| ASPHERE |
aspherical particles |
@@ -241,7 +271,7 @@ either via the make command or the Make.py tool described in | BODY |
+| BODY |
body-style particles |
@@ -254,7 +284,7 @@ either via the make command or the Make.py tool described in | CLASS2 |
+| CLASS2 |
class 2 force fields |
@@ -270,7 +300,7 @@ either via the make command or the Make.py tool described in | COLLOID |
+| COLLOID |
colloidal particles |
@@ -283,7 +313,7 @@ either via the make command or the Make.py tool described in | COMPRESS |
+| COMPRESS |
I/O compression |
Axel Kohlmeyer (Temple U) |
dump */gz |
@@ -296,7 +326,7 @@ either via the make command or the Make.py tool described in CORESHELL |
+ | CORESHELL |
adiabatic core/shell model |
Hendrik Heenen (Technical U of Munich) |
Section_howto 6.25 |
@@ -306,7 +336,7 @@ either via the make command or the Make.py tool described in DIPOLE |
+ | DIPOLE |
point dipole particles |
@@ -319,7 +349,7 @@ either via the make command or the Make.py tool described in | FLD |
+| FLD |
Fast Lubrication Dynamics |
Kumar & Bybee & Higdon (1) |
pair_style lubricateU |
@@ -332,14 +362,14 @@ either via the make command or the Make.py tool described in GPU |
+ | GPU |
GPU-enabled styles |
Mike Brown (ORNL) |
Section accelerate |
gpu |
lib/gpu |
-| GRANULAR |
+ | GRANULAR |
granular systems |
@@ -352,21 +382,21 @@ either via the make command or the Make.py tool described in | KIM |
+| KIM |
openKIM potentials |
Smirichinski & Elliot & Tadmor (3) |
pair_style kim |
kim |
KIM |
-| KOKKOS |
+ | KOKKOS |
Kokkos-enabled styles |
Trott & Edwards (4) |
Section_accelerate |
kokkos |
lib/kokkos |
-| KSPACE |
+ | KSPACE |
long-range Coulombic solvers |
@@ -379,7 +409,7 @@ either via the make command or the Make.py tool described in | MANYBODY |
+| MANYBODY |
many-body potentials |
@@ -392,14 +422,14 @@ either via the make command or the Make.py tool described in | MEAM |
+| MEAM |
modified EAM potential |
Greg Wagner (Sandia) |
pair_style meam |
meam |
lib/meam |
-| MC |
+ | MC |
Monte Carlo options |
@@ -415,7 +445,7 @@ either via the make command or the Make.py tool described in | MOLECULE |
+| MOLECULE |
molecular system force fields |
@@ -428,7 +458,7 @@ either via the make command or the Make.py tool described in | OPT |
+| OPT |
optimized pair styles |
Fischer & Richie & Natoli (2) |
Section accelerate |
@@ -441,7 +471,7 @@ either via the make command or the Make.py tool described in PERI |
+ | PERI |
Peridynamics models |
Mike Parks (Sandia) |
pair_style peri |
@@ -451,14 +481,14 @@ either via the make command or the Make.py tool described in POEMS |
+ | POEMS |
coupled rigid body motion |
Rudra Mukherjee (JPL) |
fix poems |
rigid |
lib/poems |
-| PYTHON |
+ | PYTHON |
embed Python code in an input script |
@@ -468,14 +498,14 @@ either via the make command or the Make.py tool described in | REAX |
+| REAX |
ReaxFF potential |
Aidan Thompson (Sandia) |
pair_style reax |
reax |
lib/reax |
-| REPLICA |
+ | REPLICA |
multi-replica methods |
@@ -488,7 +518,7 @@ either via the make command or the Make.py tool described in | RIGID |
+| RIGID |
rigid bodies |
@@ -501,7 +531,7 @@ either via the make command or the Make.py tool described in | SHOCK |
+| SHOCK |
shock loading methods |
@@ -517,7 +547,7 @@ either via the make command or the Make.py tool described in | SNAP |
+| SNAP |
quantum-fit potential |
Aidan Thompson (Sandia) |
pair snap |
@@ -527,7 +557,7 @@ either via the make command or the Make.py tool described in SRD |
+ | SRD |
stochastic rotation dynamics |
@@ -540,7 +570,7 @@ either via the make command or the Make.py tool described in | VORONOI |
+| VORONOI |
Voronoi tesselations |
Daniel Schwen (LANL) |
compute voronoi/atom |
@@ -550,7 +580,7 @@ either via the make command or the Make.py tool described in XTC |
+ | XTC |
dumps in XTC format |
@@ -576,9 +606,7 @@ either via the make command or the Make.py tool described in Section_howto of the manual, or an input script
-command implemented as part of the package.
+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.
@@ -601,74 +630,755 @@ 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 the src/package/README or src/package/Makefile.lammps file for
-info on where to download the library. Section start of the manual also gives details
-on how to build LAMMPS with both kinds of auxiliary libraries.
