Loading doc/rst/Build_extras.rst +49 −19 Original line number Diff line number Diff line Loading @@ -786,17 +786,40 @@ library in lib/linalg with a command like these: USER-COLVARS package --------------------------------------- This package includes into the LAMMPS distribution the Colvars library, which can be built for the most part with all major versions of the C++ language. A few of the most recent features require C++11 support. In particular, the library is optionally built together with the `Lepton <https://simtk.org/projects/lepton>`_ library, a copy of which is also included in the LAMMPS distribution. Lepton implements the `customFunction <http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction>`_ feature, and requires C++11 support. See `here <https://colvars.github.io/README-c++11.html>`_ for a detailed list of C++11-only features. **CMake build**\ : No additional settings are needed besides "-D PKG\_USER-COLVARS=yes". This is the recommended build recipe: no additional settings are normally needed besides "-D PKG\_USER-COLVARS=yes". Building and linking of Lepton (or other C++11-only features) is enabled automatically when compilation is carried out with C++11 support, and disabled otherwise. Optionally, Lepton build may be manually controlled with the flag "-D COLVARS\_LEPTON=yes\|no". **Traditional make**\ : Before building LAMMPS, you must build the COLVARS library in lib/colvars. You can do this manually if you prefer; follow the instructions in lib/colvars/README. You can also do it in one step from the lammps/src dir, using a command like these, which simply invoke the lib/colvars/Install.py script with the specified args: Before building LAMMPS, one must build the Colvars library in lib/colvars. This can be done manually in the same folder by using or adapting one of the provided Makefiles: for example, Makefile.g++ for the GNU compiler. In general, it is safer to use build setting consistent with the rest of LAMMPS. This is best carried out from the LAMMPS src directory using a command like these, which simply invoke the lib/colvars/Install.py script with the specified args: .. parsed-literal:: Loading @@ -806,13 +829,20 @@ invoke the lib/colvars/Install.py script with the specified args: make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi") make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled The build should produce two files: lib/colvars/libcolvars.a and lib/colvars/Makefile.lammps. The latter is copied from an existing Makefile.lammps.\* and has settings needed to build LAMMPS with the COLVARS library (though typically the settings are just blank). If necessary, you can edit/create a new lib/colvars/Makefile.machine file for your system, which should define an EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine file. The "machine" argument of the "-m" flag is used to find a Makefile.machine to use as build recipe. If it does not already exist in lib/colvars, it will be auto-generated by using compiler flags consistent with those parsed from the core LAMMPS makefiles. Optional flags may be specified as environment variables: COLVARS\_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower) COLVARS\_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise) The build should produce two files: the library lib/colvars/libcolvars.a (which also includes Lepton objects if enabled) and the specification file lib/colvars/Makefile.lammps. The latter is auto-generated, and normally does not need to be edited. ---------- Loading Loading @@ -972,7 +1002,7 @@ lib/h5md/Install.py script with the specified args: .. parsed-literal:: make lib-h5md # print help message make lib-hm5d args="-m h5cc" # build with h5cc compiler make lib-h5md args="-m h5cc" # build with h5cc compiler The build should produce two files: lib/h5md/libch5md.a and lib/h5md/Makefile.lammps. The latter is copied from an existing Loading doc/rst/Build_settings.rst +42 −0 Original line number Diff line number Diff line Loading @@ -4,6 +4,7 @@ Optional build settings LAMMPS can be built with several optional settings. Each sub-section explain how to do this for building both with CMake and make. | :ref:`C++11 standard compliance test <cxx11>` when building all of LAMMPS | :ref:`FFT library <fft>` for use with the :doc:`kspace\_style pppm <kspace_style>` command | :ref:`Size of LAMMPS data types <size>` | :ref:`Read or write compressed files <gzip>` Loading @@ -18,6 +19,47 @@ explain how to do this for building both with CMake and make. ---------- .. _cxx11: C++11 standard compliance test ------------------------------------------ The LAMMPS developers plan to transition to make the C++11 standard the minimum requirement for compiling LAMMPS. Currently this only applies to some packages like KOKKOS while the rest aims to be compatible with the C++98 standard. Most currently used compilers are compatible with C++11; some need to set extra flags to switch. To determine the impact of requiring C++11, we have added a simple compliance test to the