diff --git a/src/GPU/README b/src/GPU/README new file mode 100644 index 0000000000000000000000000000000000000000..ea1fa702853bfd5881fede970be51ae3444a8211 --- /dev/null +++ b/src/GPU/README @@ -0,0 +1,11 @@ +This package implements GPU optimizations of various LAMMPS styles. + +This package uses an external library in lib/gpu which must be +compiled before making LAMMPS. See the lib/gpu/README file and the +LAMMPS manual for information on building LAMMPS with external +libraries. The settings in the Makefile.lammps file in that directory +must be correct for LAMMPS to build correctly with this package +installed. + +The people who created this package are Mike Brown (while at Sandia +and ORNL) and Trung Nguyen (while at ORNL). diff --git a/src/KOKKOS/README b/src/KOKKOS/README new file mode 100644 index 0000000000000000000000000000000000000000..e1cf04c7e84efaeb0d6fec982e414bc46867baf4 --- /dev/null +++ b/src/KOKKOS/README @@ -0,0 +1,21 @@ +This package implements optimizations of various LAMMPS styles using +the Kokkos library, which is part of Trilinos +(http://trilinos.sandia.gov/packages/kokkos). It's a templated C++ +library that provides two key abstractions for an application like +LAMMPS. First, it allows a single implementation of an application +kernel (e.g. a pair style) to run efficiently on different kinds of +hardware, such as a GPU, Intel Phi, or many-core chip. + +This package uses an external library in lib/kokkos. However the +"library" is mostly header files and is auto-built when building +LAMMPS with this package installed, so no special pre-build of the +library is necessary. See the lib/kokkos/README file and the LAMMPS +manual for information on building LAMMPS with external libraries. +The settings in the Makefile.lammps file in that directory must be +correct for LAMMPS to build correctly with this package installed. + +This package was developed primaritly by Christian Trott (Sandia) with +contributions of various styles by others, including Sikandar Mashayak +(UIUC). The underlying Kokkos library was written primarily by Carter +Edwards, Christian Trott, and Dan Sunderland (all Sandia). + diff --git a/src/MEAM/README b/src/MEAM/README new file mode 100644 index 0000000000000000000000000000000000000000..2f2bf275fb92ffcca01c794d11626b8e46c8b628 --- /dev/null +++ b/src/MEAM/README @@ -0,0 +1,11 @@ +This package implements the MEAM potential as a LAMMPS pair style. + +This package uses an external library in lib/meam which must be +compiled before making LAMMPS. See the lib/meam/README file and the +LAMMPS manual for information on building LAMMPS with external +libraries. The settings in the Makefile.lammps file in that directory +must be correct for LAMMPS to build correctly with this package +installed. + +The person who created the MEAM library and this pair style is Greg +Wagner (while at Sandia, now at Northwestern U). diff --git a/src/POEMS/README b/src/POEMS/README new file mode 100644 index 0000000000000000000000000000000000000000..3c56d5c74f619bc114a26a28e663a4a6de604746 --- /dev/null +++ b/src/POEMS/README @@ -0,0 +1,12 @@ +This package implements the fix poems command for coupling multiple +rigid bodies together. + +This package uses an external library in lib/poems which must be +compiled before making LAMMPS. See the lib/poems/README file and the +LAMMPS manual for information on building LAMMPS with external +libraries. The settings in the Makefile.lammps file in that directory +must be correct for LAMMPS to build correctly with this package +installed. + +The people who created the POEMS library and this fix are Rudranarayan +Mukherjee (while at RPI, now at NASA) and Kurt Anderson (RPI). diff --git a/src/USER-ATC/README b/src/USER-ATC/README index 85e2c1a5703fbd9b5f7362ad430d0e78e52ea92a..06ab91ed809178679532185b24e596680a13ec77 100644 --- a/src/USER-ATC/README +++ b/src/USER-ATC/README @@ -12,7 +12,9 @@ There are example scripts for using this package in examples/USER/atc. This package uses an external library in lib/atc which must be compiled before making LAMMPS. See the lib/atc/README file and the LAMMPS manual for information on building LAMMPS with external -libraries. +libraries. The settings in the Makefile.lammps file in that directory +must be correct for LAMMPS to build correctly with this package +installed. The primary people who created this package are Reese Jones (rjones at sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon diff --git a/src/USER-AWPMD/README b/src/USER-AWPMD/README index 4dd16fca46fec1efde34010ffab3352e8b27f723..4a853f5059d72bb2a1e299f273c53fff744eff6e 100644 --- a/src/USER-AWPMD/README +++ b/src/USER-AWPMD/README @@ -9,7 +9,9 @@ examples/USER/awpmd. This package uses an external library in lib/awpmd which must be compiled before making LAMMPS. See the lib/awpmd/README file and the LAMMPS manual for information on building LAMMPS with external -libraries. +libraries. The settings in the Makefile.lammps file in that directory +must be correct for LAMMPS to build correctly with this package +installed. 