-Except where explained below, all of these packages can be installed,
-and LAMMPS re-built, by issuing these commands from the src dir.
-make yes-package
+See details on all of this below for individual packages.
+
+
+
+ 4.2. ASPHERE package
+ Contents: Aspherical particle models for ellipsoids, 2d lines, 3d
+triangles.
+ To install via make or Make.py:
+ make yes-asphere
make machine
-or
-Make.py -p package -a machine
- To un-install the package and re-build LAMMPS without it:
- make no-package
-make machine
-or
-Make.py -p ^package -a machine
+Make.py -p asphere -a machine
“Package” is the name of the package in lower-case letters,
-e.g. asphere or rigid, and “machine” is the build target, e.g. mpi or
-serial.
+To un-install via make or Make.py:
+make no-asphere
+make machine
+
- 4.2. Build instructions for COMPRESS package
+ Make.py -p ^asphere -a machine
+
-
- 4.3. Build instructions for GPU package
+ Supporting info: examples/ASPHERE, examples/ellipse, Section howto
+6.14, pair gayberne
+
-
- 4.4. Build instructions for KIM package
+
+ 4.3. BODY package
+ Contents:
+ To install via make or Make.py:
+ make yes-body
+make machine
+
-
- 4.5. Build instructions for KOKKOS package
+ Make.py -p body -a machine
+
-
- 4.6. Build instructions for KSPACE package
+ To un-install via make or Make.py:
+ make no-body
+make machine
+
-
- 4.7. Build instructions for MEAM package
+ Make.py -p ^body -a machine
+
-
- 4.8. Build instructions for POEMS package
+ Supporting info: examples/body
+
-
- 4.9. Build instructions for PYTHON package
+
+ 4.4. CLASS2 package
+ Contents:
+ To install via make or Make.py:
+ make yes-class2
+make machine
+
-
- 4.10. Build instructions for REAX package
+ Make.py -p class2 -a machine
+
-
- 4.11. Build instructions for VORONOI package
+ To un-install via make or Make.py:
+ make no-class2
+make machine
+
-
- 4.12. Build instructions for XTC package
+ Make.py -p ^class2 -a machine
+
+
+ Supporting info:
+
+
+
+ 4.5. COLLOID package
+ Contents:
+ To install via make or Make.py:
+ make yes-colloid
+make machine
+
+
+ Make.py -p colloid -a machine
+
+
+ To un-install via make or Make.py:
+ make no-colloid
+make machine
+
+
+ Make.py -p ^colloid -a machine
+
+
+ Supporting info: examples/colloid, examples/srd
+
+
+
+ 4.6. COMPRESS package
+ Contents:
+ To install via make or Make.py:
+ make yes-compress
+make machine
+
+
+ Make.py -p compress -a machine
+
+
+ To un-install via make or Make.py:
+ make no-compress
+make machine
+
+
+ Make.py -p ^compress -a machine
+
+
+ Supporting info:
+
+
+
+ 4.7. CORESHELL package
+ Contents:
+ To install via make or Make.py:
+ make yes-coreshell
+make machine
+
+
+ Make.py -p coreshell -a machine
+
+
+ To un-install via make or Make.py:
+ make no-coreshell
+make machine
+
+
+ Make.py -p ^coreshell -a machine
+
+
+ Supporting info: examples/coreshell, Section howto 6.26
+
+
+
+ 4.8. DIPOLE package
+ Contents:
+ To install via make or Make.py:
+ make yes-dipole
+make machine
+
+
+ Make.py -p dipole -a machine
+
+
+ To un-install via make or Make.py:
+ make no-dipole
+make machine
+
+
+ Make.py -p ^dipole -a machine
+
+
+ Supporting info: examples/dipole
+
+
+
+ 4.9. FLD package
+ Contents:
+ To install via make or Make.py:
+ make yes-fld
+make machine
+
+
+ Make.py -p fld -a machine
+
+
+ To un-install via make or Make.py:
+ make no-fld
+make machine
+
+
+ Make.py -p ^fld -a machine
+
+
+ Supporting info:
+
+
+
+ 4.10. GPU package
+ Contents:
+ To install via make or Make.py:
+ make yes-gpu
+make machine
+
+
+ Make.py -p gpu -a machine
+
+
+ To un-install via make or Make.py:
+ make no-gpu
+make machine
+
+
+ Make.py -p ^gpu -a machine
+
+
+ Supporting info: examples/accelerate, bench/FERMI, bench/KEPLER
+
+
+
+ 4.11. GRANULAR package
+ Contents:
+ To install via make or Make.py:
+ make yes-granular
+make machine
+
+
+ Make.py -p granular -a machine
+
+
+ To un-install via make or Make.py:
+ make no-granular
+make machine
+
+
+ Make.py -p ^granular -a machine
+
+
+ Supporting info: examples/pour, bench/in.chute, Section howto 6.6
+
+
+
+ 4.12. KIM package
+ Contents:
+ To install via make or Make.py:
+ make yes-kim
+make machine
+
+
+ Make.py -p kim -a machine
+
+
+ To un-install via make or Make.py:
+ make no-kim
+make machine
+
+
+ Make.py -p ^kim -a machine
+
+
+ Supporting info: examples/kim
+
+
+
+ 4.13. KOKKOS package
+ Contents:
+ To install via make or Make.py:
+ make yes-kokkow
+make machine
+
+
+ Make.py -p kokkow -a machine
+
+
+ To un-install via make or Make.py:
+ make no-kokkow
+make machine
+
+
+ Make.py -p ^kokkow -a machine
+
+
+ Supporting info:
+ For the KOKKOS package, you have 3 choices when building. You can
+build with OMP or Cuda or Phi support. Phi support uses Xeon Phi
+chips in “native” mode. This can be done by setting the following
+variables in your Makefile.machine:
+
+- for OMP support, set OMP = yes
+- for Cuda support, set OMP = yes and CUDA = yes
+- for Phi support, set OMP = yes and MIC = yes
+
+ These can also be set as additional arguments to the make command, e.g.
