904.64676 -5199.062 0 -5131.8245 -31402.385
|
||||
60 1005.5353 -5206.5725 0 -5131.8365 -29790.442
|
||||
70 941.02343 -5201.7644 0 -5131.8232 -23046.796
|
||||
80 1020.1044 -5207.6763 0 -5131.8574 -13488.675
|
||||
90 912.75535 -5199.651 0 -5131.8108 2715.5897
|
||||
100 998.97588 -5206.1008 0 -5131.8523 6024.3651
|
||||
Loop time of 2.14363 on 1 procs for 100 steps with 576 atoms
|
||||
|
||||
Performance: 4.031 ns/day, 5.955 hours/ns, 46.650 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.0632 | 2.0632 | 2.0632 | 0.0 | 96.25
|
||||
Neigh | 0.074735 | 0.074735 | 0.074735 | 0.0 | 3.49
|
||||
Comm | 0.0039496 | 0.0039496 | 0.0039496 | 0.0 | 0.18
|
||||
Output | 0.00013208 | 0.00013208 | 0.00013208 | 0.0 | 0.01
|
||||
Modify | 0.00093484 | 0.00093484 | 0.00093484 | 0.0 | 0.04
|
||||
Other | | 0.0006742 | | | 0.03
|
||||
|
||||
Nlocal: 576 ave 576 max 576 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4926 ave 4926 max 4926 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 210470 ave 210470 max 210470 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 210470
|
||||
Ave neighs/atom = 365.399
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 10
|
||||
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -0,0 +1,86 @@
|
|||
LAMMPS (7 Sep 2016)
|
||||
# test Vashishta potential for quartz
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.quartz
|
||||
triclinic box = (0 0 0) to (4.9134 4.25513 5.4052) with tilt (-2.4567 0 0)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
9 atoms
|
||||
|
||||
replicate 4 4 4
|
||||
triclinic box = (0 0 0) to (19.6536 17.0205 21.6208) with tilt (-9.8268 0 0)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
576 atoms
|
||||
velocity all create 2000.0 277387 mom yes
|
||||
displace_atoms all move 0.05 0.9 0.4 units box
|
||||
|
||||
pair_style vashishta
|
||||
pair_coeff * * SiO.1990.vashishta Si O
|
||||
Reading potential file SiO.1990.vashishta with DATE: 2015-10-14
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz
|
||||
#dump_modify 1 element Si O
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.3
|
||||
ghost atom cutoff = 10.3
|
||||
binsize = 5.15 -> bins = 6 4 5
|
||||
Memory usage per processor = 2.50221 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 2000 -5280.875 0 -5132.2259 -20502.321
|
||||
10 895.65237 -5198.402 0 -5131.833 419.34676
|
||||
20 932.93463 -5201.1569 0 -5131.8169 -21407.961
|
||||
30 936.09591 -5201.3998 0 -5131.8248 -32531.168
|
||||
40 930.05159 -5201.0073 0 -5131.8816 -46445.212
|
||||
50 904.64676 -5199.062 0 -5131.8245 -31402.385
|
||||
60 1005.5353 -5206.5725 0 -5131.8365 -29790.442
|
||||
70 941.02343 -5201.7644 0 -5131.8232 -23046.796
|
||||
80 1020.1044 -5207.6763 0 -5131.8574 -13488.675
|
||||
90 912.75535 -5199.651 0 -5131.8108 2715.5897
|
||||
100 998.97588 -5206.1008 0 -5131.8523 6024.3651
|
||||
Loop time of 0.595482 on 4 procs for 100 steps with 576 atoms
|
||||
|
||||
Performance: 14.509 ns/day, 1.654 hours/ns, 167.931 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.5197 | 0.52697 | 0.53712 | 0.9 | 88.49
|
||||
Neigh | 0.017602 | 0.017907 | 0.018271 | 0.2 | 3.01
|
||||
Comm | 0.039021 | 0.049564 | 0.057245 | 3.0 | 8.32
|
||||
Output | 0.00021839 | 0.00024223 | 0.00028372 | 0.2 | 0.04
|
||||
Modify | 0.00027037 | 0.00027883 | 0.00028706 | 0.0 | 0.05
|
||||
Other | | 0.0005233 | | | 0.09
|
||||
|
||||
Nlocal: 144 ave 146 max 143 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Nghost: 3031 ave 3032 max 3030 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 52617.5 ave 53258 max 52208 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 210470
|
||||
Ave neighs/atom = 365.399
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 10
|
