forked from lijiext/lammps
2339 lines
73 KiB
Plaintext
2339 lines
73 KiB
Plaintext
"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws -
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"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
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Section"_Section_accelerate.html :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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4. Packages :h3
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This section gives an overview of the add-on optional packages that
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extend LAMMPS functionality. Packages are groups of files that enable
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a specific set of features. For example, force fields for molecular
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systems or granular systems are in packages. You can see the list of
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all packages by typing "make package" from within the src directory of
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the LAMMPS distribution.
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Here are links for two tables below, which list standard and user
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packages.
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4.1 "Standard packages"_#pkg_1
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4.2 "User packages"_#pkg_2 :all(b)
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"Section_start 3"_Section_start.html#start_3 of the manual describes
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the difference between standard packages and user packages. It also
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has general details on how to include/exclude specific packages as
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part of the LAMMPS build process, and on how to build auxiliary
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libraries or modify a machine Makefile if a package requires it.
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Following the two tables below, is a sub-section for each package. It
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has a summary of what the package contains. It has specific
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instructions on how to install it, build or obtain any auxiliary
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library it requires, and any Makefile.machine changes it requires. It
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also lists pointers to examples of its use or documentation provided
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in the LAMMPS distribution. If you want to know the complete list of
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commands that a package adds to LAMMPS, simply list the files in its
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directory, e.g. "ls src/GRANULAR". Source files with names that start
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with compute, fix, pair, bond, etc correspond to command styles with
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the same names.
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NOTE: The USER package sub-sections below are still being filled in,
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as of March 2016.
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Unless otherwise noted below, every package is independent of all the
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others. I.e. any package can be included or excluded in a LAMMPS
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build, independent of all other packages. However, note that some
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packages include commands derived from commands in other packages. If
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the other package is not installed, the derived command from the new
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package will also not be installed when you include the new one.
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E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package
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will not be installed as part of the USER-OMP package if the KSPACE
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package is not also installed, since it contains the pair
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lj/cut/coul/long command. If you later install the KSPACE package and
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the USER-OMP package is already installed, both the pair
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lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.
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:line
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4.1 Standard packages :h4,link(pkg_1)
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The current list of standard packages is as follows. Each package
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name links to a sub-section below with more details.
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Package, Description, Author(s), Doc page, Example, Library
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"ASPHERE"_#ASPHERE, aspherical particles, -, "Section_howto 6.14"_Section_howto.html#howto_14, ellipse, -
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"BODY"_#BODY, body-style particles, -, "body"_body.html, body, -
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"CLASS2"_#CLASS2, class 2 force fields, -, "pair_style lj/class2"_pair_class2.html, -, -
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"COLLOID"_#COLLOID, colloidal particles, Kumar (1), "atom_style colloid"_atom_style.html, colloid, -
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"COMPRESS"_#COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, -
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"CORESHELL"_#CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section_howto 6.25"_Section_howto.html#howto_25, coreshell, -
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"DIPOLE"_#DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -
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"GPU"_#GPU, GPU-enabled styles, Mike Brown (ORNL), "Section accelerate"_accelerate_gpu.html, gpu, lib/gpu
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"GRANULAR"_#GRANULAR, granular systems, -, "Section_howto 6.6"_Section_howto.html#howto_6, pour, -
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"KIM"_#KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM
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"KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Moore (4), "Section_accelerate"_accelerate_kokkos.html, kokkos, lib/kokkos
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"KSPACE"_#KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
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"MANYBODY"_#MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
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"MEAM"_#MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
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"MC"_#MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
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"MOLECULE"_#MOLECULE, molecular system force fields, -, "Section_howto 6.3"_Section_howto.html#howto_3, peptide, -
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"OPT"_#OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section accelerate"_accelerate_opt.html, -, -
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"PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
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"POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
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"PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
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"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
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"REPLICA"_#REPLICA, multi-replica methods, -, "Section_howto 6.5"_Section_howto.html#howto_5, tad, -
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"RIGID"_#RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
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"SHOCK"_#SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
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"SNAP"_#SNAP, quantum-fit potential, Aidan Thompson (Sandia), "pair snap"_pair_snap.html, snap, -
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"SRD"_#SRD, stochastic rotation dynamics, -, "fix srd"_fix_srd.html, srd, -
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"VORONOI"_#VORONOI, Voronoi tesselations, Daniel Schwen (LANL), "compute voronoi/atom"_compute_voronoi_atom.html, -, Voro++
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:tb(ea=c)
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The "Authors" column lists a name(s) if a specific person is
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responible for creating and maintaining the package.
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(1) The COLLOID package includes Fast Lubrication Dynamics pair styles
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which were created by Amit Kumar and Michael Bybee from Jonathan
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Higdon's group at UIUC.
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(2) The OPT package was created by James Fischer (High Performance
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Technologies), David Richie, and Vincent Natoli (Stone Ridge
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Technolgy).
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(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
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and Ellad Tadmor (U Minn).
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(4) The KOKKOS package was created primarily by Christian Trott and
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Stan Moore (Sandia). It uses the Kokkos library which was developed
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by Carter Edwards, Christian Trott, and others at Sandia.
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The "Doc page" column links to either a sub-section of the
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"Section_howto"_Section_howto.html of the manual, or an input script
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command implemented as part of the package, or to additional
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documentation provided within the package.
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The "Example" column is a sub-directory in the examples directory of
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the distribution which has an input script that uses the package.
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E.g. "peptide" refers to the examples/peptide directory.
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The "Library" column lists an external library which must be built
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first and which LAMMPS links to when it is built. If it is listed as
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lib/package, then the code for the library is under the lib directory
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of the LAMMPS distribution. See the lib/package/README file for info
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on how to build the library. If it is not listed as lib/package, then
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it is a third-party library not included in the LAMMPS distribution.
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See details on all of this below for individual packages.
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p.s.: are we ever going to get commit messages from you? ;-)
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:line
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ASPHERE package :link(ASPHERE),h5
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Contents: Several computes, time-integration fixes, and pair styles
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for aspherical particle models: ellipsoids, 2d lines, 3d triangles.
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To install via make or Make.py:
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make yes-asphere
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make machine :pre
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Make.py -p asphere -a machine :pre
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To un-install via make or Make.py:
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make no-asphere
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make machine :pre
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Make.py -p ^asphere -a machine :pre
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Supporting info: "Section howto 6.14"_Section_howto.html#howto_14,
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"pair_style gayberne"_pair_gayberne.html, "pair_style
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resquared"_pair_resquared.html,
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"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf,
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"doc/PDF/pair_resquared_extra.pdf"_PDF/pair_resquared_extra.pdf,
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examples/ASPHERE, examples/ellipse
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:line
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BODY package :link(BODY),h5
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Contents: Support for body-style particles. Computes,
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time-integration fixes, pair styles, as well as the body styles
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themselves. See the "body"_body.html doc page for an overview.
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To install via make or Make.py:
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make yes-body
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make machine :pre
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Make.py -p body -a machine :pre
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To un-install via make or Make.py:
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make no-body
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make machine :pre
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Make.py -p ^body -a machine :pre
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Supporting info: "atom_style body"_atom_style.html, "body"_body.html,
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"pair_style body"_pair_body.html, examples/body
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:line
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CLASS2 package :link(CLASS2),h5
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Contents: Bond, angle, dihedral, improper, and pair styles for the
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COMPASS CLASS2 molecular force field.
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To install via make or Make.py:
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make yes-class2
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make machine :pre
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Make.py -p class2 -a machine :pre
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To un-install via make or Make.py:
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make no-class2
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make machine :pre
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Make.py -p ^class2 -a machine :pre
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Supporting info: "bond_style class2"_bond_class2.html, "angle_style
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class2"_angle_class2.html, "dihedral_style
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class2"_dihedral_class2.html, "improper_style
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class2"_improper_class2.html, "pair_style lj/class2"_pair_class2.html
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:line
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COLLOID package :link(COLLOID),h5
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Contents: Support for coarse-grained colloidal particles. Wall fix
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and pair styles that implement colloidal interaction models for
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finite-size particles. This includes the Fast Lubrication Dynamics
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method for hydrodynamic interactions, which is a simplified
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approximation to Stokesian dynamics.