+ make g++ OMP=yes MIC=yes
+
+
+ Building the KOKKOS package with CUDA support requires a Makefile
+machine that uses the NVIDIA “nvcc” compiler, as well as an
+appropriate “arch” setting appropriate to the GPU hardware and NVIDIA
+software you have on your machine. See
+src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine
+Makefile.
+ Examples: examples/accelerate, bench/FERMI, bench/KEPLER
+
+
+
+ 4.14. KSPACE package
+ Contents:
+ To install via make or Make.py:
+ make yes-kspace
+make machine
+
+
+ Make.py -p kspace -a machine
+
+
+ To un-install via make or Make.py:
+ make no-kspace
+make machine
+
+
+ Make.py -p ^kspace -a machine
+
+
+ Supporting info:
+ Examples: examples/peptide, bench/in.rhodo
+ Doc: Section howto 6.7, Section howto 6.8, Section howto 6.9
+
+
+
+ 4.15. MANYBODY package
+ Contents:
+ To install via make or Make.py:
+ make yes-manybody
+make machine
+
+
+ Make.py -p manybody -a machine
+
+
+ To un-install via make or Make.py:
+ make no-manybody
+make machine
+
+
+ Make.py -p ^manybody -a machine
+
+
+ Supporting info:
+ Examples: examples/comb, examples/eim, examples/nb3d, examples/vashishta
+
+
+
+ 4.16. MC package
+ Contents:
+ To install via make or Make.py:
+ make yes-mc
+make machine
+
+
+ Make.py -p mc -a machine
+
+
+ To un-install via make or Make.py:
+ make no-mc
+make machine
+
+
+ Make.py -p ^mc -a machine
+
+
+ Supporting info:
+
+
+
+ 4.17. MEAM package
+ Contents:
+ To install via make or Make.py:
+ make yes-meam
+make machine
+
+
+ Make.py -p meam -a machine
+
+
+ To un-install via make or Make.py:
+ make no-meam
+make machine
+
+
+ Make.py -p ^meam -a machine
+
+
+ Supporting info: examples/meam
+
+
+
+ 4.18. MISC package
+ Contents:
+ To install via make or Make.py:
+ make yes-misc
+make machine
+
+
+ Make.py -p misc -a machine
+
+
+ To un-install via make or Make.py:
+ make no-misc
+make machine
+
+
+ Make.py -p ^misc -a machine
+
+
+ Supporting info: examples/misc
+
+
+
+ 4.19. MOLECULE package
+ Contents:
+ To install via make or Make.py:
+ make yes-molecule
+make machine
+
+
+ Make.py -p molecule -a machine
+
+
+ To un-install via make or Make.py:
+ make no-molecule
+make machine
+
+
+ Make.py -p ^molecule -a machine
+
+
+ Supporting info: examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo, Section howto 6.3
+
+
+
+ 4.20. MPIIO package
+ Contents:
+ To install via make or Make.py:
+ make yes-mpiio
+make machine
+
+
+ Make.py -p mpiio -a machine
+
+
+ To un-install via make or Make.py:
+ make no-mpiio
+make machine
+
+
+ Make.py -p ^mpiio -a machine
+
+
+ Supporting info:
+
+
+
+ 4.21. OPT package
+ Contents:
+ To install via make or Make.py:
+ make yes-opt
+make machine
+
+
+ Make.py -p opt -a machine
+
+
+ To un-install via make or Make.py:
+ make no-opt
+make machine
+
+
+ Make.py -p ^opt -a machine
+
+
+ Supporting info: examples/accelerate, bench/KEPLER
+ For the OPT package, your Makefile.machine needs an additional
+settings for CCFLAGS.
