Commit 4f0540b3 authored by iafoss's avatar iafoss
Browse files

update

parent 9c51bb6c

doc/src/Packages_details.rst

+59 −234
Original line number Diff line number Diff line
@@ -10,7 +10,7 @@ scripts, and pictures/movies (if available) that illustrate use of the 
package.



The majority of packages can be included in a LAMMPS build with a

single setting (-D PGK\_NAME for CMake) or command ("make yes-name" for

single setting (-D PGK_NAME for CMake) or command ("make yes-name" for

make).  See the :doc:`Build package <Build_package>` doc page for more

info.  A few packages may require additional steps; this is indicated

in the descriptions below.  The :doc:`Build extras <Build_extras>` doc
@@ -60,7 +60,6 @@ page gives those details. 
   * :ref:`SRD <PKG-SRD>`

   * :ref:`VORONOI <PKG-VORONOI>`





.. table_from_list::

   :columns: 6
@@ -81,7 +80,7 @@ page gives those details. 
   * :ref:`USER-LB <PKG-USER-LB>`

   * :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`

   * :ref:`USER-MEAMC <PKG-USER-MEAMC>`

   * :ref:`USER-MESO <PKG-USER-MESO>`

   * :ref:`USER-MESODPD <PKG-USER-MESODPD>`

   * :ref:`USER-MESONT <PKG-USER-MESONT>`

   * :ref:`USER-MGPT <PKG-USER-MGPT>`

   * :ref:`USER-MISC <PKG-USER-MISC>`
@@ -107,10 +106,8 @@ page gives those details. 
   * :ref:`USER-VTK <PKG-USER-VTK>`

   * :ref:`USER-YAFF <PKG-USER-YAFF>`





----------





.. _PKG-ASPHERE:



ASPHERE package
@@ -127,17 +124,15 @@ particle models including ellipsoids, 2d lines, and 3d triangles. 
* :doc:`Howto spherical <Howto_spherical>`

* :doc:`pair_style gayberne <pair_gayberne>`

* :doc:`pair_style resquared <pair_resquared>`

* `doc/PDF/pair\_gayberne\_extra.pdf <PDF/pair_gayberne_extra.pdf>`_

* `doc/PDF/pair\_resquared\_extra.pdf <PDF/pair_resquared_extra.pdf>`_

* `doc/PDF/pair_gayberne_extra.pdf <PDF/pair_gayberne_extra.pdf>`_

* `doc/PDF/pair_resquared_extra.pdf <PDF/pair_resquared_extra.pdf>`_

* examples/ASPHERE

* examples/ellipse

* http://lammps.sandia.gov/movies.html#line

* http://lammps.sandia.gov/movies.html#tri



* https://lammps.sandia.gov/movies.html#line

* https://lammps.sandia.gov/movies.html#tri



----------





.. _PKG-BODY:



BODY package
@@ -153,16 +148,14 @@ overview. 
**Supporting info:**



* src/BODY filenames -> commands

* :doc:`Howto\_body <Howto_body>`

* :doc:`Howto_body <Howto_body>`

* :doc:`atom_style body <atom_style>`

* :doc:`fix nve/body <fix_nve_body>`

* :doc:`pair_style body/nparticle <pair_body_nparticle>`

* examples/body





----------





.. _PKG-CLASS2:



CLASS2 package
@@ -182,10 +175,8 @@ CLASS2 molecular force field. 
* :doc:`improper_style class2 <improper_class2>`

* :doc:`pair_style lj/class2 <pair_class2>`





----------





.. _PKG-COLLOID:



COLLOID package
@@ -214,10 +205,8 @@ Higdon's group at UIUC. 
* examples/colloid

* examples/srd





----------





.. _PKG-COMPRESS:



COMPRESS package
@@ -247,10 +236,8 @@ This package has :ref:`specific installation instructions <compress>` on the :do 
* :doc:`dump custom/gz <dump>`

* :doc:`dump xyz/gz <dump>`





----------





.. _PKG-CORESHELL:



CORESHELL package
@@ -277,10 +264,8 @@ this package. 
* :doc:`pair_style lj/cut/coul/long/cs <pair_lj>`

* examples/coreshell





----------





.. _PKG-DIPOLE:



DIPOLE package
@@ -300,10 +285,8 @@ short-range or long-range interactions. 
* :doc:`pair_style lj/long/dipole/long <pair_dipole>`

* examples/dipole





----------





.. _PKG-GPU:



GPU package
@@ -340,12 +323,10 @@ This package has :ref:`specific installation instructions <gpu>` on the :doc:`Bu 
* :doc:`package gpu <package>`

