Merge pull request #19 from akohlmey/clean-up-docs-for-sphinx

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 <span class="xref doc">fix ave/spatial</span> command.</p>

the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> 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

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 <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>

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>

<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 <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

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

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

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 <span class="xref doc">fix ave/spatial</span> command, which determines

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

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

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 <span class="xref doc">fix ave/spatial</span> command.

monitored with the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> 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

<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> and <span class="xref doc">atom swapping</span></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><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>

<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>, <span class="xref doc">compute damage</span>,

<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 internal" href="pair_peri.html"><span class="doc">pair_style peri/pmb</span></a>, examples/peri</p>

<hr class="docutils" />

</div>

<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 <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>

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>

<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

</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>, <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>

<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>

<hr class="docutils" />

</div>

<div class="section" id="shock-package">

<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>, <span class="xref doc">compute snad/atom</span>,

<span class="xref doc">compute snav/atom</span>, 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>, <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>

<hr class="docutils" />

</div>

<div class="section" id="srd-package">

<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><span class="xref doc">compute</span></td>

<td><a class="reference internal" href="compute_tally.html"><span class="doc">compute XXX/tally</span></a></td>

<td>USER/tally</td>

<td><ul class="first last simple">

<li></li>

<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><span class="xref doc">compute custom/vtk</span></td>

<td><a class="reference internal" href="dump_custom_vtk.html"><span class="doc">compute custom/vtk</span></a></td>

<td><ul class="first last simple">

<li></li>

</ul>

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, <span class="xref doc">fix awpmd/cut</span>, examples/USER/awpmd</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>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" />

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

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>

<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>

<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>

<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

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><span class="xref std std-ref">Section_accelerate</span></p>

<p><a class="reference internal" href="Section_accelerate.html#acc-3"><span class="std std-ref">Section_accelerate</span></a></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

other programs that use them) without having to recompile the

application itself.</p>

<p>See this doc page to get started:</p>

<p><span class="xref std std-ref">dump molfile</span></p>

<p><a class="reference internal" href="dump_molfile.html"><span class="doc">dump molfile</span></a></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" />

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><span class="xref std std-ref">Section_accelerate</span></p>

<p><a class="reference internal" href="Section_accelerate.html#acc-3"><span class="std std-ref">Section_accelerate</span></a></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

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 <span class="xref std std-ref">Section 5.8</span>.</p>

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>

<ul class="simple">

<li>d or device</li>

<li>g or gpus</li>

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 <span class="xref std std-ref">this section</span>.</p>

given in <a class="reference internal" href="Section_accelerate.html#acc-3"><span class="std std-ref">this section</span></a>.</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