Loading doc/src/Build_extras.txt +44 −16 Changes for doc/src/Build_extras.txt: 44 added lines, 16 removed lines. Original line number Diff line number Diff line Loading @@ -642,33 +642,61 @@ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre USER-COLVARS package :h4,link(user-colvars) 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]: The USER-COLVARS package requires the use of a C++11 compiler to compile the included Lepton library. You can set the flag "-D COLVARS_LEPTON=no" in addition to "-D PKG_USER-COLVARS=yes" in order to instruct CMake to skip building and including the Lepton library into the USER-COLVARS code. 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: make lib-colvars # print help message make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial") 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 :pre 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. :line Loading lib/colvars/Makefile.common +1 −1 Changes for lib/colvars/Makefile.common: 1 added line, 1 removed line. Original line number Diff line number Diff line Loading @@ -54,7 +54,7 @@ LEPTON_SRCS = \ # Allow to selectively turn off Lepton ifeq ($(ENABLE_LEPTON),no) ifeq ($(COLVARS_LEPTON),no) LEPTON_INCFLAGS = COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o) else Loading lib/colvars/Makefile.g++-debug +1 −1 Changes for lib/colvars/Makefile.g++-debug: 1 added line, 1 removed line. Original line number Diff line number Diff line # -*- makefile -*- to build Colvars module with GNU compiler COLVARS_DEBUG = "YES" COLVARS_DEBUG = yes include Makefile.g++ lib/colvars/Makefile.g++-no-lepton 0 → 100644 +5 −0 Changes for lib/colvars/Makefile.g++-no-lepton: 5 added lines, 0 removed lines. Original line number Diff line number Diff line # -*- makefile -*- to build Colvars module with GNU compiler COLVARS_LEPTON = no include Makefile.g++ lib/colvars/README +55 −54 Changes for lib/colvars/README: 55 added lines, 54 removed lines. Original line number Diff line number Diff line Loading @@ -8,82 +8,83 @@ The module itself implements a variety of functions and algorithms, including free-energy estimators based on thermodynamic forces, non-equilibrium work and probability distributions. For a brief description see: http://colvars.github.io/ https://github.com/colvars/colvars/ ## How to build ## Documentation This directory has source files to build a library that LAMMPS links against when using the USER-COLVARS package. For a brief description see: https://colvars.github.io/ https://github.com/Colvars/colvars/ This library must be built with a C++ compiler, *before* LAMMPS is built and *after* packages are configured, so that LAMMPS can link against it. You can use the provided Makefile.* files or create your own, specific to your compiler and system. For example: For the reference manual see: http://colvars.github.io/colvars-refman-lammps cd src make yes-user-colvars cd ../lib/colvars make -f Makefile.g++ A PDF copy is also at: doc/PDF/colvars-refman-lammps.pdf where Makefile.g++ uses the GNU C++ compiler and is a good template to start. Also available is a Doxygen-based developer documentation: http://colvars.github.io/doxygen/html/ **Optional**: if you use the Install.py script provided in this folder, you can give the machine name as the '-m' argument. This can be the suffix of one of the files from either this folder, or from src/MAKE/MACHINES. *This is only supported by the Install.py within the lib/colvars folder*. The reference article is: G. Fiorin, M. L. Klein, and J. Hénin, Molecular Physics 111, 3345 (2013). http://dx.doi.org/10.1080/00268976.2013.813594 When you are done building this library, two files should exist in this directory: libcolvars.a the library LAMMPS will link against Makefile.lammps settings the LAMMPS Makefile will import ## Requirements IMPORTANT: You must examine the final Makefile.lammps to insure it is correct for your system, else the LAMMPS build will likely fail. The Colvars library can be built for the most part with all major versions of the C++ language. If you want to set a debug flag recognized by the library, the settings in Makefile.common should work. 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. Note: some Colvars functions use the Lepton mathematical expression parser, which is here included (no additional steps required). For more details, see: https://simtk.org/projects/lepton Starting from 2019-06-02, Lepton requires C++11. Please see: https://colvars.github.io/README-c++11.html https://lammps.sandia.gov/doc/Build_settings.html#cxx11 See "here"_https://colvars.github.io/README-c++11.html for a detailed list of C++11-only features. ## Documentation ## How to build (CMake) For the reference manual see: http://colvars.github.io/colvars-refman-lammps This is the recommended build recipe: no additional settings are normally needed besides "-D PKG_USER-COLVARS=yes". A copy of the reference manual is also in: doc/PDF/colvars-refman-lammps.pdf 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". Also available is a Doxygen-based developer documentation: http://colvars.github.io/doxygen/html/ The reference article is: G. Fiorin, M. L. Klein, and J. Henin, Molecular Physics 111, 3345 (2013). http://dx.doi.org/10.1080/00268976.2013.813594 ## How to build (traditional make) Before building LAMMPS, one must build the Colvars library in lib/colvars. ## Updating to the latest version 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. To recompile LAMMPS with the most recent version of this module, the `master` branch of this repository from GitHub, or clone it via git: 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: git clone https://github.com/colvars/colvars.git make lib-colvars # print help message make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial") 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 :pre and run the provided `update-colvars-code.sh` script against the unpacked LAMMPS source tree: 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. ./update-colvars-code.sh /path/to/lammps/folder Optional flags may be specified as environment variables: Please report bugs and request new features at: https://github.com/colvars/colvars/issues 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