* :doc:`Commands <Commands_all>` pages (:doc:`pair <Commands_pair>`, :doc:`kspace <Commands_kspace>`)

  for styles followed by (g)

* `Benchmarks page <http://lammps.sandia.gov/bench.html>`_ of web site



* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site



----------





.. _PKG-GRANULAR:



GRANULAR package
@@ -368,16 +349,14 @@ potentials. 
* examples/granregion

* examples/pour

* bench/in.chute

* http://lammps.sandia.gov/pictures.html#jamming

* http://lammps.sandia.gov/movies.html#hopper

* http://lammps.sandia.gov/movies.html#dem

* http://lammps.sandia.gov/movies.html#brazil

* http://lammps.sandia.gov/movies.html#granregion



* https://lammps.sandia.gov/pictures.html#jamming

* https://lammps.sandia.gov/movies.html#hopper

* https://lammps.sandia.gov/movies.html#dem

* https://lammps.sandia.gov/movies.html#brazil

* https://lammps.sandia.gov/movies.html#granregion



----------





.. _PKG-KIM:



KIM package
@@ -389,7 +368,7 @@ This package contains a set of commands that serve as a wrapper on the 
`Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_

repository of interatomic models (IMs)

enabling compatible ones to be used in LAMMPS simulations.

This includes :doc:`kim_init and kim\_interactions <kim_commands>`

This includes :doc:`kim_init and kim_interactions <kim_commands>`

commands to select, initialize and instantiate the IM, and a

:doc:`kim_query <kim_commands>` command to perform web queries

for material property predictions of OpenKIM IMs.
@@ -399,7 +378,7 @@ is provided by the :doc:`pair_style kim <pair_kim>` command. 


.. note::



   The command *pair\_style kim* is called by *kim\_interactions* and

   The command *pair_style kim* is called by *kim_interactions* and

   is not recommended to be directly used in input scripts.



To use this package you must have the KIM API library available on your
@@ -414,7 +393,7 @@ The KIM project is led by Ellad Tadmor and Ryan Elliott (U Minnesota) 
and is funded by the `National Science Foundation <https://www.nsf.gov/>`_.



**Authors:** Ryan Elliott (U Minnesota) is the main developer for the KIM

API and the *pair\_style kim* command. Axel Kohlmeyer (Temple U) and

API and the *pair_style kim* command. Axel Kohlmeyer (Temple U) and

Ellad Tadmor (U Minnesota) contributed to the :doc:`kim_commands <kim_commands>`

interface in close collaboration with Ryan Elliott.
@@ -431,10 +410,8 @@ This package has :ref:`specific installation instructions <kim>` on the :doc:`Bu 
* lib/kim/README

* examples/kim





----------





.. _PKG-KOKKOS:



KOKKOS package
@@ -485,12 +462,10 @@ This package has :ref:`specific installation instructions <kokkos>` on the :doc: 
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,

  :doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,

  :doc:`kspace <Commands_kspace>`) for styles followed by (k)

* `Benchmarks page <http://lammps.sandia.gov/bench.html>`_ of web site



* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site



----------





.. _PKG-KSPACE:



KSPACE package
@@ -524,10 +499,8 @@ different FFT options for your LAMPMS build. 
* examples/peptide

* bench/in.rhodo





----------





.. _PKG-LATTE:



LATTE package
@@ -545,8 +518,6 @@ description is given with the :doc:`fix latte <fix_latte>` command. 


.. _latte-home: https://github.com/lanl/LATTE







**Authors:** Christian Negre (LANL) and Steve Plimpton (Sandia).  LATTE

itself is developed at Los Alamos National Laboratory by Marc

Cawkwell, Anders Niklasson, and Christian Negre.
@@ -564,10 +535,8 @@ This package has :ref:`specific installation instructions <latte>` on the :doc:` 
* examples/latte

* `LAMMPS-LATTE tutorial <https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS>`_





----------





.. _PKG-MANYBODY:



MANYBODY package
@@ -590,10 +559,8 @@ A variety of many-body and bond-order potentials. These include 
* examples/vashishta

* bench/in.eam





----------





.. _PKG-MC:



MC package
@@ -615,12 +582,10 @@ bonds, for performing atomic swaps, and performing grand-canonical MC 
* :doc:`fix bond/swap <fix_bond_swap>`

* :doc:`fix gcmc <fix_gcmc>`

* :doc:`pair_style dsmc <pair_dsmc>`

* http://lammps.sandia.gov/movies.html#gcmc



* https://lammps.sandia.gov/movies.html#gcmc



----------





.. _PKG-MESSAGE:



