Loading cmake/CMakeLists.txt +12 −7 Original line number Diff line number Diff line Loading @@ -178,7 +178,7 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM) USER-QUIP USER-QMMM USER-YAFF) set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) set(OTHER_PACKAGES CORESHELL QEQ) foreach(PKG ${DEFAULT_PACKAGES}) Loading Loading @@ -559,10 +559,15 @@ if(PKG_USER-PLUMED) message(STATUS "PLUMED download requested - we will build our own") include(ExternalProject) ExternalProject_Add(plumed_build URL https://github.com/plumed/plumed2/releases/download/v2.4.3/plumed-src-2.4.3.tgz URL_MD5 b1be7c48971627febc11c61b70767fc5 URL https://github.com/plumed/plumed2/releases/download/v2.4.4/plumed-src-2.4.4.tgz URL_MD5 71ed465bdc7c2059e282dbda8d564e71 BUILD_IN_SOURCE 1 CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> ${CONFIGURE_REQUEST_PIC}) CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> ${CONFIGURE_REQUEST_PIC} --enable-modules=all CXX=${CMAKE_MPI_CXX_COMPILER} CC=${CMAKE_MPI_C_COMPILER} ) ExternalProject_get_property(plumed_build INSTALL_DIR) set(PLUMED_INSTALL_DIR ${INSTALL_DIR}) list(APPEND LAMMPS_DEPS plumed_build) Loading Loading @@ -614,8 +619,8 @@ if(PKG_USER-SMD) message(STATUS "Eigen3 download requested - we will build our own") include(ExternalProject) ExternalProject_Add(Eigen3_build URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz URL_MD5 1a47e78efe365a97de0c022d127607c3 URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07 CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" ) ExternalProject_get_property(Eigen3_build SOURCE_DIR) Loading Loading @@ -762,7 +767,7 @@ endif() # Basic system tests (standard libraries, headers, functions, types) # ######################################################################## include(CheckIncludeFileCXX) foreach(HEADER math.h) foreach(HEADER cmath) check_include_file_cxx(${HEADER} FOUND_${HEADER}) if(NOT FOUND_${HEADER}) message(FATAL_ERROR "Could not find needed header - ${HEADER}") Loading doc/github-development-workflow.md +11 −8 Original line number Diff line number Diff line Loading @@ -50,8 +50,8 @@ This is indicated by who the pull request is assigned to. LAMMPS core developers can self-assign or they can decide to assign a pull request to a different LAMMPS developer. Being assigned to a pull request means, that this pull request may need some work and the assignee is tasked to determine what this might be needed or not, and may either implement the required changes or ask the submitter of the pull request to implement determine whether this might be needed or not, and may either implement the required changes or ask the submitter of the pull request to implement them. Even though, all LAMMPS developers may have write access to pull requests (if enabled by the submitter, which is the default), only the submitter or the assignee of a pull request may do so. During this Loading @@ -76,12 +76,15 @@ People can be assigned to review a pull request in two ways: Reviewers are requested to state their appraisal of the proposed changes and either approve or request changes. People may unassign themselves from review, if they feel not competent about the changes proposed. At least one review from a LAMMPS developer with write access is required before merging in addition to the automated compilation tests. The feature, that reviews from code owners are "hard" reviews (i.e. they must all be approved before merging is allowed), is currently disabled and it is in the discretion of the merge maintainer to assess when a sufficient degree of approval has been reached. Reviews may be least two approvals from LAMMPS developers with write access are required before merging in addition to the automated compilation tests. Merging counts as implicit approval, so does submission of a pull request (by a LAMMPS developer). So the person doing the merge may not also submit an approving review. The feature, that reviews from code owners are "hard" reviews (i.e. they must all be approved before merging is allowed), is currently disabled and it is in the discretion of the merge maintainer to assess when a sufficient degree of approval, especially from external contributors, has been reached in these cases. Reviews may be (automatically) dismissed, when the reviewed code has been changed, and then approval is required a second time. Loading doc/src/Build_extras.txt +2 −1 Original line number Diff line number Diff line Loading @@ -95,6 +95,7 @@ which GPU hardware to build for. GPU_ARCH settings for different GPU hardware is as follows: sm_12 or sm_13 for GT200 (supported by CUDA 3.2 until CUDA 6.5) sm_20 or sm_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5) sm_30 or sm_35 or sm_37 for Kepler (supported since CUDA 5) sm_50 or sm_52 