||||
|
||||
Total wall time: 0:00:00
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,89 @@
|
|||
LAMMPS (7 Sep 2016)
|
||||
# test Vashishta potential for quartz
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
variable ntable index 100000
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.quartz
|
||||
triclinic box = (0 0 0) to (4.9134 4.25513 5.4052) with tilt (-2.4567 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
9 atoms
|
||||
|
||||
replicate 4 4 4
|
||||
triclinic box = (0 0 0) to (19.6536 17.0205 21.6208) with tilt (-9.8268 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
576 atoms
|
||||
velocity all create 2000.0 277387 mom yes
|
||||
displace_atoms all move 0.05 0.9 0.4 units box
|
||||
|
||||
pair_style vashishta/table ${ntable} 0.2
|
||||
pair_style vashishta/table 100000 0.2
|
||||
pair_coeff * * SiO.1990.vashishta Si O
|
||||
Reading potential file SiO.1990.vashishta with DATE: 2015-10-14
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz
|
||||
#dump_modify 1 element Si O
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.3
|
||||
ghost atom cutoff = 10.3
|
||||
binsize = 5.15 -> bins = 6 4 5
|
||||
Memory usage per processor = 8.64433 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 2000 -5280.8748 0 -5132.2257 -20501.94
|
||||
10 895.65274 -5198.4018 0 -5131.8328 419.5556
|
||||
20 932.93469 -5201.1567 0 -5131.8167 -21407.92
|
||||
30 936.0957 -5201.3996 0 -5131.8246 -32531.15
|
||||
40 930.05185 -5201.0072 0 -5131.8815 -46445.195
|
||||
50 904.6467 -5199.0618 0 -5131.8243 -31402.296
|
||||
60 1005.5353 -5206.5723 0 -5131.8363 -29790.426
|
||||
70 941.02343 -5201.7642 0 -5131.8231 -23046.844
|
||||
80 1020.1046 -5207.6761 0 -5131.8572 -13488.691
|
||||
90 912.75537 -5199.6508 0 -5131.8106 2715.7189
|
||||
100 998.97595 -5206.1006 0 -5131.8521 6024.5628
|
||||
Loop time of 0.558684 on 1 procs for 100 steps with 576 atoms
|
||||
|
||||
Performance: 15.465 ns/day, 1.552 hours/ns, 178.992 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.47882 | 0.47882 | 0.47882 | 0.0 | 85.71
|
||||
Neigh | 0.07425 | 0.07425 | 0.07425 | 0.0 | 13.29
|
||||
Comm | 0.0038991 | 0.0038991 | 0.0038991 | 0.0 | 0.70
|
||||
Output | 0.00013018 | 0.00013018 | 0.00013018 | 0.0 | 0.02
|
||||
Modify | 0.00092959 | 0.00092959 | 0.00092959 | 0.0 | 0.17
|
||||
Other | | 0.0006537 | | | 0.12
|
||||
|
||||
Nlocal: 576 ave 576 max 576 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4926 ave 4926 max 4926 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 210470 ave 210470 max 210470 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 210470
|
||||
Ave neighs/atom = 365.399
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 10
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,89 @@
|
|||
LAMMPS (7 Sep 2016)
|
||||
# test Vashishta potential for quartz
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
variable ntable index 100000
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.quartz
|
||||
triclinic box = (0 0 0) to (4.9134 4.25513 5.4052) with tilt (-2.4567 0 0)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
9 atoms
|
||||
|
||||
replicate 4 4 4
|
||||
triclinic box = (0 0 0) to (19.6536 17.0205 21.6208) with tilt (-9.8268 0 0)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
576 atoms
|
||||
velocity all create 2000.0 277387 mom yes
|
||||
displace_atoms all move 0.05 0.9 0.4 units box
|
||||
|
||||
pair_style vashishta/table ${ntable} 0.2
|
||||
pair_style vashishta/table 100000 0.2
|
||||
pair_coeff * * SiO.1990.vashishta Si O
|
||||
Reading potential file SiO.1990.vashishta with DATE: 2015-10-14
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz
|
||||
#dump_modify 1 element Si O