MESSAGE package
@@ -645,10 +610,8 @@ This package has :ref:`specific installation instructions <message>` on the :doc 
* :doc:`server mc <server_mc>`

* examples/message





----------





.. _PKG-MISC:



MISC package
@@ -676,13 +639,11 @@ listing, "ls src/MISC", to see the list of commands. 
* :doc:`fix viscosity <fix_viscosity>`

* examples/KAPPA

* examples/VISCOSITY

* http://lammps.sandia.gov/pictures.html#ttm

* http://lammps.sandia.gov/movies.html#evaporation



* https://lammps.sandia.gov/pictures.html#ttm

* https://lammps.sandia.gov/movies.html#evaporation



----------





.. _PKG-MOLECULE:



MOLECULE package
@@ -713,10 +674,8 @@ force fields, and a TIP4P water model. 
* bench/in.chain

* bench/in.rhodo





----------





.. _PKG-MPIIO:



MPIIO package
@@ -737,10 +696,8 @@ written and read in parallel. 
* :doc:`write_restart <write_restart>`

* :doc:`read_restart <read_restart>`





----------





.. _PKG-mscg:



MSCG package
@@ -753,8 +710,6 @@ Multi-Scale Coarse-Graining (MSCG) model using the open-source `MS-CG library <m 


.. _mscg-home: https://github.com/uchicago-voth/MSCG-release







To use this package you must have the MS-CG library available on your

system.
@@ -773,10 +728,8 @@ This package has :ref:`specific installation instructions <mscg>` on the :doc:`B 
* lib/mscg/README

* examples/mscg





----------





.. _PKG-OPT:



OPT package
@@ -794,7 +747,7 @@ invoked at run time via the "-sf opt" or "-suffix opt" :doc:`command-line switch 
have styles optimized for CPU performance.



**Authors:** James Fischer (High Performance Technologies), David Richie,

and Vincent Natoli (Stone Ridge Technolgy).

and Vincent Natoli (Stone Ridge Technology).



**Install:**
@@ -807,12 +760,10 @@ This package has :ref:`specific installation instructions <opt>` on the :doc:`Bu 
* :doc:`Speed opt <Speed_opt>`

* :doc:`Section 2.6 -sf opt <Run_options>`

* Search the :doc:`pair style <Commands_pair>` page for styles followed by (t)

* `Benchmarks page <http://lammps.sandia.gov/bench.html>`_ of web site



* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site



----------





.. _PKG-PERI:



PERI package
@@ -832,20 +783,18 @@ Foster (UTSA). 
**Supporting info:**



* src/PERI: filenames -> commands

* `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>`_

* `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>`_

* :doc:`atom_style peri <atom_style>`

* :doc:`pair_style peri/\* <pair_peri>`

* :doc:`compute damage/atom <compute_damage_atom>`

* :doc:`compute plasticity/atom <compute_plasticity_atom>`

* examples/peri

* http://lammps.sandia.gov/movies.html#peri



* https://lammps.sandia.gov/movies.html#peri



----------





.. _PKG-POEMS:



POEMS package
@@ -873,10 +822,8 @@ This package has :ref:`specific installation instructions <poems>` on the :doc:` 
* :doc:`fix poems <fix_poems>`

* examples/rigid





----------





.. _PKG-PYTHON:



PYTHON package
@@ -908,10 +855,8 @@ This package has :ref:`specific installation instructions <python>` on the :doc: 
* lib/python/README

* examples/python





----------





.. _PKG-QEQ:



QEQ package
@@ -930,10 +875,8 @@ part of their formulation. 
* examples/qeq

* examples/streitz





----------





.. _PKG-REPLICA:



REPLICA package
@@ -963,10 +906,8 @@ another set. 
* examples/prd

* examples/tad





----------





.. _PKG-RIGID:



RIGID package
@@ -989,13 +930,11 @@ Also several computes which calculate properties of rigid bodies. 
* examples/ASPHERE

* examples/rigid

* bench/in.rhodo

* http://lammps.sandia.gov/movies.html#box

* http://lammps.sandia.gov/movies.html#star



* https://lammps.sandia.gov/movies.html#box

* https://lammps.sandia.gov/movies.html#star



----------





.. _PKG-SHOCK:



SHOCK package
@@ -1016,10 +955,8 @@ a material. 
* examples/hugoniostat

* examples/msst





----------





.. _PKG-SNAP:



