forked from lijiext/lammps
final version of pair vashishta/table
This commit is contained in:
Steve Plimpton
parent
956af8cebb
commit
944289b018
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@ -145,12 +145,8 @@ pair_style style args
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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> args = none
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<em>vashishta/omp</em> args = none
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<em>vashishta/table</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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<em>vashishta/table/omp</em> args = Ntable cutinner
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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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@ -169,13 +165,13 @@ pair_coeff * * SiC.vashishta Si C
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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> and <em>vashishta/table</em> styles compute the combined
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2-body and 3-body family of potentials developed in the group of
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Vashishta and co-workers. By combining repulsive, screened Coulombic,
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screened charge-dipole, and dispersion interactions with a bond-angle
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energy based on the Stillinger-Weber potential, this potential has
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been used to describe a variety of inorganic compounds, including SiO2
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<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>,
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and InP <a class="reference internal" href="#branicio2009"><span class="std std-ref">Branicio2009</span></a>.</p>
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2-body and 3-body family of potentials developed in the group of Priya
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Vashishta and collaborators. By combining repulsive, screened
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Coulombic, screened charge-dipole, and dispersion interactions with a
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bond-angle energy based on the Stillinger-Weber potential, this
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potential has been used to describe a variety of inorganic compounds,
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including SiO2 <a class="reference internal" href="#vashishta1990"><span class="std std-ref">Vashishta1990</span></a>, SiC
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<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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@ -323,16 +319,17 @@ script that reads a restart file.</p>
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<hr class="docutils" />
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<div class="section" id="restrictions">
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<h2>Restrictions</h2>
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<p>This pair style is part of the MANYBODY package. It is only enabled
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if LAMMPS was built with that package (which it is by default). See
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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>
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<p>This pair style requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be “on”
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<p>These pair style are part of the MANYBODY package. They is only
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enabled if LAMMPS was built with that package (which it is by
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default). See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section
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for more info.</p>
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<p>These pair styles requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be “on”
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for pair interactions.</p>
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<p>The Vashishta potential files provided with LAMMPS (see the potentials
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directory) are parameterized for metal <a class="reference internal" href="units.html"><span class="doc">units</span></a>. You can
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use the Vashishta potential with any LAMMPS units, but you would need
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to create your own Vashishta potential file with coefficients listed
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in the appropriate units if your simulation doesn’t use “metal” units.</p>
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to create your own potential file with coefficients listed in the
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appropriate units if your simulation doesn’t use “metal” units.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands</h2>
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@ -17,12 +17,8 @@ pair_style style args :pre
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style = {vashishta} or {vashishta/table} or {vashishta/omp} or {vashishta/table/omp}
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args = list of arguments for a particular style :ul
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{vashishta} args = none
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{vashishta/omp} args = none
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{vashishta/table} 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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{vashishta/table/omp} args = Ntable cutinner
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{vashishta} or {vashishta/omp} args = none
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{vashishta/table} or {vashishta/table/omp} args = Ntable cutinner
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Ntable = # of tabulation points
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cutinner = tablulate from cutinner to cutoff :pre
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@ -37,13 +33,13 @@ pair_coeff * * SiC.vashishta Si C :pre
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[Description:]
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The {vashishta} and {vashishta/table} styles compute the combined
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2-body and 3-body family of potentials developed in the group of
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Vashishta and co-workers. By combining repulsive, screened Coulombic,
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screened charge-dipole, and dispersion interactions with a bond-angle
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energy based on the Stillinger-Weber potential, this potential has
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been used to describe a variety of inorganic compounds, including SiO2
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"Vashishta1990"_#Vashishta1990, SiC "Vashishta2007"_#Vashishta2007,
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and InP "Branicio2009"_#Branicio2009.
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2-body and 3-body family of potentials developed in the group of Priya
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Vashishta and collaborators. By combining repulsive, screened
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Coulombic, screened charge-dipole, and dispersion interactions with a
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bond-angle energy based on the Stillinger-Weber potential, this
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potential has been used to describe a variety of inorganic compounds,
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including SiO2 "Vashishta1990"_#Vashishta1990, SiC
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"Vashishta2007"_#Vashishta2007, and InP "Branicio2009"_#Branicio2009.
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The potential for the energy U of a system of atoms is
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@ -215,18 +211,19 @@ This pair style can only be used via the {pair} keyword of the
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[Restrictions:]
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This pair style is part of the MANYBODY package. It is only enabled
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if LAMMPS was built with that package (which it is by default). See
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the "Making LAMMPS"_Section_start.html#start_3 section for more info.