+
+- CCFLAGS: add -restrict
+
+
+
+
+ 4.22. PERI package
+ Contents:
+ To install via make or Make.py:
+ make yes-peri
+make machine
+
+
+ Make.py -p peri -a machine
+
+
+ To un-install via make or Make.py:
+ make no-peri
+make machine
+
+
+ Make.py -p ^peri -a machine
+
+
+ Supporting info: examples/peri
+
+
+
+ 4.23. POEMS package
+ Contents:
+ To install via make or Make.py:
+ make yes-poems
+make machine
+
+
+ Make.py -p poems -a machine
+
+
+ To un-install via make or Make.py:
+ make no-poems
+make machine
+
+
+ Make.py -p ^poems -a machine
+
+
+ Supporting info: examples/rigid
+
+
+
+ 4.24. PYTHON package
+ Contents:
+ To install via make or Make.py:
+ make yes-python
+make machine
+
+
+ Make.py -p python -a machine
+
+
+ To un-install via make or Make.py:
+ make no-python
+make machine
+
+
+ Make.py -p ^python -a machine
+
+
+ Supporting info: examples/python
+
+
+
+ 4.25. QEQ package
+ Contents:
+ To install via make or Make.py:
+ make yes-qeq
+make machine
+
+
+ Make.py -p qeq -a machine
+
+
+ To un-install via make or Make.py:
+ make no-qeq
+make machine
+
+
+ Make.py -p ^qeq -a machine
+
+
+ Supporting info: examples/qeq
+
+
+
+ 4.26. REAX package
+ Contents:
+ To install via make or Make.py:
+ make yes-reax
+make machine
+
+
+ Make.py -p reax -a machine
+
+
+ To un-install via make or Make.py:
+ make no-reax
+make machine
+
+
+ Make.py -p ^reax -a machine
+
+
+ Supporting info: examples/reax
+
+
+
+ 4.27. REPLICA package
+ Contents:
+ To install via make or Make.py:
+ make yes-replica
+make machine
+
+
+ Make.py -p replica -a machine
+
+
+ To un-install via make or Make.py:
+ make no-replica
+make machine
+
+
+ Make.py -p ^replica -a machine
+
+
+ Supporting info: examples/neb, examples/prd, examples/tad, Section howto 6.5
+
+
+
+ 4.28. RIGID package
+ Contents:
+ To install via make or Make.py:
+ make yes-rigid
+make machine
+
+
+ Make.py -p rigid -a machine
+
+
+ To un-install via make or Make.py:
+ make no-rigid
+make machine
+
+
+ Make.py -p ^rigid -a machine
+
+
+ Supporting info: examples/ASPHERE, examples/rigid
+
+
+
+ 4.29. SHOCK package
+ Contents:
+ To install via make or Make.py:
+ make yes-shock
+make machine
+
+
+ Make.py -p shock -a machine
+
+
+ To un-install via make or Make.py:
+ make no-shock
+make machine
+
+
+ Make.py -p ^shock -a machine
+
+
+ Supporting info: examples/hugoniostat, examples/msst
+
+
+
+ 4.30. SNAP package
+ Contents:
+ To install via make or Make.py:
+ make yes-snap
+make machine
+
+
+ Make.py -p snap -a machine
+
+
+ To un-install via make or Make.py:
+ make no-snap
+make machine
+
+
+ Make.py -p ^snap -a machine
+
+
+ Supporting info: examples/snap
+
+
+
+ 4.31. SRD package
+ Contents:
+ To install via make or Make.py:
+ make yes-srd
+make machine
+
+
+ Make.py -p srd -a machine
+
+
+ To un-install via make or Make.py:
+ make no-srd
+make machine
+
+
+ Make.py -p ^srd -a machine
+
+
+ Supporting info:
+
+
+
+ 4.32. VORONOI package
+ Contents:
+ To install via make or Make.py:
+ make yes-voronoi
+make machine
+
+
+ Make.py -p voronoi -a machine
+
+
+ To un-install via make or Make.py:
+ make no-voronoi
+make machine
+
+
+ Make.py -p ^voronoi -a machine
+
+
+ Supporting info: examples/voronoi
+
+
+
+ 4.33. XTC package
+ Contents:
+ To install via make or Make.py:
+ make yes-xtc
+make machine
+
+
+ Make.py -p xtc -a machine
+
+
+ To un-install via make or Make.py:
+ make no-xtc
+make machine
+
+
+ Make.py -p ^xtc -a machine
+
+
+ Supporting info:
- 4.13. User packages
+ 4.34. User packages
The current list of user-contributed packages is as follows:
-
-
-
-
-
-
-
+
+
+
+
+
+
+
| Package |
@@ -679,7 +1389,7 @@ serial.