SNAP package
@@ -1043,10 +980,8 @@ computes which analyze attributes of the potential. 
* :doc:`compute snav/atom <compute_sna_atom>`

* examples/snap





----------





.. _PKG-SPIN:



SPIN package
@@ -1075,10 +1010,8 @@ the usual manner via MD. Various pair, fix, and compute styles. 
* :doc:`neb/spin <neb_spin>`

* examples/SPIN





----------





.. _PKG-SRD:



SRD package
@@ -1097,14 +1030,12 @@ colloidal particles. 
* :doc:`fix wall/srd <fix_wall_srd>`

* examples/srd

* examples/ASPHERE

* http://lammps.sandia.gov/movies.html#tri

* http://lammps.sandia.gov/movies.html#line

* http://lammps.sandia.gov/movies.html#poly



* https://lammps.sandia.gov/movies.html#tri

* https://lammps.sandia.gov/movies.html#line

* https://lammps.sandia.gov/movies.html#poly



----------





.. _PKG-VORONOI:



VORONOI package
@@ -1119,8 +1050,6 @@ neighbors. 


.. _voro-home: http://math.lbl.gov/voro++







To use this package you must have the Voro++ library available on your

system.
@@ -1140,10 +1069,8 @@ This package has :ref:`specific installation instructions <voronoi>` on the :doc 
* :doc:`compute voronoi/atom <compute_voronoi_atom>`

* examples/voronoi





----------





.. _PKG-USER-ADIOS:



USER-ADIOS package
@@ -1172,11 +1099,8 @@ This package has :ref:`specific installation instructions <user-adios>` on the : 
* :doc:`dump custom/adios <dump_adios>`

* :doc:`read_dump <read_dump>`







----------





.. _PKG-USER-ATC:



USER-ATC package
@@ -1200,12 +1124,10 @@ This package has :ref:`specific installation instructions <user-atc>` on the :do 
* src/USER-ATC/README

* :doc:`fix atc <fix_atc>`

* examples/USER/atc

* http://lammps.sandia.gov/pictures.html#atc



* https://lammps.sandia.gov/pictures.html#atc



----------





.. _PKG-USER-AWPMD:



USER-AWPMD package
@@ -1231,10 +1153,8 @@ This package has :ref:`specific installation instructions <user-awpmd>` on the : 
* :doc:`pair_style awpmd/cut <pair_awpmd>`

* examples/USER/awpmd





----------





.. _PKG-USER-BOCS:



USER-BOCS package
@@ -1266,10 +1186,8 @@ J. Phys. Chem. B. 122, 13, 3363-3377 (2018). 


Example inputs are in the examples/USER/bocs folder.





----------





.. _PKG-USER-CGDNA:



USER-CGDNA package
@@ -1296,10 +1214,8 @@ rigid-body integrators with improved stability. 
* :doc:`bond_style oxrna2/\* <bond_oxdna>`

* :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`





----------





.. _PKG-USER-CGSDK:



USER-CGSDK package
@@ -1321,12 +1237,10 @@ acids. 
* :doc:`pair_style lj/sdk/\* <pair_sdk>`

* :doc:`angle_style sdk <angle_sdk>`

* examples/USER/cgsdk

* http://lammps.sandia.gov/pictures.html#cg



* https://lammps.sandia.gov/pictures.html#cg



----------





.. _PKG-USER-COLVARS:



USER-COLVARS package
@@ -1360,10 +1274,8 @@ This package has :ref:`specific installation instructions <user-colvars>` on the 
* :doc:`fix colvars <fix_colvars>`

* examples/USER/colvars





----------





.. _PKG-USER-PLUMED:



USER-PLUMED package
@@ -1380,9 +1292,7 @@ script by using the :doc:`fix plumed <fix_plumed>` command. 
Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth

Tribello.



.. _PLUMED: http://www.plumed.org





.. _PLUMED: https://www.plumed.org



**Install:**
@@ -1395,10 +1305,8 @@ This package has :ref:`specific installation instructions <user-plumed>` on the 
* :doc:`fix plumed <fix_plumed>`

* examples/USER/plumed





----------





.. _PKG-USER-DIFFRACTION:



USER-DIFFRACTION package
@@ -1419,10 +1327,8 @@ intensities based on kinematic diffraction theory. 
* :doc:`fix saed/vtk <fix_saed_vtk>`

* examples/USER/diffraction





----------





.. _PKG-USER-DPD:



USER-DPD package
@@ -1462,10 +1368,8 @@ Brennan (ARL). 
* :doc:`pair_style multi/lucy/rx <pair_multi_lucy_rx>`