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To install via make or Make.py:
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make yes-colloid
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make machine :pre
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Make.py -p colloid -a machine :pre
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To un-install via make or Make.py:
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make no-colloid
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make machine :pre
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Make.py -p ^colloid -a machine :pre
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Supporting info: "fix wall/colloid"_fix_wall.html, "pair_style
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colloid"_pair_colloid.html, "pair_style
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yukawa/colloid"_pair_yukawa_colloid.html, "pair_style
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brownian"_pair_brownian.html, "pair_style
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lubricate"_pair_lubricate.html, "pair_style
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lubricateU"_pair_lubricateU.html, examples/colloid, examples/srd
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:line
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COMPRESS package :link(COMPRESS),h5
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Contents: Support for compressed output of dump files via the zlib
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compression library, using dump styles with a "gz" in their style
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name.
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Building with the COMPRESS package assumes you have the zlib
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compression library available on your system. The build uses the
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lib/compress/Makefile.lammps file in the compile/link process. You
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should only need to edit this file if the LAMMPS build cannot find the
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zlib info it specifies.
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To install via make or Make.py:
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make yes-compress
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make machine :pre
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Make.py -p compress -a machine :pre
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To un-install via make or Make.py:
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make no-compress
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make machine :pre
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Make.py -p ^compress -a machine :pre
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Supporting info: src/COMPRESS/README, lib/compress/README, "dump
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atom/gz"_dump.html, "dump cfg/gz"_dump.html, "dump
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custom/gz"_dump.html, "dump xyz/gz"_dump.html
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:line
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CORESHELL package :link(CORESHELL),h5
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Contents: Compute and pair styles that implement the adiabatic
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core/shell model for polarizability. The compute temp/cs command
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measures the temperature of a system with core/shell particles. The
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pair styles augment Born, Buckingham, and Lennard-Jones styles with
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core/shell capabilities. See "Section howto
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6.26"_Section_howto.html#howto_26 for an overview of how to use the
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package.
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To install via make or Make.py:
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make yes-coreshell
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make machine :pre
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Make.py -p coreshell -a machine :pre
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To un-install via make or Make.py:
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make no-coreshell
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make machine :pre
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Make.py -p ^coreshell -a machine :pre
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Supporting info: "Section howto
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6.26"_Section_howto.html#howto_26, "compute temp/cs"_compute_temp_cs.html,
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"pair_style born/coul/long/cs"_pair_cs.html, "pair_style
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buck/coul/long/cs"_pair_cs.html, pair_style
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lj/cut/coul/long/cs"_pair_lj.html, examples/coreshell
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:line
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DIPOLE package :link(DIPOLE),h5
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Contents: An atom style and several pair styles to support point
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dipole models with short-range or long-range interactions.
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To install via make or Make.py:
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make yes-dipole
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make machine :pre
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Make.py -p dipole -a machine :pre
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To un-install via make or Make.py:
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make no-dipole
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make machine :pre
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Make.py -p ^dipole -a machine :pre
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Supporting info: "atom_style dipole"_atom_style.html, "pair_style
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lj/cut/dipole/cut"_pair_dipole.html, "pair_style
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lj/cut/dipole/long"_pair_dipole.html, "pair_style
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lj/long/dipole/long"_pair_dipole.html, examples/dipole
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:line
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GPU package :link(GPU),h5
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Contents: Dozens of pair styles and a version of the PPPM long-range
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Coulombic solver for NVIDIA GPUs. All of them have a "gpu" in their
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style name. "Section accelerate gpu"_accelerate_gpu.html gives
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details of what hardware and Cuda software is required on your system,
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and how to build and use this package. See the KOKKOS and USER-CUDA
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packages, which also have GPU-enabled styles.
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Building LAMMPS with the GPU package requires first building the GPU
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library itself, which is a set of C and Cuda files in lib/gpu.
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Details of how to do this are in lib/gpu/README. As illustrated
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below, perform a "make" using one of the Makefile.machine files in
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lib/gpu which should create a lib/reax/libgpu.a file.
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Makefile.linux.* and Makefile.xk7 are examples for different
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platforms. There are 3 important settings in the Makefile.machine you
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use:
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CUDA_HOME = where NVIDIA Cuda software is installed on your system
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CUDA_ARCH = appropriate to your GPU hardware
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CUDA_PREC = precision (double, mixed, single) you desire :ul
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See example Makefile.machine files in lib/gpu for the syntax of these
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settings. See lib/gpu/Makefile.linux.double for ARCH settings for
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various NVIDIA GPUs. The "make" also creates a
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lib/gpu/Makefile.lammps file. This file has settings that enable
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LAMMPS to link with Cuda libraries. If the settings in
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Makefile.lammps for your machine are not correct, the LAMMPS link will
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fail. Note that the Make.py script has a "-gpu" option to allow the
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GPU library (with several of its options) and LAMMPS to be built in
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one step, with Type "python src/Make.py -h -gpu" to see the details.
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To install via make or Make.py:
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cd ~/lammps/lib/gpu
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make -f Makefile.linux.mixed # for example
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cd ~/lammps/src
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make yes-gpu
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make machine :pre
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Make.py -p gpu -gpu mode=mixed arch=35 -a machine :pre
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To un-install via make or Make.py:
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make no-gpu
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make machine :pre
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Make.py -p ^gpu -a machine :pre
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Supporting info: src/GPU/README, lib/gpu/README, "Section
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acclerate"_Section_accelerate.html, "Section accelerate
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gpu"_accelerate_gpu.html, Pair Styles section of "Section commands
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3.5"_Section_commands.html#cmd_5 for any pair style listed with a (g),
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"kspace_style"_kspace_style.html, "package gpu"_package.html,
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examples/accelerate, bench/FERMI, bench/KEPLER
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:line
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GRANULAR package :link(GRANULAR),h5
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Contents: Fixes and pair styles that support models of finite-size
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granular particles, which interact with each other and boundaries via
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frictional and dissipative potentials.
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To install via make or Make.py:
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make yes-granular
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make machine :pre
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Make.py -p granular -a machine :pre
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To un-install via make or Make.py:
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make no-granular
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make machine :pre
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Make.py -p ^granular -a machine :pre
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Supporting info: "Section howto 6.6"_Section_howto.html#howto_6, "fix
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pour"_fix_pour.html, "fix wall/gran"_fix_wall_gran.html, "pair_style
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gran/hooke"_pair_gran.html, "pair_style
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gran/hertz/history"_pair_gran.html, examples/pour, bench/in.chute
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:line
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KIM package :link(KIM),h5
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Contents: A pair style that interfaces to the Knowledge Base for
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Interatomic Models (KIM) repository of interatomic potentials, so that
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KIM potentials can be used in a LAMMPS simulation.
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To build LAMMPS with the KIM package you must have previously
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installed the KIM API (library) on your system. The lib/kim/README
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file explains how to download and install KIM. Building with the KIM
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package also uses the lib/kim/Makefile.lammps file in the compile/link
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process. You should not need to edit this file.
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To install via make or Make.py:
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make yes-kim
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make machine :pre
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Make.py -p kim -a machine :pre
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To un-install via make or Make.py:
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make no-kim
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make machine :pre
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Make.py -p ^kim -a machine :pre
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Supporting info: src/KIM/README, lib/kim/README, "pair_style
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kim"_pair_kim.html, examples/kim
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:line
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KOKKOS package :link(KOKKOS),h5
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Contents: Dozens of atom, pair, bond, angle, dihedral, improper styles
|
|
which run with the Kokkos library to provide optimization for
|
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multicore CPUs (via OpenMP), NVIDIA GPUs, or the Intel Xeon Phi (in
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native mode). All of them have a "kk" in their style name. "Section
|
|
accelerate kokkos"_accelerate_kokkos.html gives details of what
|
|
hardware and software is required on your system, and how to build and
|
|
use this package. See the GPU, OPT, USER-CUDA, USER-INTEL, USER-OMP
|
|
packages, which also provide optimizations for the same range of
|
|
hardware.
|
|
|
|
Building with the KOKKOS package requires choosing which of 3 hardware
|
|
options you are optimizing for: CPU acceleration via OpenMP, GPU
|
|
acceleration, or Intel Xeon Phi. (You can build multiple times to
|
|
create LAMMPS executables for different hardware.) It also requires a
|
|
C++11 compatible compiler. For GPUs, the NVIDIA "nvcc" compiler is
|
|
used, and an appopriate KOKKOS_ARCH setting should be made in your
|
|
Makefile.machine for your GPU hardware and NVIDIA software.