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.3
|
||||
ghost atom cutoff = 10.3
|
||||
binsize = 5.15 -> bins = 6 4 5
|
||||
Memory usage per processor = 8.60573 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 2000 -5280.8748 0 -5132.2257 -20501.94
|
||||
10 895.65274 -5198.4018 0 -5131.8328 419.5556
|
||||
20 932.93469 -5201.1567 0 -5131.8167 -21407.92
|
||||
30 936.0957 -5201.3996 0 -5131.8246 -32531.15
|
||||
40 930.05185 -5201.0072 0 -5131.8815 -46445.195
|
||||
50 904.6467 -5199.0618 0 -5131.8243 -31402.296
|
||||
60 1005.5353 -5206.5723 0 -5131.8363 -29790.426
|
||||
70 941.02343 -5201.7642 0 -5131.8231 -23046.844
|
||||
80 1020.1046 -5207.6761 0 -5131.8572 -13488.691
|
||||
90 912.75537 -5199.6508 0 -5131.8106 2715.7189
|
||||
100 998.97595 -5206.1006 0 -5131.8521 6024.5628
|
||||
Loop time of 0.168748 on 4 procs for 100 steps with 576 atoms
|
||||
|
||||
Performance: 51.201 ns/day, 0.469 hours/ns, 592.599 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.12804 | 0.13513 | 0.1384 | 1.1 | 80.08
|
||||
Neigh | 0.01754 | 0.017732 | 0.017853 | 0.1 | 10.51
|
||||
Comm | 0.011786 | 0.014872 | 0.021839 | 3.3 | 8.81
|
||||
Output | 0.00026298 | 0.00027776 | 0.00031996 | 0.1 | 0.16
|
||||
Modify | 0.00025988 | 0.00027919 | 0.00029302 | 0.1 | 0.17
|
||||
Other | | 0.0004623 | | | 0.27
|
||||
|
||||
Nlocal: 144 ave 146 max 143 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Nghost: 3031 ave 3032 max 3030 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 52617.5 ave 53258 max 52208 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 210470
|
||||
Ave neighs/atom = 365.399
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 10
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,313 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Anders Hafreager (UiO), andershaf@gmail.com
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "pair_vashishta_table.h"
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_request.h"
|
||||
#include "force.h"
|
||||
#include "comm.h"
|
||||
#include "memory.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairVashishtaTable::PairVashishtaTable(LAMMPS *lmp) : PairVashishta(lmp)
|
||||
{
|
||||
neigh3BodyMax = 0;
|
||||
neigh3BodyCount = NULL;
|
||||
neigh3Body = NULL;
|
||||
forceTable = NULL;
|
||||
potentialTable = NULL;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
check if allocated, since class can be destructed when incomplete
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
PairVashishtaTable::~PairVashishtaTable()
|
||||
{
|
||||
memory->destroy(forceTable);
|
||||
memory->destroy(potentialTable);
|
||||
memory->destroy(neigh3BodyCount);
|
||||
memory->destroy(neigh3Body);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairVashishtaTable::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
|
||||
int itype,jtype,ktype,ijparam,ikparam,ijkparam;
|
||||
tagint itag,jtag;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
||||
double rsq,rsq1,rsq2;
|
||||
double delr1[3],delr2[3],fj[3],fk[3];
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
tagint *tag = atom->tag;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// reallocate 3-body neighbor list if necessary
|
||||
// NOTE: using 1000 is inefficient
|
||||
// could make this a LAMMPS paged neighbor list
|
||||
|
||||
if (nlocal > neigh3BodyMax) {
|
||||
neigh3BodyMax = atom->nmax;
|
||||
memory->destroy(neigh3BodyCount);
|
||||
memory->destroy(neigh3Body);
|
||||
memory->create(neigh3BodyCount,neigh3BodyMax,
|
||||
"pair:vashishta:neigh3BodyCount");
|
||||
memory->create(neigh3Body,neigh3BodyMax,1000,
|
||||
"pair:vashishta:neigh3Body");
|
||||
}
|
||||
|
||||
// loop over full neighbor list of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