* examples/USER/dpd





----------





.. _PKG-USER-DRUDE:



USER-DRUDE package
@@ -1496,10 +1400,8 @@ Devemy (CNRS), and Agilio Padua (U Blaise Pascal). 
* examples/USER/drude

* tools/drude





----------





.. _PKG-USER-EFF:



USER-EFF package
@@ -1532,12 +1434,10 @@ tools/eff; see its README file. 
* examples/USER/eff

* tools/eff/README

* tools/eff

* http://lammps.sandia.gov/movies.html#eff



* https://lammps.sandia.gov/movies.html#eff



----------





.. _PKG-USER-FEP:



USER-FEP package
@@ -1563,10 +1463,8 @@ for using this package in tools/fep; see its README file. 
* tools/fep/README

* tools/fep





----------





.. _PKG-USER-H5MD:



USER-H5MD package
@@ -1582,8 +1480,6 @@ LAMMPS snapshots in this format. 


.. _HDF5: http://www.hdfgroup.org/HDF5







To use this package you must have the HDF5 library available on your

system.
@@ -1601,10 +1497,8 @@ This package has :ref:`specific installation instructions <user-h5md>` on the :d 
* lib/h5md/README

* :doc:`dump h5md <dump_h5md>`





----------





.. _PKG-USER-INTEL:



USER-INTEL package
@@ -1648,12 +1542,10 @@ This package has :ref:`specific installation instructions <user-intel>` on the : 
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,

  :doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`, :doc:`kspace <Commands_kspace>`) for styles followed by (i)

* src/USER-INTEL/TEST

* `Benchmarks page <http://lammps.sandia.gov/bench.html>`_ of web site



* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site



----------





.. _PKG-USER-LB:



USER-LB package
@@ -1676,10 +1568,8 @@ Ontario). 
* :doc:`fix lb/viscous <fix_lb_viscous>`

* examples/USER/lb





----------





.. _PKG-USER-MGPT:



USER-MGPT package
@@ -1705,10 +1595,8 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. 
* :doc:`pair_style mgpt <pair_mgpt>`

* examples/USER/mgpt





----------





.. _PKG-USER-MISC:



USER-MISC package
@@ -1730,10 +1618,8 @@ src/USER-MISC/README file. 
* one doc page per individual command listed in src/USER-MISC/README

* examples/USER/misc





----------





.. _PKG-USER-MANIFOLD:



USER-MANIFOLD package
@@ -1761,12 +1647,10 @@ Waltham, MA, USA) 
* :doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>`

* :doc:`fix nvt/manifold/rattle <fix_nvt_manifold_rattle>`

* examples/USER/manifold

* http://lammps.sandia.gov/movies.html#manifold



* https://lammps.sandia.gov/movies.html#manifold



----------





.. _PKG-USER-MEAMC:



USER-MEAMC package
@@ -1790,14 +1674,12 @@ Sandia. 
* :doc:`pair_style meam/c <pair_meamc>`

* examples/meamc





----------



.. _PKG-USER-MESODPD:



.. _PKG-USER-MESO:



USER-MESO package

-----------------

USER-MESODPD package

--------------------



**Contents:**
@@ -1813,20 +1695,21 @@ algorithm. 


**Supporting info:**



* src/USER-MESO: filenames -> commands

* src/USER-MESO/README

* src/USER-MESODPD: filenames -> commands

* src/USER-MESODPD/README

* :doc:`atom_style edpd <atom_style>`

* :doc:`pair_style edpd <pair_meso>`

* :doc:`pair_style mdpd <pair_meso>`

* :doc:`pair_style tdpd <pair_meso>`

* :doc:`pair_style edpd <pair_mesodpd>`

* :doc:`pair_style mdpd <pair_mesodpd>`

* :doc:`pair_style tdpd <pair_mesodpd>`

* :doc:`fix mvv/dpd <fix_mvv_dpd>`

* examples/USER/mesodpd

* https://lammps.sandia.gov/movies.html#mesodpd



* examples/USER/meso

* http://lammps.sandia.gov/movies.html#mesodpd





----------





.. _PKG-USER-MESONT:



USER-MESONT package
@@ -1855,10 +1738,8 @@ is provided in the papers listed below. 
* examples/USER/mesont

* tools/mesont





----------





.. _PKG-USER-MOFFF:



USER-MOFFF package
@@ -1877,8 +1758,6 @@ well as the `MOF+ <MOFplus_>`_ website. 