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These pair style are part of the MANYBODY package. They is only
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enabled if LAMMPS was built with that package (which it is by
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default). See the "Making LAMMPS"_Section_start.html#start_3 section
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for more info.
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This pair style requires the "newton"_newton.html setting to be "on"
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These pair styles requires the "newton"_newton.html setting to be "on"
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for pair interactions.
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The Vashishta potential files provided with LAMMPS (see the potentials
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directory) are parameterized for metal "units"_units.html. You can
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use the Vashishta potential with any LAMMPS units, but you would need
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to create your own Vashishta potential file with coefficients listed
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in the appropriate units if your simulation doesn't use "metal" units.
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to create your own potential file with coefficients listed in the
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appropriate units if your simulation doesn't use "metal" units.
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[Related commands:]
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@ -247,4 +244,3 @@ J. P. Rino. J. Appl. Phys. 101, 103515 (2007).
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:link(Branicio2009)
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[(Branicio2009)] Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed
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Matter 21 (2009) 095002
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@ -0,0 +1,75 @@
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# calculate the energy volume curve for InP zincblende
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# define volume range and filename
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variable ndelta equal 100
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variable volatom_min equal 20.0
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variable volatom_max equal 29.0
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variable evsvolfile string evsvol.dat
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# set up cell
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units metal
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boundary p p p
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# setup loop variables for box volume
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variable amin equal ${volatom_min}^(1/3)*2
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variable delta equal (${volatom_max}-${volatom_min})/${ndelta}
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variable scale equal (${delta}/v_volatom+1)^(1/3)
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# set up 8 atom InP zincblende unit cell
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lattice diamond ${amin}
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region box prism &
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0 1 &
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0 1 &
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0 1 &
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0 0 0
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create_box 2 box
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create_atoms 1 box &
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basis 5 2 &
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basis 6 2 &
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basis 7 2 &
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basis 8 2
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mass 1 114.76
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mass 2 30.98
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# choose potential
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pair_style vashishta
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pair_coeff * * InP.vashishta In P
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# setup neighbor style
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neighbor 1.0 nsq
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neigh_modify once no every 1 delay 0 check yes
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# setup output
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thermo_style custom step temp pe press vol
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thermo_modify norm no
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variable volatom equal vol/atoms
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variable eatom equal pe/atoms
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print "# Volume [A^3/atom] Energy [eV/atom]" file ${evsvolfile}
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# loop over range of volumes
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label loop
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variable i loop ${ndelta}
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change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap
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# calculate energy
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# no energy minimization needed for zincblende
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run 0
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print "${volatom} ${eatom}" append ${evsvolfile}
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next i
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jump SELF loop
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@ -0,0 +1,28 @@
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# test Vashishta potential for quartz
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units metal
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boundary p p p
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atom_style atomic
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read_data data.quartz
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replicate 4 4 4
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velocity all create 2000.0 277387 mom yes
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displace_atoms all move 0.05 0.9 0.4 units box
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pair_style vashishta
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pair_coeff * * SiO.1990.vashishta Si O
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neighbor 0.3 bin
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neigh_modify delay 10
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fix 1 all nve
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thermo 10
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timestep 0.001
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#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz
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#dump_modify 1 element Si O
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run 100
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@ -0,0 +1,75 @@
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# calculate the energy volume curve for InP zincblende
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# define volume range and filename
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variable ndelta equal 100
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variable volatom_min equal 20.0
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variable volatom_max equal 29.0
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variable evsvolfile string evsvol.dat
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# set up cell
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units metal
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boundary p p p
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# setup loop variables for box volume
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variable amin equal ${volatom_min}^(1/3)*2
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variable delta equal (${volatom_max}-${volatom_min})/${ndelta}
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variable scale equal (${delta}/v_volatom+1)^(1/3)
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# set up 8 atom InP zincblende unit cell
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lattice diamond ${amin}
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region box prism &
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0 1 &
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0 1 &
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0 1 &
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0 0 0
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create_box 2 box
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create_atoms 1 box &
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basis 5 2 &
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basis 6 2 &
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basis 7 2 &
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basis 8 2