Pic/movie |
Library |
-| USER-ATC |
+ | USER-ATC |
atom-to-continuum coupling |
Jones & Templeton & Zimmerman (1) |
fix atc |
@@ -687,7 +1397,7 @@ serial.
atc |
lib/atc |
-| USER-AWPMD |
+ | USER-AWPMD |
wave-packet MD |
Ilya Valuev (JIHT) |
pair_style awpmd/cut |
@@ -698,7 +1408,7 @@ serial.
lib/awpmd |
-| USER-CG-CMM |
+ | USER-CG-CMM |
coarse-graining model |
Axel Kohlmeyer (Temple U) |
pair_style lj/sdk |
@@ -709,7 +1419,7 @@ serial.
-| USER-COLVARS |
+ | USER-COLVARS |
collective variables |
Fiorin & Henin & Kohlmeyer (2) |
fix colvars |
@@ -717,7 +1427,7 @@ serial.
colvars |
lib/colvars |
-| USER-CUDA |
+ | USER-CUDA |
NVIDIA GPU styles |
Christian Trott (U Tech Ilmenau) |
Section accelerate |
@@ -728,7 +1438,7 @@ serial.
lib/cuda |
-| USER-DIFFRACTION |
+ | USER-DIFFRACTION |
virutal x-ray and electron diffraction |
Shawn Coleman (ARL) |
compute xrd |
@@ -742,7 +1452,7 @@ serial.
-| USER-DPD |
+ | USER-DPD |
dissipative particle dynamics (DPD) |
Larentzos & Mattox & Brennan (5) |
src/USER-DPD/README |
@@ -756,7 +1466,7 @@ serial.
-| USER-DRUDE |
+ | USER-DRUDE |
Drude oscillators |
Dequidt & Devemy & Padua (3) |
tutorial |
@@ -770,7 +1480,7 @@ serial.
-| USER-EFF |
+ | USER-EFF |
electron force field |
Andres Jaramillo-Botero (Caltech) |
pair_style eff/cut |
@@ -781,7 +1491,7 @@ serial.
-| USER-FEP |
+ | USER-FEP |
free energy perturbation |
Agilio Padua (U Blaise Pascal Clermont-Ferrand) |
compute fep |
@@ -795,7 +1505,7 @@ serial.
-| USER-H5MD |
+ | USER-H5MD |
dump output via HDF5 |
Pierre de Buyl (KU Leuven) |
dump h5md |
@@ -809,7 +1519,7 @@ serial.
lib/h5md |
-| USER-INTEL |
+ | USER-INTEL |
Vectorized CPU and Intel(R) coprocessor styles |
- Michael Brown (Intel)
@@ -826,7 +1536,7 @@ serial.
|
-| USER-LB |
+ | USER-LB |
Lattice Boltzmann fluid |
Colin Denniston (U Western Ontario) |
fix lb/fluid |
@@ -840,7 +1550,7 @@ serial.
-| USER-MGPT |
+ | USER-MGPT |
fast MGPT multi-ion potentials |
Tomas Oppelstrup & John Moriarty (LLNL) |
pair_style mgpt |
@@ -854,7 +1564,7 @@ serial.
-| USER-MISC |
+ | USER-MISC |
single-file contributions |
USER-MISC/README |
USER-MISC/README |
@@ -871,7 +1581,7 @@ serial.
-| USER-MOLFILE |
+ | USER-MOLFILE |
VMD molfile plug-ins |
Axel Kohlmeyer (Temple U) |
dump molfile |
@@ -885,7 +1595,7 @@ serial.
VMD-MOLFILE |
-| USER-OMP |
+ | USER-OMP |
OpenMP threaded styles |
Axel Kohlmeyer (Temple U) |
Section accelerate |
@@ -902,7 +1612,7 @@ serial.
-| USER-PHONON |
+ | USER-PHONON |
phonon dynamical matrix |
Ling-Ti Kong (Shanghai Jiao Tong U) |
fix phonon |
@@ -916,7 +1626,7 @@ serial.
-| USER-QMMM |
+ | USER-QMMM |
QM/MM coupling |
Axel Kohlmeyer (Temple U) |
fix qmmm |
@@ -927,7 +1637,7 @@ serial.
lib/qmmm |
-| USER-QTB |
+ | USER-QTB |
quantum nuclear effects |
Yuan Shen (Stanford) |
fix qtb fix_qbmsst |
@@ -941,7 +1651,7 @@ serial.
-| USER-QUIP |
+ | USER-QUIP |
QUIP/libatoms interface |
Albert Bartok-Partay (U Cambridge) |
pair_style quip |
@@ -952,7 +1662,7 @@ serial.
lib/quip |
-| USER-REAXC |
+ | USER-REAXC |
C version of ReaxFF |
Metin Aktulga (LBNL) |
pair_style reaxc |
@@ -966,7 +1676,7 @@ serial.
-| USER-SMD |
+ | USER-SMD |
smoothed Mach dynamics |
Georg Ganzenmuller (EMI) |
userguide.pdf |
@@ -980,7 +1690,7 @@ serial.
-| USER-SMTBQ |
+ | USER-SMTBQ |
Second Moment Tight Binding - QEq potential |
Salles & Maras & Politano & Tetot (4) |
pair_style smtbq |
@@ -994,7 +1704,7 @@ serial.
-| USER-SPH |
+ | USER-SPH |
smoothed particle hydrodynamics |
Georg Ganzenmuller (EMI) |
userguide.pdf |
@@ -1005,7 +1715,7 @@ serial.
-| USER-TALLY |
+ | USER-TALLY |
Pairwise tallied computes |
Axel Kohlmeyer (Temple U) |
compute |
@@ -1019,7 +1729,21 @@ serial.
-| |
+ | USER-VTK |
+VTK-style dumps |
+Berger and Queteschiner (6) |
+compute custom/vtk |
+
+ |
+
+ |
+lib/vtk |
+
+| |
|
|
|
@@ -1041,13 +1765,11 @@ 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).
-(4) The USER-DPD package was created by James Larentzos, Timothy
-Mattox, and John Brennan (Army Research Lab (ARL) and Engility Corp).
-If the Library is not listed as lib/package, then it is a third-party
-library not included in the LAMMPS distribution. See the
-src/package/Makefile.lammps file for info on where to download the
-library from.
-The “Doc page” column links to either a portion of the
+ (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 of the manual, or an input script
command implemented as part of the package, or to additional
documentation provided within the package.
@@ -1061,31 +1783,15 @@ 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 the src/package/Makefile.lammps file for info on where to download
-the library. Section start of the
-manual also gives details on how to build LAMMPS with both kinds of
-auxiliary libraries.
-Except where explained below, all of these packages can be installed,
-and LAMMPS re-built, by issuing these commands from the src dir.
-make yes-user-package
-make machine
-or
-Make.py -p package -a machine
-
- To un-install the package and re-build LAMMPS without it:
-make no-user-package
-make machine
-or
-Make.py -p ^package -a machine
-
- “Package” is the name of the package (in this case without the user
-prefix) in lower-case letters, e.g. drude or phonon, and “machine” is
-the build target, e.g. mpi or serial.
+See details on all of this below for individual packages.
+
- 4.14. USER-ATC package
+ 4.35. USER-ATC package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ Supporting info:
This package implements a “fix atc” command which can be used in a
LAMMPS input script. This fix can be employed to either do concurrent
coupling of MD with FE-based physics surrogates or on-the-fly
@@ -1102,10 +1808,15 @@ libraries.
sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
you have questions.
- Examples: examples/USER/atc
+
- 4.15. USER-AWPMD package
+ 4.36. USER-AWPMD package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ Supporting info:
This package contains a LAMMPS implementation of the Antisymmetrized
Wave Packet Molecular Dynamics (AWPMD) method.
See the doc page for the pair_style awpmd/cut command to get started.
@@ -1117,10 +1828,29 @@ libraries.
The person who created this package is Ilya Valuev at the JIHT in
Russia (valuev at physik.hu-berlin.de). Contact him directly if you
have questions.
- Examples: examples/USER/awpmd
+
- 4.16. USER-CG-CMM package
+ 4.37. USER-CG-CMM package
+ Contents:
+ To install via make or Make.py:
+ make yes-body
+make machine
+
+
+ Make.py -p body -a machine
+
+
+ To un-install via make or Make.py:
+ make no-body
+make machine
+
+
+ Make.py -p ^body -a machine
+
+
+ Supporting info:
This package implements 3 commands which can be used in a LAMMPS input
script:
@@ -1152,10 +1882,15 @@ have not been testing with all kinds of potential parameters and
simulation systems.
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
- Examples: examples/USER/cg-cmm
+
- 4.17. USER-COLVARS package
+ 4.38. USER-COLVARS package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ Supporting info:
This package implements the “fix colvars” command which can be
used in a LAMMPS input script.
This fix allows to use “collective variables” to implement
@@ -1181,10 +1916,15 @@ Thus the current version of this package should be considered
beta quality.
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
- Examples: examples/USER/colvars
+Contents:
+To install via make or Make.py:
+To un-install via make or Make.py:
+Supporting info:
+
- 4.18. USER-CUDA package
+ 4.39. USER-CUDA package
This package provides acceleration of various LAMMPS pair styles, fix
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
GPUs.
@@ -1199,10 +1939,15 @@ 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
+Contents:
+To install via make or Make.py:
+To un-install via make or Make.py:
+Supporting info:
+
- 4.19. USER-DIFFRACTION package
+ 4.40. USER-DIFFRACTION package
This package contains the commands neeed to calculate x-ray and
electron diffraction intensities based on kinematic diffraction
theory.
@@ -1215,10 +1960,29 @@ theory.
The person who created this package is Shawn P. Coleman
(shawn.p.coleman8.ctr at mail.mil) while at the University of
Arkansas. Contact him directly if you have questions.
