Update from master

endif()

include(ExternalProject)

set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball")

mark_as_advanced(GTEST_URL)

ExternalProject_Add(googletest

                    GIT_REPOSITORY  https://github.com/google/googletest.git

                    GIT_TAG         release-1.10.0

                    URL ${GTEST_URL}

                    URL_MD5         ecd1fa65e7de707cd5c00bdac56022cd

                    SOURCE_DIR      "${CMAKE_BINARY_DIR}/gtest-src"

                    BINARY_DIR      "${CMAKE_BINARY_DIR}/gtest-build"

                    CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}

.TH LAMMPS "21 July 2020" "2020-07-21"

.TH LAMMPS "24 August 2020" "2020-08-24"

.SH NAME

.B LAMMPS

\- Molecular Dynamics Simulator.

.. _cmake_presets:

CMake presets for installing many packages

""""""""""""""""""""""""""""""""""""""""""

Instead of specifying all the CMake options via the command-line,

CMake allows initializing its settings cache using script files.

   in a single cmake run, or change settings incrementally by running

   cmake with new flags.

**Example:**

Example

"""""""

.. code-block:: bash

   * :doc:`manifoldforce <fix_manifoldforce>`

   * :doc:`meso/move <fix_meso_move>`

   * :doc:`momentum (k) <fix_momentum>`

   * :doc:`momentum/chunk <fix_momentum>`

   * :doc:`move <fix_move>`

   * :doc:`mscg <fix_mscg>`

   * :doc:`msst <fix_msst>`

twice, once on the CPU and once with an offload flag. This allows

LAMMPS to run on the CPU cores and co-processor cores simultaneously.

**Currently Available USER-INTEL Styles:**

Currently Available USER-INTEL Styles

"""""""""""""""""""""""""""""""""""""

* Angle Styles: charmm, harmonic

* Bond Styles: fene, fourier, harmonic

   support computing per-atom stress.  If any compute or fix in your

   input requires it, LAMMPS will abort with an error message.

**Speed-ups to expect:**

Speed-up to expect

"""""""""""""""""""

The speedups will depend on your simulation, the hardware, which

The speedup will depend on your simulation, the hardware, which

styles are used, the number of atoms, and the floating-point

precision mode. Performance improvements are shown compared to

LAMMPS *without using other acceleration packages* as these are

----------

**Accuracy and order of operations:**

Accuracy and order of operations

""""""""""""""""""""""""""""""""

In most molecular dynamics software, parallelization parameters

(# of MPI, OpenMP, and vectorization) can change the results due

----------

**Quick Start for Experienced Users:**

Quick Start for Experienced Users

"""""""""""""""""""""""""""""""""

LAMMPS should be built with the USER-INTEL package installed.

Simulations should be run with 1 MPI task per physical *core*\ ,

----------

**Required hardware/software:**

Required hardware/software

""""""""""""""""""""""""""

When using Intel compilers version 16.0 or later is required.

"Cache" mode can also be used, although the performance might be

slightly lower.

**Notes about Simultaneous Multithreading:**

Notes about Simultaneous Multithreading

"""""""""""""""""""""""""""""""""""""""

Modern CPUs often support Simultaneous Multithreading (SMT). On

Intel processors, this is called Hyper-Threading (HT) technology.

   cat /proc/cpuinfo

**Building LAMMPS with the USER-INTEL package:**

Building LAMMPS with the USER-INTEL package

"""""""""""""""""""""""""""""""""""""""""""

See the :ref:`Build extras <user-intel>` doc page for

instructions.  Some additional details are covered here.

   in most of the example Makefiles is to use "-xHost", however this

   should not be used when cross-compiling.

**Running LAMMPS with the USER-INTEL package:**

Running LAMMPS with the USER-INTEL package

""""""""""""""""""""""""""""""""""""""""""

Running LAMMPS with the USER-INTEL package is similar to normal use

with the exceptions that one should 1) specify that LAMMPS should use

   recommended, especially when running on a machine with Intel

   Hyper-Threading technology disabled.

**Run with the USER-INTEL package from the command line:**

Run with the USER-INTEL package from the command line

"""""""""""""""""""""""""""""""""""""""""""""""""""""

To enable USER-INTEL optimizations for all available styles used in

the input script, the "-sf intel" :doc:`command-line switch <Run_options>` can be used without any requirement for

   mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script                                 # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads

   mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double   # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision

**Or run with the USER-INTEL package by editing an input script:**

Or run with the USER-INTEL package by editing an input script

"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

As an alternative to adding command-line arguments, the input script

can be edited to enable the USER-INTEL package. This requires adding

the input script to enable USER-INTEL styles for the commands that

follow in the input script.

**Tuning for Performance:**

Tuning for Performance

""""""""""""""""""""""

.. note::

consult your system documentation for the best approach to specify

that MPI runs are performed in MCDRAM.

**Tuning for Offload Performance:**

Tuning for Offload Performance

""""""""""""""""""""""""""""""

The default settings for offload should give good performance.

:doc:`run_style respa <run_style>` command; only the "pair" option is

supported.

**References:**

References

""""""""""

* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.

* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <http://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).