|
|
|
|
The simplest way to do this is to use Makefile.kokkos_cuda or
|
|
Makefile.kokkos_omp or Makefile.kokkos_phi in src/MAKE/OPTIONS, via
|
|
"make kokkos_cuda" or "make kokkos_omp" or "make kokkos_phi". (Check
|
|
the KOKKOS_ARCH setting in Makefile.kokkos_cuda), Or, as illustrated
|
|
below, you can use the Make.py script with its "-kokkos" option to
|
|
choose which hardware to build for. Type "python src/Make.py -h
|
|
-kokkos" to see the details. If these methods do not work on your
|
|
system, you will need to read the "Section accelerate
|
|
kokkos"_accelerate_kokkos.html doc page for details of what
|
|
Makefile.machine settings are needed.
|
|
|
|
To install via make or Make.py for each of 3 hardware options:
|
|
|
|
make yes-kokkos
|
|
make kokkos_omp # for CPUs with OpenMP
|
|
make kokkos_cuda # for GPUs, check the KOKKOS_ARCH setting in Makefile.kokkos_cuda
|
|
make kokkos_phi # for Xeon Phis :pre
|
|
|
|
Make.py -p kokkos -kokkos omp -a machine # for CPUs with OpenMP
|
|
Make.py -p kokkos -kokkos cuda arch=35 -a machine # for GPUs of style arch
|
|
Make.py -p kokkos -kokkos phi -a machine # for Xeon Phis
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-kokkos
|
|
make machine :pre
|
|
|
|
Make.py -p ^kokkos -a machine :pre
|
|
|
|
Supporting info: src/KOKKOS/README, lib/kokkos/README, "Section
|
|
acclerate"_Section_accelerate.html, "Section accelerate
|
|
kokkos"_accelerate_kokkos.html, Pair Styles section of "Section
|
|
commands 3.5"_Section_commands.html#cmd_5 for any pair style listed
|
|
with a (k), "package kokkos"_package.html,
|
|
examples/accelerate, bench/FERMI, bench/KEPLER
|
|
|
|
:line
|
|
|
|
KSPACE package :link(KSPACE),h5
|
|
|
|
Contents: A variety of long-range Coulombic solvers, and pair styles
|
|
which compute the corresponding short-range portion of the pairwise
|
|
Coulombic interactions. These include Ewald, particle-particle
|
|
particle-mesh (PPPM), and multilevel summation method (MSM) solvers.
|
|
|
|
Building with the KSPACE package requires a 1d FFT library be present
|
|
on your system for use by the PPPM solvers. This can be the KISS FFT
|
|
library provided with LAMMPS, or 3rd party libraries like FFTW or a
|
|
vendor-supplied FFT library. See step 6 of "Section start
|
|
2.2.2"_Section_start.html#start_2_2 of the manual for details of how
|
|
to select different FFT options in your machine Makefile. The Make.py
|
|
tool has an "-fft" option which can insert these settings into your
|
|
machine Makefile automatically. Type "python src/Make.py -h -fft" to
|
|
see the details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-kspace
|
|
make machine :pre
|
|
|
|
Make.py -p kspace -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-kspace
|
|
make machine :pre
|
|
|
|
Make.py -p ^kspace -a machine :pre
|
|
|
|
Supporting info: "kspace_style"_kspace_style.html,
|
|
"doc/PDF/kspace.pdf"_PDF/kspace.pdf, "Section howto
|
|
6.7"_Section_howto.html#howto_7, "Section howto
|
|
6.8"_Section_howto.html#howto_8, "Section howto
|
|
6.9"_Section_howto.html#howto_9, "pair_style coul"_pair_coul.html,
|
|
other pair style command doc pages which have "long" or "msm" in their
|
|
style name, examples/peptide, bench/in.rhodo
|
|
|
|
:line
|
|
|
|
MANYBODY package :link(MANYBODY),h5
|
|
|
|
Contents: A variety of many-body and bond-order potentials. These
|
|
include (AI)REBO, EAM, EIM, BOP, Stillinger-Weber, and Tersoff
|
|
potentials. Do a directory listing, "ls src/MANYBODY", to see
|
|
the full list.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-manybody
|
|
make machine :pre
|
|
|
|
Make.py -p manybody -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-manybody
|
|
make machine :pre
|
|
|
|
Make.py -p ^manybody -a machine :pre
|
|
|
|
Supporting info:
|
|
|
|
Examples: Pair Styles section of "Section commands
|
|
3.5"_Section_commands.html#cmd_5, examples/comb, examples/eim,
|
|
examples/nb3d, examples/vashishta
|
|
|
|
:line
|
|
|
|
MC package :link(MC),h5
|
|
|
|
Contents: Several fixes and a pair style that have Monte Carlo (MC) or
|
|
MC-like attributes. These include fixes for creating, breaking, and
|
|
swapping bonds, and for performing atomic swaps and grand-canonical MC
|
|
in conjuction with dynamics.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-mc
|
|
make machine :pre
|
|
|
|
Make.py -p mc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-mc
|
|
make machine :pre
|
|
|
|
Make.py -p ^mc -a machine :pre
|
|
|
|
Supporting info: "fix atom/swap"_fix_atom_swap.html, "fix
|
|
bond/break"_fix_bond_break.html, "fix
|
|
bond/create"_fix_bond_create.html, "fix bond/swap"_fix_bond_swap.html,
|
|
"fix gcmc"_fix_gcmc.html, "pair_style dsmc"_pair_dsmc.html
|
|
|
|
:line
|
|
|
|
MEAM package :link(MEAM),h5
|
|
|
|
Contents: A pair style for the modified embedded atom (MEAM)
|
|
potential.
|
|
|
|
Building LAMMPS with the MEAM package requires first building the MEAM
|
|
library itself, which is a set of Fortran 95 files in lib/meam.
|
|
Details of how to do this are in lib/meam/README. As illustrated
|
|
below, perform a "make" using one of the Makefile.machine files in
|
|
lib/meam which should create a lib/meam/libmeam.a file.
|
|
Makefile.gfortran and Makefile.ifort are examples for the GNU Fortran
|
|
and Intel Fortran compilers. The "make" also copies a
|
|
lib/meam/Makefile.lammps.machine file to lib/meam/Makefile.lammps.
|
|
This file has settings that enable the C++ compiler used to build
|
|
LAMMPS to link with a Fortran library (typically the 2 compilers to be
|
|
consistent e.g. both Intel compilers, or both GNU compilers). If the
|
|
settings in Makefile.lammps for your compilers and machine are not
|
|
correct, the LAMMPS link will fail. Note that the Make.py script has
|
|
a "-meam" option to allow the MEAM library and LAMMPS to be built in
|
|
one step. Type "python src/Make.py -h -meam" to see the details.
|
|
|
|
NOTE: The MEAM potential can run dramatically faster if built with the
|
|
Intel Fortran compiler, rather than the GNU Fortran compiler.