+ Examples: examples/USER/diffraction
+ Contents:
+ To install via make or Make.py:
+ make yes-body
+make machine
+
+ Make.py -p body -a machine
+
+
+ To un-install via make or Make.py:
+ make no-body
+make machine
+
+
+ Make.py -p ^body -a machine
+
+
+ Supporting info:
+
- 4.20. USER-DPD package
+ 4.41. USER-DPD package
This package implements the dissipative particle dynamics (DPD) method
under isothermal, isoenergetic, isobaric and isenthalpic conditions.
The DPD equations of motion are integrated efficiently through the
@@ -1239,10 +2003,31 @@ Shardlow splitting algorithm.
(james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at
engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil).
Contact them directly if you have questions.
+ To install via make or Make.py:
+ make yes-body
+make machine
+
+ Make.py -p body -a machine
+
+
+ To un-install via make or Make.py:
+ make no-body
+make machine
+
+
+ Make.py -p ^body -a machine
+
+
+ Examples: examples/USER/dpd
+
- 4.21. USER-DRUDE package
+ 4.42. USER-DRUDE package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ Supporting info:
This package implements methods for simulating polarizable systems
in LAMMPS using thermalized Drude oscillators.
See these doc pages and their related commands to get started:
@@ -1259,10 +2044,32 @@ in LAMMPS using thermalized Drude oscillators.
Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
Contact him directly if you have questions. Co-authors: Julien Devemy,
Agilio Padua.
+ To install via make or Make.py:
+ make yes-body
+make machine
+
+ Make.py -p body -a machine
+
+
+ To un-install via make or Make.py:
+ make no-body
+make machine
+
+
+ Make.py -p ^body -a machine
+
+
+ Examples: examples/USER/drude
+ Doc: Section howto 6.27
+
- 4.22. USER-EFF package
+ 4.43. USER-EFF package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ Supporting info:
This package contains a LAMMPS implementation of the electron Force
Field (eFF) currently under development at Caltech, as described in
A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
@@ -1293,10 +2100,31 @@ examples/USER/eff.
The person who created this package is Andres Jaramillo-Botero at
CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
have questions.
+ To install via make or Make.py:
+ make yes-body
+make machine
+
+ Make.py -p body -a machine
+
+
+ To un-install via make or Make.py:
+ make no-body
+make machine
+
+
+ Make.py -p ^body -a machine
+
+
+ Examples: examples/USER/eff
+
- 4.23. USER-FEP package
+ 4.44. USER-FEP package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ Supporting info:
This package provides methods for performing free energy perturbation
simulations with soft-core pair potentials in LAMMPS.
See these doc pages and their related commands to get started:
@@ -1308,10 +2136,31 @@ simulations with soft-core pair potentials in LAMMPS.
The person who created this package is Agilio Padua at Universite
Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
Contact him directly if you have questions.
+ To install via make or Make.py:
+ make yes-body
+make machine
+
+ Make.py -p body -a machine
+
+
+ To un-install via make or Make.py:
+ make no-body
+make machine
+
+
+ Make.py -p ^body -a machine
+
+
+ Examples: examples/USER/fep
+
- 4.24. USER-H5MD package
+ 4.45. USER-H5MD package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ Supporting info:
This package contains a dump h5md command for
performing a dump of atom properties in HDF5 format. HDF5 files are binary, portable and self-describing and can be
examined and used by a variety of auxiliary tools. The output HDF5
@@ -1322,10 +2171,14 @@ citation to a paper describing the format.
The person who created this package and the underlying H5MD format is
Pierre de Buyl at KU Leuven (see http://pdebuyl.be). Contact him
directly if you have questions.
-
+
- 4.25. USER-INTEL package
+ 4.46. USER-INTEL package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ Supporting info:
This package provides options for performing neighbor list and
non-bonded force calculations in single, mixed, or double precision
and also a capability for accelerating calculations with an
@@ -1334,10 +2187,33 @@ Intel(R) Xeon Phi(TM) coprocessor.
Section_accelerate
The person who created this package is W. Michael 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
+
+For Phi mode add the following in addition to the CPU mode flags:
+
+- CCFLAGS: add -DLMP_INTEL_OFFLOAD and
+- LINKFLAGS: add -offload
+
+And also add this to CCFLAGS:
+
+-offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs="gather_scatter_loop_unroll=4""
+
+Examples: examples/accelerate, bench/KEPLER
+
- 4.26. USER-LB package
+ 4.47. USER-LB package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ 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.
@@ -1346,10 +2222,31 @@ influenced by hydrodynamic forces.
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.
+ To install via make or Make.py:
+ make yes-body
+make machine
+
+ Make.py -p body -a machine
+
+
+ To un-install via make or Make.py:
+ make no-body
+make machine
+
+
+ Make.py -p ^body -a machine
+
+
+ Examples: examples/USER/lb
+
- 4.27. USER-MGPT package
+ 4.48. USER-MGPT package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ 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
@@ -1369,10 +2266,31 @@ Oppelstrup at LLNL.