itag = tag[i];
|
||||
itype = map[type[i]];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
|
||||
// reset the 3-body neighbor list
|
||||
|
||||
neigh3BodyCount[i] = 0;
|
||||
|
||||
// two-body interactions, skip half of them
|
||||
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
jtag = tag[j];
|
||||
|
||||
jtype = map[type[j]];
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
ijparam = elem2param[itype][jtype][jtype];
|
||||
|
||||
if (rsq <= params[ijparam].cutsq2) {
|
||||
neigh3Body[i][neigh3BodyCount[i]] = j;
|
||||
neigh3BodyCount[i]++;
|
||||
}
|
||||
|
||||
if (rsq > params[ijparam].cutsq) continue;
|
||||
|
||||
if (itag > jtag) {
|
||||
if ((itag+jtag) % 2 == 0) continue;
|
||||
} else if (itag < jtag) {
|
||||
if ((itag+jtag) % 2 == 1) continue;
|
||||
} else {
|
||||
if (x[j][2] < ztmp) continue;
|
||||
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
|
||||
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
||||
}
|
||||
|
||||
twobody_table(params[ijparam],rsq,fpair,eflag,evdwl);
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,0.0,fpair,delx,dely,delz);
|
||||
}
|
||||
|
||||
jlist = neigh3Body[i];
|
||||
jnum = neigh3BodyCount[i];
|
||||
jnumm1 = jnum - 1;
|
||||
|
||||
for (jj = 0; jj < jnumm1; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
jtype = map[type[j]];
|
||||
ijparam = elem2param[itype][jtype][jtype];
|
||||
delr1[0] = x[j][0] - xtmp;
|
||||
delr1[1] = x[j][1] - ytmp;
|
||||
delr1[2] = x[j][2] - ztmp;
|
||||
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
|
||||
if (rsq1 >= params[ijparam].cutsq2) continue;
|
||||
|
||||
for (kk = jj+1; kk < jnum; kk++) {
|
||||
k = jlist[kk];
|
||||
k &= NEIGHMASK;
|
||||
ktype = map[type[k]];
|
||||
ikparam = elem2param[itype][ktype][ktype];
|
||||
ijkparam = elem2param[itype][jtype][ktype];
|
||||
|
||||
delr2[0] = x[k][0] - xtmp;
|
||||
delr2[1] = x[k][1] - ytmp;
|
||||
delr2[2] = x[k][2] - ztmp;
|
||||
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
|
||||
if (rsq2 >= params[ikparam].cutsq2) continue;
|
||||
|
||||
threebody(¶ms[ijparam],¶ms[ikparam],¶ms[ijkparam],
|
||||
rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl);
|
||||
|
||||
f[i][0] -= fj[0] + fk[0];
|
||||
f[i][1] -= fj[1] + fk[1];
|
||||
f[i][2] -= fj[2] + fk[2];
|
||||
f[j][0] += fj[0];
|
||||
f[j][1] += fj[1];
|
||||
f[j][2] += fj[2];
|
||||
f[k][0] += fk[0];
|
||||
f[k][1] += fk[1];
|
||||
f[k][2] += fk[2];
|
||||
|
||||
if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,delr1,delr2);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairVashishtaTable::twobody_table(const Param ¶m, double rsq,
|
||||
double &fforce, int eflag, double &eng)
|
||||
{
|
||||
// use analytic form if rsq is inside inner cutoff
|
||||
|
||||
if (rsq < tabinnersq) {
|
||||
Param *pparam = const_cast<Param *> (¶m);
|
||||
PairVashishta::twobody(pparam,rsq,fforce,eflag,eng);
|
||||
return;
|
||||
}
|
||||
|
||||
// double -> int will only keep the 0.xxxx part
|
||||
|
||||
const int tableIndex = (rsq - tabinnersq)*oneOverDeltaR2;
|
||||
const double fraction = (rsq - tabinnersq)*oneOverDeltaR2 - tableIndex;
|
||||
|
||||
// force/energy are linearly interpolated between two adjacent values
|
||||
|
||||
double force0 = forceTable[param.ielement][param.jelement][tableIndex];
|
||||
double force1 = forceTable[param.ielement][param.jelement][tableIndex+1];
|
||||
fforce = (1.0 - fraction)*force0 + fraction*force1;
|
||||
|
||||
if (evflag) {
|
||||
double energy0 = potentialTable[param.ielement][param.jelement][tableIndex];
|
||||
double energy1 = potentialTable[param.ielement][param.jelement]
|
||||
[tableIndex+1];
|
||||