.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF







**Author:** Hendrik Heenen (Technical U of Munich),

Rochus Schmid (Ruhr-University Bochum).
@@ -1892,10 +1771,8 @@ Rochus Schmid (Ruhr-University Bochum). 
* :doc:`improper_style inversion/harmonic <improper_inversion_harmonic>`

* examples/USER/mofff





----------





.. _PKG-USER-MOLFILE:



USER-MOLFILE package
@@ -1936,10 +1813,8 @@ This package has :ref:`specific installation instructions <user-molfile>` on the 
* lib/molfile/README

* :doc:`dump molfile <dump_molfile>`





----------





.. _PKG-USER-NETCDF:



USER-NETCDF package
@@ -1960,20 +1835,11 @@ tools: 


* `Ovito <ovito_>`_ (Ovito supports the AMBER convention and the extensions mentioned above)

* `VMD <vmd-home_>`_

* `AtomEye <atomeye_>`_ (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution)



.. _ovito: http://www.ovito.org







.. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/







.. _atomeye: http://www.libatoms.org







**Author:** Lars Pastewka (Karlsruhe Institute of Technology).



**Install:**
@@ -1987,10 +1853,8 @@ This package has :ref:`specific installation instructions <user-netcdf>` on the 
* lib/netcdf/README

* :doc:`dump netcdf <dump_netcdf>`





----------





.. _PKG-USER-OMP:



USER-OMP package
@@ -2041,12 +1905,10 @@ This package has :ref:`specific installation instructions <user-omp>` on the :do 
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,

  :doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,

  :doc:`kspace <Commands_kspace>`) for styles followed by (o)

* `Benchmarks page <http://lammps.sandia.gov/bench.html>`_ of web site



* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site



----------





.. _PKG-USER-PHONON:



USER-PHONON package
@@ -2062,7 +1924,7 @@ And a :doc:`dynamical_matrix <dynamical_matrix>` as well as a 
and third order tensor from finite differences.



**Authors:** Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"

and Charlie Sievers (UC Davis) for "dynamical\_matrix" and "third\_order"

and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order"



**Supporting info:**
@@ -2073,10 +1935,8 @@ and Charlie Sievers (UC Davis) for "dynamical\_matrix" and "third\_order" 
* :doc:`third_order <third_order>`

* examples/USER/phonon





----------





.. _PKG-USER-PTM:



USER-PTM package
@@ -2092,15 +1952,13 @@ Matching methodology. 


**Supporting info:**



* src/USER-PTM: filenames not starting with ptm\\_ -> commands

* src/USER-PTM: filenames starting with ptm\\_ -> supporting code

* src/USER-PTM: filenames not starting with ptm\_ -> commands

* src/USER-PTM: filenames starting with ptm\_ -> supporting code

* src/USER-PTM/LICENSE

* :doc:`compute ptm/atom <compute_ptm_atom>`





----------





.. _PKG-USER-QMMM:



USER-QMMM package
@@ -2130,7 +1988,6 @@ changes to LAMMPS itself. 


**Authors:** Axel Kohlmeyer (Temple U). Mariella Ippolito and Carlo Cavazzoni (CINECA, Italy)





**Install:**



This package has :ref:`specific installation instructions <user-qmmm>`
@@ -2145,10 +2002,8 @@ on the :doc:`Build extras <Build_extras>` doc page. 
* lib/qmmm/example-ec/README

* lib/qmmm/example-mc/README





----------





.. _PKG-USER-QTB:



USER-QTB package
@@ -2175,10 +2030,8 @@ simulation. 
* :doc:`fix qbmsst <fix_qbmsst>`

* examples/USER/qtb





----------





.. _PKG-USER-QUIP:



USER-QUIP package
@@ -2192,8 +2045,6 @@ developed by the Cambridge University group. 


.. _quip: https://github.com/libAtoms/QUIP







To use this package you must have the QUIP libAtoms library available

on your system.
@@ -2210,10 +2061,8 @@ This package has :ref:`specific installation instructions <user-quip>` on the :d 
* :doc:`pair_style quip <pair_quip>`

* examples/USER/quip





----------





.. _PKG-USER-REACTION:



USER-REACTION package
@@ -2243,10 +2092,8 @@ molecules, and chiral-sensitive reactions. 
* `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_

* disarmmd.org





----------





.. _PKG-USER-REAXC:



USER-REAXC package
@@ -2270,10 +2117,8 @@ for monitoring molecules as bonds are created and destroyed. 
* :doc:`fix reax/c/species <fix_reaxc_species>`

* examples/reax





----------





.. _PKG-USER-SCAFACOS:



USER-SCAFACOS package
@@ -2307,10 +2152,8 @@ This package has :ref:`specific installation instructions <user-scafacos>` on th 
* :doc:`kspace_modify <kspace_modify>`

* examples/USER/scafacos





----------





.. _PKG-USER-SDPD:



USER-SDPD package
@@ -2323,7 +2166,7 @@ is an extension of smoothed particle hydrodynamics (SPH) to mesoscale 
where thermal fluctuations are important (see the

:ref:`USER-SPH package <PKG-USER-SPH>`).