source code, that will cause the compilation to abort, if C++11 compliance is not available or enabled. To bypass this check, you need to change a setting in the makefile or when calling CMake. **CMake variable**\ : .. parsed-literal:: -D DISABLE_CXX11_REQUIREMENT=yes You can set additional C++ compiler flags (beyond those selected by CMake) through the CMAKE\_CXX\_FLAGS variable. Example for CentOS 7: .. parsed-literal:: -D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -DNDEBUG -std=c++11" **Makefile.machine setting**\ : .. parsed-literal:: LMP_INC = -DLAMMPS_CXX98 ---------- .. _fft: FFT library Loading doc/rst/Commands_all.rst +3 −3 Original line number Diff line number Diff line Loading @@ -46,11 +46,11 @@ An alphabetic list of all general LAMMPS commands. +-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+ | :doc:`tad <tad>` | :doc:`temper <temper>` | :doc:`temper/grem <temper_grem>` | :doc:`temper/npt <temper_npt>` | :doc:`thermo <thermo>` | :doc:`thermo\_modify <thermo_modify>` | +-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+ | :doc:`thermo\_style <thermo_style>` | :doc:`timer <timer>` | :doc:`timestep <timestep>` | :doc:`uncompute <uncompute>` | :doc:`undump <undump>` | :doc:`unfix <unfix>` | | :doc:`thermo\_style <thermo_style>` | :doc:`third\_order <third_order>` | :doc:`timer <timer>` | :doc:`timestep <timestep>` | :doc:`uncompute <uncompute>` | :doc:`undump <undump>` | +-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+ | :doc:`units <units>` | :doc:`variable <variable>` | :doc:`velocity <velocity>` | :doc:`write\_coeff <write_coeff>` | :doc:`write\_data <write_data>` | :doc:`write\_dump <write_dump>` | | :doc:`unfix <unfix>` | :doc:`units <units>` | :doc:`variable <variable>` | :doc:`velocity <velocity>` | :doc:`write\_coeff <write_coeff>` | :doc:`write\_data <write_data>` | +-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+ | :doc:`write\_restart <write_restart>` | | | | | | | :doc:`write\_dump <write_dump>` | :doc:`write\_restart <write_restart>` | | | | | +-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+ Loading doc/rst/Commands_bond.rst +13 −13 Original line number Diff line number Diff line Loading @@ -66,19 +66,19 @@ have accelerated versions. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. +-------------------------------------------+------------------------------------------+-------------------------------------------+---------------------------------------------------------+ +-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+ | :doc:`none <dihedral_none>` | :doc:`zero <dihedral_zero>` | :doc:`hybrid <dihedral_hybrid>` | | +-------------------------------------------+------------------------------------------+-------------------------------------------+---------------------------------------------------------+ +-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+ | | | | | +-------------------------------------------+------------------------------------------+-------------------------------------------+---------------------------------------------------------+ +-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+ | :doc:`charmm (iko) <dihedral_charmm>` | :doc:`charmmfsw <dihedral_charmm>` | :doc:`class2 (ko) <dihedral_class2>` | :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>` | +-------------------------------------------+------------------------------------------+-------------------------------------------+---------------------------------------------------------+ | :doc:`fourier (io) <dihedral_fourier>` | :doc:`harmonic (io) <dihedral_harmonic>` | :doc:`helix (o) <dihedral_helix>` | :doc:`multi/harmonic (o) <dihedral_multi_harmonic>` | +-------------------------------------------+------------------------------------------+-------------------------------------------+---------------------------------------------------------+ +-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+ | :doc:`fourier (io) <dihedral_fourier>` | :doc:`harmonic (iko) <dihedral_harmonic>` | :doc:`helix (o) <dihedral_helix>` | :doc:`multi/harmonic (o) <dihedral_multi_harmonic>` | +-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+ | :doc:`nharmonic (o) <dihedral_nharmonic>` | :doc:`opls (iko) <dihedral_opls>` | :doc:`quadratic (o) <dihedral_quadratic>` | :doc:`spherical <dihedral_spherical>` | +-------------------------------------------+------------------------------------------+-------------------------------------------+---------------------------------------------------------+ +-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+ | :doc:`table (o) <dihedral_table>` | :doc:`table/cut <dihedral_table_cut>` | | | +-------------------------------------------+------------------------------------------+-------------------------------------------+---------------------------------------------------------+ +-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+ ---------- Loading doc/rst/Commands_pair.rst +115 −115 File changed.Preview size limit exceeded, changes collapsed. Show changes Loading
doc/rst/Build_extras.rst +49 −19 Original line number Diff line number Diff line Loading @@ -786,17 +786,40 @@ library in lib/linalg with a command like these: USER-COLVARS package --------------------------------------- This package includes into the LAMMPS distribution the Colvars library, which can be built for the most part with all major versions of the C++ language. A few of the most recent features require C++11 support. In particular, the library is optionally built together with the `Lepton <https://simtk.org/projects/lepton>`_ library, a copy of which is also included in the LAMMPS distribution. Lepton implements the `customFunction <http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction>`_ feature, and requires C++11 support. See `here <https://colvars.github.io/README-c++11.html>`_ for a detailed list of C++11-only features. **CMake build**\ : No additional settings are needed besides "-D PKG\_USER-COLVARS=yes". This is the recommended build recipe: no additional settings are normally needed besides "-D PKG\_USER-COLVARS=yes". Building and linking of Lepton (or other C++11-only features) is enabled automatically when compilation is carried out with C++11 support, and disabled otherwise. Optionally, Lepton build may be manually controlled with the flag "-D COLVARS\_LEPTON=yes\|no". **Traditional make**\ : Before building LAMMPS, you must build the COLVARS library in lib/colvars. You can do this manually if you prefer; follow the instructions in lib/colvars/README. You can also do it in one step from the lammps/src dir, using a command like these, which simply invoke the lib/colvars/Install.py script with the specified args: Before building LAMMPS, one must build the Colvars library in lib/colvars. This can be done manually in the same folder by using or adapting one of the provided Makefiles: for example, Makefile.g++ for the GNU compiler. In general, it is safer to use build setting consistent with the rest of LAMMPS. This is best carried out from the LAMMPS src directory using a command like these, which simply invoke the lib/colvars/Install.py script with the specified args: .. parsed-literal:: Loading @@ -806,13 +829,20 @@ invoke the lib/colvars/Install.py script with the specified args: make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi") make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled The build should produce two files: lib/colvars/libcolvars.a and lib/colvars/Makefile.lammps. The latter is copied from an existing Makefile.lammps.\* and has settings needed to build LAMMPS with the COLVARS library (though typically the settings are just blank). If necessary, you can edit/create a new lib/colvars/Makefile.machine file for your system, which should define an EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine file. The "machine" argument of the "-m" flag is used to find a Makefile.machine to use as build recipe. If it does not already exist in lib/colvars, it will be auto-generated by using compiler flags consistent with those parsed from the core LAMMPS makefiles. Optional flags may be specified as environment variables: COLVARS\_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower) COLVARS\_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise) The build should produce two files: the library lib/colvars/libcolvars.a (which also includes Lepton objects if enabled) and the specification file lib/colvars/Makefile.lammps. The latter is auto-generated, and normally does not need to be edited. ---------- Loading Loading @@ -972,7 +1002,7 @@ lib/h5md/Install.py script with the specified args: .. parsed-literal:: make lib-h5md # print help message make lib-hm5d args="-m h5cc" # build with h5cc compiler make lib-h5md args="-m h5cc" # build with h5cc compiler The build should produce two files: lib/h5md/libch5md.a and lib/h5md/Makefile.lammps. The latter is copied from an existing Loading
doc/rst/Build_settings.rst +42 −0 Original line number Diff line number Diff line Loading @@ -4,6 +4,7 @@ Optional build settings LAMMPS can be built with several optional settings. Each sub-section explain how to do this for building both with CMake and make. | :ref:`C++11 standard compliance test <cxx11>` when building all of LAMMPS | :ref:`FFT library <fft>` for use with the :doc:`kspace\_style pppm <kspace_style>` command | :ref:`Size of LAMMPS data types <size>` | :ref:`Read or write compressed files <gzip>` Loading @@ -18,6 +19,47 @@ explain how to do this for building both with CMake and make. ---------- .. _cxx11: C++11 standard compliance test ------------------------------------------ The LAMMPS developers plan to transition to make the C++11 standard the minimum requirement for compiling LAMMPS. Currently this only applies to some packages like KOKKOS while the rest aims to be compatible with the C++98 standard. Most currently used compilers are compatible with C++11; some need to set extra flags to switch. To determine the impact of requiring C++11, we have added a simple compliance test to the source code, that will cause the compilation to abort, if C++11 compliance is not available or enabled. To bypass this check, you need to change a setting in the makefile or when calling CMake. **CMake variable**\ : .. parsed-literal:: -D DISABLE_CXX11_REQUIREMENT=yes You can set additional C++ compiler flags (beyond those selected by CMake) through the CMAKE\_CXX\_FLAGS variable. Example for CentOS 7: .. parsed-literal:: -D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -DNDEBUG -std=c++11" **Makefile.machine setting**\ : .. parsed-literal:: LMP_INC = -DLAMMPS_CXX98 ---------- .. _fft: FFT library Loading