eng = (1.0 - fraction)*energy0 + fraction*energy1;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairVashishtaTable::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
ntable = force->inumeric(FLERR,arg[0]);
|
||||
tabinner = force->numeric(FLERR,arg[1]);
|
||||
|
||||
if (tabinner <= 0.0)
|
||||
error->all(FLERR,"Illegal inner cutoff for tabulation");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairVashishtaTable::setup_params()
|
||||
{
|
||||
PairVashishta::setup_params();
|
||||
|
||||
create_tables();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairVashishtaTable::create_tables()
|
||||
{
|
||||
memory->destroy(forceTable);
|
||||
memory->destroy(potentialTable);
|
||||
forceTable = NULL;
|
||||
potentialTable = NULL;
|
||||
|
||||
tabinnersq = tabinner*tabinner;
|
||||
|
||||
deltaR2 = (cutmax*cutmax - tabinnersq) / (ntable-1);
|
||||
oneOverDeltaR2 = 1.0/deltaR2;
|
||||
|
||||
memory->create(forceTable,nelements,nelements,ntable+1,
|
||||
"pair:vashishta:forceTable");
|
||||
memory->create(potentialTable,nelements,nelements,ntable+1,
|
||||
"pair:vashishta:potentialTable");
|
||||
|
||||
// tabulalate energy/force via analytic twobody() in parent
|
||||
|
||||
int i,j,idx;
|
||||
double rsq,fpair,eng;
|
||||
|
||||
for (i = 0; i < nelements; i++) {
|
||||
for (j = 0; j < nelements; j++) {
|
||||
int ijparam = elem2param[i][j][j];
|
||||
for (idx = 0; idx <= ntable; idx++) {
|
||||
rsq = tabinnersq + idx*deltaR2;
|
||||
PairVashishta::twobody(¶ms[ijparam],rsq,fpair,1,eng);
|
||||
forceTable[i][j][idx] = fpair;
|
||||
potentialTable[i][j][idx] = eng;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of tabulation arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairVashishtaTable::memory_usage()
|
||||
{
|
||||
double bytes = 2*nelements*nelements*sizeof(double)*ntable;
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,105 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(vashishta/table,PairVashishtaTable)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_VASHISHITA_TABLE_H
|
||||
#define LMP_PAIR_VASHISHITA_TABLE_H
|
||||
|
||||
#include "pair_vashishta.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairVashishtaTable : public PairVashishta {
|
||||
public:
|
||||
PairVashishtaTable(class LAMMPS *);
|
||||
~PairVashishtaTable();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
double memory_usage();
|
||||
|
||||
protected:
|
||||
int ntable;
|
||||
double deltaR2;
|
||||
double oneOverDeltaR2;
|
||||
double ***forceTable; // table of forces per element pair
|
||||
double ***potentialTable; // table of potential energies
|
||||
|
||||
int neigh3BodyMax; // max size of short neighborlist
|
||||
int *neigh3BodyCount; // # of neighbors in short range
|
||||
// 3 particle forces neighbor list
|
||||
int **neigh3Body; // neighlist for short range 3 particle forces
|
||||
|
||||
void twobody_table(const Param &, double, double &, int, double &);
|
||||
void setup_params();
|
||||
void create_tables();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Pair style Vashishta requires atom IDs
|
||||
|
||||
This is a requirement to use the Vashishta potential.
|
||||
|
||||
E: Pair style Vashishta requires newton pair on
|
||||
|
||||
See the newton command. This is a restriction to use the Vashishta
|
||||
potential.
|
||||
|
||||
E: All pair coeffs are not set
|
||||
|
||||
All pair coefficients must be set in the data file or by the
|
||||
pair_coeff command before running a simulation.
|
||||
|
||||
E: Cannot open Vashishta potential file %s
|
||||
|
||||
The specified Vashishta potential file cannot be opened. Check that the path
|
||||
and name are correct.
|
||||
|
||||
E: Incorrect format in Vashishta potential file
|
||||
|
||||
Incorrect number of words per line in the potential file.