|
|
|
|
To install via make or Make.py:
|
|
|
|
cd ~/lammps/lib/meam
|
|
make -f Makefile.gfortran # for example
|
|
cd ~/lammps/src
|
|
make yes-meam
|
|
make machine :pre
|
|
|
|
Make.py -p meam -meam make=gfortran -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-meam
|
|
make machine :pre
|
|
|
|
Make.py -p ^meam -a machine :pre
|
|
|
|
Supporting info: lib/meam/README, "pair_style meam"_pair_meam.html,
|
|
examples/meam
|
|
|
|
:line
|
|
|
|
MISC package :link(MISC),h5
|
|
|
|
Contents: A variety of computes, fixes, and pair styles that are not
|
|
commonly used, but don't align with other packages. Do a directory
|
|
listing, "ls src/MISC", to see the list of commands.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-misc
|
|
make machine :pre
|
|
|
|
Make.py -p misc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-misc
|
|
make machine :pre
|
|
|
|
Make.py -p ^misc -a machine :pre
|
|
|
|
Supporting info: "compute ti"_compute_ti.html, "fix
|
|
evaporate"_fix_evaporate.html, "fix tmm"_fix_ttm.html, "fix
|
|
viscosity"_fix_viscosity.html, examples/misc
|
|
|
|
:line
|
|
|
|
MOLECULE package :link(MOLECULE),h5
|
|
|
|
Contents: A large number of atom, pair, bond, angle, dihedral,
|
|
improper styles that are used to model molecular systems with fixed
|
|
covalent bonds. The pair styles include terms for the Dreiding
|
|
(hydrogen-bonding) and CHARMM force fields, and TIP4P water model.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-molecule
|
|
make machine :pre
|
|
|
|
Make.py -p molecule -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-molecule
|
|
make machine :pre
|
|
|
|
Make.py -p ^molecule -a machine :pre
|
|
|
|
Supporting info:"atom_style"_atom_style.html,
|
|
"bond_style"_bond_style.html, "angle_style"_angle_style.html,
|
|
"dihedral_style"_dihedral_style.html,
|
|
"improper_style"_improper_style.html, "pair_style
|
|
hbond/dreiding/lj"_pair_hbond_dreiding.html, "pair_style
|
|
lj/charmm/coul/charmm"_pair_charmm.html, "Section howto
|
|
6.3"_Section_howto.html#howto_3, examples/micelle, examples/peptide,
|
|
bench/in.chain, bench/in.rhodo
|
|
|
|
:line
|
|
|
|
MPIIO package :link(MPIIO),h5
|
|
|
|
Contents: Support for parallel output/input of dump and restart files
|
|
via the MPIIO library, which is part of the standard message-passing
|
|
interface (MPI) library. It adds "dump styles"_dump.html with a
|
|
"mpiio" in their style name. Restart files with an ".mpiio" suffix
|
|
are also written and read in parallel.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-mpiio
|
|
make machine :pre
|
|
|
|
Make.py -p mpiio -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-mpiio
|
|
make machine :pre
|
|
|
|
Make.py -p ^mpiio -a machine :pre
|
|
|
|
Supporting info: "dump"_dump.html, "restart"_restart.html,
|
|
"write_restart"_write_restart.html, "read_restart"_read_restart.html
|
|
|
|
:line
|
|
|
|
OPT package :link(OPT),h5
|
|
|
|
Contents: A handful of pair styles with an "opt" in their style name
|
|
which are optimized for improved CPU performance on single or multiple
|
|
cores. These include EAM, LJ, CHARMM, and Morse potentials. "Section
|
|
accelerate opt"_accelerate_opt.html gives details of how to build and
|
|
use this package. See the KOKKOS, USER-INTEL, and USER-OMP packages,
|
|
which also have styles optimized for CPU performance.
|
|
|
|
Some C++ compilers, like the Intel compiler, require the compile flag
|
|
"-restrict" to build LAMMPS with the OPT package. It should be added
|
|
to the CCFLAGS line of your Makefile.machine. Or use Makefile.opt in
|
|
src/MAKE/OPTIONS, via "make opt". For compilers that use the flag,
|
|
the Make.py command adds it automatically to the Makefile.auto file it
|
|
creates and uses.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-opt
|
|
make machine :pre
|
|
|
|
Make.py -p opt -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-opt
|
|
make machine :pre
|
|
|
|
Make.py -p ^opt -a machine :pre
|
|
|
|
Supporting info: "Section acclerate"_Section_accelerate.html, "Section
|
|
accelerate opt"_accelerate_opt.html, Pair Styles section of "Section
|
|
commands 3.5"_Section_commands.html#cmd_5 for any pair style listed
|
|
with an (o), examples/accelerate, bench/KEPLER
|
|
|
|
:line
|
|
|
|
PERI package :link(PERI),h5
|
|
|
|
Contents: Support for the Peridynamics method, a particle-based
|
|
meshless continuum model. The package includes an atom style, several
|
|
computes which calculate diagnostics, and several Peridynamic pair
|
|
styles which implement different materials models.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-peri
|
|
make machine :pre
|
|
|
|
Make.py -p peri -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-peri
|
|
make machine :pre
|
|
|
|
Make.py -p ^peri -a machine :pre
|
|
|
|
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"_compute_damage.html,
|
|
"pair_style peri/pmb"_pair_peri.html, examples/peri
|
|
|
|
:line
|
|
|
|
POEMS package :link(POEMS),h5
|
|
|
|
Contents: A fix that wraps the Parallelizable Open source Efficient
|
|
Multibody Software (POEMS) librar, which is able to simulate the
|
|
dynamics of articulated body systems. These are systems with multiple
|
|
rigid bodies (collections of atoms or particles) whose motion is
|
|
coupled by connections at hinge points.
|
|
|
|
Building LAMMPS with the POEMS package requires first building the
|
|
POEMS library itself, which is a set of C++ files in lib/poems.
|
|
Details of how to do this are in lib/poems/README. As illustrated
|
|
below, perform a "make" using one of the Makefile.machine files in
|
|
lib/poems which should create a lib/meam/libpoems.a file.
|
|
Makefile.g++ and Makefile.icc are examples for the GNU and Intel C++
|
|
compilers. The "make" also creates a lib/poems/Makefile.lammps file
|
|
which you should not need to change. Note the Make.py script has a
|
|
"-poems" option to allow the POEMS library and LAMMPS to be built in
|
|
one step. Type "python src/Make.py -h -poems" to see the details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
cd ~/lammps/lib/poems
|
|
make -f Makefile.g++ # for example
|
|
cd ~/lammps/src
|
|
make yes-poems
|
|
make machine :pre
|
|
|
|
Make.py -p poems -poems make=g++ -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-meam
|
|
make machine :pre
|
|
|
|
Make.py -p ^meam -a machine :pre
|
|
|
|
Supporting info: src/POEMS/README, lib/poems/README,
|
|
"fix poems"_fix_poems.html, examples/rigid
|
|
|
|
:line
|
|
|
|
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#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
|
|
version, 2.6 or later. Python 3 is not supported. The build uses the
|
|
contents of the lib/python/Makefile.lammps file to find all the Python
|
|
files required in the build/link process. See the lib/python/README
|
|
file if the settings in that file do not work on your system. Note
|
|
that the Make.py script has a "-python" option to allow an alternate
|
|
lib/python/Makefile.lammps file to be specified and LAMMPS to be built
|
|
in one step. Type "python src/Make.py -h -python" to see the details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-python
|
|
make machine :pre
|
|
|
|
Make.py -p python -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-python
|
|
make machine :pre
|
|
|
|
Make.py -p ^python -a machine :pre
|
|
|
|
Supporting info: examples/python
|
|
|
|
:line
|
|
|
|
QEQ package :link(QEQ),h5
|
|
|
|
Contents: Several fixes for performing charge equilibration (QEq) via
|
|
severeal different algorithms. These can be used with pair styles
|
|
that use QEq as part of their formulation.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-qeq
|
|
make machine :pre
|
|
|
|
Make.py -p qeq -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-qeq
|
|
make machine :pre
|
|
|
|
Make.py -p ^qeq -a machine :pre
|
|
|
|
Supporting info: "fix qeq/*"_fix_qeq.html, examples/qeq
|
|
|
|
:line
|
|
|
|
REAX package :link(REAX),h5
|
|
|
|
Contents: A pair style for the ReaxFF potential, a universal reactive
|
|
force field, as well as a "fix reax/bonds"_fix_reax_bonds.html command
|
|
for monitoring molecules as bonds are created and destroyed.
|
|
|
|
Building LAMMPS with the REAX package requires first building the REAX
|
|
library itself, which is a set of Fortran 95 files in lib/reax.
|
|
Details of how to do this are in lib/reax/README. As illustrated
|
|
below, perform a "make" using one of the Makefile.machine files in
|
|
lib/reax which should create a lib/reax/libreax.a file.
|
|
Makefile.gfortran and Makefile.ifort are examples for the GNU Fortran
|
|
and Intel Fortran compilers. The "make" also copies a
|
|
lib/reax/Makefile.lammps.machine file to lib/reax/Makefile.lammps.