Also two fixes for moving and rigid body integration of SPH/SDPD particles

(particles of atom\_style meso).

(particles of atom_style meso).



**Author:** Morteza Jalalvand (Institute for Advanced Studies in Basic

Sciences, Iran).
@@ -2337,10 +2180,8 @@ Sciences, Iran). 
* :doc:`fix rigid/meso <fix_rigid_meso>`

* examples/USER/sdpd





----------





.. _PKG-USER-SMD:



USER-SMD package
@@ -2373,14 +2214,12 @@ This package has :ref:`specific installation instructions <user-smd>` on the :do 


* src/USER-SMD: filenames -> commands

* src/USER-SMD/README

* doc/PDF/SMD\_LAMMPS\_userguide.pdf

* doc/PDF/SMD_LAMMPS_userguide.pdf

* examples/USER/smd

* http://lammps.sandia.gov/movies.html#smd



* https://lammps.sandia.gov/movies.html#smd



----------





.. _PKG-USER-SMTBQ:



USER-SMTBQ package
@@ -2402,10 +2241,8 @@ Tetot (LAAS-CNRS, France). 
* :doc:`pair_style smtbq <pair_smtbq>`

* examples/USER/smtbq





----------





.. _PKG-USER-SPH:



USER-SPH package
@@ -2434,14 +2271,12 @@ Dynamics, Ernst Mach Institute, Germany). 


* src/USER-SPH: filenames -> commands

* src/USER-SPH/README

* doc/PDF/SPH\_LAMMPS\_userguide.pdf

* doc/PDF/SPH_LAMMPS_userguide.pdf

* examples/USER/sph

* http://lammps.sandia.gov/movies.html#sph



* https://lammps.sandia.gov/movies.html#sph



----------





.. _PKG-USER-TALLY:



USER-TALLY package
@@ -2462,10 +2297,8 @@ stress, etc) about individual interactions. 
* :doc:`compute \*/tally <compute_tally>`

* examples/USER/tally





----------





.. _PKG-USER-UEF:



USER-UEF package
@@ -2490,10 +2323,8 @@ supporting compute styles and an output option. 
* :doc:`dump cfg/uef <dump_cfg_uef>`

* examples/uef





----------





.. _PKG-USER-VTK:



USER-VTK package
@@ -2507,12 +2338,8 @@ other visualization packages. 


.. _vtk: http://www.vtk.org







.. _paraview: http://www.paraview.org







To use this package you must have VTK library available on your

system.
@@ -2529,10 +2356,8 @@ This package has :ref:`specific installation instructions <user-vtk>` on the :do 
* lib/vtk/README

* :doc:`dump vtk <dump_vtk>`





----------





.. _PKG-USER-YAFF:



USER-YAFF package
@@ -2548,8 +2373,8 @@ The expressions and their use are discussed in the following papers 


which discuss the `QuickFF <quickff_>`_ methodology.



.. _vanduyfhuys2015: http://dx.doi.org/10.1002/jcc.23877

.. _vanduyfhuys2018: http://dx.doi.org/10.1002/jcc.25173

.. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877

.. _vanduyfhuys2018: https://doi.org/10.1002/jcc.25173

.. _quickff: http://molmod.github.io/QuickFF

.. _yaff: https://github.com/molmod/yaff

doc/src/Packages_user.rst

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doc/src/compute.rst

+11 −23
Original line number Diff line number Diff line
@@ -6,7 +6,6 @@ compute command 
Syntax

""""""





.. parsed-literal::



   compute ID group-ID style args
@@ -19,8 +18,7 @@ Syntax 
Examples

""""""""





.. parsed-literal::

.. code-block:: LAMMPS



   compute 1 all temp

   compute newtemp flow temp/partial 1 1 0
@@ -43,10 +41,8 @@ various LAMMPS output options, many of which involve computes. 
The ID of a compute can only contain alphanumeric characters and

underscores.