|
||||
|
||||
E: Illegal Vashishta parameter
|
||||
|
||||
One or more of the coefficients defined in the potential file is
|
||||
invalid.
|
||||
|
||||
E: Potential file has duplicate entry
|
||||
|
||||
The potential file has more than one entry for the same element.
|
||||
|
||||
E: Potential file is missing an entry
|
||||
|
||||
The potential file does not have a needed entry.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,239 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
This software is distributed under the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include "pair_vashishta_table_omp.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairVashishtaTableOMP::PairVashishtaTableOMP(LAMMPS *lmp) :
|
||||
PairVashishtaTable(lmp), ThrOMP(lmp, THR_PAIR)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairVashishtaTableOMP::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) {
|
||||
ev_setup(eflag,vflag);
|
||||
} else evflag = vflag_fdotr = 0;
|
||||
|
||||
// reallocate 3-body neighbor list if necessary
|
||||
// NOTE: using 1000 is inefficient
|
||||
// could make this a LAMMPS paged neighbor list
|
||||
|
||||
if (atom->nlocal > neigh3BodyMax) {
|
||||
neigh3BodyMax = atom->nmax;
|
||||
memory->destroy(neigh3BodyCount);
|
||||
memory->destroy(neigh3Body);
|
||||
memory->create(neigh3BodyCount,neigh3BodyMax,
|
||||
"pair:vashishta:neigh3BodyCount");
|
||||
memory->create(neigh3Body,neigh3BodyMax,1000,
|
||||
"pair:vashishta:neigh3Body");
|
||||
}
|
||||
|
||||
const int nall = atom->nlocal + atom->nghost;
|
||||
const int nthreads = comm->nthreads;
|
||||
const int inum = list->inum;
|
||||
|
||||
#if defined(_OPENMP)
|
||||
#pragma omp parallel default(none) shared(eflag,vflag)
|
||||
#endif
|
||||
{
|
||||
int ifrom, ito, tid;
|
||||
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
thr->timer(Timer::START);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
|
||||
if (evflag) {
|
||||
if (eflag) {
|
||||
eval<1,1>(ifrom, ito, thr);
|
||||
} else {
|
||||
eval<1,0>(ifrom, ito, thr);
|
||||
}
|
||||
} else eval<0,0>(ifrom, ito, thr);
|
||||
|
||||
thr->timer(Timer::PAIR);
|
||||
reduce_thr(this, eflag, vflag, thr);
|
||||
} // end of omp parallel region
|
||||
}
|
||||
|
||||
template <int EVFLAG, int EFLAG>
|
||||
void PairVashishtaTableOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
int i,j,k,ii,jj,kk,jnum,jnumm1;
|
||||
tagint itag,jtag;
|
||||
int itype,jtype,ktype,ijparam,ikparam,ijkparam;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
||||
double rsq,rsq1,rsq2;
|
||||
double delr1[3],delr2[3],fj[3],fk[3];
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
|
||||
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
|
||||
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
|
||||
const tagint * _noalias const tag = atom->tag;
|
||||
const int * _noalias const type = atom->type;
|
||||
const int nlocal = atom->nlocal;
|
||||
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
double fxtmp,fytmp,fztmp;
|
||||
|
||||
// loop over full neighbor list of my atoms
|
||||
|
||||
for (ii = iifrom; ii < iito; ++ii) {
|
||||
|
||||
i = ilist[ii];
|
||||
itag = tag[i];
|
||||
itype = map[type[i]];
|
||||
xtmp = x[i].x;
|
||||
ytmp = x[i].y;
|
||||
ztmp = x[i].z;
|
||||
fxtmp = fytmp = fztmp = 0.0;
|
||||
|
||||
// reset the 3-body neighbor list
|
||||
|
||||
neigh3BodyCount[i] = 0;
|
||||
|
||||
// two-body interactions, skip half of them
|
||||
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