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.
+ To install via make or Make.py:
+ make yes-body
+make machine
+
+ Make.py -p body -a machine
+
+
+ To un-install via make or Make.py:
+ make no-body
+make machine
+
+
+ Make.py -p ^body -a machine
+
+
+ Examples: examples/USER/mgpt
+
- 4.28. USER-MISC package
+ 4.49. USER-MISC package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ 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).
@@ -1386,10 +2304,31 @@ compute, pair, etc sections.
src/USER-MISC/README file.
You should contact the author directly if you have specific questions
about the feature or its coding.
+ To install via make or Make.py:
+ make yes-body
+make machine
+
+ Make.py -p body -a machine
+
+
+ To un-install via make or Make.py:
+ make no-body
+make machine
+
+
+ Make.py -p ^body -a machine
+
+
+ Examples: examples/USER/misc
+
- 4.29. USER-MOLFILE package
+ 4.50. USER-MOLFILE package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ Supporting info:
This package contains a dump molfile command which uses molfile
plugins that are bundled with the
VMD molecular visualization and
@@ -1405,10 +2344,14 @@ application itself.
dump molfile
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
-
+
- 4.30. USER-OMP package
+ 4.51. USER-OMP package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ Supporting info:
This package provides OpenMP multi-threading support and
other optimizations of various LAMMPS pair styles, dihedral
styles, and fix styles.
@@ -1416,10 +2359,17 @@ styles, and fix styles.
Section_accelerate
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
+
+Examples: examples/accelerate, bench/KEPLER
+
- 4.31. USER-PHONON package
+ 4.52. USER-PHONON package
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.
@@ -1428,10 +2378,31 @@ relations, directly from molecular dynamics simulations.
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.
+ To install via make or Make.py:
+ make yes-body
+make machine
+
+ Make.py -p body -a machine
+
+
+ To un-install via make or Make.py:
+ make no-body
+make machine
+
+
+ Make.py -p ^body -a machine
+
+
+ Examples: examples/USER/phonon
+
- 4.32. USER-QMMM package
+ 4.53. USER-QMMM package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ 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 package.
@@ -1445,10 +2416,14 @@ without changes to LAMMPS itself.
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.
-
+
- 4.33. USER-QTB package
+ 4.54. USER-QTB package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ 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
@@ -1467,10 +2442,54 @@ 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.
+ To install via make or Make.py:
+ make yes-body
+make machine
+
+ Make.py -p body -a machine
+
+
+ To un-install via make or Make.py:
+ make no-body
+make machine
+
+
+ Make.py -p ^body -a machine
+
+
+ Examples: examples/USER/qtb
+
+ 4.55. USER-QUIP package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ Supporting info:
+ Examples: examples/USER/quip
+
+
- 4.34. USER-REAXC package
+ 4.56. USER-REAXC package
+ Contents:
+ To install via make or Make.py:
+ make yes-body
+make machine
+
+
+ Make.py -p body -a machine
+
+
+ To un-install via make or Make.py:
+ make no-body
+make machine
+
+
+ Make.py -p ^body -a machine
+
+
+ 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
@@ -1495,10 +2514,15 @@ of how to use it in LAMMPS.
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
+
- 4.35. USER-SMD package
+ 4.57. USER-SMD package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ Supporting info:
This package implements smoothed Mach dynamics (SMD) in
LAMMPS. Currently, the package has the following features:
@@ -1519,10 +2543,29 @@ from *.STL files.
- Examples: examples/USER/smd
+
- 4.36. USER-SMTBQ package
+ 4.58. USER-SMTBQ package
+ Contents:
+ To install via make or Make.py:
+ make yes-body
+make machine
+
+
+ Make.py -p body -a machine
+
+
+ To un-install via make or Make.py:
+ make no-body
+make machine
+
+
+ Make.py -p ^body -a machine
+
+
+ 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
@@ -1533,10 +2576,29 @@ examples/USER/smtbq.
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
+
- 4.37. USER-SPH package
+ 4.59. USER-SPH package
+ Contents:
+ To install via make or Make.py:
+ make yes-body
+make machine
+
+
+ Make.py -p body -a machine
+
+
+ To un-install via make or Make.py:
+ make no-body
+make machine
+
+
+ Make.py -p ^body -a machine
+
+
+ Supporting info:
This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:
+ 4.60. USER-TALLY package
+ Contents:
+ To install via make or Make.py:
+ make yes-body
+make machine
+
+
+ Make.py -p body -a machine
+
+
+ To un-install via make or Make.py:
+ make no-body
+make machine
+
+
+ Make.py -p ^body -a machine
+
+
+ Supporting info:
+ Examples: examples/USER/tally
+
+
+ 4.61. USER-VTK package
+ Contents:
+ To install via make or Make.py:
+ To un-install via make or Make.py:
+ Supporting info:
+ Examples: examples/USER/tally
| | | | | | | | | | | | | | | |