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add pppm/kk and fix reax/c issues

This commit is contained in:
Steve Plimpton 2016-09-06 10:46:51 -06:00
parent c543cba95c
commit 3bb3c1a45c
112 changed files with 5582 additions and 260 deletions
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10
doc/html/Section_howto.html
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@ -1086,7 +1086,7 @@ the sheared fluid and integrate the SLLOD equations of motion for the
system. Fix nvt/sllod uses <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a> to compute a thermal temperature
by subtracting out the streaming velocity of the shearing atoms. The
velocity profile or other properties of the fluid can be monitored via
the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command.</p>
the <span class="xref doc">fix ave/spatial</span> command.</p>
<p>As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by
LAMMPS for computational efficiency to be 1/2 of the parallel box
@ -2011,13 +2011,13 @@ on each of two regions to add/subtract specified amounts of energy to
both regions. In both cases, the resulting temperatures of the two
regions can be monitored with the &#8220;compute temp/region&#8221; command and
the temperature profile of the intermediate region can be monitored
with the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> and <a class="reference internal" href="compute_ke_atom.html"><span class="doc">compute ke/atom</span></a> commands.</p>
with the <span class="xref doc">fix ave/spatial</span> and <a class="reference internal" href="compute_ke_atom.html"><span class="doc">compute ke/atom</span></a> commands.</p>
<p>The third method is to perform a reverse non-equilibrium MD simulation
using the <a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">fix thermal/conductivity</span></a>
command which implements the rNEMD algorithm of Muller-Plathe.
Kinetic energy is swapped between atoms in two different layers of the
simulation box. This induces a temperature gradient between the two
layers which can be monitored with the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> and <a class="reference internal" href="compute_ke_atom.html"><span class="doc">compute ke/atom</span></a> commands. The fix tallies the
layers which can be monitored with the <span class="xref doc">fix ave/spatial</span> and <a class="reference internal" href="compute_ke_atom.html"><span class="doc">compute ke/atom</span></a> commands. The fix tallies the
cumulative energy transfer that it performs. See the <a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">fix thermal/conductivity</span></a> command for
details.</p>
<p>The fourth method is based on the Green-Kubo (GK) formula which
@ -2060,7 +2060,7 @@ used to shear the fluid in between them, again with some kind of
thermostat that modifies only the thermal (non-shearing) components of
velocity to prevent the fluid from heating up.</p>
<p>In both cases, the velocity profile setup in the fluid by this
procedure can be monitored by the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command, which determines
procedure can be monitored by the <span class="xref doc">fix ave/spatial</span> command, which determines
grad(Vstream) in the equation above. E.g. the derivative in the
y-direction of the Vx component of fluid motion or grad(Vstream) =
dVx/dy. The Pxy off-diagonal component of the pressure or stress
@ -2073,7 +2073,7 @@ using the <a class="reference internal" href="fix_viscosity.html"><span class="d
the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is
swapped between atoms in two different layers of the simulation box in
a different dimension. This induces a velocity gradient which can be
monitored with the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command.
monitored with the <span class="xref doc">fix ave/spatial</span> command.
The fix tallies the cummulative momentum transfer that it performs.
See the <a class="reference internal" href="fix_viscosity.html"><span class="doc">fix viscosity</span></a> command for details.</p>
<p>The fourth method is based on the Green-Kubo (GK) formula which

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@ -391,7 +391,7 @@ molecular dynamics options:</p>
<li>coupled rigid body integration via the <a class="reference internal" href="fix_poems.html"><span class="doc">POEMS</span></a> library</li>
<li><a class="reference internal" href="fix_qmmm.html"><span class="doc">QM/MM coupling</span></a></li>
<li><a class="reference internal" href="fix_ipi.html"><span class="doc">path-integral molecular dynamics (PIMD)</span></a> and <a class="reference internal" href="fix_pimd.html"><span class="doc">this as well</span></a></li>
<li>Monte Carlo via <a class="reference internal" href="fix_gcmc.html"><span class="doc">GCMC</span></a> and <a class="reference internal" href="fix_tfmc.html"><span class="doc">tfMC</span></a> <a class="reference internal" href="fix_atom_swap.html"><span class="doc">atom swapping</span></a> and <a class="reference internal" href="fix_bond_swap.html"><span class="doc">bond swapping</span></a></li>
<li>Monte Carlo via <a class="reference internal" href="fix_gcmc.html"><span class="doc">GCMC</span></a> and <a class="reference internal" href="fix_tfmc.html"><span class="doc">tfMC</span></a> and <span class="xref doc">atom swapping</span></li>
<li><a class="reference internal" href="pair_dsmc.html"><span class="doc">Direct Simulation Monte Carlo</span></a> for low-density fluids</li>
<li><a class="reference internal" href="pair_peri.html"><span class="doc">Peridynamics mesoscale modeling</span></a></li>
<li><a class="reference internal" href="fix_lb_fluid.html"><span class="doc">Lattice Boltzmann fluid</span></a></li>

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@ -1224,7 +1224,7 @@ styles which implement different materials models.</p>
<p>Supporting info:
<a class="reference external" href="PDF/PDLammps_overview.pdf">doc/PDF/PDLammps_overview.pdf</a>,
<a class="reference external" href="PDF/PDLammps_EPS.pdf">doc/PDF/PDLammps_EPS.pdf</a>,
<a class="reference external" href="PDF/PDLammps_VES.pdf">doc/PDF/PDLammps_VES.pdf</a>, <a class="reference internal" href="atom_style.html"><span class="doc">atom_style peri</span></a>, <a class="reference internal" href="compute_damage_atom.html"><span class="doc">compute damage/atom</span></a>,
<a class="reference external" href="PDF/PDLammps_VES.pdf">doc/PDF/PDLammps_VES.pdf</a>, <a class="reference internal" href="atom_style.html"><span class="doc">atom_style peri</span></a>, <span class="xref doc">compute damage</span>,
<a class="reference internal" href="pair_peri.html"><span class="doc">pair_style peri/pmb</span></a>, examples/peri</p>
<hr class="docutils" />
</div>
@ -1272,8 +1272,9 @@ one step. Type &#8220;python src/Make.py -h -poems&#8221; to see the details.</
<span id="python"></span><h3>4.1.22. PYTHON package</h3>
<p>Contents: A <a class="reference internal" href="python.html"><span class="doc">python</span></a> command which allow you to execute
Python code from a LAMMPS input script. The code can be in a separate
file or embedded in the input script itself. See <a class="reference external" href="Section_python.html&quot;">Section python 11.2</a> for an overview of using Python from
LAMMPS and for other ways to use LAMMPS and Python together.</p>
file or embedded in the input script itself. See <span class="xref std std-ref">Section python 11.2</span> for an overview of using Python from
LAMMPS and <a class="reference external" href="Section_python.html&quot;">Section python</a> for other ways to use
LAMMPS and Python together.</p>
<p>Building with the PYTHON package assumes you have a Python shared
library available on your system, which needs to be a Python 2
version, 2.6 or later. Python 3 is not supported. The build uses the
@ -1426,7 +1427,7 @@ few large bodies or many small bodies.</p>
</pre></div>
</div>
<p>Supporting info: <a class="reference internal" href="compute_erotate_rigid.html"><span class="doc">compute erotate/rigid</span></a>,
<a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a>, <a class="reference internal" href="fix_shake.html"><span class="doc">fix rattle</span></a>, <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/*</span></a>, examples/ASPHERE, examples/rigid</p>
<a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a>, <span class="xref doc">fix rattle</span>, <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/*</span></a>, examples/ASPHERE, examples/rigid</p>
<hr class="docutils" />
</div>
<div class="section" id="shock-package">
@ -1474,8 +1475,8 @@ properties of the potential are also included.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">snap</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
</pre></div>
</div>
<p>Supporting info: <a class="reference internal" href="pair_snap.html"><span class="doc">pair snap</span></a>, <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute sna/atom</span></a>, <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute snad/atom</span></a>,
<a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute snav/atom</span></a>, examples/snap</p>
<p>Supporting info: <a class="reference internal" href="pair_snap.html"><span class="doc">pair snap</span></a>, <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute sna/atom</span></a>, <span class="xref doc">compute snad/atom</span>,
<span class="xref doc">compute snav/atom</span>, examples/snap</p>
<hr class="docutils" />
</div>
<div class="section" id="srd-package">
@ -1899,7 +1900,7 @@ src/Make.py -h -voronoi&#8221; to see the details.</p>
<tr class="row-odd"><td><a class="reference internal" href="#user-tally"><span class="std std-ref">USER-TALLY</span></a></td>
<td>Pairwise tallied computes</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="compute_tally.html"><span class="doc">compute XXX/tally</span></a></td>
<td><span class="xref doc">compute</span></td>
<td>USER/tally</td>
<td><ul class="first last simple">
<li></li>
@ -1913,7 +1914,7 @@ src/Make.py -h -voronoi&#8221; to see the details.</p>
<tr class="row-even"><td><a class="reference internal" href="#user-vtk"><span class="std std-ref">USER-VTK</span></a></td>
<td>VTK-style dumps</td>
<td>Berger and Queteschiner (6)</td>
<td><a class="reference internal" href="dump_custom_vtk.html"><span class="doc">compute custom/vtk</span></a></td>
<td><span class="xref doc">compute custom/vtk</span></td>
<td><ul class="first last simple">
<li></li>
</ul>
@ -2003,7 +2004,7 @@ Dynamics. This package implements an atom, pair, and fix style which
allows electrons to be treated as explicit particles in an MD
calculation. See src/USER-AWPMD/README for more details.</p>
<p>To build LAMMPS with this package ...</p>
<p>Supporting info: src/USER-AWPMD/README, <a class="reference internal" href="pair_awpmd.html"><span class="doc">fix awpmd/cut</span></a>, examples/USER/awpmd</p>
<p>Supporting info: src/USER-AWPMD/README, <span class="xref doc">fix awpmd/cut</span>, examples/USER/awpmd</p>
<p>Author: Ilya Valuev at the JIHT in Russia (valuev at
physik.hu-berlin.de). Contact him directly if you have questions.</p>
<hr class="docutils" />
@ -2046,7 +2047,7 @@ have questions.</p>
calculating x-ray and electron diffraction intensities based on
kinematic diffraction theory. See src/USER-DIFFRACTION/README for
more details.</p>
<p>Supporting info: <a class="reference internal" href="compute_saed.html"><span class="doc">compute saed</span></a>, <a class="reference internal" href="compute_xrd.html"><span class="doc">compute xrd</span></a>, <a class="reference internal" href="fix_saed_vtk.html"><span class="doc">fix saed/vtk</span></a>,
<p>Supporting info: <a class="reference internal" href="compute_saed.html"><span class="doc">compute saed</span></a>, <a class="reference internal" href="compute_xrd.html"><span class="doc">compute xrd</span></a>, <a class="reference internal" href="fix_saed_vtk.html"><span class="doc">fix saed.vtk</span></a>,
examples/USER/diffraction</p>
<p>Author: Shawn P. Coleman (shawn.p.coleman8.ctr at mail.mil) while at
the University of Arkansas. Contact him directly if you have
@ -2064,13 +2065,11 @@ equations of motion are integrated efficiently through the Shardlow
splitting algorithm. See src/USER-DPD/README for more details.</p>
<p>Supporting info: /src/USER-DPD/README, <a class="reference internal" href="compute_dpd.html"><span class="doc">compute dpd</span></a>
<a class="reference internal" href="compute_dpd_atom.html"><span class="doc">compute dpd/atom</span></a>
<a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/cv</span></a> <a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/table</span></a></p>
<blockquote>
<div><a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">fix eos/table/rx</span></a> <a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a></div></blockquote>
<p><a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> <a class="reference internal" href="pair_table_rx.html"><span class="doc">pair table/rx</span></a>
<a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair dpd/fdt</span></a> <a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair dpd/fdt/energy</span></a>
<a class="reference internal" href="pair_exp6_rx.html"><span class="doc">pair exp6/rx</span></a> <a class="reference internal" href="pair_multi_lucy.html"><span class="doc">pair multi/lucy</span></a>
<a class="reference internal" href="pair_multi_lucy_rx.html"><span class="doc">pair multi/lucy/rx</span></a>, examples/USER/dpd</p>
<a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/cv</span></a> <a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/table</span></a>
<a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a>
<span class="xref doc">pair_dpd/conservative</span>
<a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair_dpd/fdt</span></a>
<a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair_dpd/fdt/energy</span></a>, examples/USER/dpd</p>
<p>Authors: James Larentzos (ARL) (james.p.larentzos.civ at mail.mil),
Timothy Mattox (Engility Corp) (Timothy.Mattox at engilitycorp.com)
and John Brennan (ARL) (john.k.brennan.civ at mail.mil). Contact them
@ -2145,7 +2144,7 @@ this package. Also see src/USER-INTEL/README for more details. See
the KOKKOS, OPT, and USER-OMP packages, which also have CPU and
Phi-enabled styles.</p>
<p>Supporting info: examples/accelerate, src/USER-INTEL/TEST</p>
<p><a class="reference internal" href="Section_accelerate.html#acc-3"><span class="std std-ref">Section_accelerate</span></a></p>
<p><span class="xref std std-ref">Section_accelerate</span></p>
<p>Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact
him directly if you have questions.</p>
<p>For the USER-INTEL package, you have 2 choices when building. You can
@ -2262,7 +2261,7 @@ to VMD, support for new file formats can be added to LAMMPS (or VMD or
other programs that use them) without having to recompile the
application itself.</p>
<p>See this doc page to get started:</p>
<p><a class="reference internal" href="dump_molfile.html"><span class="doc">dump molfile</span></a></p>
<p><span class="xref std std-ref">dump molfile</span></p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
<hr class="docutils" />
@ -2274,7 +2273,7 @@ application itself.</p>
other optimizations of various LAMMPS pair styles, dihedral
styles, and fix styles.</p>
<p>See this section of the manual to get started:</p>
<p><a class="reference internal" href="Section_accelerate.html#acc-3"><span class="std std-ref">Section_accelerate</span></a></p>
<p><span class="xref std std-ref">Section_accelerate</span></p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
<p>For the USER-OMP package, your Makefile.machine needs additional

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@ -1365,7 +1365,7 @@ supercomputer there may be dozens or 1000s of physical nodes.</p>
Note that the keywords do not use a leading minus sign. I.e. the
keyword is &#8220;t&#8221;, not &#8220;-t&#8221;. Also note that each of the keywords has a
default setting. Example of when to use these options and what
settings to use on different platforms is given in <a class="reference internal" href="Section_accelerate.html#acc-3"><span class="std std-ref">Section 5.8</span></a>.</p>
settings to use on different platforms is given in <span class="xref std std-ref">Section 5.8</span>.</p>
<ul class="simple">
<li>d or device</li>
<li>g or gpus</li>

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@ -351,7 +351,7 @@ used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
provides alternative methods via environment variables for binding
threads to hardware cores. More info on binding threads to cores is
given in <a class="reference internal" href="Section_accelerate.html#acc-3"><span class="std std-ref">this section</span></a>.</p>
given in <span class="xref std std-ref">this section</span>.</p>
<p>KOKKOS_ARCH=KNC enables compiler switches needed when compling for an
Intel Phi processor.</p>
<p>KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism

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@ -302,6 +302,11 @@ sphere is determined by the <em>bflag1</em> parameter for the <em>body</em> keyw
The <em>bflag2</em> argument is ignored.</p>
<hr class="docutils" />
<p><strong>Specifics of body style rounded/polygon:</strong></p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Aug 2016 - This body style has not yet been added to LAMMPS.
The info below is a placeholder.</p>
</div>
<p>The <em>rounded/polygon</em> body style represents body particles as a convex
polygon with a variable number N &gt; 2 of vertices, which can only be
used for 2d models. One example use of this body style is for 2d
@ -359,8 +364,9 @@ particles whose edge length is sqrt(2):</p>
<span class="mf">1.0</span>
</pre></div>
</div>
<p>The <span class="xref doc">pair_style body/rounded/polygon</span> command
can be used with this body style to compute body/body interactions.</p>
<p>The <span class="xref doc">pair_style body/rounded/polygon</span>
command can be used with this body style to compute body/body
interactions.</p>
<p>For output purposes via the <a class="reference internal" href="compute_body_local.html"><span class="doc">compute body/local</span></a> and <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>
commands, this body style produces one datum for each of the N
sub-particles in a body particle. The datum has 3 values:</p>

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@ -170,8 +170,7 @@ LAMMPS was built with that package. See the <a class="reference internal" href=
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="compute_dilatation_atom.html"><span class="doc">compute dilatation/atom</span></a>,
<a class="reference internal" href="compute_plasticity_atom.html"><span class="doc">compute plasticity/atom</span></a></p>
<p><span class="xref doc">compute dilatation</span>, <span class="xref doc">compute plasticity</span></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

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@ -172,8 +172,7 @@ LAMMPS was built with that package. See the <a class="reference internal" href=
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="compute_damage_atom.html"><span class="doc">compute damage/atom</span></a>,
<a class="reference internal" href="compute_plasticity_atom.html"><span class="doc">compute plasticity/atom</span></a></p>
<p><span class="xref doc">compute damage</span>, <span class="xref doc">compute plasticity</span></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

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@ -172,7 +172,7 @@ LAMMPS was built with that package. See the <a class="reference internal" href=
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="compute_ke_rigid.html"><span class="doc">compute ke/rigid</span></a></p>
<p><span class="xref doc">compute ke/rigid</span></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

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@ -168,8 +168,7 @@ LAMMPS was built with that package. See the <a class="reference internal" href=
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="compute_damage_atom.html"><span class="doc">compute damage/atom</span></a>,
<a class="reference internal" href="compute_dilatation_atom.html"><span class="doc">compute dilatation/atom</span></a></p>
<p><span class="xref doc">compute damage</span>, <span class="xref doc">compute dilatation</span></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="mitchell"><strong>(Mitchell)</strong> Mitchell, &#8220;A non-local, ordinary-state-based

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@ -220,7 +220,7 @@ asterisk means all indices from n to N (inclusive). A middle asterisk
means all indices from m to n (inclusive).</p>
<p>Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 compute reduce commands are
equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
equivalent, since the <span class="xref doc">compute stress/atom</span>
command creates a per-atom array with 6 columns:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myPress</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">myPress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>

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@ -149,11 +149,11 @@ nuclei and electrons in the <a class="reference internal" href="pair_eff.html"><
model, after subtracting out a streaming velocity induced by the
simulation box changing size and/or shape, for example in a
non-equilibrium MD (NEMD) simulation. The size/shape change is
induced by use of the <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> command. A
induced by use of the <span class="xref doc">fix deform/eff</span> command. A
compute of this style is created by the <a class="reference internal" href="fix_nvt_sllod_eff.html"><span class="doc">fix nvt/sllod/eff</span></a> command to compute the thermal
temperature of atoms for thermostatting purposes. A compute of this
style can also be used by any command that computes a temperature,
e.g. <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a>, <a class="reference internal" href="fix_nh_eff.html"><span class="doc">fix npt/eff</span></a>,
e.g. <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt/eff</span></a>,
etc.</p>
<p>The calculation performed by this compute is exactly like that
described by the <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a>
@ -180,8 +180,7 @@ LAMMPS was built with that package. See the <a class="reference internal" href=
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="compute_temp_ramp.html"><span class="doc">compute temp/ramp</span></a>, <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a>,
<a class="reference internal" href="fix_nvt_sllod_eff.html"><span class="doc">fix nvt/sllod/eff</span></a></p>
<p><a class="reference internal" href="compute_temp_ramp.html"><span class="doc">compute temp/ramp</span></a>, <span class="xref doc">fix deform/eff</span>, <a class="reference internal" href="fix_nvt_sllod_eff.html"><span class="doc">fix nvt/sllod/eff</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

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@ -148,7 +148,7 @@
<p>Define a computation that calculates the temperature of a group of
nuclei and electrons in the <a class="reference internal" href="pair_eff.html"><span class="doc">electron force field</span></a>
model. A compute of this style can be used by commands that compute a
temperature, e.g. <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a>, <a class="reference internal" href="fix_nh_eff.html"><span class="doc">fix npt/eff</span></a>, etc.</p>
temperature, e.g. <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a>, <span class="xref doc">fix npt/eff</span>, etc.</p>
<p>The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2 for
nuclei and sum of 1/2 (m v^2 + 3/4 m s^2) for electrons, where s

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@ -301,7 +301,7 @@ more instructions on how to use the accelerated styles effectively.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This dihedral style can only be used if LAMMPS was built with the
USER-MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
USER-MISC package. See the <span class="xref std std-ref">Making LAMMPS</span>
section for more info on packages.</p>
</div>
<div class="section" id="related-commands">

2
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@ -550,7 +550,7 @@ indices from n to N (inclusive). A middle asterisk means all indices
from m to n (inclusive).</p>
<p>Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 dump commands are
equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
equivalent, since the <span class="xref doc">compute stress/atom</span>
command creates a per-atom array with 6 columns:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myPress</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
<span class="n">dump</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="nb">id</span> <span class="n">myPress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>

26
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@ -157,7 +157,7 @@ mol = molecule ID
proc = ID of processor that owns atom
procp1 = ID+1 of processor that owns atom
type = atom type
element = name of atom element, as defined by <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command
element = name of atom element, as defined by <span class="xref doc">dump_modify</span> command
mass = atom mass
x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates
@ -194,7 +194,7 @@ depending on the filename extension specified. This can be either
for the XML format; see the <a class="reference external" href="http://www.vtk.org/VTK/img/file-formats.pdf">VTK homepage</a> for a detailed
description of these formats. Since this naming convention conflicts
with the way binary output is usually specified (see below),
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify binary</span></a> allows to set the binary
<span class="xref doc">dump_modify binary</span> allows to set the binary
flag for this dump style explicitly.</p>
</div>
<div class="section" id="description">
@ -203,9 +203,9 @@ flag for this dump style explicitly.</p>
timesteps in a format readable by the <a class="reference external" href="http://www.vtk.org">VTK visualization toolkit</a> or other visualization tools that use it,
e.g. <a class="reference external" href="http://www.paraview.org">ParaView</a>. The timesteps on which dump
output is written can also be controlled by a variable; see the
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify every</span></a> command for details.</p>
<span class="xref doc">dump_modify every</span> command for details.</p>
<p>Only information for atoms in the specified group is dumped. The
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify thresh and region</span></a> commands can also
<span class="xref doc">dump_modify thresh and region</span> commands can also
alter what atoms are included; see details below.</p>
<p>As described below, special characters (&#8220;*&#8221;, &#8220;%&#8221;) in the filename
determine the kind of output.</p>
@ -218,7 +218,7 @@ box.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Unless the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify sort</span></a>
<p class="last">Unless the <span class="xref doc">dump_modify sort</span>
option is invoked, the lines of atom information written to dump files
will be in an indeterminate order for each snapshot. This is even
true when running on a single processor, if the <a class="reference internal" href="atom_modify.html"><span class="doc">atom_modify sort</span></a> option is on, which it is by default. In this
@ -228,7 +228,7 @@ data for a single snapshot is collected from multiple processors, each
of which owns a subset of the atoms.</p>
</div>
<p>For the <em>custom/vtk</em> style, sorting is off by default. See the
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> doc page for details.</p>
<span class="xref doc">dump_modify</span> doc page for details.</p>
<hr class="docutils" />
<p>The dimensions of the simulation box are written to a separate file
for each snapshot (either in legacy VTK or XML format depending on
@ -261,20 +261,20 @@ timestep 0) and on the last timestep of a minimization if the
minimization converges. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of N. This behavior can be
changed via the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify first</span></a> command, which
changed via the <span class="xref doc">dump_modify first</span> command, which
can also be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by
using the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify every</span></a> command.
The <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify every</span></a> command
using the <span class="xref doc">dump_modify every</span> command.
The <span class="xref doc">dump_modify every</span> command
also allows a variable to be used to determine the sequence of
timesteps on which dump files are written. In this mode a dump on the
first timestep of a run will also not be written unless the
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify first</span></a> command is used.</p>
<span class="xref doc">dump_modify first</span> command is used.</p>
<p>Dump filenames can contain two wildcard characters. If a &#8220;*&#8221;
character appears in the filename, then one file per snapshot is
written and the &#8220;*&#8221; character is replaced with the timestep value.
For example, tmp.dump*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
tmp.dump20000.vtk, etc. Note that the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify pad</span></a>
tmp.dump20000.vtk, etc. Note that the <span class="xref doc">dump_modify pad</span>
command can be used to insure all timestep numbers are the same length
(e.g. 00010), which can make it easier to read a series of dump files
in order with some post-processing tools.</p>
@ -286,7 +286,7 @@ tmp.dump_P-1.vtp, etc. This creates smaller files and can be a fast
mode of output on parallel machines that support parallel I/O for output.</p>
<p>By default, P = the number of processors meaning one file per
processor, but P can be set to a smaller value via the <em>nfile</em> or
<em>fileper</em> keywords of the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command.
<em>fileper</em> keywords of the <span class="xref doc">dump_modify</span> command.
These options can be the most efficient way of writing out dump files
when running on large numbers of processors.</p>
<p>For the legacy VTK format &#8220;%&#8221; is ignored and P = 1, i.e., only
@ -305,7 +305,7 @@ part of the <em>custom/vtk</em> style.</p>
<p><em>id</em> is the atom ID. <em>mol</em> is the molecule ID, included in the data
file for molecular systems. <em>type</em> is the atom type. <em>element</em> is
typically the chemical name of an element, which you must assign to
each type via the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify element</span></a> command.
each type via the <span class="xref doc">dump_modify element</span> command.
More generally, it can be any string you wish to associate with an
atom type. <em>mass</em> is the atom mass. <em>vx</em>, <em>vy</em>, <em>vz</em>, <em>fx</em>, <em>fy</em>,
<em>fz</em>, and <em>q</em> are components of atom velocity and force and atomic

5
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@ -481,6 +481,11 @@ change this via the <a class="reference internal" href="dump_modify.html"><span
<p>The <em>fix</em> keyword can be used with a <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> that produces
objects to be drawn. An example is the <span class="xref doc">fix surface/global</span> command which can draw lines
or triangles for 2d/3d simulations.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Aug 2016 - The fix surface/global command is not yet added to
LAMMPS.</p>
</div>
<p>The <em>fflag1</em> and <em>fflag2</em> settings are numerical values which are
passed to the fix to affect how the drawing of its objects is done.
See the individual fix doc page for a description of what these

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@ -251,7 +251,7 @@ asterisk means all indices from n to N (inclusive). A middle asterisk
means all indices from m to n (inclusive).</p>
<p>Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 fix ave/chunk commands are
equivalent, since the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command creates, in this
equivalent, since the <span class="xref doc">compute property/atom</span> command creates, in this
case, a per-atom array with 3 columns:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myAng</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">angmomx</span> <span class="n">angmomy</span> <span class="n">angmomz</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">cc1</span> <span class="n">c_myAng</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">angmom</span>
@ -262,7 +262,7 @@ case, a per-atom array with 3 columns:</p>
<p class="first admonition-title">Note</p>
<p class="last">This fix works by creating an array of size <em>Nchunk</em> by Nvalues
on each processor. <em>Nchunk</em> is the number of chunks which is defined
by the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.
by the <span class="xref doc">compute chunk/atom</span> command.
Nvalues is the number of input values specified. Each processor loops
over its atoms, tallying its values to the appropriate chunk. Then
the entire array is summed across all processors. This means that

2
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@ -237,7 +237,7 @@ become one moleclue due to the created bond, all atoms in the new
moleclue retain their original molecule IDs.</p>
</div>
<p>If the <em>atype</em> keyword is used and if an angle potential is defined
via the <a class="reference internal" href="angle_style.html"><span class="doc">angle_style</span></a> command, then any new 3-body
via the <span class="xref doc">angle_style</span> command, then any new 3-body
interactions inferred by the creation of a bond will create new angles
of type <em>angletype</em>, with parameters assigned by the corresponding
<a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a> command. Likewise, the <em>dtype</em> and

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@ -570,7 +570,7 @@ is not consistent with fix nvt/sllod.</p>
<p class="last">For non-equilibrium MD (NEMD) simulations using &#8220;remap v&#8221; it is
usually desirable that the fluid (or flowing material, e.g. granular
particles) stream with a velocity profile consistent with the
deforming box. As mentioned above, using a thermostat such as <a class="reference internal" href="fix_nvt_sllod.html"><span class="doc">fix nvt/sllod</span></a> or <a class="reference internal" href="fix_langevin.html"><span class="doc">fix lavgevin</span></a>
deforming box. As mentioned above, using a thermostat such as <a class="reference internal" href="fix_nvt_sllod.html"><span class="doc">fix nvt/sllod</span></a> or <span class="xref doc">fix lavgevin</span>
(with a bias provided by <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a>), will typically accomplish
that. If you do not use a thermostat, then there is no driving force
pushing the atoms to flow in a manner consistent with the deforming

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@ -264,7 +264,7 @@ time a molecule is deposited, a random number is used to sample from
the list of relative probabilities. The N values must sum to 1.0.</p>
<p>If you wish to insert molecules via the <em>mol</em> keyword, that will be
treated as rigid bodies, use the <em>rigid</em> keyword, specifying as its
value the ID of a separate <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/small</span></a>
value the ID of a separate <span class="xref doc">fix rigid/small</span>
command which also appears in your input script.</p>
<p>If you wish to insert molecules via the <em>mol</em> keyword, that will have
their bonds or angles constrained via SHAKE, use the <em>shake</em> keyword,

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@ -231,7 +231,7 @@ resulting temperature profile will therefore be the same.</p>
the keyword <em>hex</em> is specified.</p>
<hr class="docutils" />
<p><strong>Compatibility with SHAKE and RATTLE (rigid molecules)</strong>:</p>
<p>This fix is compatible with <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> and <a class="reference internal" href="fix_shake.html"><span class="doc">fix rattle</span></a>. If either of these constraining algorithms is
<p>This fix is compatible with <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> and <span class="xref doc">fix rattle</span>. If either of these constraining algorithms is
specified in the input script and the keyword <em>constrain</em> is set, the
bond distances will be corrected a second time at the end of the
integration step. It is recommended to specify the keyword <em>com</em> in
@ -244,7 +244,7 @@ rescaling takes place if the centre of mass lies outside the region.</p>
<p class="first admonition-title">Note</p>
<p class="last">You can only use the keyword <em>com</em> along with <em>constrain</em>.</p>
</div>
<p>To achieve the highest accuracy it is recommended to use <a class="reference internal" href="fix_shake.html"><span class="doc">fix rattle</span></a> with the keywords <em>constrain</em> and <em>com</em> as
<p>To achieve the highest accuracy it is recommended to use <span class="xref doc">fix rattle</span> with the keywords <em>constrain</em> and <em>com</em> as
shown in the second example. Only if RATTLE is employed, the velocity
constraints will be satisfied.</p>
<div class="admonition note">

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@ -187,7 +187,7 @@ identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the fix command.</p>
<p>The next line lists the number of table entries. The parameter &#8220;N&#8221; is
required and its value is the number of table entries that follow.
Note that this may be different than the <em>N</em> specified in the <a class="reference internal" href="#"><span class="doc">fix eos/table</span></a> command. Let Ntable = <em>N</em> in the fix
Note that this may be different than the <em>N</em> specified in the <span class="xref doc">fix eos/table</span> command. Let Ntable = <em>N</em> in the fix
command, and Nfile = &#8220;N&#8221; in the tabulated file. What LAMMPS does is a
preliminary interpolation by creating splines using the Nfile
tabulated values as nodal points. It uses these to interpolate as
@ -220,7 +220,7 @@ are not within the table cutoffs.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a>, <a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair dpd/fdt</span></a></p>
<p><a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a>, <span class="xref doc">pair dpd/fdt</span></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

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@ -242,7 +242,7 @@ are not within the table cutoffs.</p>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a>,
<a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair dpd/fdt</span></a></p>
<span class="xref doc">pair dpd/fdt</span></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
</div>

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@ -172,7 +172,7 @@ dimension.</p>
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can be
by this fix for access by various <span class="xref std std-ref">output commands</span>. No parameter of this fix can be
used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.
This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
</div>

2
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@ -154,7 +154,7 @@ algorithm if the force coupling constant has been set by default.</p>
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can be
by this fix for access by various <span class="xref std std-ref">output commands</span>. No parameter of this fix can be
used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.
This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
</div>

2
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@ -203,7 +203,7 @@ to the temperature or kinetic energy from the electron radial velocity.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">there are two different pressures that can be reported for eFF
when defining the pair_style (see <a class="reference internal" href="pair_eff.html"><span class="doc">pair eff/cut</span></a> to
when defining the pair_style (see <span class="xref doc">pair eff/cut</span> to
understand these settings), one (default) that considers electrons do
not contribute radial virial components (i.e. electrons treated as
incompressible &#8216;rigid&#8217; spheres) and one that does. The radial

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@ -247,7 +247,7 @@ corresponding reciprocal lattice.</p>
fix. You can use it to change the temperature compute from thermo_temp
to the one that reflects the true temperature of atoms in the group.</p>
<p>No global scalar or vector or per-atom quantities are stored by this
fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.</p>
fix for access by various <span class="xref std std-ref">output commands</span>.</p>
<p>Instead, this fix outputs its initialization information (including
mapping information) and the calculated dynamical matrices to the file
<em>prefix</em>.log, with the specified <em>prefix</em>. The dynamical matrices are

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@ -232,7 +232,7 @@ time a molecule is inserted, a random number is used to sample from
the list of relative probabilities. The N values must sum to 1.0.</p>
<p>If you wish to insert molecules via the <em>mol</em> keyword, that will be
treated as rigid bodies, use the <em>rigid</em> keyword, specifying as its
value the ID of a separate <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/small</span></a>
value the ID of a separate <span class="xref doc">fix rigid/small</span>
command which also appears in your input script.</p>
<p>If you wish to insert molecules via the <em>mol</em> keyword, that will have
their bonds or angles constrained via SHAKE, use the <em>shake</em> keyword,

2
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@ -155,7 +155,7 @@ specified by <a class="reference internal" href="pair_reax.html"><span class="do
stand-alone ReaxFF code of Adri van Duin. The bond information is
written to <em>filename</em> on timesteps that are multiples of <em>Nevery</em>,
including timestep 0. For time-averaged chemical species analysis,
please see the <a class="reference internal" href="fix_reaxc_species.html"><span class="doc">fix reaxc/c/species</span></a> command.</p>
please see the <span class="xref doc">fix species</span> command.</p>
<p>The format of the output file should be self-explantory.</p>
</div>
<hr class="docutils" />

2
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@ -292,7 +292,7 @@ enthalpy DPD simulation.</p>
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">fix eos/table/rx</span></a>,
<a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a>,
<a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair dpd/fdt/energy</span></a></p>
<span class="xref doc">pair dpd/fdt/energy</span></p>
<p><strong>Default:</strong> none</p>
</div>
</div>

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@ -148,7 +148,7 @@
integrate the DPD equations of motion. The SSA splits the integration
into a stochastic and deterministic integration step. The fix
<em>shardlow</em> performs the stochastic integration step and must be used
in conjunction with a deterministic integrator (e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>). The stochastic
in conjunction with a deterministic integrator (e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <span class="xref doc">fix nph</span>). The stochastic
integration of the dissipative and random forces is performed prior to
the deterministic integration of the conservative force. Further
details regarding the method are provided in <a class="reference internal" href="pair_dpd_fdt.html#lisal"><span class="std std-ref">(Lisal)</span></a> and

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@ -168,10 +168,10 @@
<div class="section" id="description">
<h2>Description</h2>
<p>This fix implements several options of steered MD (SMD) as reviewed in
<a class="reference internal" href="#izrailev"><span class="std std-ref">(Izrailev)</span></a>, which allows to induce conformational changes
<span class="xref std std-ref">(Izrailev)</span>, which allows to induce conformational changes
in systems and to compute the potential of mean force (PMF) along the
assumed reaction coordinate <a class="reference internal" href="#park"><span class="std std-ref">(Park)</span></a> based on Jarzynski&#8217;s
equality <a class="reference internal" href="#jarzynski"><span class="std std-ref">(Jarzynski)</span></a>. This fix borrows a lot from <a class="reference internal" href="fix_spring.html"><span class="doc">fix spring</span></a> and <a class="reference internal" href="fix_setforce.html"><span class="doc">fix setforce</span></a>.</p>
assumed reaction coordinate <span class="xref std std-ref">(Park)</span> based on Jarzynski&#8217;s
equality <span class="xref std std-ref">(Jarzynski)</span>. This fix borrows a lot from <a class="reference internal" href="fix_spring.html"><span class="doc">fix spring</span></a> and <a class="reference internal" href="fix_setforce.html"><span class="doc">fix setforce</span></a>.</p>
<p>You can apply a moving spring force to a group of atoms (<em>tether</em>
style) or between two groups of atoms (<em>couple</em> style). The spring
can then be used in either constant velocity (<em>cvel</em>) mode or in
@ -249,12 +249,14 @@ LAMMPS was built with that package. See the <a class="reference internal" href=
<a class="reference internal" href="fix_spring_rg.html"><span class="doc">fix spring/rg</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="izrailev"><strong>(Izrailev)</strong> Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar,
<p id="israilev"><strong>(Izrailev)</strong> Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar,
Wriggers, Schulten. Computational Molecular Dynamics: Challenges,
Methods, Ideas, volume 4 of Lecture Notes in Computational Science and
Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.</p>
<p id="park"><strong>(Park)</strong> Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)</p>
<p id="jarzynski"><strong>(Jarzynski)</strong> Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)</p>
<p><strong>(Park)</strong>
Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)</p>
<p><strong>(Jarzynski)</strong>
Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)</p>
</div>
</div>

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@ -205,7 +205,7 @@ define the lattice spacings.</p>
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
by this fix for access by various <span class="xref std std-ref">output commands</span>. No parameter of this fix can
be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.
This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
</div>

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@ -132,7 +132,7 @@
</pre></div>
</div>
<ul class="simple">
<li>style = <em>none</em> or <em>ewald</em> or <em>ewald/disp</em> or <em>ewald/omp</em> or <em>pppm</em> or <em>pppm/cg</em> or <em>pppm/disp</em> or <em>pppm/tip4p</em> or <em>pppm/stagger</em> or <em>pppm/disp/tip4p</em> or <em>pppm/gpu</em> or <em>pppm/omp</em> or <em>pppm/cg/omp</em> or <em>pppm/tip4p/omp</em> or <em>msm</em> or <em>msm/cg</em> or <em>msm/omp</em> or <em>msm/cg/omp</em></li>
<li>style = <em>none</em> or <em>ewald</em> or <em>ewald/disp</em> or <em>ewald/omp</em> or <em>pppm</em> or <em>pppm/cg</em> or <em>pppm/disp</em> or <em>pppm/tip4p</em> or <em>pppm/stagger</em> or <em>pppm/disp/tip4p</em> or <em>pppm/gpu</em> or <em>pppm/kk</em> or <em>pppm/omp</em> or <em>pppm/cg/omp</em> or <em>pppm/tip4p/omp</em> or <em>msm</em> or <em>msm/cg</em> or <em>msm/omp</em> or <em>msm/cg/omp</em></li>
</ul>
<pre class="literal-block">
<em>none</em> value = none
@ -155,6 +155,8 @@
accuracy = desired relative error in forces
<em>pppm/gpu</em> value = accuracy
accuracy = desired relative error in forces
<em>pppm/kk</em> value = accuracy
accuracy = desired relative error in forces
<em>pppm/omp</em> value = accuracy
accuracy = desired relative error in forces
<em>pppm/cg/omp</em> value = accuracy
@ -195,7 +197,7 @@ style, the cutoff for Coulombic or 1/r^N interactions is effectively
infinite. If the Coulombic case, this means each charge in the system
interacts with charges in an infinite array of periodic images of the
simulation domain.</p>
<p>Note that using a long-range solver requires use of a matching <a class="reference internal" href="pair_style.html"><span class="doc">pair style</span></a> to perform consistent short-range pairwise
<p>Note that using a long-range solver requires use of a matching <span class="xref doc">pair style</span> to perform consistent short-range pairwise
calculations. This means that the name of the pair style contains a
matching keyword to the name of the KSpace style, as in this table:</p>
<table border="1" class="docutils">
@ -385,6 +387,9 @@ If <em>pppm/gpu</em> is used with a GPU-enabled pair style, part of the PPPM
calculation can be performed concurrently on the GPU while other
calculations for non-bonded and bonded force calculation are performed
on the CPU.</p>
<p>The <em>pppm/kk</em> style also performs charge assignment and force
interpolation calculations on the GPU while the FFTs themselves are
calculated on the CPU in non-threaded mode.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL,
KOKKOS, USER-OMP, and OPT packages respectively. They are only
enabled if LAMMPS was built with those packages. 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>
@ -406,10 +411,10 @@ the KSPACE package is installed by default.</p>
<p>For MSM, a simulation must be 3d and one can use any combination of
periodic, non-periodic, or shrink-wrapped boundaries (specified using
the <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command).</p>
<p>For Ewald and PPPM, a simulation must be 3d and periodic in all dimensions.
The only exception is if the slab option is set with <a class="reference internal" href="kspace_modify.html"><span class="doc">kspace_modify</span></a>,
in which case the xy dimensions must be periodic and the z dimension must be
non-periodic.</p>
<p>For Ewald and PPPM, a simulation must be 3d and periodic in all
dimensions. The only exception is if the slab option is set with
<a class="reference internal" href="kspace_modify.html"><span class="doc">kspace_modify</span></a>, in which case the xy dimensions
must be periodic and the z dimension must be non-periodic.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
@ -435,9 +440,10 @@ and Computation 5, 2322 (2009)</p>
<p id="veld"><strong>(Veld)</strong> In &#8216;t Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).</p>
<p id="toukmaji"><strong>(Toukmaji)</strong> Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
10913 (2000).</p>
<p id="isele-holder"><strong>(Isele-Holder)</strong> Isele-Holder, Mitchell, Ismail, J Chem Phys, 137, 174107 (2012).</p>
<p id="isele-holder2"><strong>(Isele-Holder2)</strong> Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J Chem Theory
Comput 9, 5412 (2013).</p>
<p id="isele-holder"><strong>(Isele-Holder)</strong> Isele-Holder, Mitchell, Ismail, J Chem Phys, 137,
174107 (2012).</p>
<p id="isele-holder2"><strong>(Isele-Holder2)</strong> Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail,
J Chem Theory Comput 9, 5412 (2013).</p>
<p id="hardy"><strong>(Hardy)</strong> David Hardy thesis: Multilevel Summation for the Fast
Evaluation of Forces for the Simulation of Biomolecules, University of
Illinois at Urbana-Champaign, (2006).</p>

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@ -297,7 +297,7 @@ manner.</p>
<p class="last">Whether a section is required depends on how the molecule
template is used by other LAMMPS commands. For example, to add a
molecule via the <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a> command, the Coords
and Types sections are required. To add a rigid body via the <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a> command, the Bonds (Angles, etc) sections are not
and Types sections are required. To add a rigid body via the <span class="xref doc">fix pour</span> command, the Bonds (Angles, etc) sections are not
required, since the molecule will be treated as a rigid body. Some
sections are optional. For example, the <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a>
command can be used to add &#8220;molecules&#8221; which are clusters of

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@ -192,7 +192,7 @@ are printed to the screen and log file. See <a class="reference internal" href=
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify</span></a>, <a class="reference internal" href="units.html"><span class="doc">units</span></a>,
<a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify</span></a></p>
<span class="xref doc">comm_modify</span></p>
</div>
<div class="section" id="default">
<h2>Default</h2>

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@ -227,7 +227,7 @@ to be specified in an input script that reads a restart file.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>These styles are part of the COLLOID package. They are only enabled
if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
if LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
<p>Only spherical monodisperse particles are allowed for pair_style
brownian.</p>
<p>Only spherical particles are allowed for pair_style brownian/poly.</p>

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@ -268,15 +268,17 @@ dipole interactions. The long-range portion is calculated by using
<em>ewald_disp</em> of the <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> command. If
<em>flag_coul</em> is set to <em>off</em>, Coulombic and dipole interactions are not
computed at all.</p>
<p>Atoms with dipole moments should be integrated using the <a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix nve/sphere update dipole</span></a> or the <a class="reference internal" href="fix_nvt_sphere.html"><span class="doc">fix nvt/sphere update dipole</span></a> command to rotate the
<p>Atoms with dipole moments should be integrated using the <a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix nve/sphere update dipole</span></a> command to rotate the
dipole moments. The <em>omega</em> option on the <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> command can be used to thermostat the
rotational motion. The <a class="reference internal" href="compute_temp_sphere.html"><span class="doc">compute temp/sphere</span></a>
command can be used to monitor the temperature, since it includes
rotational degrees of freedom. The <a class="reference internal" href="atom_style.html"><span class="doc">atom_style hybrid dipole sphere</span></a> command should be used since
it defines the point dipoles and their rotational state.
The magnitude and orientation of the dipole moment for each particle
can be defined by the <a class="reference internal" href="set.html"><span class="doc">set</span></a> command or in the &#8220;Atoms&#8221; section
of the data file read in by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command.</p>
rotational degrees of freedom. The <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dipole</span></a> command should be used since it defines the
point dipoles and their rotational state. The magnitude of the dipole
moment for each type of particle can be defined by the
<span class="xref doc">dipole</span> command or in the &#8220;Dipoles&#8221; section of the data
file read in by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command. Their initial
orientation can be defined by the <a class="reference internal" href="set.html"><span class="doc">set dipole</span></a> command or in
the &#8220;Atoms&#8221; section of the data file.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as in the examples
above, or in the data file or restart files read by the
@ -346,8 +348,7 @@ currently supported.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a>, <a class="reference internal" href="set.html"><span class="doc">set</span></a>, <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>,
<a class="reference internal" href="fix_nve_sphere.html"><span class="doc">fix nve/sphere</span></a>, <a class="reference internal" href="fix_nvt_sphere.html"><span class="doc">fix nvt/sphere</span></a></p>
<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="allen"><strong>(Allen)</strong> Allen and Tildesley, Computer Simulation of Liquids,

2
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@ -230,7 +230,7 @@ specified.</p>
<p>These commands are part of the USER-DPD package. They are only
enabled if LAMMPS was built with that package. 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>Pair styles <em>dpd/fdt</em> and <em>dpd/fdt/energy</em> require use of the
<a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify vel yes</span></a> option so that velocites are
<span class="xref doc">communicate vel yes</span> option so that velocites are
stored by ghost atoms.</p>
<p>Pair style <em>dpd/fdt/energy</em> requires <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a>
to be used in order to properly account for the particle internal

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@ -288,7 +288,7 @@ enabled if LAMMPS was built with that package. See the <a class="reference inte
<p>These pair style require that atoms store torque and a quaternion to
represent their orientation, as defined by the
<a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a>. It also require they store a per-type
<a class="reference internal" href="set.html"><span class="doc">shape</span></a>. The particles cannot store a per-particle
<span class="xref doc">shape</span>. The particles cannot store a per-particle
diameter.</p>
<p>This pair style requires that atoms be ellipsoids as defined by the
<a class="reference internal" href="atom_style.html"><span class="doc">atom_style ellipsoid</span></a> command.</p>

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@ -238,7 +238,7 @@ shift, table, and tail options.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This style is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. 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>
LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
<p>Defining particles to be line segments so they participate in
line/line or line/particle interactions requires the use the
<a class="reference internal" href="atom_style.html"><span class="doc">atom_style line</span></a> command.</p>

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@ -180,7 +180,7 @@ it also allows for mixing pair coefficients instead of listing them all.
The <em>lj/cut/thole/long</em> pair style is also a bit faster because it avoids an
overlay and can benefit from OMP acceleration. Moreover, it uses a more
precise approximation of the direct Coulomb interaction at short range similar
to <a class="reference internal" href="pair_cs.html"><span class="doc">coul/long/cs</span></a>, which stabilizes the temperature of
to <span class="xref doc">coul/long/cs</span>, which stabilizes the temperature of
Drude particles.</p>
<p>The <em>thole</em> pair styles compute the Coulomb interaction damped at
short distances by a function</p>

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@ -210,7 +210,7 @@ shift, table, and tail options.</p>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This style is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. 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>
LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
<p>Defining particles to be triangles so they participate in tri/tri or
tri/particle interactions requires the use the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style tri</span></a> command.</p>
</div>

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@ -554,7 +554,7 @@ building LAMMPS. LAMMPS must also be built as a shared library and
your Python function must be able to to load the Python module in
python/lammps.py that wraps the LAMMPS library interface. These are
the same steps required to use Python by itself to wrap LAMMPS.
Details on these steps are explained in <a class="reference internal" href="Section_python.html"><span class="doc">Section python</span></a>. Note that it is important that the
Details on these steps are explained in <span class="xref doc">Section python</span>. Note that it is important that the
stand-alone LAMMPS executable and the LAMMPS shared library be
consistent (built from the same source code files) in order for this
to work. If the two have been built at different times using

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@ -174,7 +174,7 @@ initial simulation produced the dump file:</p>
<li>Calculate one or more diagnostic quantities on the snapshots that
weren&#8217;t computed in the initial run. These can also be computed with
settings not used in the initial run, e.g. computing an RDF via the
<a class="reference internal" href="compute_rdf.html"><span class="doc">compute rdf</span></a> command with a longer cutoff than was
<span class="xref doc">compute rdf</span> command with a longer cutoff than was
used initially.</li>
<li>Calculate the portion of per-atom forces resulting from a subset of
the potential. E.g. compute only Coulombic forces. This can be done

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@ -1192,7 +1192,7 @@ with a leading $ sign (e.g. $x or ${abc}) versus with a leading &#8220;<a href="
(e.g. v_x or v_abc). The former can be used in any input script
command, including a variable command. The input script parser
evaluates the reference variable immediately and substitutes its value
into the command. As explained in <a class="reference internal" href="Section_commands.html#cmd-2"><span class="std std-ref">Section commands 3.2</span></a> for &#8220;Parsing rules&#8221;, you can also use
into the command. As explained in <span class="xref std std-ref">Section commands 3.2</span> for &#8220;Parsing rules&#8221;, you can also use
un-named &#8220;immediate&#8221; variables for this purpose. For example, a
string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script
command evaluates the string between the parenthesis as an equal-style

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@ -1010,7 +1010,7 @@ system. Fix nvt/sllod uses "compute
temp/deform"_compute_temp_deform.html to compute a thermal temperature
by subtracting out the streaming velocity of the shearing atoms. The
velocity profile or other properties of the fluid can be monitored via
the "fix ave/chunk"_fix_ave_chunk.html command.
the "fix ave/spatial"_fix_ave_spatial.html command.
As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by
@ -1970,7 +1970,7 @@ on each of two regions to add/subtract specified amounts of energy to
both regions. In both cases, the resulting temperatures of the two
regions can be monitored with the "compute temp/region" command and
the temperature profile of the intermediate region can be monitored
with the "fix ave/chunk"_fix_ave_chunk.html and "compute
with the "fix ave/spatial"_fix_ave_spatial.html and "compute
ke/atom"_compute_ke_atom.html commands.
The third method is to perform a reverse non-equilibrium MD simulation
@ -1979,7 +1979,7 @@ command which implements the rNEMD algorithm of Muller-Plathe.
Kinetic energy is swapped between atoms in two different layers of the
simulation box. This induces a temperature gradient between the two
layers which can be monitored with the "fix
ave/chunk"_fix_ave_chunk.html and "compute
ave/spatial"_fix_ave_spatial.html and "compute
ke/atom"_compute_ke_atom.html commands. The fix tallies the
cumulative energy transfer that it performs. See the "fix
thermal/conductivity"_fix_thermal_conductivity.html command for
@ -2036,7 +2036,7 @@ velocity to prevent the fluid from heating up.
In both cases, the velocity profile setup in the fluid by this
procedure can be monitored by the "fix
ave/chunk"_fix_ave_chunk.html command, which determines
ave/spatial"_fix_ave_spatial.html command, which determines
grad(Vstream) in the equation above. E.g. the derivative in the
y-direction of the Vx component of fluid motion or grad(Vstream) =
dVx/dy. The Pxy off-diagonal component of the pressure or stress
@ -2050,7 +2050,7 @@ using the "fix viscosity"_fix_viscosity.html command which implements
the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is
swapped between atoms in two different layers of the simulation box in
a different dimension. This induces a velocity gradient which can be
monitored with the "fix ave/chunk"_fix_ave_chunk.html command.
monitored with the "fix ave/spatial"_fix_ave_spatial.html command.
The fix tallies the cummulative momentum transfer that it performs.
See the "fix viscosity"_fix_viscosity.html command for details.

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@ -260,7 +260,7 @@ calculate "virtual diffraction patterns"_compute_xrd.html
coupled rigid body integration via the "POEMS"_fix_poems.html library
"QM/MM coupling"_fix_qmmm.html
"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html
Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html "atom swapping"_fix_atom_swap.html and "bond swapping"_fix_bond_swap.html
Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html and "atom swapping"_fix_swap.html
"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
"Peridynamics mesoscale modeling"_pair_peri.html
"Lattice Boltzmann fluid"_fix_lb_fluid.html

36
doc/src/Section_packages.txt
View File

@ -795,7 +795,7 @@ Supporting info:
"doc/PDF/PDLammps_overview.pdf"_PDF/PDLammps_overview.pdf,
"doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf,
"doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf, "atom_style
peri"_atom_style.html, "compute damage/atom"_compute_damage_atom.html,
peri"_atom_style.html, "compute damage"_compute_damage.html,
"pair_style peri/pmb"_pair_peri.html, examples/peri
:line
@ -846,8 +846,9 @@ PYTHON package :link(PYTHON),h5
Contents: A "python"_python.html command which allow you to execute
Python code from a LAMMPS input script. The code can be in a separate
file or embedded in the input script itself. See "Section python
11.2"_Section_python.html" for an overview of using Python from
LAMMPS and for other ways to use LAMMPS and Python together.
11.2"_Section_python.html#py_2" for an overview of using Python from
LAMMPS and "Section python"_Section_python.html" for other ways to use
LAMMPS and Python together.
Building with the PYTHON package assumes you have a Python shared
library available on your system, which needs to be a Python 2
@ -1002,7 +1003,7 @@ make machine :pre
Make.py -p ^rigid -a machine :pre
Supporting info: "compute erotate/rigid"_compute_erotate_rigid.html,
"fix shake"_fix_shake.html, "fix rattle"_fix_shake.html, "fix
"fix shake"_fix_shake.html, "fix rattle"_fix_rattle.html, "fix
rigid/*"_fix_rigid.html, examples/ASPHERE, examples/rigid
:line
@ -1054,8 +1055,8 @@ make machine :pre
Make.py -p ^snap -a machine :pre
Supporting info: "pair snap"_pair_snap.html, "compute
sna/atom"_compute_sna_atom.html, "compute snad/atom"_compute_sna_atom.html,
"compute snav/atom"_compute_sna_atom.html, examples/snap
sna/atom"_compute_sna_atom.html, "compute snad/atom"_compute_sna.html,
"compute snav/atom"_compute_sna.html, examples/snap
:line
@ -1163,8 +1164,8 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
"USER-SMD"_#USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, -
"USER-SMTBQ"_#USER-SMTBQ, Second Moment Tight Binding - QEq potential, Salles & Maras & Politano & Tetot (4), "pair_style smtbq"_pair_smtbq.html, USER/smtbq, -, -
"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
"USER-TALLY"_#USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute XXX/tally"_compute_tally.html, USER/tally, -, -
"USER-VTK"_#USER-VTK, VTK-style dumps, Berger and Queteschiner (6), "compute custom/vtk"_dump_custom_vtk.html, -, -, lib/vtk
"USER-TALLY"_#USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute <...>/tally"_compute_tally.html, USER/tally, -, -
"USER-VTK"_#USER-VTK, VTK-style dumps, Berger and Queteschiner (6), "compute custom/vtk"_compute_custom_vtk.html, -, -, lib/vtk
:tb(ea=c)
:link(atc,http://lammps.sandia.gov/pictures.html#atc)
@ -1259,7 +1260,7 @@ calculation. See src/USER-AWPMD/README for more details.
To build LAMMPS with this package ...
Supporting info: src/USER-AWPMD/README, "fix
awpmd/cut"_pair_awpmd.html, examples/USER/awpmd
awpmd/cut"_pair_awpmd_cut.html, examples/USER/awpmd
Author: Ilya Valuev at the JIHT in Russia (valuev at
physik.hu-berlin.de). Contact him directly if you have questions.
@ -1314,7 +1315,7 @@ kinematic diffraction theory. See src/USER-DIFFRACTION/README for
more details.
Supporting info: "compute saed"_compute_saed.html, "compute
xrd"_compute_xrd.html, "fix saed/vtk"_fix_saed_vtk.html,
xrd"_compute_xrd.html, "fix saed.vtk"_fix_saed_vtk.html,
examples/USER/diffraction
Author: Shawn P. Coleman (shawn.p.coleman8.ctr at mail.mil) while at
@ -1336,11 +1337,10 @@ splitting algorithm. See src/USER-DPD/README for more details.
Supporting info: /src/USER-DPD/README, "compute dpd"_compute_dpd.html
"compute dpd/atom"_compute_dpd_atom.html
"fix eos/cv"_fix_eos_table.html "fix eos/table"_fix_eos_table.html
"fix eos/table/rx"_fix_eos_table_rx.html "fix shardlow"_fix_shardlow.html
"fix rx"_fix_rx.html "pair table/rx"_pair_table_rx.html
"pair dpd/fdt"_pair_dpd_fdt.html "pair dpd/fdt/energy"_pair_dpd_fdt.html
"pair exp6/rx"_pair_exp6_rx.html "pair multi/lucy"_pair_multi_lucy.html
"pair multi/lucy/rx"_pair_multi_lucy_rx.html, examples/USER/dpd
"fix shardlow"_fix_shardlow.html
"pair_dpd/conservative"_pair_dpd_conservative.html
"pair_dpd/fdt"_pair_dpd_fdt.html
"pair_dpd/fdt/energy"_pair_dpd_fdt.html, examples/USER/dpd
Authors: James Larentzos (ARL) (james.p.larentzos.civ at mail.mil),
Timothy Mattox (Engility Corp) (Timothy.Mattox at engilitycorp.com)
@ -1440,7 +1440,7 @@ Phi-enabled styles.
Supporting info: examples/accelerate, src/USER-INTEL/TEST
"Section_accelerate"_Section_accelerate.html#acc_3
"Section_accelerate"_Section_accelerate.html#acc_9
Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact
him directly if you have questions.
@ -1592,7 +1592,7 @@ application itself.
See this doc page to get started:
"dump molfile"_dump_molfile.html
"dump molfile"_dump_molfile.html#acc_5
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
@ -1609,7 +1609,7 @@ styles, and fix styles.
See this section of the manual to get started:
"Section_accelerate"_Section_accelerate.html#acc_3
"Section_accelerate"_Section_accelerate.html#acc_5
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.

2
doc/src/Section_start.txt
View File

@ -1353,7 +1353,7 @@ Note that the keywords do not use a leading minus sign. I.e. the
keyword is "t", not "-t". Also note that each of the keywords has a
default setting. Example of when to use these options and what
settings to use on different platforms is given in "Section
5.8"_Section_accelerate.html#acc_3.
5.8"_Section_accelerate.html#acc_8.
d or device
g or gpus

2
doc/src/accelerate_kokkos.txt
View File

@ -246,7 +246,7 @@ used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
provides alternative methods via environment variables for binding
threads to hardware cores. More info on binding threads to cores is
given in "this section"_Section_accelerate.html#acc_3.
given in "this section"_Section_accelerate.html#acc_8.
KOKKOS_ARCH=KNC enables compiler switches needed when compling for an
Intel Phi processor.

8
doc/src/body.txt
View File

@ -175,6 +175,9 @@ The {bflag2} argument is ignored.
[Specifics of body style rounded/polygon:]
NOTE: Aug 2016 - This body style has not yet been added to LAMMPS.
The info below is a placeholder.
The {rounded/polygon} body style represents body particles as a convex
polygon with a variable number N > 2 of vertices, which can only be
used for 2d models. One example use of this body style is for 2d
@ -235,8 +238,9 @@ particles whose edge length is sqrt(2):
0 1 1 2 2 3 3 0
1.0 :pre
The "pair_style body/rounded/polygon"_pair_body_rounded_polygon.html command
can be used with this body style to compute body/body interactions.
The "pair_style body/rounded/polygon"_pair_body_rounded_polygon.html
command can be used with this body style to compute body/body
interactions.
For output purposes via the "compute
body/local"_compute_body_local.html and "dump local"_dump.html

4
doc/src/compute_damage_atom.txt
View File

@ -57,7 +57,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"compute dilatation/atom"_compute_dilatation_atom.html,
"compute plasticity/atom"_compute_plasticity_atom.html
"compute dilatation"_compute_dilatation.html, "compute
plasticity"_compute_plasticity.html
[Default:] none

4
doc/src/compute_dilatation_atom.txt
View File

@ -60,7 +60,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"compute damage/atom"_compute_damage_atom.html,
"compute plasticity/atom"_compute_plasticity_atom.html
"compute damage"_compute_damage.html, "compute
plasticity"_compute_plasticity.html
[Default:] none

2
doc/src/compute_erotate_rigid.txt
View File

@ -56,6 +56,6 @@ LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"compute ke/rigid"_compute_ke_rigid.html
"compute ke/rigid"_compute_erotate_ke_rigid.html
[Default:] none

4
doc/src/compute_plasticity_atom.txt
View File

@ -54,8 +54,8 @@ LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"compute damage/atom"_compute_damage_atom.html,
"compute dilatation/atom"_compute_dilatation_atom.html
"compute damage"_compute_damage.html, "compute
dilatation"_compute_dilatation.html
[Default:] none

2
doc/src/compute_reduce.txt
View File

@ -93,7 +93,7 @@ means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 compute reduce commands are
equivalent, since the "compute stress/atom"_compute_stress_atom.html
equivalent, since the "compute stress/atom"_compute_stress/atom.html
command creates a per-atom array with 6 columns:
compute myPress all stress/atom NULL

9
doc/src/compute_temp_deform_eff.txt
View File

@ -26,12 +26,12 @@ nuclei and electrons in the "electron force field"_pair_eff.html
model, after subtracting out a streaming velocity induced by the
simulation box changing size and/or shape, for example in a
non-equilibrium MD (NEMD) simulation. The size/shape change is
induced by use of the "fix deform"_fix_deform.html command. A
induced by use of the "fix deform/eff"_fix_deform_eff.html command. A
compute of this style is created by the "fix
nvt/sllod/eff"_fix_nvt_sllod_eff.html command to compute the thermal
temperature of atoms for thermostatting purposes. A compute of this
style can also be used by any command that computes a temperature,
e.g. "thermo_modify"_thermo_modify.html, "fix npt/eff"_fix_nh_eff.html,
e.g. "thermo_modify"_thermo_modify.html, "fix npt/eff"_fix_nh.html,
etc.
The calculation performed by this compute is exactly like that
@ -66,7 +66,8 @@ LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"compute temp/ramp"_compute_temp_ramp.html, "fix deform"_fix_deform.html,
"fix nvt/sllod/eff"_fix_nvt_sllod_eff.html
"compute temp/ramp"_compute_temp_ramp.html, "fix
deform/eff"_fix_deform_eff.html, "fix
nvt/sllod/eff"_fix_nvt_sllod_eff.html
[Default:] none

2
doc/src/compute_temp_eff.txt
View File

@ -26,7 +26,7 @@ Define a computation that calculates the temperature of a group of
nuclei and electrons in the "electron force field"_pair_eff.html
model. A compute of this style can be used by commands that compute a
temperature, e.g. "thermo_modify"_thermo_modify.html, "fix
npt/eff"_fix_nh_eff.html, etc.
npt/eff"_fix_npt_eff.html, etc.
The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2 for

2
doc/src/dihedral_table.txt
View File

@ -195,7 +195,7 @@ more instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
USER-MISC package. See the "Making LAMMPS"_Section_start.html#2_3
section for more info on packages.
[Related commands:]

2
doc/src/dump.txt
View File

@ -441,7 +441,7 @@ from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 dump commands are
equivalent, since the "compute stress/atom"_compute_stress_atom.html
equivalent, since the "compute stress/atom"_compute_stress/atom.html
command creates a per-atom array with 6 columns:
compute myPress all stress/atom NULL

26
doc/src/dump_custom_vtk.txt
View File

@ -34,7 +34,7 @@ args = list of arguments for a particular style :l
proc = ID of processor that owns atom
procp1 = ID+1 of processor that owns atom
type = atom type
element = name of atom element, as defined by "dump_modify"_dump_modify.html command
element = name of atom element, as defined by "dump_modify"_dump_modify_vtk.html command
mass = atom mass
x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates
@ -71,7 +71,7 @@ for the XML format; see the "VTK
homepage"_http://www.vtk.org/VTK/img/file-formats.pdf for a detailed
description of these formats. Since this naming convention conflicts
with the way binary output is usually specified (see below),
"dump_modify binary"_dump_modify.html allows to set the binary
"dump_modify binary"_dump_modify_vtk.html allows to set the binary
flag for this dump style explicitly.
[Description:]
@ -81,10 +81,10 @@ timesteps in a format readable by the "VTK visualization
toolkit"_http://www.vtk.org or other visualization tools that use it,
e.g. "ParaView"_http://www.paraview.org. The timesteps on which dump
output is written can also be controlled by a variable; see the
"dump_modify every"_dump_modify.html command for details.
"dump_modify every"_dump_modify_vtk.html command for details.
Only information for atoms in the specified group is dumped. The
"dump_modify thresh and region"_dump_modify.html commands can also
"dump_modify thresh and region"_dump_modify_vtk.html commands can also
alter what atoms are included; see details below.
As described below, special characters ("*", "%") in the filename
@ -95,7 +95,7 @@ on timesteps when neighbor lists are rebuilt, the coordinates of an
atom written to a dump file may be slightly outside the simulation
box.
IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify.html
IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify_vtk.html
option is invoked, the lines of atom information written to dump files
will be in an indeterminate order for each snapshot. This is even
true when running on a single processor, if the "atom_modify
@ -106,7 +106,7 @@ data for a single snapshot is collected from multiple processors, each
of which owns a subset of the atoms.
For the {custom/vtk} style, sorting is off by default. See the
"dump_modify"_dump_modify.html doc page for details.
"dump_modify"_dump_modify_vtk.html doc page for details.
:line
@ -148,21 +148,21 @@ timestep 0) and on the last timestep of a minimization if the
minimization converges. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of N. This behavior can be
changed via the "dump_modify first"_dump_modify.html command, which
changed via the "dump_modify first"_dump_modify_vtk.html command, which
can also be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by
using the "dump_modify every"_dump_modify.html command.
The "dump_modify every"_dump_modify.html command
using the "dump_modify every"_dump_modify_vtk.html command.
The "dump_modify every"_dump_modify_vtk.html command
also allows a variable to be used to determine the sequence of
timesteps on which dump files are written. In this mode a dump on the
first timestep of a run will also not be written unless the
"dump_modify first"_dump_modify.html command is used.
"dump_modify first"_dump_modify_vtk.html command is used.
Dump filenames can contain two wildcard characters. If a "*"
character appears in the filename, then one file per snapshot is
written and the "*" character is replaced with the timestep value.
For example, tmp.dump*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
tmp.dump20000.vtk, etc. Note that the "dump_modify pad"_dump_modify.html
tmp.dump20000.vtk, etc. Note that the "dump_modify pad"_dump_modify_vtk.html
command can be used to insure all timestep numbers are the same length
(e.g. 00010), which can make it easier to read a series of dump files
in order with some post-processing tools.
@ -176,7 +176,7 @@ mode of output on parallel machines that support parallel I/O for output.
By default, P = the number of processors meaning one file per
processor, but P can be set to a smaller value via the {nfile} or
{fileper} keywords of the "dump_modify"_dump_modify.html command.
{fileper} keywords of the "dump_modify"_dump_modify_vtk.html command.
These options can be the most efficient way of writing out dump files
when running on large numbers of processors.
@ -202,7 +202,7 @@ The {id}, {mol}, {proc}, {procp1}, {type}, {element}, {mass}, {vx},
{id} is the atom ID. {mol} is the molecule ID, included in the data
file for molecular systems. {type} is the atom type. {element} is
typically the chemical name of an element, which you must assign to
each type via the "dump_modify element"_dump_modify.html command.
each type via the "dump_modify element"_dump_modify_vtk.html command.
More generally, it can be any string you wish to associate with an
atom type. {mass} is the atom mass. {vx}, {vy}, {vz}, {fx}, {fy},
{fz}, and {q} are components of atom velocity and force and atomic

3
doc/src/dump_image.txt
View File

@ -388,6 +388,9 @@ objects to be drawn. An example is the "fix
surface/global"_fix_surface_global.html command which can draw lines
or triangles for 2d/3d simulations.
NOTE: Aug 2016 - The fix surface/global command is not yet added to
LAMMPS.
The {fflag1} and {fflag2} settings are numerical values which are
passed to the fix to affect how the drawing of its objects is done.
See the individual fix doc page for a description of what these

4
doc/src/fix_ave_chunk.txt
View File

@ -141,7 +141,7 @@ means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 fix ave/chunk commands are
equivalent, since the "compute
property/atom"_compute_property_atom.html command creates, in this
property/atom"_compute_property/atom.html command creates, in this
case, a per-atom array with 3 columns:
compute myAng all property/atom angmomx angmomy angmomz
@ -150,7 +150,7 @@ fix 2 all ave/chunk 100 1 100 cc1 c_myAng\[1\] c_myAng\[2\] c_myAng\[3\] file tm
NOTE: This fix works by creating an array of size {Nchunk} by Nvalues
on each processor. {Nchunk} is the number of chunks which is defined
by the "compute chunk/atom"_compute_chunk_atom.html command.
by the "compute chunk/atom"_doc/compute_chunk_atom.html command.
Nvalues is the number of input values specified. Each processor loops
over its atoms, tallying its values to the appropriate chunk. Then
the entire array is summed across all processors. This means that

2
doc/src/fix_bond_create.txt
View File

@ -122,7 +122,7 @@ become one moleclue due to the created bond, all atoms in the new
moleclue retain their original molecule IDs.
If the {atype} keyword is used and if an angle potential is defined
via the "angle_style"_angle_style.html command, then any new 3-body
via the "angle_style"_angle.html command, then any new 3-body
interactions inferred by the creation of a bond will create new angles
of type {angletype}, with parameters assigned by the corresponding
"angle_coeff"_angle_coeff.html command. Likewise, the {dtype} and

2
doc/src/fix_deform.txt
View File

@ -487,7 +487,7 @@ NOTE: For non-equilibrium MD (NEMD) simulations using "remap v" it is
usually desirable that the fluid (or flowing material, e.g. granular
particles) stream with a velocity profile consistent with the
deforming box. As mentioned above, using a thermostat such as "fix
nvt/sllod"_fix_nvt_sllod.html or "fix lavgevin"_fix_langevin.html
nvt/sllod"_fix_nvt_sllod.html or "fix lavgevin"_doc/fix_langevin.html
(with a bias provided by "compute
temp/deform"_compute_temp_deform.html), will typically accomplish
that. If you do not use a thermostat, then there is no driving force

2
doc/src/fix_deposit.txt
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@ -147,7 +147,7 @@ the list of relative probabilities. The N values must sum to 1.0.
If you wish to insert molecules via the {mol} keyword, that will be
treated as rigid bodies, use the {rigid} keyword, specifying as its
value the ID of a separate "fix rigid/small"_fix_rigid.html
value the ID of a separate "fix rigid/small"_fix_rigid_small.html
command which also appears in your input script.
If you wish to insert molecules via the {mol} keyword, that will have

4
doc/src/fix_ehex.txt
View File

@ -111,7 +111,7 @@ the keyword {hex} is specified.
[Compatibility with SHAKE and RATTLE (rigid molecules)]:
This fix is compatible with "fix shake"_fix_shake.html and "fix
rattle"_fix_shake.html. If either of these constraining algorithms is
rattle"_fix_rattle.html. If either of these constraining algorithms is
specified in the input script and the keyword {constrain} is set, the
bond distances will be corrected a second time at the end of the
integration step. It is recommended to specify the keyword {com} in
@ -124,7 +124,7 @@ rescaling takes place if the centre of mass lies outside the region.
NOTE: You can only use the keyword {com} along with {constrain}.
To achieve the highest accuracy it is recommended to use "fix
rattle"_fix_shake.html with the keywords {constrain} and {com} as
rattle"_fix_rattle.html with the keywords {constrain} and {com} as
shown in the second example. Only if RATTLE is employed, the velocity
constraints will be satisfied.

4
doc/src/fix_eos_table.txt
View File

@ -71,7 +71,7 @@ initial text must match the argument specified in the fix command.
The next line lists the number of table entries. The parameter "N" is
required and its value is the number of table entries that follow.
Note that this may be different than the {N} specified in the "fix
eos/table"_fix_eos_table.html command. Let Ntable = {N} in the fix
eos/table"_fix_style.html command. Let Ntable = {N} in the fix
command, and Nfile = "N" in the tabulated file. What LAMMPS does is a
preliminary interpolation by creating splines using the Nfile
tabulated values as nodal points. It uses these to interpolate as
@ -112,6 +112,6 @@ are not within the table cutoffs.
[Related commands:]
"fix shardlow"_fix_shardlow.html, "pair dpd/fdt"_pair_dpd_fdt.html
"fix shardlow"_fix_shardlow.html, "pair dpd/fdt"_dpd_fdt.html
[Default:] none

2
doc/src/fix_eos_table_rx.txt
View File

@ -135,7 +135,7 @@ are not within the table cutoffs.
[Related commands:]
"fix rx"_fix_rx.html,
"pair dpd/fdt"_pair_dpd_fdt.html
"pair dpd/fdt"_dpd_fdt.html
[Default:] none

2
doc/src/fix_lb_momentum.txt
View File

@ -50,7 +50,7 @@ No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can be
commands"_Section_howto.html#4_15. No parameter of this fix can be
used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.

2
doc/src/fix_lb_pc.txt
View File

@ -35,7 +35,7 @@ No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can be
commands"_Section_howto.html#4_15. No parameter of this fix can be
used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.

2
doc/src/fix_nh_eff.txt
View File

@ -75,7 +75,7 @@ doc page), are performed with computes that include the eFF contribution
to the temperature or kinetic energy from the electron radial velocity.
NOTE: there are two different pressures that can be reported for eFF
when defining the pair_style (see "pair eff/cut"_pair_eff.html to
when defining the pair_style (see "pair eff/cut"_pair_eff_cut.html to
understand these settings), one (default) that considers electrons do
not contribute radial virial components (i.e. electrons treated as
incompressible 'rigid' spheres) and one that does. The radial

2
doc/src/fix_phonon.txt
View File

@ -148,7 +148,7 @@ fix. You can use it to change the temperature compute from thermo_temp
to the one that reflects the true temperature of atoms in the group.
No global scalar or vector or per-atom quantities are stored by this
fix for access by various "output commands"_Section_howto.html#howto_15.
fix for access by various "output commands"_Section_howto.html#4_15.
Instead, this fix outputs its initialization information (including
mapping information) and the calculated dynamical matrices to the file

2
doc/src/fix_pour.txt
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@ -114,7 +114,7 @@ the list of relative probabilities. The N values must sum to 1.0.
If you wish to insert molecules via the {mol} keyword, that will be
treated as rigid bodies, use the {rigid} keyword, specifying as its
value the ID of a separate "fix rigid/small"_fix_rigid.html
value the ID of a separate "fix rigid/small"_fix_rigid_small.html
command which also appears in your input script.
If you wish to insert molecules via the {mol} keyword, that will have

2
doc/src/fix_reax_bonds.txt
View File

@ -31,7 +31,7 @@ reax/c"_pair_reax_c.html in the exact same format as the original
stand-alone ReaxFF code of Adri van Duin. The bond information is
written to {filename} on timesteps that are multiples of {Nevery},
including timestep 0. For time-averaged chemical species analysis,
please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
please see the "fix species"_fix_species.html command.
The format of the output file should be self-explantory.

2
doc/src/fix_rx.txt
View File

@ -198,6 +198,6 @@ enthalpy DPD simulation.
"fix eos/table/rx"_fix_eos_table_rx.html,
"fix shardlow"_fix_shardlow.html,
"pair dpd/fdt/energy"_pair_dpd_fdt.html
"pair dpd/fdt/energy"_dpd_fdt_energy.html
[Default:] none

2
doc/src/fix_shardlow.txt
View File

@ -26,7 +26,7 @@ integrate the DPD equations of motion. The SSA splits the integration
into a stochastic and deterministic integration step. The fix
{shardlow} performs the stochastic integration step and must be used
in conjunction with a deterministic integrator (e.g. "fix
nve"_fix_nve.html or "fix nph"_fix_nh.html). The stochastic
nve"_fix_nve.html or "fix nph"_fix_nph.html). The stochastic
integration of the dissipative and random forces is performed prior to
the deterministic integration of the conservative force. Further
details regarding the method are provided in "(Lisal)"_#Lisal and

10
doc/src/fix_smd.txt
View File

@ -138,14 +138,14 @@ LAMMPS"_Section_start.html#start_3 section for more info.
:line
:link(Izrailev)
:link(Israilev)
[(Izrailev)] Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar,
Wriggers, Schulten. Computational Molecular Dynamics: Challenges,
Methods, Ideas, volume 4 of Lecture Notes in Computational Science and
Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.
:link(Park)
[(Park)] Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
[(Park)]
Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
:link(Jarzynski)
[(Jarzynski)] Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)
[(Jarzynski)]
Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)

2
doc/src/fix_wall_piston.txt
View File

@ -92,7 +92,7 @@ No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
commands"_Section_howto.html#howoto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.

25
doc/src/kspace_style.txt
View File

@ -12,7 +12,7 @@ kspace_style command :h3
kspace_style style value :pre
style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/stagger} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} or {msm/cg} or {msm/omp} or {msm/cg/omp} :ulb,l
style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/stagger} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/kk} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} or {msm/cg} or {msm/omp} or {msm/cg/omp} :ulb,l
{none} value = none
{ewald} value = accuracy
accuracy = desired relative error in forces
@ -33,6 +33,8 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
accuracy = desired relative error in forces
{pppm/gpu} value = accuracy
accuracy = desired relative error in forces
{pppm/kk} value = accuracy
accuracy = desired relative error in forces
{pppm/omp} value = accuracy
accuracy = desired relative error in forces
{pppm/cg/omp} value = accuracy
@ -74,7 +76,7 @@ interacts with charges in an infinite array of periodic images of the
simulation domain.
Note that using a long-range solver requires use of a matching "pair
style"_pair_style.html to perform consistent short-range pairwise
style"_pair.html to perform consistent short-range pairwise
calculations. This means that the name of the pair style contains a
matching keyword to the name of the KSpace style, as in this table:
@ -271,6 +273,10 @@ calculation can be performed concurrently on the GPU while other
calculations for non-bonded and bonded force calculation are performed
on the CPU.
The {pppm/kk} style also performs charge assignment and force
interpolation calculations on the GPU while the FFTs themselves are
calculated on the CPU in non-threaded mode.
These accelerated styles are part of the GPU, USER-INTEL,
KOKKOS, USER-OMP, and OPT packages respectively. They are only
enabled if LAMMPS was built with those packages. See the "Making
@ -299,10 +305,10 @@ For MSM, a simulation must be 3d and one can use any combination of
periodic, non-periodic, or shrink-wrapped boundaries (specified using
the "boundary"_boundary.html command).
For Ewald and PPPM, a simulation must be 3d and periodic in all dimensions.
The only exception is if the slab option is set with "kspace_modify"_kspace_modify.html,
in which case the xy dimensions must be periodic and the z dimension must be
non-periodic.
For Ewald and PPPM, a simulation must be 3d and periodic in all
dimensions. The only exception is if the slab option is set with
"kspace_modify"_kspace_modify.html, in which case the xy dimensions
must be periodic and the z dimension must be non-periodic.
[Related commands:]
@ -354,11 +360,12 @@ and Computation 5, 2322 (2009)
10913 (2000).
:link(Isele-Holder)
[(Isele-Holder)] Isele-Holder, Mitchell, Ismail, J Chem Phys, 137, 174107 (2012).
[(Isele-Holder)] Isele-Holder, Mitchell, Ismail, J Chem Phys, 137,
174107 (2012).
:link(Isele-Holder2)
[(Isele-Holder2)] Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J Chem Theory
Comput 9, 5412 (2013).
[(Isele-Holder2)] Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail,
J Chem Theory Comput 9, 5412 (2013).
:link(Hardy)
[(Hardy)] David Hardy thesis: Multilevel Summation for the Fast

2
doc/src/molecule.txt
View File

@ -184,7 +184,7 @@ NOTE: Whether a section is required depends on how the molecule
template is used by other LAMMPS commands. For example, to add a
molecule via the "fix deposit"_fix_deposit.html command, the Coords
and Types sections are required. To add a rigid body via the "fix
pour"_fix_pour.html command, the Bonds (Angles, etc) sections are not
pour"_fix_pout.html command, the Bonds (Angles, etc) sections are not
required, since the molecule will be treated as a rigid body. Some
sections are optional. For example, the "fix pour"_fix_pour.html
command can be used to add "molecules" which are clusters of

2
doc/src/neighbor.txt
View File

@ -73,7 +73,7 @@ section"_Section_start.html#start_8 for details.
[Related commands:]
"neigh_modify"_neigh_modify.html, "units"_units.html,
"comm_modify"_comm_modify.html
"comm_modify"_cmom_modify.html
[Default:]

2
doc/src/pair_brownian.txt
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@ -123,7 +123,7 @@ This pair style can only be used via the {pair} keyword of the
These styles are part of the COLLOID package. They are only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
LAMMPS"_Section_start.html#2_3 section for more info.
Only spherical monodisperse particles are allowed for pair_style
brownian.

18
doc/src/pair_dipole.txt
View File

@ -138,18 +138,19 @@ dipole interactions. The long-range portion is calculated by using
computed at all.
Atoms with dipole moments should be integrated using the "fix
nve/sphere update dipole"_fix_nve_sphere.html or the "fix
nvt/sphere update dipole"_fix_nvt_sphere.html command to rotate the
nve/sphere update dipole"_fix_nve_sphere.html command to rotate the
dipole moments. The {omega} option on the "fix
langevin"_fix_langevin.html command can be used to thermostat the
rotational motion. The "compute temp/sphere"_compute_temp_sphere.html
command can be used to monitor the temperature, since it includes
rotational degrees of freedom. The "atom_style
hybrid dipole sphere"_atom_style.html command should be used since
it defines the point dipoles and their rotational state.
The magnitude and orientation of the dipole moment for each particle
can be defined by the "set"_set.html command or in the "Atoms" section
of the data file read in by the "read_data"_read_data.html command.
dipole"_atom_style.html command should be used since it defines the
point dipoles and their rotational state. The magnitude of the dipole
moment for each type of particle can be defined by the
"dipole"_dipole.html command or in the "Dipoles" section of the data
file read in by the "read_data"_read_data.html command. Their initial
orientation can be defined by the "set dipole"_set.html command or in
the "Atoms" section of the data file.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
@ -241,8 +242,7 @@ currently supported.
[Related commands:]
"pair_coeff"_pair_coeff.html, "set"_set.html, "read_data"_read_data.html,
"fix nve/sphere"_fix_nve_sphere.html, "fix nvt/sphere"_fix_nvt_sphere.html
"pair_coeff"_pair_coeff.html
[Default:] none

2
doc/src/pair_dpd_fdt.txt
View File

@ -115,7 +115,7 @@ enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
Pair styles {dpd/fdt} and {dpd/fdt/energy} require use of the
"comm_modify vel yes"_comm_modify.html option so that velocites are
"communicate vel yes"_communicate.html option so that velocites are
stored by ghost atoms.
Pair style {dpd/fdt/energy} requires "atom_style dpd"_atom_style.html

2
doc/src/pair_gayberne.txt
View File

@ -191,7 +191,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
These pair style require that atoms store torque and a quaternion to
represent their orientation, as defined by the
"atom_style"_atom_style.html. It also require they store a per-type
"shape"_set.html. The particles cannot store a per-particle
"shape"_shape.html. The particles cannot store a per-particle
diameter.
This pair style requires that atoms be ellipsoids as defined by the

2
doc/src/pair_line_lj.txt
View File

@ -131,7 +131,7 @@ This pair style can only be used via the {pair} keyword of the
This style is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
LAMMPS"_Section_start.html#2_3 section for more info.
Defining particles to be line segments so they participate in
line/line or line/particle interactions requires the use the

2
doc/src/pair_thole.txt
View File

@ -60,7 +60,7 @@ it also allows for mixing pair coefficients instead of listing them all.
The {lj/cut/thole/long} pair style is also a bit faster because it avoids an
overlay and can benefit from OMP acceleration. Moreover, it uses a more
precise approximation of the direct Coulomb interaction at short range similar
to "coul/long/cs"_pair_cs.html, which stabilizes the temperature of
to "coul/long/cs"_pair_coul_long_cs.html, which stabilizes the temperature of
Drude particles.
The {thole} pair styles compute the Coulomb interaction damped at

2
doc/src/pair_tri_lj.txt
View File

@ -102,7 +102,7 @@ This pair style can only be used via the {pair} keyword of the
This style is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
LAMMPS"_Section_start.html#2_3 section for more info.
Defining particles to be triangles so they participate in tri/tri or
tri/particle interactions requires the use the "atom_style

2
doc/src/python.txt
View File

@ -460,7 +460,7 @@ your Python function must be able to to load the Python module in
python/lammps.py that wraps the LAMMPS library interface. These are
the same steps required to use Python by itself to wrap LAMMPS.
Details on these steps are explained in "Section
python"_Section_python.html. Note that it is important that the
python"_Section.python.html. Note that it is important that the
stand-alone LAMMPS executable and the LAMMPS shared library be
consistent (built from the same source code files) in order for this
to work. If the two have been built at different times using

2
doc/src/rerun.txt
View File

@ -53,7 +53,7 @@ Compute the energy and forces of snaphots using a different potential.
Calculate one or more diagnostic quantities on the snapshots that
weren't computed in the initial run. These can also be computed with
settings not used in the initial run, e.g. computing an RDF via the
"compute rdf"_compute_rdf.html command with a longer cutoff than was
"compute rdf"_compute.rdf.html command with a longer cutoff than was
used initially. :l
Calculate the portion of per-atom forces resulting from a subset of

2
doc/src/variable.txt
View File

@ -1108,7 +1108,7 @@ with a leading $ sign (e.g. $x or $\{abc\}) versus with a leading "v_"
command, including a variable command. The input script parser
evaluates the reference variable immediately and substitutes its value
into the command. As explained in "Section commands
3.2"_Section_commands.html#cmd_2 for "Parsing rules", you can also use
3.2"_Section_commands.html#3_2 for "Parsing rules", you can also use
un-named "immediate" variables for this purpose. For example, a
string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script
command evaluates the string between the parenthesis as an equal-style

6
src/KOKKOS/Install.sh
View File

@ -87,6 +87,8 @@ action fix_setforce_kokkos.cpp
action fix_setforce_kokkos.h
action fix_wall_reflect_kokkos.cpp
action fix_wall_reflect_kokkos.h
action gridcomm_kokkos.cpp gridcomm.cpp
action gridcomm_kokkos.h gridcomm.h
action improper_harmonic_kokkos.cpp improper_harmonic.cpp
action improper_harmonic_kokkos.h improper_harmonic.h
action kokkos.cpp
@ -102,6 +104,8 @@ action neigh_list_kokkos.cpp
action neigh_list_kokkos.h
action neighbor_kokkos.cpp
action neighbor_kokkos.h
action math_special_kokkos.cpp
action math_special_kokkos.h
action pair_buck_coul_cut_kokkos.cpp
action pair_buck_coul_cut_kokkos.h
action pair_buck_coul_long_kokkos.cpp pair_buck_coul_long.cpp
@ -167,6 +171,8 @@ action pair_tersoff_mod_kokkos.cpp pair_tersoff_mod.cpp
action pair_tersoff_mod_kokkos.h pair_tersoff_mod.h
action pair_tersoff_zbl_kokkos.cpp pair_tersoff_zbl.cpp
action pair_tersoff_zbl_kokkos.h pair_tersoff_zbl.h
action pppm_kokkos.cpp pppm.cpp
action pppm_kokkos.h pppm.h
action region_block_kokkos.cpp
action region_block_kokkos.h
action verlet_kokkos.cpp

614
src/KOKKOS/gridcomm_kokkos.cpp Normal file
View File

@ -0,0 +1,614 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include <mpi.h>
#include "gridcomm_kokkos.h"
#include "comm.h"
#include "kspace.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define SWAPDELTA 8
/* ---------------------------------------------------------------------- */
template<class DeviceType>
GridCommKokkos<DeviceType>::GridCommKokkos(LAMMPS *lmp, MPI_Comm gcomm, int forward, int reverse,
int ixlo, int ixhi, int iylo, int iyhi, int izlo, int izhi,
int oxlo, int oxhi, int oylo, int oyhi, int ozlo, int ozhi,
int pxlo, int pxhi, int pylo, int pyhi, int pzlo, int pzhi)
: Pointers(lmp)
{
gridcomm = gcomm;
MPI_Comm_rank(gridcomm,&me);
nforward = forward;
nreverse = reverse;
inxlo = ixlo;
inxhi = ixhi;
inylo = iylo;
inyhi = iyhi;
inzlo = izlo;
inzhi = izhi;
outxlo = oxlo;
outxhi = oxhi;
outylo = oylo;
outyhi = oyhi;
outzlo = ozlo;
outzhi = ozhi;
outxlo_max = oxlo;
outxhi_max = oxhi;
outylo_max = oylo;
outyhi_max = oyhi;
outzlo_max = ozlo;
outzhi_max = ozhi;
procxlo = pxlo;
procxhi = pxhi;
procylo = pylo;
procyhi = pyhi;
proczlo = pzlo;
proczhi = pzhi;
nswap = 0;
swap = NULL;
//buf1 = buf2 = NULL;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
GridCommKokkos<DeviceType>::GridCommKokkos(LAMMPS *lmp, MPI_Comm gcomm, int forward, int reverse,
int ixlo, int ixhi, int iylo, int iyhi, int izlo, int izhi,
int oxlo, int oxhi, int oylo, int oyhi, int ozlo, int ozhi,
int oxlo_max, int oxhi_max, int oylo_max, int oyhi_max,
int ozlo_max, int ozhi_max,
int pxlo, int pxhi, int pylo, int pyhi, int pzlo, int pzhi)
: Pointers(lmp)
{
gridcomm = gcomm;
MPI_Comm_rank(gridcomm,&me);
nforward = forward;
nreverse = reverse;
inxlo = ixlo;
inxhi = ixhi;
inylo = iylo;
inyhi = iyhi;
inzlo = izlo;
inzhi = izhi;
outxlo = oxlo;
outxhi = oxhi;
outylo = oylo;
outyhi = oyhi;
outzlo = ozlo;
outzhi = ozhi;
outxlo_max = oxlo_max;
outxhi_max = oxhi_max;
outylo_max = oylo_max;
outyhi_max = oyhi_max;
outzlo_max = ozlo_max;
outzhi_max = ozhi_max;
procxlo = pxlo;
procxhi = pxhi;
procylo = pylo;
procyhi = pyhi;
proczlo = pzlo;
proczhi = pzhi;
nswap = 0;
swap = NULL;
//buf1 = buf2 = NULL;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
GridCommKokkos<DeviceType>::~GridCommKokkos()
{
for (int i = 0; i < nswap; i++) {
//memory->destroy_kokkos(swap[i].k_packlist,swap[i].packlist);
//memory->destroy_kokkos(swap[i].k_unpacklist,swap[i].unpacklist);
}
memory->sfree(swap);
//memory->destroy(buf1);
//memory->destroy(buf2);
}
/* ----------------------------------------------------------------------
notify 6 neighbor procs how many ghost grid planes I need from them
ghostxlo = # of lower grid planes I own that are needed from me
by procxlo to become its upper ghost planes
ghostxhi = # of upper grid planes I own that are needed from me
by procxhi to become its lower ghost planes
if no neighbor proc, value is from self
------------------------------------------------------------------------- */
template<class DeviceType>
void GridCommKokkos<DeviceType>::ghost_notify()
{
int nplanes = inxlo - outxlo;
if (procxlo != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,procxlo,0,
&ghostxhi,1,MPI_INT,procxhi,0,gridcomm,MPI_STATUS_IGNORE);
else ghostxhi = nplanes;
nplanes = outxhi - inxhi;
if (procxhi != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,procxhi,0,
&ghostxlo,1,MPI_INT,procxlo,0,gridcomm,MPI_STATUS_IGNORE);
else ghostxlo = nplanes;
nplanes = inylo - outylo;
if (procylo != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,procylo,0,
&ghostyhi,1,MPI_INT,procyhi,0,gridcomm,MPI_STATUS_IGNORE);
else ghostyhi = nplanes;
nplanes = outyhi - inyhi;
if (procyhi != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,procyhi,0,
&ghostylo,1,MPI_INT,procylo,0,gridcomm,MPI_STATUS_IGNORE);
else ghostylo = nplanes;
nplanes = inzlo - outzlo;
if (proczlo != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,proczlo,0,
&ghostzhi,1,MPI_INT,proczhi,0,gridcomm,MPI_STATUS_IGNORE);
else ghostzhi = nplanes;
nplanes = outzhi - inzhi;
if (proczhi != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,proczhi,0,
&ghostzlo,1,MPI_INT,proczlo,0,gridcomm,MPI_STATUS_IGNORE);
else ghostzlo = nplanes;
}
/* ----------------------------------------------------------------------
check if all ghost grid comm needs overlap into non nearest-neighbor proc
if yes, return 1, else return 0
------------------------------------------------------------------------- */
template<class DeviceType>
int GridCommKokkos<DeviceType>::ghost_overlap()
{
int nearest = 0;
if (ghostxlo > inxhi-inxlo+1) nearest = 1;
if (ghostxhi > inxhi-inxlo+1) nearest = 1;
if (ghostylo > inyhi-inylo+1) nearest = 1;
if (ghostyhi > inyhi-inylo+1) nearest = 1;
if (ghostzlo > inzhi-inzlo+1) nearest = 1;
if (ghostzhi > inzhi-inzlo+1) nearest = 1;
int nearest_all;
MPI_Allreduce(&nearest,&nearest_all,1,MPI_INT,MPI_MIN,gridcomm);
return nearest_all;
}
/* ----------------------------------------------------------------------
create swap stencil for grid own/ghost communication
swaps covers all 3 dimensions and both directions
swaps cover multiple iterations in a direction if need grid pts
from further away than nearest-neighbor proc
same swap list used by forward and reverse communication
------------------------------------------------------------------------- */
template<class DeviceType>
void GridCommKokkos<DeviceType>::setup()
{
int nsent,sendfirst,sendlast,recvfirst,recvlast;
int sendplanes,recvplanes;
int notdoneme,notdone;
int maxswap = 6;
swap = (Swap *) memory->smalloc(maxswap*sizeof(Swap),"Commgrid:swap");
k_packlist = DAT::tdual_int_2d("Commgrid:packlist",maxswap,1);
k_unpacklist = DAT::tdual_int_2d("Commgrid:unpacklist",maxswap,1);
nswap = 0;
// send own grid pts to -x processor, recv ghost grid pts from +x processor
nsent = 0;
sendfirst = inxlo;
sendlast = inxhi;
recvfirst = inxhi+1;
notdone = 1;
while (notdone) {
if (nswap == maxswap) {
maxswap += SWAPDELTA;
swap = (Swap *)
memory->srealloc(swap,maxswap*sizeof(Swap),"Commgrid:swap");
k_packlist.resize(maxswap,k_packlist.dimension_1());
k_unpacklist.resize(maxswap,k_unpacklist.dimension_1());
}
swap[nswap].sendproc = procxlo;
swap[nswap].recvproc = procxhi;
sendplanes = MIN(sendlast-sendfirst+1,ghostxlo-nsent);
swap[nswap].npack =
indices(k_packlist,nswap,
sendfirst,sendfirst+sendplanes-1,inylo,inyhi,inzlo,inzhi);
if (procxlo != me)
MPI_Sendrecv(&sendplanes,1,MPI_INT,procxlo,0,
&recvplanes,1,MPI_INT,procxhi,0,gridcomm,MPI_STATUS_IGNORE);
else recvplanes = sendplanes;
swap[nswap].nunpack =
indices(k_unpacklist,nswap,
recvfirst,recvfirst+recvplanes-1,inylo,inyhi,inzlo,inzhi);
nsent += sendplanes;
sendfirst += sendplanes;
sendlast += recvplanes;
recvfirst += recvplanes;
nswap++;
if (nsent < ghostxlo) notdoneme = 1;
else notdoneme = 0;
MPI_Allreduce(&notdoneme,&notdone,1,MPI_INT,MPI_SUM,gridcomm);
}
// send own grid pts to +x processor, recv ghost grid pts from -x processor
nsent = 0;
sendfirst = inxlo;
sendlast = inxhi;
recvlast = inxlo-1;
notdone = 1;
while (notdone) {
if (nswap == maxswap) {
maxswap += 1;
swap = (Swap *)
memory->srealloc(swap,maxswap*sizeof(Swap),"Commgrid:swap");
k_packlist.resize(maxswap,k_packlist.dimension_1());
k_unpacklist.resize(maxswap,k_unpacklist.dimension_1());
}
swap[nswap].sendproc = procxhi;
swap[nswap].recvproc = procxlo;
sendplanes = MIN(sendlast-sendfirst+1,ghostxhi-nsent);
swap[nswap].npack =
indices(k_packlist,nswap,
sendlast-sendplanes+1,sendlast,inylo,inyhi,inzlo,inzhi);
if (procxhi != me)
MPI_Sendrecv(&sendplanes,1,MPI_INT,procxhi,0,
&recvplanes,1,MPI_INT,procxlo,0,gridcomm,MPI_STATUS_IGNORE);
else recvplanes = sendplanes;
swap[nswap].nunpack =
indices(k_unpacklist,nswap,
recvlast-recvplanes+1,recvlast,inylo,inyhi,inzlo,inzhi);
nsent += sendplanes;
sendfirst -= recvplanes;
sendlast -= sendplanes;
recvlast -= recvplanes;
nswap++;
if (nsent < ghostxhi) notdoneme = 1;
else notdoneme = 0;
MPI_Allreduce(&notdoneme,&notdone,1,MPI_INT,MPI_SUM,gridcomm);
}
// send own grid pts to -y processor, recv ghost grid pts from +y processor
nsent = 0;
sendfirst = inylo;
sendlast = inyhi;
recvfirst = inyhi+1;
notdone = 1;
while (notdone) {
if (nswap == maxswap) {
maxswap += SWAPDELTA;
swap = (Swap *)
memory->srealloc(swap,maxswap*sizeof(Swap),"Commgrid:swap");
k_packlist.resize(maxswap,k_packlist.dimension_1());
k_unpacklist.resize(maxswap,k_unpacklist.dimension_1());
}
swap[nswap].sendproc = procylo;
swap[nswap].recvproc = procyhi;
sendplanes = MIN(sendlast-sendfirst+1,ghostylo-nsent);
swap[nswap].npack =
indices(k_packlist,nswap,
outxlo,outxhi,sendfirst,sendfirst+sendplanes-1,inzlo,inzhi);
if (procylo != me)
MPI_Sendrecv(&sendplanes,1,MPI_INT,procylo,0,
&recvplanes,1,MPI_INT,procyhi,0,gridcomm,MPI_STATUS_IGNORE);
else recvplanes = sendplanes;
swap[nswap].nunpack =
indices(k_unpacklist,nswap,
outxlo,outxhi,recvfirst,recvfirst+recvplanes-1,inzlo,inzhi);
nsent += sendplanes;
sendfirst += sendplanes;
sendlast += recvplanes;
recvfirst += recvplanes;
nswap++;
if (nsent < ghostylo) notdoneme = 1;
else notdoneme = 0;
MPI_Allreduce(&notdoneme,&notdone,1,MPI_INT,MPI_SUM,gridcomm);
}
// send own grid pts to +y processor, recv ghost grid pts from -y processor
nsent = 0;
sendfirst = inylo;
sendlast = inyhi;
recvlast = inylo-1;
notdone = 1;
while (notdone) {
if (nswap == maxswap) {
maxswap += 1;
swap = (Swap *)
memory->srealloc(swap,maxswap*sizeof(Swap),"Commgrid:swap");
k_packlist.resize(maxswap,k_packlist.dimension_1());
k_unpacklist.resize(maxswap,k_unpacklist.dimension_1());
}
swap[nswap].sendproc = procyhi;
swap[nswap].recvproc = procylo;
sendplanes = MIN(sendlast-sendfirst+1,ghostyhi-nsent);
swap[nswap].npack =
indices(k_packlist,nswap,
outxlo,outxhi,sendlast-sendplanes+1,sendlast,inzlo,inzhi);
if (procyhi != me)
MPI_Sendrecv(&sendplanes,1,MPI_INT,procyhi,0,
&recvplanes,1,MPI_INT,procylo,0,gridcomm,MPI_STATUS_IGNORE);
else recvplanes = sendplanes;
swap[nswap].nunpack =
indices(k_unpacklist,nswap,
outxlo,outxhi,recvlast-recvplanes+1,recvlast,inzlo,inzhi);
nsent += sendplanes;
sendfirst -= recvplanes;
sendlast -= sendplanes;
recvlast -= recvplanes;
nswap++;
if (nsent < ghostyhi) notdoneme = 1;
else notdoneme = 0;
MPI_Allreduce(&notdoneme,&notdone,1,MPI_INT,MPI_SUM,gridcomm);
}
// send own grid pts to -z processor, recv ghost grid pts from +z processor
nsent = 0;
sendfirst = inzlo;
sendlast = inzhi;
recvfirst = inzhi+1;
notdone = 1;
while (notdone) {
if (nswap == maxswap) {
maxswap += SWAPDELTA;
swap = (Swap *)
memory->srealloc(swap,maxswap*sizeof(Swap),"Commgrid:swap");
k_packlist.resize(maxswap,k_packlist.dimension_1());
k_unpacklist.resize(maxswap,k_unpacklist.dimension_1());
}
swap[nswap].sendproc = proczlo;
swap[nswap].recvproc = proczhi;
sendplanes = MIN(sendlast-sendfirst+1,ghostzlo-nsent);
swap[nswap].npack =
indices(k_packlist,nswap,
outxlo,outxhi,outylo,outyhi,sendfirst,sendfirst+sendplanes-1);
if (proczlo != me)
MPI_Sendrecv(&sendplanes,1,MPI_INT,proczlo,0,
&recvplanes,1,MPI_INT,proczhi,0,gridcomm,MPI_STATUS_IGNORE);
else recvplanes = sendplanes;
swap[nswap].nunpack =
indices(k_unpacklist,nswap,
outxlo,outxhi,outylo,outyhi,recvfirst,recvfirst+recvplanes-1);
nsent += sendplanes;
sendfirst += sendplanes;
sendlast += recvplanes;
recvfirst += recvplanes;
nswap++;
if (nsent < ghostzlo) notdoneme = 1;
else notdoneme = 0;
MPI_Allreduce(&notdoneme,&notdone,1,MPI_INT,MPI_SUM,gridcomm);
}
// send own grid pts to +z processor, recv ghost grid pts from -z processor
nsent = 0;
sendfirst = inzlo;
sendlast = inzhi;
recvlast = inzlo-1;
notdone = 1;
while (notdone) {
if (nswap == maxswap) {
maxswap += 1;
swap = (Swap *)
memory->srealloc(swap,maxswap*sizeof(Swap),"Commgrid:swap");
k_packlist.resize(maxswap,k_packlist.dimension_1());
k_unpacklist.resize(maxswap,k_unpacklist.dimension_1());
}
swap[nswap].sendproc = proczhi;
swap[nswap].recvproc = proczlo;
sendplanes = MIN(sendlast-sendfirst+1,ghostzhi-nsent);
swap[nswap].npack =
indices(k_packlist,nswap,
outxlo,outxhi,outylo,outyhi,sendlast-sendplanes+1,sendlast);
if (proczhi != me)
MPI_Sendrecv(&sendplanes,1,MPI_INT,proczhi,0,
&recvplanes,1,MPI_INT,proczlo,0,gridcomm,MPI_STATUS_IGNORE);
else recvplanes = sendplanes;
swap[nswap].nunpack =
indices(k_unpacklist,nswap,
outxlo,outxhi,outylo,outyhi,recvlast-recvplanes+1,recvlast);
nsent += sendplanes;
sendfirst -= recvplanes;
sendlast -= sendplanes;
recvlast -= recvplanes;
nswap++;
if (nsent < ghostzhi) notdoneme = 1;
else notdoneme = 0;
MPI_Allreduce(&notdoneme,&notdone,1,MPI_INT,MPI_SUM,gridcomm);
}
// nbuf = max of any forward/reverse pack/unpack
nbuf = 0;
for (int i = 0; i < nswap; i++) {
nbuf = MAX(nbuf,swap[i].npack);
nbuf = MAX(nbuf,swap[i].nunpack);
}
nbuf *= MAX(nforward,nreverse);
//memory->create(buf1,nbuf,"Commgrid:buf1");
k_buf1 = DAT::tdual_FFT_SCALAR_1d("Commgrid:buf1",nbuf);
//memory->create(buf2,nbuf,"Commgrid:buf2");
k_buf2 = DAT::tdual_FFT_SCALAR_1d("Commgrid:buf2",nbuf);
}
/* ----------------------------------------------------------------------
use swap list in forward order to acquire copy of all needed ghost grid pts
------------------------------------------------------------------------- */
template<class DeviceType>
void GridCommKokkos<DeviceType>::forward_comm(KSpace *kspace, int which)
{
k_packlist.sync<DeviceType>();
k_unpacklist.sync<DeviceType>();
for (int m = 0; m < nswap; m++) {
if (swap[m].sendproc == me)
kspace->pack_forward_kokkos(which,k_buf2,swap[m].npack,k_packlist,m);
else
kspace->pack_forward_kokkos(which,k_buf1,swap[m].npack,k_packlist,m);
if (swap[m].sendproc != me) {
MPI_Irecv(k_buf2.view<DeviceType>().ptr_on_device(),nforward*swap[m].nunpack,MPI_FFT_SCALAR,
swap[m].recvproc,0,gridcomm,&request);
MPI_Send(k_buf1.view<DeviceType>().ptr_on_device(),nforward*swap[m].npack,MPI_FFT_SCALAR,
swap[m].sendproc,0,gridcomm);
MPI_Wait(&request,MPI_STATUS_IGNORE);
}
kspace->unpack_forward_kokkos(which,k_buf2,swap[m].nunpack,k_unpacklist,m);
}
}
/* ----------------------------------------------------------------------
use swap list in reverse order to compute fully summed value
for each owned grid pt that some other proc has copy of as a ghost grid pt
------------------------------------------------------------------------- */
template<class DeviceType>
void GridCommKokkos<DeviceType>::reverse_comm(KSpace *kspace, int which)
{
k_packlist.sync<DeviceType>();
k_unpacklist.sync<DeviceType>();
for (int m = nswap-1; m >= 0; m--) {
if (swap[m].recvproc == me)
kspace->pack_reverse_kokkos(which,k_buf2,swap[m].nunpack,k_unpacklist,m);
else
kspace->pack_reverse_kokkos(which,k_buf1,swap[m].nunpack,k_unpacklist,m);
if (swap[m].recvproc != me) {
MPI_Irecv(k_buf2.view<DeviceType>().ptr_on_device(),nreverse*swap[m].npack,MPI_FFT_SCALAR,
swap[m].sendproc,0,gridcomm,&request);
MPI_Send(k_buf1.view<DeviceType>().ptr_on_device(),nreverse*swap[m].nunpack,MPI_FFT_SCALAR,
swap[m].recvproc,0,gridcomm);
MPI_Wait(&request,MPI_STATUS_IGNORE);
}
kspace->unpack_reverse_kokkos(which,k_buf2,swap[m].npack,k_packlist,m);
}
}
/* ----------------------------------------------------------------------
create 1d list of offsets into 3d array section (xlo:xhi,ylo:yhi,zlo:zhi)
assume 3d array is allocated as (0:outxhi_max-outxlo_max+1,0:outyhi_max-outylo_max+1,
0:outzhi_max-outzlo_max+1)
------------------------------------------------------------------------- */
template<class DeviceType>
int GridCommKokkos<DeviceType>::indices(DAT::tdual_int_2d &k_list, int index,
int xlo, int xhi, int ylo, int yhi, int zlo, int zhi)
{
int nmax = (xhi-xlo+1) * (yhi-ylo+1) * (zhi-zlo+1);
if (k_list.dimension_1() < nmax)
k_list.resize(k_list.dimension_0(),nmax);
int nx = (outxhi_max-outxlo_max+1);
int ny = (outyhi_max-outylo_max+1);
k_list.sync<LMPHostType>();
int n = 0;
int ix,iy,iz;
for (iz = zlo; iz <= zhi; iz++)
for (iy = ylo; iy <= yhi; iy++)
for (ix = xlo; ix <= xhi; ix++)
k_list.h_view(index,n++) = (iz-outzlo_max)*ny*nx + (iy-outylo_max)*nx + (ix-outxlo_max);
k_list.modify<LMPHostType>();
k_list.sync<DeviceType>();
return nmax;
}
/* ----------------------------------------------------------------------
memory usage of send/recv bufs
------------------------------------------------------------------------- */
template<class DeviceType>
double GridCommKokkos<DeviceType>::memory_usage()
{
double bytes = 2*nbuf * sizeof(double);
return bytes;
}
namespace LAMMPS_NS {
template class GridCommKokkos<LMPDeviceType>;
#ifdef KOKKOS_HAVE_CUDA
template class GridCommKokkos<LMPHostType>;
#endif
}

96
src/KOKKOS/gridcomm_kokkos.h Normal file
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@ -0,0 +1,96 @@
/* -*- 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.
------------------------------------------------------------------------- */
#ifndef LMP_GRIDCOMM_KOKKOS_H
#define LMP_GRIDCOMM_KOKKOS_H
#include "pointers.h"
#include "kokkos_type.h"
#ifdef FFT_SINGLE
typedef float FFT_SCALAR;
#define MPI_FFT_SCALAR MPI_FLOAT
#else
typedef double FFT_SCALAR;
#define MPI_FFT_SCALAR MPI_DOUBLE
#endif
namespace LAMMPS_NS {
template<class DeviceType>
class GridCommKokkos : protected Pointers {
public:
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
GridCommKokkos(class LAMMPS *, MPI_Comm, int, int,
int, int, int, int, int, int,
int, int, int, int, int, int,
int, int, int, int, int, int);
GridCommKokkos(class LAMMPS *, MPI_Comm, int, int,
int, int, int, int, int, int,
int, int, int, int, int, int,
int, int, int, int, int, int,
int, int, int, int, int, int);
~GridCommKokkos();
void ghost_notify();
int ghost_overlap();
void setup();
void forward_comm(class KSpace *, int);
void reverse_comm(class KSpace *, int);
double memory_usage();
private:
int me;
int nforward,nreverse;
MPI_Comm gridcomm;
MPI_Request request;
// in = inclusive indices of 3d grid chunk that I own
// out = inclusive indices of 3d grid chunk I own plus ghosts I use
// proc = 6 neighbor procs that surround me
// ghost = # of my owned grid planes needed from me
// by each of 6 neighbor procs to become their ghost planes
int inxlo,inxhi,inylo,inyhi,inzlo,inzhi;
int outxlo,outxhi,outylo,outyhi,outzlo,outzhi;
int outxlo_max,outxhi_max,outylo_max,outyhi_max,outzlo_max,outzhi_max;
int procxlo,procxhi,procylo,procyhi,proczlo,proczhi;
int ghostxlo,ghostxhi,ghostylo,ghostyhi,ghostzlo,ghostzhi;
int nbuf;
//FFT_SCALAR *buf1,*buf2;
DAT::tdual_FFT_SCALAR_1d k_buf1;
DAT::tdual_FFT_SCALAR_1d k_buf2;
struct Swap {
int sendproc; // proc to send to for forward comm
int recvproc; // proc to recv from for forward comm
int npack; // # of datums to pack
int nunpack; // # of datums to unpack
//int *packlist; // 3d array offsets to pack
//int *unpacklist; // 3d array offsets to unpack
};
DAT::tdual_int_2d k_packlist;
DAT::tdual_int_2d k_unpacklist;
int nswap;
Swap *swap;
int indices(DAT::tdual_int_2d &, int, int, int, int, int, int, int);
};
}
#endif

70
src/KOKKOS/kokkos_type.h
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@ -14,6 +14,8 @@
#ifndef LMP_LMPTYPE_KOKKOS_H
#define LMP_LMPTYPE_KOKKOS_H
#include "lmptype.h"
#include <Kokkos_Core.hpp>
#include <Kokkos_DualView.hpp>
#include <impl/Kokkos_Timer.hpp>
@ -24,6 +26,21 @@
#define ISFINITE(x) std::isfinite(x)
#endif
// User-settable FFT precision
// FFT_PRECISION = 1 is single-precision complex (4-byte real, 4-byte imag)
// FFT_PRECISION = 2 is double-precision complex (8-byte real, 8-byte imag)
#ifdef FFT_SINGLE
#define FFT_PRECISION 1
#define MPI_FFT_SCALAR MPI_FLOAT
typedef float FFT_SCALAR;
#else
#define FFT_PRECISION 2
#define MPI_FFT_SCALAR MPI_DOUBLE
typedef double FFT_SCALAR;
#endif
#define MAX_TYPES_STACKPARAMS 12
#define NeighClusterSize 8
@ -567,6 +584,32 @@ typedef tdual_neighbors_2d::t_dev_um t_neighbors_2d_um;
typedef tdual_neighbors_2d::t_dev_const_um t_neighbors_2d_const_um;
typedef tdual_neighbors_2d::t_dev_const_randomread t_neighbors_2d_randomread;
//Kspace
typedef Kokkos::
DualView<FFT_SCALAR*, Kokkos::LayoutRight, LMPDeviceType> tdual_FFT_SCALAR_1d;
typedef tdual_FFT_SCALAR_1d::t_dev t_FFT_SCALAR_1d;
typedef tdual_FFT_SCALAR_1d::t_dev_um t_FFT_SCALAR_1d_um;
typedef Kokkos::DualView<FFT_SCALAR**,Kokkos::LayoutRight,LMPDeviceType> tdual_FFT_SCALAR_2d;
typedef tdual_FFT_SCALAR_2d::t_dev t_FFT_SCALAR_2d;
typedef Kokkos::DualView<FFT_SCALAR**[3],Kokkos::LayoutRight,LMPDeviceType> tdual_FFT_SCALAR_2d_3;
typedef tdual_FFT_SCALAR_2d_3::t_dev t_FFT_SCALAR_2d_3;
typedef Kokkos::DualView<FFT_SCALAR***,Kokkos::LayoutRight,LMPDeviceType> tdual_FFT_SCALAR_3d;
typedef tdual_FFT_SCALAR_3d::t_dev t_FFT_SCALAR_3d;
typedef Kokkos::
DualView<FFT_SCALAR*[2], Kokkos::LayoutRight, LMPDeviceType> tdual_FFT_DATA_1d;
typedef tdual_FFT_DATA_1d::t_dev t_FFT_DATA_1d;
typedef tdual_FFT_DATA_1d::t_dev_um t_FFT_DATA_1d_um;
typedef Kokkos::
DualView<int*, LMPDeviceType::array_layout, LMPDeviceType> tdual_int_64;
typedef tdual_int_64::t_dev t_int_64;
typedef tdual_int_64::t_dev_um t_int_64_um;
};
#ifdef KOKKOS_HAVE_CUDA
@ -801,6 +844,33 @@ typedef tdual_neighbors_2d::t_host_um t_neighbors_2d_um;
typedef tdual_neighbors_2d::t_host_const_um t_neighbors_2d_const_um;
typedef tdual_neighbors_2d::t_host_const_randomread t_neighbors_2d_randomread;
//Kspace
typedef Kokkos::
DualView<FFT_SCALAR*, Kokkos::LayoutRight, LMPDeviceType> tdual_FFT_SCALAR_1d;
typedef tdual_FFT_SCALAR_1d::t_host t_FFT_SCALAR_1d;
typedef tdual_FFT_SCALAR_1d::t_host_um t_FFT_SCALAR_1d_um;
typedef Kokkos::DualView<FFT_SCALAR**,Kokkos::LayoutRight,LMPDeviceType> tdual_FFT_SCALAR_2d;
typedef tdual_FFT_SCALAR_2d::t_host t_FFT_SCALAR_2d;
typedef Kokkos::DualView<FFT_SCALAR**[3],Kokkos::LayoutRight,LMPDeviceType> tdual_FFT_SCALAR_2d_3;
typedef tdual_FFT_SCALAR_2d_3::t_host t_FFT_SCALAR_2d_3;
typedef Kokkos::DualView<FFT_SCALAR***,Kokkos::LayoutRight,LMPDeviceType> tdual_FFT_SCALAR_3d;
typedef tdual_FFT_SCALAR_3d::t_host t_FFT_SCALAR_3d;
typedef Kokkos::
DualView<FFT_SCALAR*[2], Kokkos::LayoutRight, LMPDeviceType> tdual_FFT_DATA_1d;
typedef tdual_FFT_DATA_1d::t_host t_FFT_DATA_1d;
typedef tdual_FFT_DATA_1d::t_host_um t_FFT_DATA_1d_um;
typedef Kokkos::
DualView<int*, LMPDeviceType::array_layout, LMPDeviceType> tdual_int_64;
typedef tdual_int_64::t_host t_int_64;
typedef tdual_int_64::t_host_um t_int_64_um;
};
#endif
//default LAMMPS Types

534
src/KOKKOS/math_special_kokkos.cpp Normal file
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@ -0,0 +1,534 @@
#include <math.h>
#include <stdint.h>
#include "math_special_kokkos.h"
using namespace LAMMPS_NS;
/* Library libcerf:
* Compute complex error functions, based on a new implementation of
* Faddeeva's w_of_z. Also provide Dawson and Voigt functions.
*
* File erfcx.c:
* Compute erfcx(x) = exp(x^2) erfc(x) function, for real x,
* using a novel algorithm that is much faster than DERFC of SLATEC.
* This function is used in the computation of Faddeeva, Dawson, and
* other complex error functions.
*
* Copyright:
* (C) 2012 Massachusetts Institute of Technology
* (C) 2013 Forschungszentrum Jülich GmbH
*
* Licence:
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject to
* the following conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*
* Authors:
* Steven G. Johnson, Massachusetts Institute of Technology, 2012, core author
* Joachim Wuttke, Forschungszentrum Jülich, 2013, package maintainer
*
* Website:
* http://apps.jcns.fz-juelich.de/libcerf
*
* Revision history:
* ../CHANGELOG
*
* Manual page:
* man 3 erfcx
*/
/******************************************************************************/
/* Lookup-table for Chebyshev polynomials for smaller |x| */
/******************************************************************************/
double MathSpecialKokkos::erfcx_y100(const double y100)
{
// Steven G. Johnson, October 2012.
// Given y100=100*y, where y = 4/(4+x) for x >= 0, compute erfc(x).
// Uses a look-up table of 100 different Chebyshev polynomials
// for y intervals [0,0.01], [0.01,0.02], ...., [0.99,1], generated
// with the help of Maple and a little shell script. This allows
// the Chebyshev polynomials to be of significantly lower degree (about 1/4)
// compared to fitting the whole [0,1] interval with a single polynomial.
switch ((int) y100) {
case 0: {
double t = 2*y100 - 1;
return 0.70878032454106438663e-3 + (0.71234091047026302958e-3 + (0.35779077297597742384e-5 + (0.17403143962587937815e-7 + (0.81710660047307788845e-10 + (0.36885022360434957634e-12 + 0.15917038551111111111e-14 * t) * t) * t) * t) * t) * t;
}
case 1: {
double t = 2*y100 - 3;
return 0.21479143208285144230e-2 + (0.72686402367379996033e-3 + (0.36843175430938995552e-5 + (0.18071841272149201685e-7 + (0.85496449296040325555e-10 + (0.38852037518534291510e-12 + 0.16868473576888888889e-14 * t) * t) * t) * t) * t) * t;
}
case 2: {
double t = 2*y100 - 5;
return 0.36165255935630175090e-2 + (0.74182092323555510862e-3 + (0.37948319957528242260e-5 + (0.18771627021793087350e-7 + (0.89484715122415089123e-10 + (0.40935858517772440862e-12 + 0.17872061464888888889e-14 * t) * t) * t) * t) * t) * t;
}
case 3: {
double t = 2*y100 - 7;
return 0.51154983860031979264e-2 + (0.75722840734791660540e-3 + (0.39096425726735703941e-5 + (0.19504168704300468210e-7 + (0.93687503063178993915e-10 + (0.43143925959079664747e-12 + 0.18939926435555555556e-14 * t) * t) * t) * t) * t) * t;
}
case 4: {
double t = 2*y100 - 9;
return 0.66457513172673049824e-2 + (0.77310406054447454920e-3 + (0.40289510589399439385e-5 + (0.20271233238288381092e-7 + (0.98117631321709100264e-10 + (0.45484207406017752971e-12 + 0.20076352213333333333e-14 * t) * t) * t) * t) * t) * t;
}
case 5: {
double t = 2*y100 - 11;
return 0.82082389970241207883e-2 + (0.78946629611881710721e-3 + (0.41529701552622656574e-5 + (0.21074693344544655714e-7 + (0.10278874108587317989e-9 + (0.47965201390613339638e-12 + 0.21285907413333333333e-14 * t) * t) * t) * t) * t) * t;
}
case 6: {
double t = 2*y100 - 13;
return 0.98039537275352193165e-2 + (0.80633440108342840956e-3 + (0.42819241329736982942e-5 + (0.21916534346907168612e-7 + (0.10771535136565470914e-9 + (0.50595972623692822410e-12 + 0.22573462684444444444e-14 * t) * t) * t) * t) * t) * t;
}
case 7: {
double t = 2*y100 - 15;
return 0.11433927298290302370e-1 + (0.82372858383196561209e-3 + (0.44160495311765438816e-5 + (0.22798861426211986056e-7 + (0.11291291745879239736e-9 + (0.53386189365816880454e-12 + 0.23944209546666666667e-14 * t) * t) * t) * t) * t) * t;
}
case 8: {
double t = 2*y100 - 17;
return 0.13099232878814653979e-1 + (0.84167002467906968214e-3 + (0.45555958988457506002e-5 + (0.23723907357214175198e-7 + (0.11839789326602695603e-9 + (0.56346163067550237877e-12 + 0.25403679644444444444e-14 * t) * t) * t) * t) * t) * t;
}
case 9: {
double t = 2*y100 - 19;
return 0.14800987015587535621e-1 + (0.86018092946345943214e-3 + (0.47008265848816866105e-5 + (0.24694040760197315333e-7 + (0.12418779768752299093e-9 + (0.59486890370320261949e-12 + 0.26957764568888888889e-14 * t) * t) * t) * t) * t) * t;
}
case 10: {
double t = 2*y100 - 21;
return 0.16540351739394069380e-1 + (0.87928458641241463952e-3 + (0.48520195793001753903e-5 + (0.25711774900881709176e-7 + (0.13030128534230822419e-9 + (0.62820097586874779402e-12 + 0.28612737351111111111e-14 * t) * t) * t) * t) * t) * t;
}
case 11: {
double t = 2*y100 - 23;
return 0.18318536789842392647e-1 + (0.89900542647891721692e-3 + (0.50094684089553365810e-5 + (0.26779777074218070482e-7 + (0.13675822186304615566e-9 + (0.66358287745352705725e-12 + 0.30375273884444444444e-14 * t) * t) * t) * t) * t) * t;
}
case 12: {
double t = 2*y100 - 25;
return 0.20136801964214276775e-1 + (0.91936908737673676012e-3 + (0.51734830914104276820e-5 + (0.27900878609710432673e-7 + (0.14357976402809042257e-9 + (0.70114790311043728387e-12 + 0.32252476000000000000e-14 * t) * t) * t) * t) * t) * t;
}
case 13: {
double t = 2*y100 - 27;
return 0.21996459598282740954e-1 + (0.94040248155366777784e-3 + (0.53443911508041164739e-5 + (0.29078085538049374673e-7 + (0.15078844500329731137e-9 + (0.74103813647499204269e-12 + 0.34251892320000000000e-14 * t) * t) * t) * t) * t) * t;
}
case 14: {
double t = 2*y100 - 29;
return 0.23898877187226319502e-1 + (0.96213386835900177540e-3 + (0.55225386998049012752e-5 + (0.30314589961047687059e-7 + (0.15840826497296335264e-9 + (0.78340500472414454395e-12 + 0.36381553564444444445e-14 * t) * t) * t) * t) * t) * t;
}
case 15: {
double t = 2*y100 - 31;
return 0.25845480155298518485e-1 + (0.98459293067820123389e-3 + (0.57082915920051843672e-5 + (0.31613782169164830118e-7 + (0.16646478745529630813e-9 + (0.82840985928785407942e-12 + 0.38649975768888888890e-14 * t) * t) * t) * t) * t) * t;
}
case 16: {
double t = 2*y100 - 33;
return 0.27837754783474696598e-1 + (0.10078108563256892757e-2 + (0.59020366493792212221e-5 + (0.32979263553246520417e-7 + (0.17498524159268458073e-9 + (0.87622459124842525110e-12 + 0.41066206488888888890e-14 * t) * t) * t) * t) * t) * t;
}
case 17: {
double t = 2*y100 - 35;
return 0.29877251304899307550e-1 + (0.10318204245057349310e-2 + (0.61041829697162055093e-5 + (0.34414860359542720579e-7 + (0.18399863072934089607e-9 + (0.92703227366365046533e-12 + 0.43639844053333333334e-14 * t) * t) * t) * t) * t) * t;
}
case 18: {
double t = 2*y100 - 37;
return 0.31965587178596443475e-1 + (0.10566560976716574401e-2 + (0.63151633192414586770e-5 + (0.35924638339521924242e-7 + (0.19353584758781174038e-9 + (0.98102783859889264382e-12 + 0.46381060817777777779e-14 * t) * t) * t) * t) * t) * t;
}
case 19: {
double t = 2*y100 - 39;
return 0.34104450552588334840e-1 + (0.10823541191350532574e-2 + (0.65354356159553934436e-5 + (0.37512918348533521149e-7 + (0.20362979635817883229e-9 + (0.10384187833037282363e-11 + 0.49300625262222222221e-14 * t) * t) * t) * t) * t) * t;
}
case 20: {
double t = 2*y100 - 41;
return 0.36295603928292425716e-1 + (0.11089526167995268200e-2 + (0.67654845095518363577e-5 + (0.39184292949913591646e-7 + (0.21431552202133775150e-9 + (0.10994259106646731797e-11 + 0.52409949102222222221e-14 * t) * t) * t) * t) * t) * t;
}
case 21: {
double t = 2*y100 - 43;
return 0.38540888038840509795e-1 + (0.11364917134175420009e-2 + (0.70058230641246312003e-5 + (0.40943644083718586939e-7 + (0.22563034723692881631e-9 + (0.11642841011361992885e-11 + 0.55721092871111111110e-14 * t) * t) * t) * t) * t) * t;
}
case 22: {
double t = 2*y100 - 45;
return 0.40842225954785960651e-1 + (0.11650136437945673891e-2 + (0.72569945502343006619e-5 + (0.42796161861855042273e-7 + (0.23761401711005024162e-9 + (0.12332431172381557035e-11 + 0.59246802364444444445e-14 * t) * t) * t) * t) * t) * t;
}
case 23: {
double t = 2*y100 - 47;
return 0.43201627431540222422e-1 + (0.11945628793917272199e-2 + (0.75195743532849206263e-5 + (0.44747364553960993492e-7 + (0.25030885216472953674e-9 + (0.13065684400300476484e-11 + 0.63000532853333333334e-14 * t) * t) * t) * t) * t) * t;
}
case 24: {
double t = 2*y100 - 49;
return 0.45621193513810471438e-1 + (0.12251862608067529503e-2 + (0.77941720055551920319e-5 + (0.46803119830954460212e-7 + (0.26375990983978426273e-9 + (0.13845421370977119765e-11 + 0.66996477404444444445e-14 * t) * t) * t) * t) * t) * t;
}
case 25: {
double t = 2*y100 - 51;
return 0.48103121413299865517e-1 + (0.12569331386432195113e-2 + (0.80814333496367673980e-5 + (0.48969667335682018324e-7 + (0.27801515481905748484e-9 + (0.14674637611609884208e-11 + 0.71249589351111111110e-14 * t) * t) * t) * t) * t) * t;
}
case 26: {
double t = 2*y100 - 53;
return 0.50649709676983338501e-1 + (0.12898555233099055810e-2 + (0.83820428414568799654e-5 + (0.51253642652551838659e-7 + (0.29312563849675507232e-9 + (0.15556512782814827846e-11 + 0.75775607822222222221e-14 * t) * t) * t) * t) * t) * t;
}
case 27: {
double t = 2*y100 - 55;
return 0.53263363664388864181e-1 + (0.13240082443256975769e-2 + (0.86967260015007658418e-5 + (0.53662102750396795566e-7 + (0.30914568786634796807e-9 + (0.16494420240828493176e-11 + 0.80591079644444444445e-14 * t) * t) * t) * t) * t) * t;
}
case 28: {
double t = 2*y100 - 57;
return 0.55946601353500013794e-1 + (0.13594491197408190706e-2 + (0.90262520233016380987e-5 + (0.56202552975056695376e-7 + (0.32613310410503135996e-9 + (0.17491936862246367398e-11 + 0.85713381688888888890e-14 * t) * t) * t) * t) * t) * t;
}
case 29: {
double t = 2*y100 - 59;
return 0.58702059496154081813e-1 + (0.13962391363223647892e-2 + (0.93714365487312784270e-5 + (0.58882975670265286526e-7 + (0.34414937110591753387e-9 + (0.18552853109751857859e-11 + 0.91160736711111111110e-14 * t) * t) * t) * t) * t) * t;
}
case 30: {
double t = 2*y100 - 61;
return 0.61532500145144778048e-1 + (0.14344426411912015247e-2 + (0.97331446201016809696e-5 + (0.61711860507347175097e-7 + (0.36325987418295300221e-9 + (0.19681183310134518232e-11 + 0.96952238400000000000e-14 * t) * t) * t) * t) * t) * t;
}
case 31: {
double t = 2*y100 - 63;
return 0.64440817576653297993e-1 + (0.14741275456383131151e-2 + (0.10112293819576437838e-4 + (0.64698236605933246196e-7 + (0.38353412915303665586e-9 + (0.20881176114385120186e-11 + 0.10310784480000000000e-13 * t) * t) * t) * t) * t) * t;
}
case 32: {
double t = 2*y100 - 65;
return 0.67430045633130393282e-1 + (0.15153655418916540370e-2 + (0.10509857606888328667e-4 + (0.67851706529363332855e-7 + (0.40504602194811140006e-9 + (0.22157325110542534469e-11 + 0.10964842115555555556e-13 * t) * t) * t) * t) * t) * t;
}
case 33: {
double t = 2*y100 - 67;
return 0.70503365513338850709e-1 + (0.15582323336495709827e-2 + (0.10926868866865231089e-4 + (0.71182482239613507542e-7 + (0.42787405890153386710e-9 + (0.23514379522274416437e-11 + 0.11659571751111111111e-13 * t) * t) * t) * t) * t) * t;
}
case 34: {
double t = 2*y100 - 69;
return 0.73664114037944596353e-1 + (0.16028078812438820413e-2 + (0.11364423678778207991e-4 + (0.74701423097423182009e-7 + (0.45210162777476488324e-9 + (0.24957355004088569134e-11 + 0.12397238257777777778e-13 * t) * t) * t) * t) * t) * t;
}
case 35: {
double t = 2*y100 - 71;
return 0.76915792420819562379e-1 + (0.16491766623447889354e-2 + (0.11823685320041302169e-4 + (0.78420075993781544386e-7 + (0.47781726956916478925e-9 + (0.26491544403815724749e-11 + 0.13180196462222222222e-13 * t) * t) * t) * t) * t) * t;
}
case 36: {
double t = 2*y100 - 73;
return 0.80262075578094612819e-1 + (0.16974279491709504117e-2 + (0.12305888517309891674e-4 + (0.82350717698979042290e-7 + (0.50511496109857113929e-9 + (0.28122528497626897696e-11 + 0.14010889635555555556e-13 * t) * t) * t) * t) * t) * t;
}
case 37: {
double t = 2*y100 - 75;
return 0.83706822008980357446e-1 + (0.17476561032212656962e-2 + (0.12812343958540763368e-4 + (0.86506399515036435592e-7 + (0.53409440823869467453e-9 + (0.29856186620887555043e-11 + 0.14891851591111111111e-13 * t) * t) * t) * t) * t) * t;
}
case 38: {
double t = 2*y100 - 77;
return 0.87254084284461718231e-1 + (0.17999608886001962327e-2 + (0.13344443080089492218e-4 + (0.90900994316429008631e-7 + (0.56486134972616465316e-9 + (0.31698707080033956934e-11 + 0.15825697795555555556e-13 * t) * t) * t) * t) * t) * t;
}
case 39: {
double t = 2*y100 - 79;
return 0.90908120182172748487e-1 + (0.18544478050657699758e-2 + (0.13903663143426120077e-4 + (0.95549246062549906177e-7 + (0.59752787125242054315e-9 + (0.33656597366099099413e-11 + 0.16815130613333333333e-13 * t) * t) * t) * t) * t) * t;
}
case 40: {
double t = 2*y100 - 81;
return 0.94673404508075481121e-1 + (0.19112284419887303347e-2 + (0.14491572616545004930e-4 + (0.10046682186333613697e-6 + (0.63221272959791000515e-9 + (0.35736693975589130818e-11 + 0.17862931591111111111e-13 * t) * t) * t) * t) * t) * t;
}
case 41: {
double t = 2*y100 - 83;
return 0.98554641648004456555e-1 + (0.19704208544725622126e-2 + (0.15109836875625443935e-4 + (0.10567036667675984067e-6 + (0.66904168640019354565e-9 + (0.37946171850824333014e-11 + 0.18971959040000000000e-13 * t) * t) * t) * t) * t) * t;
}
case 42: {
double t = 2*y100 - 85;
return 0.10255677889470089531e0 + (0.20321499629472857418e-2 + (0.15760224242962179564e-4 + (0.11117756071353507391e-6 + (0.70814785110097658502e-9 + (0.40292553276632563925e-11 + 0.20145143075555555556e-13 * t) * t) * t) * t) * t) * t;
}
case 43: {
double t = 2*y100 - 87;
return 0.10668502059865093318e0 + (0.20965479776148731610e-2 + (0.16444612377624983565e-4 + (0.11700717962026152749e-6 + (0.74967203250938418991e-9 + (0.42783716186085922176e-11 + 0.21385479360000000000e-13 * t) * t) * t) * t) * t) * t;
}
case 44: {
double t = 2*y100 - 89;
return 0.11094484319386444474e0 + (0.21637548491908170841e-2 + (0.17164995035719657111e-4 + (0.12317915750735938089e-6 + (0.79376309831499633734e-9 + (0.45427901763106353914e-11 + 0.22696025653333333333e-13 * t) * t) * t) * t) * t) * t;
}
case 45: {
double t = 2*y100 - 91;
return 0.11534201115268804714e0 + (0.22339187474546420375e-2 + (0.17923489217504226813e-4 + (0.12971465288245997681e-6 + (0.84057834180389073587e-9 + (0.48233721206418027227e-11 + 0.24079890062222222222e-13 * t) * t) * t) * t) * t) * t;
}
case 46: {
double t = 2*y100 - 93;
return 0.11988259392684094740e0 + (0.23071965691918689601e-2 + (0.18722342718958935446e-4 + (0.13663611754337957520e-6 + (0.89028385488493287005e-9 + (0.51210161569225846701e-11 + 0.25540227111111111111e-13 * t) * t) * t) * t) * t) * t;
}
case 47: {
double t = 2*y100 - 95;
return 0.12457298393509812907e0 + (0.23837544771809575380e-2 + (0.19563942105711612475e-4 + (0.14396736847739470782e-6 + (0.94305490646459247016e-9 + (0.54366590583134218096e-11 + 0.27080225920000000000e-13 * t) * t) * t) * t) * t) * t;
}
case 48: {
double t = 2*y100 - 97;
return 0.12941991566142438816e0 + (0.24637684719508859484e-2 + (0.20450821127475879816e-4 + (0.15173366280523906622e-6 + (0.99907632506389027739e-9 + (0.57712760311351625221e-11 + 0.28703099555555555556e-13 * t) * t) * t) * t) * t) * t;
}
case 49: {
double t = 2*y100 - 99;
return 0.13443048593088696613e0 + (0.25474249981080823877e-2 + (0.21385669591362915223e-4 + (0.15996177579900443030e-6 + (0.10585428844575134013e-8 + (0.61258809536787882989e-11 + 0.30412080142222222222e-13 * t) * t) * t) * t) * t) * t;
}
case 50: {
double t = 2*y100 - 101;
return 0.13961217543434561353e0 + (0.26349215871051761416e-2 + (0.22371342712572567744e-4 + (0.16868008199296822247e-6 + (0.11216596910444996246e-8 + (0.65015264753090890662e-11 + 0.32210394506666666666e-13 * t) * t) * t) * t) * t) * t;
}
case 51: {
double t = 2*y100 - 103;
return 0.14497287157673800690e0 + (0.27264675383982439814e-2 + (0.23410870961050950197e-4 + (0.17791863939526376477e-6 + (0.11886425714330958106e-8 + (0.68993039665054288034e-11 + 0.34101266222222222221e-13 * t) * t) * t) * t) * t) * t;
}
case 52: {
double t = 2*y100 - 105;
return 0.15052089272774618151e0 + (0.28222846410136238008e-2 + (0.24507470422713397006e-4 + (0.18770927679626136909e-6 + (0.12597184587583370712e-8 + (0.73203433049229821618e-11 + 0.36087889048888888890e-13 * t) * t) * t) * t) * t) * t;
}
case 53: {
double t = 2*y100 - 107;
return 0.15626501395774612325e0 + (0.29226079376196624949e-2 + (0.25664553693768450545e-4 + (0.19808568415654461964e-6 + (0.13351257759815557897e-8 + (0.77658124891046760667e-11 + 0.38173420035555555555e-13 * t) * t) * t) * t) * t) * t;
}
case 54: {
double t = 2*y100 - 109;
return 0.16221449434620737567e0 + (0.30276865332726475672e-2 + (0.26885741326534564336e-4 + (0.20908350604346384143e-6 + (0.14151148144240728728e-8 + (0.82369170665974313027e-11 + 0.40360957457777777779e-13 * t) * t) * t) * t) * t) * t;
}
case 55: {
double t = 2*y100 - 111;
return 0.16837910595412130659e0 + (0.31377844510793082301e-2 + (0.28174873844911175026e-4 + (0.22074043807045782387e-6 + (0.14999481055996090039e-8 + (0.87348993661930809254e-11 + 0.42653528977777777779e-13 * t) * t) * t) * t) * t) * t;
}
case 56: {
double t = 2*y100 - 113;
return 0.17476916455659369953e0 + (0.32531815370903068316e-2 + (0.29536024347344364074e-4 + (0.23309632627767074202e-6 + (0.15899007843582444846e-8 + (0.92610375235427359475e-11 + 0.45054073102222222221e-13 * t) * t) * t) * t) * t) * t;
}
case 57: {
double t = 2*y100 - 115;
return 0.18139556223643701364e0 + (0.33741744168096996041e-2 + (0.30973511714709500836e-4 + (0.24619326937592290996e-6 + (0.16852609412267750744e-8 + (0.98166442942854895573e-11 + 0.47565418097777777779e-13 * t) * t) * t) * t) * t) * t;
}
case 58: {
double t = 2*y100 - 117;
return 0.18826980194443664549e0 + (0.35010775057740317997e-2 + (0.32491914440014267480e-4 + (0.26007572375886319028e-6 + (0.17863299617388376116e-8 + (0.10403065638343878679e-10 + 0.50190265831111111110e-13 * t) * t) * t) * t) * t) * t;
}
case 59: {
double t = 2*y100 - 119;
return 0.19540403413693967350e0 + (0.36342240767211326315e-2 + (0.34096085096200907289e-4 + (0.27479061117017637474e-6 + (0.18934228504790032826e-8 + (0.11021679075323598664e-10 + 0.52931171733333333334e-13 * t) * t) * t) * t) * t) * t;
}
case 60: {
double t = 2*y100 - 121;
return 0.20281109560651886959e0 + (0.37739673859323597060e-2 + (0.35791165457592409054e-4 + (0.29038742889416172404e-6 + (0.20068685374849001770e-8 + (0.11673891799578381999e-10 + 0.55790523093333333334e-13 * t) * t) * t) * t) * t) * t;
}
case 61: {
double t = 2*y100 - 123;
return 0.21050455062669334978e0 + (0.39206818613925652425e-2 + (0.37582602289680101704e-4 + (0.30691836231886877385e-6 + (0.21270101645763677824e-8 + (0.12361138551062899455e-10 + 0.58770520160000000000e-13 * t) * t) * t) * t) * t) * t;
}
case 62: {
double t = 2*y100 - 125;
return 0.21849873453703332479e0 + (0.40747643554689586041e-2 + (0.39476163820986711501e-4 + (0.32443839970139918836e-6 + (0.22542053491518680200e-8 + (0.13084879235290858490e-10 + 0.61873153262222222221e-13 * t) * t) * t) * t) * t) * t;
}
case 63: {
double t = 2*y100 - 127;
return 0.22680879990043229327e0 + (0.42366354648628516935e-2 + (0.41477956909656896779e-4 + (0.34300544894502810002e-6 + (0.23888264229264067658e-8 + (0.13846596292818514601e-10 + 0.65100183751111111110e-13 * t) * t) * t) * t) * t) * t;
}
case 64: {
double t = 2*y100 - 129;
return 0.23545076536988703937e0 + (0.44067409206365170888e-2 + (0.43594444916224700881e-4 + (0.36268045617760415178e-6 + (0.25312606430853202748e-8 + (0.14647791812837903061e-10 + 0.68453122631111111110e-13 * t) * t) * t) * t) * t) * t;
}
case 65: {
double t = 2*y100 - 131;
return 0.24444156740777432838e0 + (0.45855530511605787178e-2 + (0.45832466292683085475e-4 + (0.38352752590033030472e-6 + (0.26819103733055603460e-8 + (0.15489984390884756993e-10 + 0.71933206364444444445e-13 * t) * t) * t) * t) * t) * t;
}
case 66: {
double t = 2*y100 - 133;
return 0.25379911500634264643e0 + (0.47735723208650032167e-2 + (0.48199253896534185372e-4 + (0.40561404245564732314e-6 + (0.28411932320871165585e-8 + (0.16374705736458320149e-10 + 0.75541379822222222221e-13 * t) * t) * t) * t) * t) * t;
}
case 67: {
double t = 2*y100 - 135;
return 0.26354234756393613032e0 + (0.49713289477083781266e-2 + (0.50702455036930367504e-4 + (0.42901079254268185722e-6 + (0.30095422058900481753e-8 + (0.17303497025347342498e-10 + 0.79278273368888888890e-13 * t) * t) * t) * t) * t) * t;
}
case 68: {
double t = 2*y100 - 137;
return 0.27369129607732343398e0 + (0.51793846023052643767e-2 + (0.53350152258326602629e-4 + (0.45379208848865015485e-6 + (0.31874057245814381257e-8 + (0.18277905010245111046e-10 + 0.83144182364444444445e-13 * t) * t) * t) * t) * t) * t;
}
case 69: {
double t = 2*y100 - 139;
return 0.28426714781640316172e0 + (0.53983341916695141966e-2 + (0.56150884865255810638e-4 + (0.48003589196494734238e-6 + (0.33752476967570796349e-8 + (0.19299477888083469086e-10 + 0.87139049137777777779e-13 * t) * t) * t) * t) * t) * t;
}
case 70: {
double t = 2*y100 - 141;
return 0.29529231465348519920e0 + (0.56288077305420795663e-2 + (0.59113671189913307427e-4 + (0.50782393781744840482e-6 + (0.35735475025851713168e-8 + (0.20369760937017070382e-10 + 0.91262442613333333334e-13 * t) * t) * t) * t) * t) * t;
}
case 71: {
double t = 2*y100 - 143;
return 0.30679050522528838613e0 + (0.58714723032745403331e-2 + (0.62248031602197686791e-4 + (0.53724185766200945789e-6 + (0.37827999418960232678e-8 + (0.21490291930444538307e-10 + 0.95513539182222222221e-13 * t) * t) * t) * t) * t) * t;
}
case 72: {
double t = 2*y100 - 145;
return 0.31878680111173319425e0 + (0.61270341192339103514e-2 + (0.65564012259707640976e-4 + (0.56837930287837738996e-6 + (0.40035151353392378882e-8 + (0.22662596341239294792e-10 + 0.99891109760000000000e-13 * t) * t) * t) * t) * t) * t;
}
case 73: {
double t = 2*y100 - 147;
return 0.33130773722152622027e0 + (0.63962406646798080903e-2 + (0.69072209592942396666e-4 + (0.60133006661885941812e-6 + (0.42362183765883466691e-8 + (0.23888182347073698382e-10 + 0.10439349811555555556e-12 * t) * t) * t) * t) * t) * t;
}
case 74: {
double t = 2*y100 - 149;
return 0.34438138658041336523e0 + (0.66798829540414007258e-2 + (0.72783795518603561144e-4 + (0.63619220443228800680e-6 + (0.44814499336514453364e-8 + (0.25168535651285475274e-10 + 0.10901861383111111111e-12 * t) * t) * t) * t) * t) * t;
}
case 75: {
double t = 2*y100 - 151;
return 0.35803744972380175583e0 + (0.69787978834882685031e-2 + (0.76710543371454822497e-4 + (0.67306815308917386747e-6 + (0.47397647975845228205e-8 + (0.26505114141143050509e-10 + 0.11376390933333333333e-12 * t) * t) * t) * t) * t) * t;
}
case 76: {
double t = 2*y100 - 153;
return 0.37230734890119724188e0 + (0.72938706896461381003e-2 + (0.80864854542670714092e-4 + (0.71206484718062688779e-6 + (0.50117323769745883805e-8 + (0.27899342394100074165e-10 + 0.11862637614222222222e-12 * t) * t) * t) * t) * t) * t;
}
case 77: {
double t = 2*y100 - 155;
return 0.38722432730555448223e0 + (0.76260375162549802745e-2 + (0.85259785810004603848e-4 + (0.75329383305171327677e-6 + (0.52979361368388119355e-8 + (0.29352606054164086709e-10 + 0.12360253370666666667e-12 * t) * t) * t) * t) * t) * t;
}
case 78: {
double t = 2*y100 - 157;
return 0.40282355354616940667e0 + (0.79762880915029728079e-2 + (0.89909077342438246452e-4 + (0.79687137961956194579e-6 + (0.55989731807360403195e-8 + (0.30866246101464869050e-10 + 0.12868841946666666667e-12 * t) * t) * t) * t) * t) * t;
}
case 79: {
double t = 2*y100 - 159;
return 0.41914223158913787649e0 + (0.83456685186950463538e-2 + (0.94827181359250161335e-4 + (0.84291858561783141014e-6 + (0.59154537751083485684e-8 + (0.32441553034347469291e-10 + 0.13387957943111111111e-12 * t) * t) * t) * t) * t) * t;
}
case 80: {
double t = 2*y100 - 161;
return 0.43621971639463786896e0 + (0.87352841828289495773e-2 + (0.10002929142066799966e-3 + (0.89156148280219880024e-6 + (0.62480008150788597147e-8 + (0.34079760983458878910e-10 + 0.13917107176888888889e-12 * t) * t) * t) * t) * t) * t;
}
case 81: {
double t = 2*y100 - 163;
return 0.45409763548534330981e0 + (0.91463027755548240654e-2 + (0.10553137232446167258e-3 + (0.94293113464638623798e-6 + (0.65972492312219959885e-8 + (0.35782041795476563662e-10 + 0.14455745872000000000e-12 * t) * t) * t) * t) * t) * t;
}
case 82: {
double t = 2*y100 - 165;
return 0.47282001668512331468e0 + (0.95799574408860463394e-2 + (0.11135019058000067469e-3 + (0.99716373005509038080e-6 + (0.69638453369956970347e-8 + (0.37549499088161345850e-10 + 0.15003280712888888889e-12 * t) * t) * t) * t) * t) * t;
}
case 83: {
double t = 2*y100 - 167;
return 0.49243342227179841649e0 + (0.10037550043909497071e-1 + (0.11750334542845234952e-3 + (0.10544006716188967172e-5 + (0.73484461168242224872e-8 + (0.39383162326435752965e-10 + 0.15559069118222222222e-12 * t) * t) * t) * t) * t) * t;
}
case 84: {
double t = 2*y100 - 169;
return 0.51298708979209258326e0 + (0.10520454564612427224e-1 + (0.12400930037494996655e-3 + (0.11147886579371265246e-5 + (0.77517184550568711454e-8 + (0.41283980931872622611e-10 + 0.16122419680000000000e-12 * t) * t) * t) * t) * t) * t;
}
case 85: {
double t = 2*y100 - 171;
return 0.53453307979101369843e0 + (0.11030120618800726938e-1 + (0.13088741519572269581e-3 + (0.11784797595374515432e-5 + (0.81743383063044825400e-8 + (0.43252818449517081051e-10 + 0.16692592640000000000e-12 * t) * t) * t) * t) * t) * t;
}
case 86: {
double t = 2*y100 - 173;
return 0.55712643071169299478e0 + (0.11568077107929735233e-1 + (0.13815797838036651289e-3 + (0.12456314879260904558e-5 + (0.86169898078969313597e-8 + (0.45290446811539652525e-10 + 0.17268801084444444444e-12 * t) * t) * t) * t) * t) * t;
}
case 87: {
double t = 2*y100 - 175;
return 0.58082532122519320968e0 + (0.12135935999503877077e-1 + (0.14584223996665838559e-3 + (0.13164068573095710742e-5 + (0.90803643355106020163e-8 + (0.47397540713124619155e-10 + 0.17850211608888888889e-12 * t) * t) * t) * t) * t) * t;
}
case 88: {
double t = 2*y100 - 177;
return 0.60569124025293375554e0 + (0.12735396239525550361e-1 + (0.15396244472258863344e-3 + (0.13909744385382818253e-5 + (0.95651595032306228245e-8 + (0.49574672127669041550e-10 + 0.18435945564444444444e-12 * t) * t) * t) * t) * t) * t;
}
case 89: {
double t = 2*y100 - 179;
return 0.63178916494715716894e0 + (0.13368247798287030927e-1 + (0.16254186562762076141e-3 + (0.14695084048334056083e-5 + (0.10072078109604152350e-7 + (0.51822304995680707483e-10 + 0.19025081422222222222e-12 * t) * t) * t) * t) * t) * t;
}
case 90: {
double t = 2*y100 - 181;
return 0.65918774689725319200e0 + (0.14036375850601992063e-1 + (0.17160483760259706354e-3 + (0.15521885688723188371e-5 + (0.10601827031535280590e-7 + (0.54140790105837520499e-10 + 0.19616655146666666667e-12 * t) * t) * t) * t) * t) * t;
}
case 91: {
double t = 2*y100 - 183;
return 0.68795950683174433822e0 + (0.14741765091365869084e-1 + (0.18117679143520433835e-3 + (0.16392004108230585213e-5 + (0.11155116068018043001e-7 + (0.56530360194925690374e-10 + 0.20209663662222222222e-12 * t) * t) * t) * t) * t) * t;
}
case 92: {
double t = 2*y100 - 185;
return 0.71818103808729967036e0 + (0.15486504187117112279e-1 + (0.19128428784550923217e-3 + (0.17307350969359975848e-5 + (0.11732656736113607751e-7 + (0.58991125287563833603e-10 + 0.20803065333333333333e-12 * t) * t) * t) * t) * t) * t;
}
case 93: {
double t = 2*y100 - 187;
return 0.74993321911726254661e0 + (0.16272790364044783382e-1 + (0.20195505163377912645e-3 + (0.18269894883203346953e-5 + (0.12335161021630225535e-7 + (0.61523068312169087227e-10 + 0.21395783431111111111e-12 * t) * t) * t) * t) * t) * t;
}
case 94: {
double t = 2*y100 - 189;
return 0.78330143531283492729e0 + (0.17102934132652429240e-1 + (0.21321800585063327041e-3 + (0.19281661395543913713e-5 + (0.12963340087354341574e-7 + (0.64126040998066348872e-10 + 0.21986708942222222222e-12 * t) * t) * t) * t) * t) * t;
}
case 95: {
double t = 2*y100 - 191;
return 0.81837581041023811832e0 + (0.17979364149044223802e-1 + (0.22510330592753129006e-3 + (0.20344732868018175389e-5 + (0.13617902941839949718e-7 + (0.66799760083972474642e-10 + 0.22574701262222222222e-12 * t) * t) * t) * t) * t) * t;
}
case 96: {
double t = 2*y100 - 193;
return 0.85525144775685126237e0 + (0.18904632212547561026e-1 + (0.23764237370371255638e-3 + (0.21461248251306387979e-5 + (0.14299555071870523786e-7 + (0.69543803864694171934e-10 + 0.23158593688888888889e-12 * t) * t) * t) * t) * t) * t;
}
case 97: {
double t = 2*y100 - 195;
return 0.89402868170849933734e0 + (0.19881418399127202569e-1 + (0.25086793128395995798e-3 + (0.22633402747585233180e-5 + (0.15008997042116532283e-7 + (0.72357609075043941261e-10 + 0.23737194737777777778e-12 * t) * t) * t) * t) * t) * t;
}
case 98: {
double t = 2*y100 - 197;
return 0.93481333942870796363e0 + (0.20912536329780368893e-1 + (0.26481403465998477969e-3 + (0.23863447359754921676e-5 + (0.15746923065472184451e-7 + (0.75240468141720143653e-10 + 0.24309291271111111111e-12 * t) * t) * t) * t) * t) * t;
}
case 99: {
double t = 2*y100 - 199;
return 0.97771701335885035464e0 + (0.22000938572830479551e-1 + (0.27951610702682383001e-3 + (0.25153688325245314530e-5 + (0.16514019547822821453e-7 + (0.78191526829368231251e-10 + 0.24873652355555555556e-12 * t) * t) * t) * t) * t) * t;
}
}
/* we only get here if y = 1, i.e. |x| < 4*eps, in which case
* erfcx is within 1e-15 of 1.. */
return 1.0;
} /* erfcx_y100 */
/* optimizer friendly implementation of exp2(x).
*
* strategy:
*
* split argument into an integer part and a fraction:
* ipart = floor(x+0.5);
* fpart = x - ipart;
*
* compute exp2(ipart) from setting the ieee754 exponent
* compute exp2(fpart) using a pade' approximation for x in [-0.5;0.5[
*
* the result becomes: exp2(x) = exp2(ipart) * exp2(fpart)
*/
/* IEEE 754 double precision floating point data manipulation */
typedef union
{
double f;
uint64_t u;
struct {int32_t i0,i1;} s;
} udi_t;
static const double fm_exp2_q[] = {
/* 1.00000000000000000000e0, */
2.33184211722314911771e2,
4.36821166879210612817e3
};
static const double fm_exp2_p[] = {
2.30933477057345225087e-2,
2.02020656693165307700e1,
1.51390680115615096133e3
};
double MathSpecialKokkos::exp2_x86(double x)
{
double ipart, fpart, px, qx;
udi_t epart;
ipart = floor(x+0.5);
fpart = x - ipart;
epart.s.i0 = 0;
epart.s.i1 = (((int) ipart) + 1023) << 20;
x = fpart*fpart;
px = fm_exp2_p[0];
px = px*x + fm_exp2_p[1];
qx = x + fm_exp2_q[0];
px = px*x + fm_exp2_p[2];
qx = qx*x + fm_exp2_q[1];
px = px * fpart;
x = 1.0 + 2.0*(px/(qx-px));
return epart.f*x;
}

100
src/KOKKOS/math_special_kokkos.h Normal file
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/* -*- 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.
------------------------------------------------------------------------- */
#ifndef LMP_MATH_SPECIAL_KOKKOS_H
#define LMP_MATH_SPECIAL_KOKKOS_H
#include <math.h>
#include "kokkos_type.h"
namespace LAMMPS_NS {
namespace MathSpecialKokkos {
// support function for scaled error function complement
extern double erfcx_y100(const double y100);
// fast 2**x function without argument checks for little endian CPUs
extern double exp2_x86(double x);
// scaled error function complement exp(x*x)*erfc(x) for coul/long styles
static inline double my_erfcx(const double x)
{
if (x >= 0.0) return erfcx_y100(400.0/(4.0+x));
else return 2.0*exp(x*x) - erfcx_y100(400.0/(4.0-x));
}
// exp(-x*x) for coul/long styles
static inline double expmsq(double x)
{
x *= x;
x *= 1.4426950408889634074; // log_2(e)
#if defined(__BYTE_ORDER__)
#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__
return (x < 1023.0) ? exp2_x86(-x) : 0.0;
#endif
#endif
return (x < 1023.0) ? exp2(-x) : 0.0;
}
// x**2, use instead of pow(x,2.0)
KOKKOS_INLINE_FUNCTION
static double square(const double &x) { return x*x; }
// x**3, use instead of pow(x,3.0)
KOKKOS_INLINE_FUNCTION
static double cube(const double &x) { return x*x*x; }
// return -1.0 for odd n, 1.0 for even n, like pow(-1.0,n)
KOKKOS_INLINE_FUNCTION
static double powsign(const int n) { return (n & 1) ? -1.0 : 1.0; }
// optimized version of pow(x,n) with n being integer
// up to 10x faster than pow(x,y)
KOKKOS_INLINE_FUNCTION
static double powint(const double &x, const int n) {
double yy,ww;
if (x == 0.0) return 0.0;
int nn = (n > 0) ? n : -n;
ww = x;
for (yy = 1.0; nn != 0; nn >>= 1, ww *=ww)
if (nn & 1) yy *= ww;
return (n > 0) ? yy : 1.0/yy;
}
// optimized version of (sin(x)/x)**n with n being a _positive_ integer
KOKKOS_INLINE_FUNCTION
static double powsinxx(const double &x, int n) {
double yy,ww;
if (x == 0.0) return 1.0;
ww = sin(x)/x;
for (yy = 1.0; n != 0; n >>= 1, ww *=ww)
if (n & 1) yy *= ww;
return yy;
}
}
}
#endif

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