jtag = tag[j];
|
||||
|
||||
jtype = map[type[j]];
|
||||
|
||||
delx = xtmp - x[j].x;
|
||||
dely = ytmp - x[j].y;
|
||||
delz = ztmp - x[j].z;
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
ijparam = elem2param[itype][jtype][jtype];
|
||||
|
||||
if (rsq <= params[ijparam].cutsq2) {
|
||||
neigh3Body[i][neigh3BodyCount[i]] = j;
|
||||
neigh3BodyCount[i]++;
|
||||
}
|
||||
|
||||
if (rsq >= params[ijparam].cutsq) continue;
|
||||
|
||||
if (itag > jtag) {
|
||||
if ((itag+jtag) % 2 == 0) continue;
|
||||
} else if (itag < jtag) {
|
||||
if ((itag+jtag) % 2 == 1) continue;
|
||||
} else {
|
||||
if (x[j].z < ztmp) continue;
|
||||
if (x[j].z == ztmp && x[j].y < ytmp) continue;
|
||||
if (x[j].z == ztmp && x[j].y == ytmp && x[j].x < xtmp) continue;
|
||||
}
|
||||
|
||||
twobody_table(params[ijparam],rsq,fpair,EFLAG,evdwl);
|
||||
|
||||
fxtmp += delx*fpair;
|
||||
fytmp += dely*fpair;
|
||||
fztmp += delz*fpair;
|
||||
f[j].x -= delx*fpair;
|
||||
f[j].y -= dely*fpair;
|
||||
f[j].z -= delz*fpair;
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1,
|
||||
evdwl,0.0,fpair,delx,dely,delz,thr);
|
||||
}
|
||||
|
||||
jlist = neigh3Body[i];
|
||||
jnum = neigh3BodyCount[i];
|
||||
jnumm1 = jnum - 1;
|
||||
|
||||
for (jj = 0; jj < jnumm1; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
jtype = map[type[j]];
|
||||
ijparam = elem2param[itype][jtype][jtype];
|
||||
delr1[0] = x[j].x - xtmp;
|
||||
delr1[1] = x[j].y - ytmp;
|
||||
delr1[2] = x[j].z - ztmp;
|
||||
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
|
||||
if (rsq1 >= params[ijparam].cutsq2) continue;
|
||||
|
||||
double fjxtmp,fjytmp,fjztmp;
|
||||
fjxtmp = fjytmp = fjztmp = 0.0;
|
||||
|
||||
for (kk = jj+1; kk < jnum; kk++) {
|
||||
k = jlist[kk];
|
||||
k &= NEIGHMASK;
|
||||
ktype = map[type[k]];
|
||||
ikparam = elem2param[itype][ktype][ktype];
|
||||
ijkparam = elem2param[itype][jtype][ktype];
|
||||
|
||||
delr2[0] = x[k].x - xtmp;
|
||||
delr2[1] = x[k].y - ytmp;
|
||||
delr2[2] = x[k].z - ztmp;
|
||||
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
|
||||
if (rsq2 >= params[ikparam].cutsq2) continue;
|
||||
|
||||
threebody(¶ms[ijparam],¶ms[ikparam],¶ms[ijkparam],
|
||||
rsq1,rsq2,delr1,delr2,fj,fk,EFLAG,evdwl);
|
||||
|
||||
fxtmp -= fj[0] + fk[0];
|
||||
fytmp -= fj[1] + fk[1];
|
||||
fztmp -= fj[2] + fk[2];
|
||||
fjxtmp += fj[0];
|
||||
fjytmp += fj[1];
|
||||
fjztmp += fj[2];
|
||||
f[k].x += fk[0];
|
||||
f[k].y += fk[1];
|
||||
f[k].z += fk[2];
|
||||
|
||||
if (EVFLAG) ev_tally3_thr(this,i,j,k,evdwl,0.0,fj,fk,delr1,delr2,thr);
|
||||
}
|
||||
f[j].x += fjxtmp;
|
||||
f[j].y += fjytmp;
|
||||
f[j].z += fjztmp;
|
||||
}
|
||||
f[i].x += fxtmp;
|
||||
f[i].y += fytmp;
|
||||
f[i].z += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairVashishtaTableOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairVashishtaTable::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(vashishta/table/omp,PairVashishtaTableOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_VASHISHTA_TABLE_OMP_H
|
||||
#define LMP_PAIR_VASHISHTA_TABLE_OMP_H
|
||||
|
||||
#include "pair_vashishta_table.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairVashishtaTableOMP : public PairVashishtaTable, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairVashishtaTableOMP(class LAMMPS *);
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
template <int EVFLAG, int EFLAG>
|
||||
void eval(int ifrom, int ito, ThrData * const thr);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue