more conversion of parsed-literal to code-block and a bunch of other issues

constants so that the value can be evaluated and may change over the

course of a run.  This is typically done with the syntax *v\_name* for a

parameter, where name is the name of the variable. On the other hand,

immediate variable expansion with the syntax $\ *name* is performed while

immediate variable expansion with the syntax ${name} is performed while

reading the input and before parsing commands,

.. note::

determine the number of hardware threads available. On Linux systems,

this information can normally be obtained with:

.. parsed-literal::

.. code-block:: bash

   cat /proc/cpuinfo

recent installations of Intel Parallel Studio, the process can be as

simple as:

.. parsed-literal::

.. code-block:: bash

   make yes-user-intel

   source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh

Examples (see documentation for your MPI/Machine for differences in

launching MPI applications):

.. parsed-literal::

.. code-block:: bash

   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

the :doc:`package intel <package>` command to the top of the input

script. For the second example above, this would be:

.. parsed-literal::

.. code-block:: LAMMPS

   package intel 0 omp 2 mode double

To enable the USER-INTEL package only for individual styles, you can

add an "intel" suffix to the individual style, e.g.:

.. parsed-literal::

.. code-block:: LAMMPS

   pair_style lj/cut/intel 2.5

Here is a quick overview of how to use the KOKKOS package

for CPU acceleration, assuming one or more 16-core nodes.

.. parsed-literal::

.. code-block:: bash

   mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -in in.lj        # 1 node, 16 MPI tasks/node, no multi-threading

   mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj  # 2 nodes, 1 MPI task/node, 16 threads/task

   page for details and default settings. Experimenting with its options

   can provide a speed-up for specific calculations. For example:

.. parsed-literal::

.. code-block:: bash

   mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj       # Newton on, Half neighbor list, non-threaded comm

Examples of mpirun commands that follow these rules are shown below.

.. parsed-literal::

.. code-block:: bash

   Intel KNL node with 68 cores (272 threads/node via 4x hardware threading):

   # Running on an Intel KNL node with 68 cores (272 threads/node via 4x hardware threading):

   mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj      # 1 node, 64 MPI tasks/node, 4 threads/task

   mpirun -np 66 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj      # 1 node, 66 MPI tasks/node, 4 threads/task

   mpirun -np 32 lmp_kokkos_phi -k on t 8 -sf kk -in in.lj      # 1 node, 32 MPI tasks/node, 8 threads/task

   details and default settings. Experimenting with its options can provide

   a speed-up for specific calculations. For example:

.. parsed-literal::

.. code-block:: bash

   mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax      #  Newton on, half neighbor list, threaded comm

   mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton off neigh full comm no -in in.lj      # Newton off, full neighbor list, non-threaded comm

Here are examples of how to use the KOKKOS package for GPUs, assuming

one or more nodes, each with two GPUs:

.. parsed-literal::

.. code-block:: bash

   mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj          # 1 node,   2 MPI tasks/node, 2 GPUs/node

   mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj  # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total)

   default settings. Experimenting with its options can provide a speed-up

   for specific calculations. For example:

.. parsed-literal::

.. code-block:: bash

   mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighbor list, set binsize = neighbor ghost cutoff

You can use the :doc:`suffix kk <suffix>` command, or you can explicitly add a

"kk" suffix to individual styles in your input script, e.g.

.. parsed-literal::

.. code-block:: LAMMPS

   pair_style lj/cut/kk 2.5

KOKKOS\_DEVICES variable must include both "Cuda" and "OpenMP", as is

the case for /src/MAKE/OPTIONS/Makefile.kokkos\_cuda\_mpi

.. parsed-literal::

.. code-block:: bash

   KOKKOS_DEVICES=Cuda,OpenMP

For example, the command to run with 1 GPU and 8 OpenMP threads is then:

.. parsed-literal::

.. code-block:: bash

   mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk

Examples

""""""""

.. code-block:: LAMMPS

   compute 1 all dpd/atom

Description

Examples

""""""""

.. parsed-literal::

.. code-block:: LAMMPS

   dump myDump all atom 100 dump.atom

   dump myDump all atom/mpiio 100 dump.atom.mpiio

   dump myDump all atom/gz 100 dump.atom.gz

   dump 2 subgroup atom 50 dump.run.bin

   dump 2 subgroup atom 50 dump.run.mpiio.bin

   dump 4a all custom 100 dump.myforce.\* id type x y vx fx

   dump 4a all custom 100 dump.myforce.* id type x y vx fx

   dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke

   dump 4b flow custom 100 dump.%.myforce id type c_myF[\*] v_ke

   dump 2 inner cfg 10 dump.snap.\*.cfg mass type xs ys zs vx vy vz

   dump snap all cfg 100 dump.config.\*.cfg mass type xs ys zs id type c_Stress[2]

   dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz

   dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]

   dump 1 all xtc 1000 file.xtc

Description

Using MPI-IO requires two steps.  First, build LAMMPS with its MPIIO

package installed, e.g.

.. parsed-literal::

.. code-block:: bash

   make yes-mpiio    # installs the MPIIO package

   make mpi          # build LAMMPS for your platform

equivalent, since the :doc:`compute stress/atom <compute_stress_atom>`

command creates a per-atom array with 6 columns:

.. parsed-literal::

.. code-block:: LAMMPS

   compute myPress all stress/atom NULL

   dump 2 all custom 100 tmp.dump id myPress[\*]

   dump 2 all custom 100 tmp.dump id myPress[*]

   dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] &

                                     myPress[4] myPress[5] myPress[6]

Here is an example of how to dump bond info for a system, including

the distance and energy of each bond:

.. parsed-literal::

.. code-block:: LAMMPS

   compute 1 all property/local batom1 batom2 btype

   compute 2 all bond/local dist eng