doc/rst/Commands_all.rst +3 −3 Original line number Diff line number Diff line Loading @@ -46,11 +46,11 @@ An alphabetic list of all general LAMMPS commands. +-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+ | :doc:`tad <tad>` | :doc:`temper <temper>` | :doc:`temper/grem <temper_grem>` | :doc:`temper/npt <temper_npt>` | :doc:`thermo <thermo>` | :doc:`thermo\_modify <thermo_modify>` | +-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+ | :doc:`thermo\_style <thermo_style>` | :doc:`timer <timer>` | :doc:`timestep <timestep>` | :doc:`uncompute <uncompute>` | :doc:`undump <undump>` | :doc:`unfix <unfix>` | | :doc:`thermo\_style <thermo_style>` | :doc:`third\_order <third_order>` | :doc:`timer <timer>` | :doc:`timestep <timestep>` | :doc:`uncompute <uncompute>` | :doc:`undump <undump>` | +-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+ | :doc:`units <units>` | :doc:`variable <variable>` | :doc:`velocity <velocity>` | :doc:`write\_coeff <write_coeff>` | :doc:`write\_data <write_data>` | :doc:`write\_dump <write_dump>` | | :doc:`unfix <unfix>` | :doc:`units <units>` | :doc:`variable <variable>` | :doc:`velocity <velocity>` | :doc:`write\_coeff <write_coeff>` | :doc:`write\_data <write_data>` | +-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+ | :doc:`write\_restart <write_restart>` | | | | | | | :doc:`write\_dump <write_dump>` | :doc:`write\_restart <write_restart>` | | | | | +-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+ Loading
doc/rst/Commands_bond.rst +13 −13 Original line number Diff line number Diff line Loading @@ -66,19 +66,19 @@ have accelerated versions. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. +-------------------------------------------+------------------------------------------+-------------------------------------------+---------------------------------------------------------+ +-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+ | :doc:`none <dihedral_none>` | :doc:`zero <dihedral_zero>` | :doc:`hybrid <dihedral_hybrid>` | | +-------------------------------------------+------------------------------------------+-------------------------------------------+---------------------------------------------------------+ +-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+ | | | | | +-------------------------------------------+------------------------------------------+-------------------------------------------+---------------------------------------------------------+ +-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+ | :doc:`charmm (iko) <dihedral_charmm>` | :doc:`charmmfsw <dihedral_charmm>` | :doc:`class2 (ko) <dihedral_class2>` | :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>` | +-------------------------------------------+------------------------------------------+-------------------------------------------+---------------------------------------------------------+ | :doc:`fourier (io) <dihedral_fourier>` | :doc:`harmonic (io) <dihedral_harmonic>` | :doc:`helix (o) <dihedral_helix>` | :doc:`multi/harmonic (o) <dihedral_multi_harmonic>` | +-------------------------------------------+------------------------------------------+-------------------------------------------+---------------------------------------------------------+ +-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+ | :doc:`fourier (io) <dihedral_fourier>` | :doc:`harmonic (iko) <dihedral_harmonic>` | :doc:`helix (o) <dihedral_helix>` | :doc:`multi/harmonic (o) <dihedral_multi_harmonic>` | +-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+ | :doc:`nharmonic (o) <dihedral_nharmonic>` | :doc:`opls (iko) <dihedral_opls>` | :doc:`quadratic (o) <dihedral_quadratic>` | :doc:`spherical <dihedral_spherical>` | +-------------------------------------------+------------------------------------------+-------------------------------------------+---------------------------------------------------------+ +-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+ | :doc:`table (o) <dihedral_table>` | :doc:`table/cut <dihedral_table_cut>` | | | +-------------------------------------------+------------------------------------------+-------------------------------------------+---------------------------------------------------------+ +-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+ ---------- Loading
doc/rst/Commands_pair.rst +115 −115 File changed.Preview size limit exceeded, changes collapsed. Show changes