|
|
This file has settings that enable the C++ compiler used to build
|
|
LAMMPS to link with a Fortran library (typically the 2 compilers to be
|
|
consistent e.g. both Intel compilers, or both GNU compilers). If the
|
|
settings in Makefile.lammps for your compilers and machine are not
|
|
correct, the LAMMPS link will fail. Note that the Make.py script has
|
|
a "-reax" option to allow the REAX library and LAMMPS to be built in
|
|
one step. Type "python src/Make.py -h -reax" to see the details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
cd ~/lammps/lib/reax
|
|
make -f Makefile.gfortran # for example
|
|
cd ~/lammps/src
|
|
make yes-reax
|
|
make machine :pre
|
|
|
|
Make.py -p reax -reax make=gfortran -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-reax
|
|
make machine :pre
|
|
|
|
Make.py -p ^reax -a machine :pre
|
|
|
|
Supporting info: lib/reax/README, "pair_style reax"_pair_reax.html,
|
|
"fix reax/bonds"_fix_reax_bonds.html, examples/reax
|
|
|
|
:line
|
|
|
|
REPLICA package :link(REPLICA),h5
|
|
|
|
Contents: A collection of multi-replica methods that are used by
|
|
invoking multiple instances (replicas) of LAMMPS
|
|
simulations. Communication between individual replicas is performed in
|
|
different ways by the different methods. See "Section howto
|
|
6.5"_Section_howto.html#howto_5 for an overview of how to run
|
|
multi-replica simulations in LAMMPS. Multi-replica methods included
|
|
in the package are nudged elastic band (NEB), parallel replica
|
|
dynamics (PRD), temperature accelerated dynamics (TAD), parallel
|
|
tempering, and a verlet/split algorithm for performing long-range
|
|
Coulombics on one set of processors, and the remainded of the force
|
|
field calcalation on another set.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-replica
|
|
make machine :pre
|
|
|
|
Make.py -p replica -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-replica
|
|
make machine :pre
|
|
|
|
Make.py -p ^replica -a machine :pre
|
|
|
|
Supporting info: "Section howto 6.5"_Section_howto.html#howto_5,
|
|
"neb"_neb.html, "prd"_prd.html, "tad"_tad.html, "temper"_temper.html,
|
|
"run_style verlet/split"_run_style.html, examples/neb, examples/prd,
|
|
examples/tad
|
|
|
|
:line
|
|
|
|
RIGID package :link(RIGID),h5
|
|
|
|
Contents: A collection of computes and fixes which enforce rigid
|
|
constraints on collections of atoms or particles. This includes SHAKE
|
|
and RATTLE, as well as variants of rigid-body time integrators for a
|
|
few large bodies or many small bodies.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-rigid
|
|
make machine :pre
|
|
|
|
Make.py -p rigid -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-rigid
|
|
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_rattle.html, "fix
|
|
rigid/*"_fix_rigid.html, examples/ASPHERE, examples/rigid
|
|
|
|
:line
|
|
|
|
SHOCK package :link(SHOCK),h5
|
|
|
|
Contents: A small number of fixes useful for running impact
|
|
simulations where a shock-wave passes through a material.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-shock
|
|
make machine :pre
|
|
|
|
Make.py -p shock -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-shock
|
|
make machine :pre
|
|
|
|
Make.py -p ^shock -a machine :pre
|
|
|
|
Supporting info: "fix append/atoms"_fix_append_atoms.html, "fix
|
|
msst"_fix_msst.html, "fix nphug"_fix_nphug.html, "fix
|
|
wall/piston"_fix_wall_piston.html, examples/hugoniostat, examples/msst
|
|
|
|
:line
|
|
|
|
SNAP package :link(SNAP),h5
|
|
|
|
Contents: A pair style for the spectral neighbor analysis potential
|
|
(SNAP), which is an empirical potential which can be quantum accurate
|
|
when fit to an archive of DFT data. Computes useful for analyzing
|
|
properties of the potential are also included.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-snap
|
|
make machine :pre
|
|
|
|
Make.py -p snap -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-snap
|
|
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.html,
|
|
"compute snav/atom"_compute_sna.html, examples/snap
|
|
|
|
:line
|
|
|
|
SRD package :link(SRD),h5
|
|
|
|
Contents: Two fixes which implement the Stochastic Rotation Dynamics
|
|
(SRD) method for coarse-graining of a solvent, typically around large
|
|
colloidal-scale particles.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-srd
|
|
make machine :pre
|
|
|
|
Make.py -p srd -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-srd
|
|
make machine :pre
|
|
|
|
Make.py -p ^srd -a machine :pre
|
|
|
|
Supporting info: "fix srd"_fix_srd.html, "fix
|
|
wall/srd"_fix_wall_srd.html, examples/srd, examples/ASPHERE
|
|
|
|
:line
|
|
|
|
VORONOI package :link(VORONOI),h5
|
|
|
|
Contents: A "compute voronoi/atom"_compute_voronoi_atom.html command
|
|
which computes the Voronoi tesselation of a collection of atoms or
|
|
particles by wrapping the Voro++ lib
|
|
|
|
To build LAMMPS with the KIM package you must have previously
|
|
installed the KIM API (library) on your system. The lib/kim/README
|
|
file explains how to download and install KIM. Building with the KIM
|
|
package also uses the lib/kim/Makefile.lammps file in the compile/link
|
|
process. You should not need to edit this file.
|
|
|
|
|
|
To build LAMMPS with the VORONOI package you must have previously
|
|
installed the Voro++ library on your system. The lib/voronoi/README
|
|
file explains how to download and install Voro++. There is a
|
|
lib/voronoi/install.py script which automates the process. Type
|
|
"python install.py" to see instructions. The final step is to create
|
|
soft links in the lib/voronoi directory for "includelink" and
|
|
"liblink" which point to installed Voro++ directories. Building with
|
|
the VORONOI package uses the contents of the
|
|
lib/voronoi/Makefile.lammps file in the compile/link process. You
|
|
should not need to edit this file. Note that the Make.py script has a
|
|
"-voronoi" option to allow the Voro++ library to be downloaded and/or
|
|
installed and LAMMPS to be built in one step. Type "python
|
|
src/Make.py -h -voronoi" to see the details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
cd ~/lammps/lib/voronoi
|
|
python install.py -g -b -l # download Voro++, build in lib/voronoi, create links
|
|
cd ~/lammps/src
|
|
make yes-voronoi
|
|
make machine :pre
|
|
|
|
Make.py -p voronoi -voronoi install="-g -b -l" -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-voronoi
|
|
make machine :pre
|
|
|
|
Make.py -p ^voronoi -a machine :pre
|
|
|
|
Supporting info: src/VORONOI/README, lib/voronoi/README, "compute
|
|
voronoi/atom"_compute_voronoi_atom.html, examples/voronoi
|
|
|
|
:line
|
|
|
|
4.2 User packages :h4,link(pkg_2)
|
|
|
|
The current list of user-contributed packages is as follows:
|
|
|
|
Package, Description, Author(s), Doc page, Example, Pic/movie, Library
|
|
"USER-ATC"_#USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
|
|
"USER-AWPMD"_#USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
|
|
"USER-CG-CMM"_#USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
|
|
"USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
|
|
"USER-CUDA"_#USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda
|
|
"USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
|
|
"USER-DPD"_#USER-DPD, dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
|
|
"USER-DRUDE"_#USER-DRUDE, Drude oscillators, Dequidt & Devemy & Padua (3), "tutorial"_tutorial_drude.html, USER/drude, -, -
|
|
"USER-EFF"_#USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
|
|
"USER-FEP"_#USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
|
|
"USER-H5MD"_#USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md
|
|
"USER-INTEL"_#USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, -
|
|
"USER-LB"_#USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
|
|
"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, -
|
|
"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
|
|
"USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
|
|
"USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, -
|
|
"USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
|
|
"USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
|
|
"USER-QTB"_#USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -, -
|
|
"USER-QUIP"_#USER-QUIP, QUIP/libatoms interface, Albert Bartok-Partay (U Cambridge), "pair_style quip"_pair_quip.html, USER/quip, -, lib/quip
|
|
"USER-REAXC"_#USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, -
|
|
"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 <...>/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)
|
|
:link(cg,http://lammps.sandia.gov/pictures.html#cg)
|
|
:link(eff,http://lammps.sandia.gov/movies.html#eff)
|
|
:link(sph,http://lammps.sandia.gov/movies.html#sph)
|
|
:link(VMD,http://www.ks.uiuc.edu/Research/vmd)
|
|
|
|
The "Authors" column lists a name(s) if a specific person is
|
|
responible for creating and maintaining the package.
|
|
|
|
(1) The ATC package was created by Reese Jones, Jeremy Templeton, and
|
|
Jon Zimmerman (Sandia).
|
|
|
|
(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
|
|
the colvars module library written by Giacomo Fiorin (Temple U) and
|
|
Jerome Henin (LISM, Marseille, France).
|
|
|
|
(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal
|
|
Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
|
|
(U Blaise Pascal).
|
|
|
|
(4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
|
|
Olivier Politano, and Robert Tetot (LAAS-CNRS, France).
|
|
|
|
(5) The USER-DPD package was created by James Larentzos (ARL), Timothy
|
|
Mattox (Engility), and John Brennan (ARL).