for Maxwell (supported since CUDA 6) Loading Loading @@ -135,7 +136,7 @@ specified by the "-m" switch. For your convenience, machine makefiles for "mpi" and "serial" are provided, which have the same settings as the corresponding machine makefiles in the main LAMMPS source folder. In addition you can alter 4 important settings in the Makefile.machine you start from via the corresponding -h, -a, -p, -e Makefile.machine you start from via the corresponding -c, -a, -p, -e switches (as in the examples above), and also save a copy of the new Makefile if desired: Loading doc/src/Build_link.txt +1 −1 Original line number Diff line number Diff line Loading @@ -78,7 +78,7 @@ description of the Python interface to LAMMPS, which wraps the C-style interface. See the sample codes in examples/COUPLE/simple for examples of C++ and C and Fortran codes that invoke LAMMPS thru its library interface. C and Fortran codes that invoke LAMMPS through its library interface. Other examples in the COUPLE directory use coupling ideas discussed on the "Howto couple"_Howto_couple.html doc page. Loading doc/src/Commands_bond.txt +5 −0 Original line number Diff line number Diff line Loading @@ -37,6 +37,7 @@ OPT. "harmonic (iko)"_bond_harmonic.html, "harmonic/shift (o)"_bond_harmonic_shift.html, "harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html, "mm3"_bond_mm3.html, "morse (o)"_bond_morse.html, "nonlinear (o)"_bond_nonlinear.html, "oxdna/fene"_bond_oxdna.html, Loading Loading @@ -67,10 +68,12 @@ OPT. "cosine/shift (o)"_angle_cosine_shift.html, "cosine/shift/exp (o)"_angle_cosine_shift_exp.html, "cosine/squared (o)"_angle_cosine_squared.html, "cross"_angle_cross.html, "dipole (o)"_angle_dipole.html, "fourier (o)"_angle_fourier.html, "fourier/simple (o)"_angle_fourier_simple.html, "harmonic (iko)"_angle_harmonic.html, "mm3"_angle_mm3.html, "quartic (o)"_angle_quartic.html, "sdk (o)"_angle_sdk.html, "table (o)"_angle_table.html :tb(c=4,ea=c) Loading Loading @@ -120,8 +123,10 @@ OPT. "cossq (o)"_improper_cossq.html, "cvff (io)"_improper_cvff.html, "distance"_improper_distance.html, "distharm"_improper_distharm.html, "fourier (o)"_improper_fourier.html, "harmonic (iko)"_improper_harmonic.html, "inversion/harmonic"_improper_inversion_harmonic.html, "ring (o)"_improper_ring.html, "sqdistharm"_improper_sqdistharm.html, "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c) Loading
cmake/CMakeLists.txt +12 −7 Original line number Diff line number Diff line Loading @@ -178,7 +178,7 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM) USER-QUIP USER-QMMM USER-YAFF) set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) set(OTHER_PACKAGES CORESHELL QEQ) foreach(PKG ${DEFAULT_PACKAGES}) Loading Loading @@ -559,10 +559,15 @@ if(PKG_USER-PLUMED) message(STATUS "PLUMED download requested - we will build our own") include(ExternalProject) ExternalProject_Add(plumed_build URL https://github.com/plumed/plumed2/releases/download/v2.4.3/plumed-src-2.4.3.tgz URL_MD5 b1be7c48971627febc11c61b70767fc5 URL https://github.com/plumed/plumed2/releases/download/v2.4.4/plumed-src-2.4.4.tgz URL_MD5 71ed465bdc7c2059e282dbda8d564e71 BUILD_IN_SOURCE 1 CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> ${CONFIGURE_REQUEST_PIC}) CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> ${CONFIGURE_REQUEST_PIC} --enable-modules=all CXX=${CMAKE_MPI_CXX_COMPILER} CC=${CMAKE_MPI_C_COMPILER} ) ExternalProject_get_property(plumed_build INSTALL_DIR) set(PLUMED_INSTALL_DIR ${INSTALL_DIR}) list(APPEND LAMMPS_DEPS plumed_build) Loading Loading @@ -614,8 +619,8 @@ if(PKG_USER-SMD) message(STATUS "Eigen3 download requested - we will build our own") include(ExternalProject) ExternalProject_Add(Eigen3_build URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz URL_MD5 1a47e78efe365a97de0c022d127607c3 URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07 CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" ) ExternalProject_get_property(Eigen3_build SOURCE_DIR) Loading Loading @@ -762,7 +767,7 @@ endif() # Basic system tests (standard libraries, headers, functions, types) # ######################################################################## include(CheckIncludeFileCXX) foreach(HEADER math.h) foreach(HEADER cmath) check_include_file_cxx(${HEADER} FOUND_${HEADER}) if(NOT FOUND_${HEADER}) message(FATAL_ERROR "Could not find needed header - ${HEADER}") Loading