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 diff --git a/src/USER-COLVARS/README b/src/USER-COLVARS/README index 3a0593946c0d39b9d9d86309960c6e4bd95747f6..20551986cd9141801d0f733aafe7cff51475c7e4 100644 --- a/src/USER-COLVARS/README +++ b/src/USER-COLVARS/README @@ -1,36 +1,37 @@ 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 -Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella -Sampling and Restraints. This code consists of two parts: +This fix allows use of "collective variables" to implement Adaptive +Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and +Restraints. -- a portable collective variable module library written - and maintained by Giacomo Fiorin (ICMS, Temple University, - Philadelphia, PA, USA) and Jerome Henin (IBPC, CNRS, - Paris, France). +This package uses an external library in lib/colvars which must be +compiled before making LAMMPS. See the lib/colvars/README file and +the LAMMPS manual for information on building LAMMPS with external +libraries. The settings in the Makefile.lammps file in that directory +must be correct for LAMMPS to build correctly with this package +installed. - A copy of this code is located in the directory lib/colvars - and needs to be compiled first. More info about this code - can be found at: http://colvars.github.io +The external library is a portable collective variable module library +written and maintained by Giacomo Fiorin (ICMS, Temple University, +Philadelphia, PA, USA) and Jerome Henin (IBPC, CNRS, Paris, France). - and in the publications: +More info about this library can be found at: http://colvars.github.io - Using collective variables to drive molecular dynamics - simulations, +and in these publications: - Giacomo Fiorin, Michael L. Klein & Jérôme Hénin: - Molecular Physics, 111, 3345-3362 (2013) +Using collective variables to drive molecular dynamics simulations, +Giacomo Fiorin, Michael L. Klein & Jérôme Hénin: Molecular Physics, +111, 3345-3362 (2013) - Exploring Multidimensional Free Energy Landscapes Using - Time-Dependent Biases on Collective Variables, - J. Hénin, G. Fiorin, C. Chipot, and M. L. Klein, - J. Chem. Theory Comput., 6, 35-47 (2010). +Exploring Multidimensional Free Energy Landscapes Using Time-Dependent +Biases on Collective Variables, J. Hénin, G. Fiorin, C. Chipot, and +M. L. Klein, J. Chem. Theory Comput., 6, 35-47 (2010). -- the colvars fix and a thin interface layer, which exchanges - information between LAMMPS and the collective variable module. - This interface was written and is maintained by - Axel Kohlmeyer (akohlmey@gmail.com) +The colvars fix implementes a thin interface layer, which exchanges +information between LAMMPS and the collective variable module. This +interface was written and is maintained by Axel Kohlmeyer +(akohlmey@gmail.com) See the doc page of fix colvars for more details. @@ -45,5 +46,4 @@ The person who created this package is Axel Kohlmeyer at Temple U --------------------------------- - Version: 2014-08-13 diff --git a/src/USER-CUDA/README b/src/USER-CUDA/README index 74e5ad60c00f412e63a2143fa7059ea6b4080000..b9d2c07f8a5235d57b0e445cab59831536923486 100644 --- a/src/USER-CUDA/README +++ b/src/USER-CUDA/README @@ -12,7 +12,9 @@ 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. +libraries. The settings in the Makefile.lammps file in that directory +must be correct for LAMMPS to build correctly with this package +installed. The person who created this package is Christian Trott at the University of Technology Ilmenau, Germany (christian.trott at diff --git a/src/USER-QMMM/README b/src/USER-QMMM/README index 16bbdcc708ba9c09c7668ab2060feae8e85d82d0..909c5bd286ea758010e574b64e0f418cb836dea0 100644 --- a/src/USER-QMMM/README +++ b/src/USER-QMMM/README @@ -4,6 +4,13 @@ in a LAMMPS input script. This fix enables LAMMPS to be used in a QM/MM simulation, currently only in combination with pw.x code from the Quantum ESPRESSO package. +This package uses an external library in lib/qmmm which must be +compiled before making LAMMPS. See the lib/qmmm/README file and the +LAMMPS manual for information on building LAMMPS with external +libraries. The settings in the Makefile.lammps file in that directory +must be correct for LAMMPS to build correctly with this package +installed. + The person who created this package is Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact him directly if you have questions. diff --git a/src/VORONOI/README b/src/VORONOI/README index 118abfa296c68daff2d88021a29f3dd3b02609b6..ef408d088e0d75d7b63b1c47ae706a7ef430425e 100644 --- a/src/VORONOI/README +++ b/src/VORONOI/README @@ -2,35 +2,22 @@ The VORONOI package adds a compute voronoi/atom command which calculates a Voronoi tesselation of the system. It uses the Voro++ library, available at http://math.lbl.gov/voro++ to -compute the tesselation locally on each processor. +compute the tesselation locally on each processor. Voro++ was +develped by Chris H. Rycroft while at UC Berkeley / Lawrence Berkeley +Laboratory. + +That library can be downloaded and built in lib/voronoi or elsewhere +on your system, which must be done before bulding LAMMPS with this +package. Details of the download, build, and install process for +Voro++ are given in the lib/voronoi/README file, and scripts are +provided to help automate the process. Also see the LAMMPS manual for +general information on building LAMMPS with external libraries. The +settings in the Makefile.lammps file in lib/voronoi must be correct +for LAMMPS to build correctly with this package installed. + +Once you have successfully built LAMMPS with this package and Voro++, +you can test it using an input file from the examples dir: -== Installation of the Voro++ library == - -1. Download Voro++ at http://math.lbl.gov/voro++/download - which gives instructions for using SVN to check-out the source: - % svn checkout https://codeforge.lbl.gov/anonscm/voro/trunk - -2. compile Voro++ - % make - -3. install Voro++ at the default location (/usr/local) - % sudo make install - -3b. ..or change the PREFIX variable in the config.mk file - to a location that is writable by the user i.e. - PREFIX=/home/maxuser/install/ - -4. In the LAMMPS src directory add the VORONOI package - % make yes-voronoi - -4b. if a different PREFIX than the default was used to install Voro++ - update the paths in the src/VORONOI/Makefile.lammps file - -5. Compile LAMMPS (you should know how that works) - -== Run tests == - -Run the includes test input file ./lmp_serial < lammps/examples/voronoi/in.voronoi | grep '^TEST_' The output should conclude with 'TEST_DONE' and every line should