|
|
|
|
(6) The USER-VTK package was created by Richard Berger (JKU) and
|
|
Daniel Queteschiner (DCS Computing).
|
|
|
|
The "Doc page" column links to either a sub-section of the
|
|
"Section_howto"_Section_howto.html of the manual, or an input script
|
|
command implemented as part of the package, or to additional
|
|
documentation provided within the package.
|
|
|
|
The "Example" column is a sub-directory in the examples directory of
|
|
the distribution which has an input script that uses the package.
|
|
E.g. "peptide" refers to the examples/peptide directory. USER/cuda
|
|
refers to the examples/USER/cuda directory.
|
|
|
|
The "Library" column lists an external library which must be built
|
|
first and which LAMMPS links to when it is built. If it is listed as
|
|
lib/package, then the code for the library is under the lib directory
|
|
of the LAMMPS distribution. See the lib/package/README file for info
|
|
on how to build the library. If it is not listed as lib/package, then
|
|
it is a third-party library not included in the LAMMPS distribution.
|
|
See details on all of this below for individual packages.
|
|
|
|
:line
|
|
|
|
USER-ATC package :link(USER-ATC),h5
|
|
|
|
Contents: ATC stands for atoms-to-continuum. This package implements
|
|
a "fix atc"_fix_atc.html command to either couple MD with continuum
|
|
finite element equations or perform on-the-fly post-processing of
|
|
atomic information to continuum fields. See src/USER-ATC/README for
|
|
more details.
|
|
|
|
To build LAMMPS with this package ...
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info:src/USER-ATC/README, "fix atc"_fix_atc.html,
|
|
examples/USER/atc
|
|
|
|
Authors: Reese Jones (rjones at sandia.gov), Jeremy Templeton (jatempl
|
|
at sandia.gov) and Jon Zimmerman (jzimmer at sandia.gov) at Sandia.
|
|
Contact them directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-AWPMD package :link(USER-AWPMD),h5
|
|
|
|
Contents: AWPMD stands for Antisymmetrized Wave Packet Molecular
|
|
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.
|
|
|
|
To build LAMMPS with this package ...
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: src/USER-AWPMD/README, "fix
|
|
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.
|
|
|
|
:line
|
|
|
|
USER-CG-CMM package :link(USER-CG-CMM),h5
|
|
|
|
Contents: CG-CMM stands for coarse-grained ??. This package
|
|
implements several pair styles and an angle style using the coarse
|
|
grained parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27
|
|
(2007) (SDK), with extensions to simulate ionic liquids, electrolytes,
|
|
lipids and charged amino acids. See src/USER-CG-CMM/README for more
|
|
details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: src/USER-CG-CMM/README, "pair lj/sdk"_pair_sdk.html,
|
|
"pair lj/sdk/coul/long"_pair_sdk.html, "angle sdk"_angle_sdk.html,
|
|
examples/USER/cg-cmm
|
|
|
|
Author: Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact
|
|
him directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-COLVARS package :link(USER-COLVARS),h5
|
|
|
|
Contents: COLVARS stands for collective variables which can be used to
|
|
implement Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
|
|
Sampling and Restraints. This package implements a "fix
|
|
colvars"_fix_colvars.html command which wraps a COLVARS library which
|
|
can perform those kinds of simulations. See src/USER-COLVARS/README
|
|
for more details.
|
|
|
|
To build LAMMPS with this package ...
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info:
|
|
"doc/PDF/colvars-refman-lammps.pdf"_PDF/colvars-refman-lammps.pdf,
|
|
src/USER-COLVARS/README, lib/colvars/README, "fix
|
|
colvars"_fix_colvars.html, examples/USER/colvars
|
|
|
|
Authors: Axel Kohlmeyer at Temple U (akohlmey at gmail.com) wrote the
|
|
fix. The COLVARS library itself is written and maintained by Giacomo
|
|
Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and Jerome
|
|
Henin (LISM, CNRS, Marseille, France). Contact them directly if you
|
|
have questions.
|
|
|
|
:line
|
|
|
|
USER-CUDA package :link(USER-CUDA),h5
|
|
|
|
Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
|
|
either couple of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields. See
|
|
src/USER-ATC/README for more details.
|
|
|
|
To build LAMMPS with this package ...
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
|
|
|
|
|
|
This package provides acceleration of various LAMMPS pair styles, fix
|
|
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
|
|
GPUs.
|
|
|
|
See this section of the manual to get started:
|
|
|
|
"Section_accelerate"_Section_accelerate.html#acc_7
|
|
|
|
There are example scripts for using this package in
|
|
examples/USER/cuda.
|
|
|
|
This package uses an external library in lib/cuda which must be
|
|
compiled before making LAMMPS. See the lib/cuda/README file and the
|
|
LAMMPS manual for information on building LAMMPS with external
|
|
libraries.
|
|
|
|
The person who created this package is Christian Trott at the
|
|
University of Technology Ilmenau, Germany (christian.trott at
|
|
tu-ilmenau.de). Contact him directly if you have questions.
|
|
|
|
Examples: examples/accelerate, bench/FERMI, bench/KEPLER
|
|
|
|
:line
|
|
|
|
USER-DIFFRACTION package :link(USER-DIFFRACTION),h5
|
|
|
|
Contents: This packages implements two computes and a fix for
|
|
calculating x-ray and electron diffraction intensities based on
|
|
kinematic diffraction theory. See src/USER-DIFFRACTION/README for
|
|
more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "compute saed"_compute_saed.html, "compute
|
|
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
|
|
the University of Arkansas. Contact him directly if you have
|
|
questions.
|
|
|
|
:line
|
|
|
|
USER-DPD package :link(USER-DPD),h5
|
|
|
|
Contents: DPD stands for dissipative particle dynamics, This package
|
|
implements DPD for isothermal, isoenergetic, isobaric and isenthalpic
|
|
conditions. The DPD equations of motion are integrated efficiently
|
|
through the Shardlow splitting algorithm. See src/USER-DPD/README for
|
|
more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
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 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)
|
|
and John Brennan (ARL) (john.k.brennan.civ at mail.mil). Contact them
|
|
directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-DRUDE package :link(USER-DRUDE),h5
|
|
|
|
Contents: This package contains methods for simulating polarizable
|
|
systems using thermalized Drude oscillators. It has computes, fixes,
|
|
and pair styles for this purpose. See "Section howto
|
|
6.27"_Section_howto.html#howto_27 for an overview of how to use the
|
|
package. See src/USER-DRUDE/README for additional details. There are
|
|
auxiliary tools for using this package in tools/drude.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "Section howto 6.27"_Section_howto.html#howto_27,
|
|
src/USER-DRUDE/README, "fix drude"_fix_drude.html, "fix
|
|
drude/transform/*"_fix_drude_transform.html, "compute
|
|
temp/drude"_compute_temp_drude.html, "pair thole"_pair_thole.html,
|
|
"pair lj/cut/thole/long"_pair_thole.html, examples/USER/drude,
|
|
tools/drude
|
|
|
|
Authors: Alain Dequidt at Universite Blaise Pascal Clermont-Ferrand
|
|
(alain.dequidt at univ-bpclermont.fr); co-authors: Julien Devemy,
|
|
Agilio Padua. Contact them directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-EFF package :link(USER-EFF),h5
|
|
|
|
Contents: EFF stands for electron force field. This package contains
|
|
atom, pair, fix and compute styles which implement the eFF as
|
|
described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III,
|
|
JCC, 2010. The eFF potential was first introduced by Su and Goddard,
|
|
in 2007. See src/USER-EFF/README for more details. There are
|
|
auxiliary tools for using this package in tools/eff; see its README
|
|
file.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "atom_style electron"_atom_style.html, "compute
|
|
temp/eff"_compute_temp_eff.html, "fix
|
|
langevin/eff"_fix_langevin_eff.html, "fix nve/eff"_fix_nve_eff.html,
|
|
"pair eff/cut"_pair_eff.html, examples/USER/eff, tools/eff
|
|
|
|
Supporting info:
|
|
|
|
Author: Andres Jaramillo-Botero at CalTech (ajaramil at
|
|
wag.caltech.edu). Contact him directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-FEP package :link(USER-FEP),h5
|
|
|
|
Contents: FEP stands for free energy perturbation. This package
|
|
provides methods for performing FEP simulations by using a "fix
|
|
adapt/fep"_fix_adapt_fep.html command with soft-core pair potentials,
|
|
which have a "soft" in their style name. See src/USER-FEP/README for
|
|
more details. There are auxiliary tools for using this package in
|
|
tools/fep; see its README file.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: src/USER-FEP/README, "fix
|
|
adapt/fep"_fix_adapt_fep.html, "compute fep"_compute_fep.html,
|
|
"pair_style */soft"_pair_lj_soft.html, examples/USER/fep
|
|
|
|
Author: Agilio Padua at Universite Blaise Pascal Clermont-Ferrand
|
|
(agilio.padua at univ-bpclermont.fr). Contact him directly if you have
|
|
questions.