----------





Computes calculate one of three styles of quantities: global,

per-atom, or local.  A global quantity is one or more system-wide

values, e.g. the temperature of the system.  A per-atom quantity is
@@ -76,11 +72,11 @@ discussed below, it can be referenced via the following bracket 
notation, where ID is the ID of the compute:



+-------------+--------------------------------------------+

| c\_ID       | entire scalar, vector, or array            |

| c_ID        | entire scalar, vector, or array            |

+-------------+--------------------------------------------+

| c\_ID[I]    | one element of vector, one column of array |

| c_ID[I]     | one element of vector, one column of array |

+-------------+--------------------------------------------+

| c\_ID[I][J] | one element of array                       |

| c_ID[I][J]  | one element of array                       |

+-------------+--------------------------------------------+



In other words, using one bracket reduces the dimension of the
@@ -92,14 +88,12 @@ vector or array. 
Note that commands and :doc:`variables <variable>` which use compute

quantities typically do not allow for all kinds, e.g. a command may

require a vector of values, not a scalar.  This means there is no

ambiguity about referring to a compute quantity as c\_ID even if it

ambiguity about referring to a compute quantity as c_ID even if it

produces, for example, both a scalar and vector.  The doc pages for

various commands explain the details.





----------





In LAMMPS, the values generated by a compute can be used in several

ways:
@@ -115,7 +109,6 @@ ways: 
  command.  Or the per-atom values can be referenced in an :doc:`atom-style variable <variable>`.

* Local values can be reduced by the :doc:`compute reduce <compute_reduce>` command, or histogrammed by the :doc:`fix ave/histo <fix_ave_histo>` command, or output by the :doc:`dump local <dump>` command.





The results of computes that calculate global quantities can be either

"intensive" or "extensive" values.  Intensive means the value is

independent of the number of atoms in the simulation,
@@ -123,23 +116,20 @@ e.g. temperature. Extensive means the value scales with the number of 
atoms in the simulation, e.g. total rotational kinetic energy.

:doc:`Thermodynamic output <thermo_style>` will normalize extensive

values by the number of atoms in the system, depending on the

"thermo\_modify norm" setting.  It will not normalize intensive values.

"thermo_modify norm" setting.  It will not normalize intensive values.

If a compute value is accessed in another way, e.g. by a

:doc:`variable <variable>`, you may want to know whether it is an

intensive or extensive value.  See the doc page for individual

computes for further info.





----------





LAMMPS creates its own computes internally for thermodynamic output.

Three computes are always created, named "thermo\_temp",

"thermo\_press", and "thermo\_pe", as if these commands had been invoked

Three computes are always created, named "thermo_temp",

"thermo_press", and "thermo_pe", as if these commands had been invoked

in the input script:





.. parsed-literal::

.. code-block:: LAMMPS



   compute thermo_temp all temp

   compute thermo_press all pressure thermo_temp
@@ -166,10 +156,8 @@ Code for new computes can be added to LAMMPS; see the 
:doc:`Modify <Modify>` doc page for details.  The results of their

calculations accessed in the various ways described above.





----------





Each compute style has its own doc page which describes its arguments

and what it does.  Here is an alphabetic list of compute styles

available in LAMMPS.  They are also listed in more compact form on the
@@ -237,7 +225,6 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc 
* :doc:`ke/atom/eff <compute_ke_atom_eff>` - per-atom translational and radial kinetic energy in the electron force field model

* :doc:`ke/eff <compute_ke_eff>` - kinetic energy of a group of nuclei and electrons in the electron force field model

* :doc:`ke/rigid <compute_ke_rigid>` - translational kinetic energy of rigid bodies

* :doc:`mesont <compute_mesont>` - Nanotube bending,stretching, and intertube energies

* :doc:`meso/e/atom <compute_meso_e_atom>` - per-atom internal energy of Smooth-Particle Hydrodynamics atoms

* :doc:`meso/rho/atom <compute_meso_rho_atom>` - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms

* :doc:`meso/t/atom <compute_meso_t_atom>` - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
@@ -251,6 +238,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc 
* :doc:`pair/local <compute_pair_local>` - distance/energy/force of each pairwise interaction

* :doc:`pe <compute_pe>` - potential energy

* :doc:`pe/atom <compute_pe_atom>` - potential energy for each atom

* :doc:`mesont <compute_mesont>` - Nanotube bending,stretching, and intertube energies

* :doc:`pe/mol/tally <compute_tally>` -

* :doc:`pe/tally <compute_tally>` -

* :doc:`plasticity/atom <compute_plasticity_atom>` - Peridynamic plasticity for each atom

doc/src/pair_airebo.rst

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