doc/github-development-workflow.md +11 −8 Original line number Diff line number Diff line Loading @@ -50,8 +50,8 @@ This is indicated by who the pull request is assigned to. LAMMPS core developers can self-assign or they can decide to assign a pull request to a different LAMMPS developer. Being assigned to a pull request means, that this pull request may need some work and the assignee is tasked to determine what this might be needed or not, and may either implement the required changes or ask the submitter of the pull request to implement determine whether this might be needed or not, and may either implement the required changes or ask the submitter of the pull request to implement them. Even though, all LAMMPS developers may have write access to pull requests (if enabled by the submitter, which is the default), only the submitter or the assignee of a pull request may do so. During this Loading @@ -76,12 +76,15 @@ People can be assigned to review a pull request in two ways: Reviewers are requested to state their appraisal of the proposed changes and either approve or request changes. People may unassign themselves from review, if they feel not competent about the changes proposed. At least one review from a LAMMPS developer with write access is required before merging in addition to the automated compilation tests. The feature, that reviews from code owners are "hard" reviews (i.e. they must all be approved before merging is allowed), is currently disabled and it is in the discretion of the merge maintainer to assess when a sufficient degree of approval has been reached. Reviews may be least two approvals from LAMMPS developers with write access are required before merging in addition to the automated compilation tests. Merging counts as implicit approval, so does submission of a pull request (by a LAMMPS developer). So the person doing the merge may not also submit an approving review. The feature, that reviews from code owners are "hard" reviews (i.e. they must all be approved before merging is allowed), is currently disabled and it is in the discretion of the merge maintainer to assess when a sufficient degree of approval, especially from external contributors, has been reached in these cases. Reviews may be (automatically) dismissed, when the reviewed code has been changed, and then approval is required a second time. Loading
doc/src/Build_extras.txt +2 −1 Original line number Diff line number Diff line Loading @@ -95,6 +95,7 @@ which GPU hardware to build for. GPU_ARCH settings for different GPU hardware is as follows: sm_12 or sm_13 for GT200 (supported by CUDA 3.2 until CUDA 6.5) sm_20 or sm_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5) sm_30 or sm_35 or sm_37 for Kepler (supported since CUDA 5) sm_50 or sm_52 for Maxwell (supported since CUDA 6) Loading Loading @@ -135,7 +136,7 @@ specified by the "-m" switch. For your convenience, machine makefiles for "mpi" and "serial" are provided, which have the same settings as the corresponding machine makefiles in the main LAMMPS source folder. In addition you can alter 4 important settings in the Makefile.machine you start from via the corresponding -h, -a, -p, -e Makefile.machine you start from via the corresponding -c, -a, -p, -e switches (as in the examples above), and also save a copy of the new Makefile if desired: Loading
doc/src/Build_link.txt +1 −1 Original line number Diff line number Diff line Loading @@ -78,7 +78,7 @@ description of the Python interface to LAMMPS, which wraps the C-style interface. See the sample codes in examples/COUPLE/simple for examples of C++ and C and Fortran codes that invoke LAMMPS thru its library interface. C and Fortran codes that invoke LAMMPS through its library interface. Other examples in the COUPLE directory use coupling ideas discussed on the "Howto couple"_Howto_couple.html doc page. Loading
doc/src/Commands_bond.txt +5 −0 Original line number Diff line number Diff line Loading @@ -37,6 +37,7 @@ OPT. "harmonic (iko)"_bond_harmonic.html, "harmonic/shift (o)"_bond_harmonic_shift.html, "harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html, "mm3"_bond_mm3.html, "morse (o)"_bond_morse.html, "nonlinear (o)"_bond_nonlinear.html, "oxdna/fene"_bond_oxdna.html, Loading Loading @@ -67,10 +68,12 @@ OPT. "cosine/shift (o)"_angle_cosine_shift.html, "cosine/shift/exp (o)"_angle_cosine_shift_exp.html, "cosine/squared (o)"_angle_cosine_squared.html, "cross"_angle_cross.html, "dipole (o)"_angle_dipole.html, "fourier (o)"_angle_fourier.html, "fourier/simple (o)"_angle_fourier_simple.html, "harmonic (iko)"_angle_harmonic.html, "mm3"_angle_mm3.html, "quartic (o)"_angle_quartic.html, "sdk (o)"_angle_sdk.html, "table (o)"_angle_table.html :tb(c=4,ea=c) Loading Loading @@ -120,8 +123,10 @@ OPT. "cossq (o)"_improper_cossq.html, "cvff (io)"_improper_cvff.html, "distance"_improper_distance.html, "distharm"_improper_distharm.html, "fourier (o)"_improper_fourier.html, "harmonic (iko)"_improper_harmonic.html, "inversion/harmonic"_improper_inversion_harmonic.html, "ring (o)"_improper_ring.html, "sqdistharm"_improper_sqdistharm.html, "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