|
|
|
|
:line
|
|
|
|
USER-H5MD package :link(USER-H5MD),h5
|
|
|
|
Contents: H5MD stands for HDF5 for MD. "HDF5"_HDF5 is a binary,
|
|
portable, self-describing file format, used by many scientific
|
|
simulations. H5MD is a format for molecular simulations, built on top
|
|
of HDF5. This package implements a "dump h5md"_dump_h5md.html command
|
|
to output LAMMPS snapshots in this format. See src/USER-H5MD/README
|
|
for more details.
|
|
|
|
:link(HDF5,http://www.hdfgroup.org/HDF5/)
|
|
|
|
To build LAMMPS with this package ...
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: src/USER-H5MD/README, lib/h5md/README, "dump
|
|
h5md"_dump_h5md.html
|
|
|
|
Author: Pierre de Buyl at KU Leuven (see http://pdebuyl.be) created
|
|
this package as well as the H5MD format and library. Contact him
|
|
directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-INTEL package :link(USER-INTEL),h5
|
|
|
|
Contents: Dozens of pair, bond, angle, dihedral, and improper styles
|
|
that are optimized for Intel CPUs and the Intel Xeon Phi (in offload
|
|
mode). All of them have an "intel" in their style name. "Section
|
|
accelerate intel"_accelerate_intel.html gives details of what hardware
|
|
and compilers are required on your system, and how to build and use
|
|
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.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: examples/accelerate, src/USER-INTEL/TEST
|
|
|
|
"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.
|
|
|
|
For the USER-INTEL package, you have 2 choices when building. You can
|
|
build with CPU or Phi support. The latter uses Xeon Phi chips in
|
|
"offload" mode. Each of these modes requires additional settings in
|
|
your Makefile.machine for CCFLAGS and LINKFLAGS.
|
|
|
|
For CPU mode (if using an Intel compiler):
|
|
|
|
CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
|
|
LINKFLAGS: add -fopenmp :ul
|
|
|
|
For Phi mode add the following in addition to the CPU mode flags:
|
|
|
|
CCFLAGS: add -DLMP_INTEL_OFFLOAD and
|
|
LINKFLAGS: add -offload :ul
|
|
|
|
And also add this to CCFLAGS:
|
|
|
|
-offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\"" :pre
|
|
|
|
Examples:
|
|
|
|
:line
|
|
|
|
USER-LB package :link(USER-LB),h5
|
|
|
|
Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
|
|
either couple of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields. See
|
|
src/USER-ATC/README for more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
|
|
|
|
Supporting info:
|
|
|
|
This package contains a LAMMPS implementation of a background
|
|
Lattice-Boltzmann fluid, which can be used to model MD particles
|
|
influenced by hydrodynamic forces.
|
|
|
|
See this doc page and its related commands to get started:
|
|
|
|
"fix lb/fluid"_fix_lb_fluid.html
|
|
|
|
The people who created this package are Frances Mackay (fmackay at
|
|
uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
|
|
Western Ontario. Contact them directly if you have questions.
|
|
|
|
Examples: examples/USER/lb
|
|
|
|
:line
|
|
|
|
USER-MGPT package :link(USER-MGPT),h5
|
|
|
|
Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
|
|
either couple of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields. See
|
|
src/USER-ATC/README for more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
|
|
|
|
Supporting info:
|
|
|
|
This package contains a fast implementation for LAMMPS of
|
|
quantum-based MGPT multi-ion potentials. The MGPT or model GPT method
|
|
derives from first-principles DFT-based generalized pseudopotential
|
|
theory (GPT) through a series of systematic approximations valid for
|
|
mid-period transition metals with nearly half-filled d bands. The
|
|
MGPT method was originally developed by John Moriarty at Lawrence
|
|
Livermore National Lab (LLNL).
|
|
|
|
In the general matrix representation of MGPT, which can also be
|
|
applied to f-band actinide metals, the multi-ion potentials are
|
|
evaluated on the fly during a simulation through d- or f-state matrix
|
|
multiplication, and the forces that move the ions are determined
|
|
analytically. The {mgpt} pair style in this package calculates forces
|
|
and energies using an optimized matrix-MGPT algorithm due to Tomas
|
|
Oppelstrup at LLNL.
|
|
|
|
See this doc page to get started:
|
|
|
|
"pair_style mgpt"_pair_mgpt.html
|
|
|
|
The persons who created the USER-MGPT package are Tomas Oppelstrup
|
|
(oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov)
|
|
Contact them directly if you have any questions.
|
|
|
|
Examples: examples/USER/mgpt
|
|
|
|
:line
|
|
|
|
USER-MISC package :link(USER-MISC),h5
|
|
|
|
Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
|
|
either couple of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields. See
|
|
src/USER-ATC/README for more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
|
|
|
|
Supporting info:
|
|
|
|
The files in this package are a potpourri of (mostly) unrelated
|
|
features contributed to LAMMPS by users. Each feature is a single
|
|
pair of files (*.cpp and *.h).
|
|
|
|
More information about each feature can be found by reading its doc
|
|
page in the LAMMPS doc directory. The doc page which lists all LAMMPS
|
|
input script commands is as follows:
|
|
|
|
"Section_commands"_Section_commands.html#cmd_5
|
|
|
|
User-contributed features are listed at the bottom of the fix,
|
|
compute, pair, etc sections.
|
|
|
|
The list of features and author of each is given in the
|
|
src/USER-MISC/README file.
|
|
|
|
You should contact the author directly if you have specific questions
|
|
about the feature or its coding.
|
|
|
|
Examples: examples/USER/misc
|
|
|
|
:line
|
|
|
|
USER-MOLFILE package :link(USER-MOLFILE),h5
|
|
|
|
Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
|
|
either couple of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields. See
|
|
src/USER-ATC/README for more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
|
|
|
|
Supporting info:
|
|
|
|
This package contains a dump molfile command which uses molfile
|
|
plugins that are bundled with the
|
|
"VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
|
|
analysis program, to enable LAMMPS to dump its information in formats
|
|
compatible with various molecular simulation tools.
|
|
|
|
The package only provides the interface code, not the plugins. These
|
|
can be obtained from a VMD installation which has to match the
|
|
platform that you are using to compile LAMMPS for. By adding plugins
|
|
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.
|
|
|
|
See this doc page to get started:
|
|
|
|
"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.
|
|
|
|
:line
|
|
|
|
USER-OMP package :link(USER-OMP),h5
|
|
|
|
Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
|
|
either couple of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields. See
|
|
src/USER-ATC/README for more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
|
|
|
|
Supporting info:
|
|
|
|
This package provides OpenMP multi-threading support and
|
|
other optimizations of various LAMMPS pair styles, dihedral
|
|
styles, and fix styles.
|
|
|
|
See this section of the manual to get started:
|
|
|
|
"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.
|
|
|
|
For the USER-OMP package, your Makefile.machine needs additional
|
|
settings for CCFLAGS and LINKFLAGS.
|
|
|
|
CCFLAGS: add -fopenmp and -restrict
|
|
LINKFLAGS: add -fopenmp :ul
|
|
|
|
Examples: examples/accelerate, bench/KEPLER
|
|
|
|
:line
|
|
|
|
USER-PHONON package :link(USER-PHONON),h5
|
|
|
|
Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
|
|
either couple of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields. See
|
|
src/USER-ATC/README for more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
|
|
|
|
This package contains a fix phonon command that calculates dynamical
|
|
matrices, which can then be used to compute phonon dispersion
|
|
relations, directly from molecular dynamics simulations.
|
|
|
|
See this doc page to get started:
|
|
|
|
"fix phonon"_fix_phonon.html
|
|
|
|
The person who created this package is Ling-Ti Kong (konglt at
|
|
sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly
|
|
if you have questions.
|
|
|
|
Examples: examples/USER/phonon
|
|
|
|
:line
|
|
|
|
USER-QMMM package :link(USER-QMMM),h5
|
|
|
|
Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
|
|
either couple of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields. See
|
|
src/USER-ATC/README for more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
|
|
|
|
Supporting info:
|
|
|
|
This package provides a fix qmmm command which allows LAMMPS to be
|
|
used in a QM/MM simulation, currently only in combination with pw.x
|
|
code from the "Quantum ESPRESSO"_espresso package.
|
|
|
|
:link(espresso,http://www.quantum-espresso.org)
|
|
|
|
The current implementation only supports an ONIOM style mechanical
|
|
coupling to the Quantum ESPRESSO plane wave DFT package.
|
|
Electrostatic coupling is in preparation and the interface has been
|
|
written in a manner that coupling to other QM codes should be possible
|
|
without changes to LAMMPS itself.
|
|
|
|
See this doc page to get started:
|
|
|
|
"fix qmmm"_fix_qmmm.html
|
|
|
|
as well as the lib/qmmm/README file.
|
|
|
|
The person who created this package is Axel Kohlmeyer at Temple U
|
|
(akohlmey at gmail.com). Contact him directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-QTB package :link(USER-QTB),h5
|
|
|
|
Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
|
|
either couple of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields. See
|
|
src/USER-ATC/README for more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
|
|
|
|
Supporting info:
|
|
|
|
This package provides a self-consistent quantum treatment of the
|
|
vibrational modes in a classical molecular dynamics simulation. By
|
|
coupling the MD simulation to a colored thermostat, it introduces zero
|
|
point energy into the system, alter the energy power spectrum and the
|
|
heat capacity towards their quantum nature. This package could be of
|
|
interest if one wants to model systems at temperatures lower than
|
|
their classical limits or when temperatures ramp up across the
|
|
classical limits in the simulation.
|
|
|
|
See these two doc pages to get started:
|
|
|
|
"fix qtb"_fix_qtb.html provides quantum nulcear correction through a
|
|
colored thermostat and can be used with other time integration schemes
|
|
like "fix nve"_fix_nve.html or "fix nph"_fix_nh.html.
|
|
|
|
"fix qbmsst"_fix_qbmsst.html enables quantum nuclear correction of a
|
|
multi-scale shock technique simulation by coupling the quantum thermal
|
|
bath with the shocked system.
|
|
|
|
The person who created this package is Yuan Shen (sy0302 at
|
|
stanford.edu) at Stanford University. Contact him directly if you
|
|
have questions.
|
|
|
|
Examples: examples/USER/qtb
|
|
|
|
:line
|
|
|
|
USER-QUIP package :link(USER-QUIP),h5
|
|
|
|
Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
|
|
either couple of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields. See
|
|
src/USER-ATC/README for more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
|
|
|
|
Supporting info:
|
|
|
|
Examples: examples/USER/quip
|
|
|
|
:line
|
|
|
|
USER-REAXC package :link(USER-REAXC),h5
|
|
|
|
Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
|
|
either couple of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields. See
|
|
src/USER-ATC/README for more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
|
|
|
|
Supporting info:
|
|
|
|
This package contains a implementation for LAMMPS of the ReaxFF force
|
|
field. ReaxFF uses distance-dependent bond-order functions to
|
|
represent the contributions of chemical bonding to the potential
|
|
energy. It was originally developed by Adri van Duin and the Goddard
|
|
group at CalTech.
|
|
|
|
The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
|
|
C, should give identical or very similar results to pair_style reax,
|
|
which is a ReaxFF implementation on top of a Fortran library, a
|
|
version of which library was originally authored by Adri van Duin.
|
|
|
|
The reax/c version should be somewhat faster and more scalable,
|
|
particularly with respect to the charge equilibration calculation. It
|
|
should also be easier to build and use since there are no complicating
|
|
issues with Fortran memory allocation or linking to a Fortran library.
|
|
|
|
For technical details about this implemention of ReaxFF, see
|
|
this paper:
|
|
|
|
Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
|
|
and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
|
|
S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011).
|
|
|
|
See the doc page for the pair_style reax/c command for details
|
|
of how to use it in LAMMPS.
|
|
|
|
The person who created this package is Hasan Metin Aktulga (hmaktulga
|
|
at lbl.gov), while at Purdue University. Contact him directly, or
|
|
Aidan Thompson at Sandia (athomps at sandia.gov), if you have
|
|
questions.
|
|
|
|
Examples: examples/reax
|
|
|
|
:line
|
|
|
|
USER-SMD package :link(USER-SMD),h5
|
|
|
|
Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
|
|
either couple of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields. See
|
|
src/USER-ATC/README for more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
|
|
|
|
Supporting info:
|
|
|
|
This package implements smoothed Mach dynamics (SMD) in
|
|
LAMMPS. Currently, the package has the following features:
|
|
|
|
* Does liquids via traditional Smooth Particle Hydrodynamics (SPH)
|
|
|
|
* Also solves solids mechanics problems via a state of the art
|
|
stabilized meshless method with hourglass control.
|
|
|
|
* Can specify hydrostatic interactions independently from material
|
|
strength models, i.e. pressure and deviatoric stresses are separated.
|
|
|
|
* Many material models available (Johnson-Cook, plasticity with
|
|
hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
|
|
material models.
|
|
|
|
* Rigid boundary conditions (walls) can be loaded as surface geometries
|
|
from *.STL files.
|
|
|
|
See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.
|
|
|
|
There are example scripts for using this package in examples/USER/smd.
|
|
|
|
The person who created this package is Georg Ganzenmuller at the
|
|
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
|
|
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
|
|
you have questions.
|
|
|
|
Examples: examples/USER/smd
|
|
|
|
:line
|
|
|
|
USER-SMTBQ package :link(USER-SMTBQ),h5
|
|
|
|
Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
|
|
either couple of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields. See
|
|
src/USER-ATC/README for more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
|
|
|
|
Supporting info:
|
|
|
|
This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
|
|
potential for the description of ionocovalent bonds in oxides.
|
|
|
|
There are example scripts for using this package in
|
|
examples/USER/smtbq.
|
|
|
|
See this doc page to get started:
|
|
|
|
"pair_style smtbq"_pair_smtbq.html
|
|
|
|
The persons who created the USER-SMTBQ package are Nicolas Salles,
|
|
Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at
|
|
these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact
|
|
them directly if you have any questions.
|
|
|
|
Examples: examples/USER/smtbq
|
|
|
|
:line
|
|
|
|
USER-SPH package :link(USER-SPH),h5
|
|
|
|
Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
|
|
either couple of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields. See
|
|
src/USER-ATC/README for more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
|
|
|
|
Supporting info:
|
|
|
|
This package implements smoothed particle hydrodynamics (SPH) in
|
|
LAMMPS. Currently, the package has the following features:
|
|
|
|
* Tait, ideal gas, Lennard-Jones equation of states, full support for
|
|
complete (i.e. internal-energy dependent) equations of state
|
|
|
|
* Plain or Monaghans XSPH integration of the equations of motion
|
|
|
|
* Density continuity or density summation to propagate the density field
|
|
|
|
* Commands to set internal energy and density of particles from the
|
|
input script
|
|
|
|
* Output commands to access internal energy and density for dumping and
|
|
thermo output
|
|
|
|
See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.
|
|
|
|
There are example scripts for using this package in examples/USER/sph.
|
|
|
|
The person who created this package is Georg Ganzenmuller at the
|
|
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
|
|
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
|
|
you have questions.
|
|
|
|
Examples: examples/USER/sph
|
|
|
|
:line
|
|
|
|
USER-TALLY package :link(USER-TALLY),h5
|
|
|
|
Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
|
|
either couple of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields. See
|
|
src/USER-ATC/README for more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
|
|
|
|
Supporting info:
|
|
|
|
Examples: examples/USER/tally
|
|
|
|
:line
|
|
|
|
USER-VTK package :link(USER-VTK),h5
|
|
|
|
Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
|
|
either couple of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields. See
|
|
src/USER-ATC/README for more details.
|
|
|
|
To install via make or Make.py:
|
|
|
|
make yes-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p atc -a machine :pre
|
|
|
|
To un-install via make or Make.py:
|
|
|
|
make no-user-atc
|
|
make machine :pre
|
|
|
|
Make.py -p ^atc -a machine :pre
|
|
|
|
Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
|
|
|
|
Examples: examples/USER/tally
|