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mass 1 114.76
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mass 2 30.98
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# choose potential
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pair_style vashishta/table 100000 0.2
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pair_coeff * * InP.vashishta In P
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# setup neighbor style
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neighbor 1.0 nsq
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neigh_modify once no every 1 delay 0 check yes
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# setup output
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thermo_style custom step temp pe press vol
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thermo_modify norm no
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variable volatom equal vol/atoms
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variable eatom equal pe/atoms
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print "# Volume [A^3/atom] Energy [eV/atom]" file ${evsvolfile}
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# loop over range of volumes
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label loop
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variable i loop ${ndelta}
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change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap
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# calculate energy
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# no energy minimization needed for zincblende
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run 0
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print "${volatom} ${eatom}" append ${evsvolfile}
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next i
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jump SELF loop
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@ -0,0 +1,30 @@
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# test Vashishta potential for quartz
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units metal
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boundary p p p
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variable ntable index 100000
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atom_style atomic
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read_data data.quartz
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replicate 4 4 4
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velocity all create 2000.0 277387 mom yes
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displace_atoms all move 0.05 0.9 0.4 units box
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pair_style vashishta/table ${ntable} 0.2
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pair_coeff * * SiO.1990.vashishta Si O
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neighbor 0.3 bin
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neigh_modify delay 10
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fix 1 all nve
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thermo 10
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timestep 0.001
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#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz
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#dump_modify 1 element Si O
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run 100
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,86 @@
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LAMMPS (7 Sep 2016)
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# test Vashishta potential for quartz
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units metal
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boundary p p p
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atom_style atomic
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read_data data.quartz
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triclinic box = (0 0 0) to (4.9134 4.25513 5.4052) with tilt (-2.4567 0 0)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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9 atoms
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replicate 4 4 4
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triclinic box = (0 0 0) to (19.6536 17.0205 21.6208) with tilt (-9.8268 0 0)
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1 by 1 by 1 MPI processor grid
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576 atoms
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velocity all create 2000.0 277387 mom yes
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displace_atoms all move 0.05 0.9 0.4 units box
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pair_style vashishta
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pair_coeff * * SiO.1990.vashishta Si O
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Reading potential file SiO.1990.vashishta with DATE: 2015-10-14
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neighbor 0.3 bin
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neigh_modify delay 10
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fix 1 all nve
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thermo 10
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timestep 0.001
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#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz
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#dump_modify 1 element Si O
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run 100
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 10.3
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ghost atom cutoff = 10.3
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binsize = 5.15 -> bins = 6 4 5
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Memory usage per processor = 2.54081 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 2000 -5280.875 0 -5132.2259 -20502.321
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10 895.65237 -5198.402 0 -5131.833 419.34676
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20 932.93463 -5201.1569 0 -5131.8169 -21407.961
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30 936.09591 -5201.3998 0 -5131.8248 -32531.168
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40 930.05159 -5201.0073 0 -5131.8816 -46445.212
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50 904.64676 -5199.062 0 -5131.8245 -31402.385
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60 1005.5353 -5206.5725 0 -5131.8365 -29790.442
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70 941.02343 -5201.7644 0 -5131.8232 -23046.796
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80 1020.1044 -5207.6763 0 -5131.8574 -13488.675
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90 912.75535 -5199.651 0 -5131.8108 2715.5897
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100 998.97588 -5206.1008 0 -5131.8523 6024.3651
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Loop time of 2.14363 on 1 procs for 100 steps with 576 atoms
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Performance: 4.031 ns/day, 5.955 hours/ns, 46.650 timesteps/s
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99.9% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 2.0632 | 2.0632 | 2.0632 | 0.0 | 96.25
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Neigh | 0.074735 | 0.074735 | 0.074735 | 0.0 | 3.49
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Comm | 0.0039496 | 0.0039496 | 0.0039496 | 0.0 | 0.18
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Output | 0.00013208 | 0.00013208 | 0.00013208 | 0.0 | 0.01
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Modify | 0.00093484 | 0.00093484 | 0.00093484 | 0.0 | 0.04
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Other | | 0.0006742 | | | 0.03
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Nlocal: 576 ave 576 max 576 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 4926 ave 4926 max 4926 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 210470 ave 210470 max 210470 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 210470
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Ave neighs/atom = 365.399
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Neighbor list builds = 10
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Dangerous builds = 10
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Total wall time: 0:00:02
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@ -0,0 +1,86 @@
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LAMMPS (7 Sep 2016)
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# test Vashishta potential for quartz
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units metal
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boundary p p p
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|
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atom_style atomic
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read_data data.quartz
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triclinic box = (0 0 0) to (4.9134 4.25513 5.4052) with tilt (-2.4567 0 0)
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2 by 1 by 2 MPI processor grid
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reading atoms ...
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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
|
||||
Loading…
Reference in New Issue