doc/src/Build_extras.txt +44 −16 Changes for doc/src/Build_extras.txt: 44 added lines, 16 removed lines. Original line number Diff line number Diff line Loading @@ -642,33 +642,61 @@ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre USER-COLVARS package :h4,link(user-colvars) 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]: The USER-COLVARS package requires the use of a C++11 compiler to compile the included Lepton library. You can set the flag "-D COLVARS_LEPTON=no" in addition to "-D PKG_USER-COLVARS=yes" in order to instruct CMake to skip building and including the Lepton library into the USER-COLVARS code. 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: make lib-colvars # print help message make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial") 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 :pre 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. :line Loading
lib/colvars/Makefile.common +1 −1 Changes for lib/colvars/Makefile.common: 1 added line, 1 removed line. Original line number Diff line number Diff line Loading @@ -54,7 +54,7 @@ LEPTON_SRCS = \ # Allow to selectively turn off Lepton ifeq ($(ENABLE_LEPTON),no) ifeq ($(COLVARS_LEPTON),no) LEPTON_INCFLAGS = COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o) else Loading
lib/colvars/Makefile.g++-debug +1 −1 Changes for lib/colvars/Makefile.g++-debug: 1 added line, 1 removed line. Original line number Diff line number Diff line # -*- makefile -*- to build Colvars module with GNU compiler COLVARS_DEBUG = "YES" COLVARS_DEBUG = yes include Makefile.g++
lib/colvars/Makefile.g++-no-lepton 0 → 100644 +5 −0 Changes for lib/colvars/Makefile.g++-no-lepton: 5 added lines, 0 removed lines. Original line number Diff line number Diff line # -*- makefile -*- to build Colvars module with GNU compiler COLVARS_LEPTON = no include Makefile.g++
lib/colvars/README +55 −54 Changes for lib/colvars/README: 55 added lines, 54 removed lines. Original line number Diff line number Diff line Loading @@ -8,82 +8,83 @@ The module itself implements a variety of functions and algorithms, including free-energy estimators based on thermodynamic forces, non-equilibrium work and probability distributions. For a brief description see: http://colvars.github.io/ https://github.com/colvars/colvars/ ## How to build ## Documentation This directory has source files to build a library that LAMMPS links against when using the USER-COLVARS package. For a brief description see: https://colvars.github.io/ https://github.com/Colvars/colvars/ This library must be built with a C++ compiler, *before* LAMMPS is built and *after* packages are configured, so that LAMMPS can link against it. You can use the provided Makefile.* files or create your own, specific to your compiler and system. For example: For the reference manual see: http://colvars.github.io/colvars-refman-lammps cd src make yes-user-colvars cd ../lib/colvars make -f Makefile.g++ A PDF copy is also at: doc/PDF/colvars-refman-lammps.pdf where Makefile.g++ uses the GNU C++ compiler and is a good template to start. Also available is a Doxygen-based developer documentation: http://colvars.github.io/doxygen/html/ **Optional**: if you use the Install.py script provided in this folder, you can give the machine name as the '-m' argument. This can be the suffix of one of the files from either this folder, or from src/MAKE/MACHINES. *This is only supported by the Install.py within the lib/colvars folder*. The reference article is: G. Fiorin, M. L. Klein, and J. Hénin, Molecular Physics 111, 3345 (2013). http://dx.doi.org/10.1080/00268976.2013.813594 When you are done building this library, two files should exist in this directory: libcolvars.a the library LAMMPS will link against Makefile.lammps settings the LAMMPS Makefile will import ## Requirements IMPORTANT: You must examine the final Makefile.lammps to insure it is correct for your system, else the LAMMPS build will likely fail. The Colvars library can be built for the most part with all major versions of the C++ language. If you want to set a debug flag recognized by the library, the settings in Makefile.common should work. 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. Note: some Colvars functions use the Lepton mathematical expression parser, which is here included (no additional steps required). For more details, see: https://simtk.org/projects/lepton Starting from 2019-06-02, Lepton requires C++11. Please see: https://colvars.github.io/README-c++11.html https://lammps.sandia.gov/doc/Build_settings.html#cxx11 See "here"_https://colvars.github.io/README-c++11.html for a detailed list of C++11-only features. ## Documentation ## How to build (CMake) For the reference manual see: http://colvars.github.io/colvars-refman-lammps This is the recommended build recipe: no additional settings are normally needed besides "-D PKG_USER-COLVARS=yes". A copy of the reference manual is also in: doc/PDF/colvars-refman-lammps.pdf 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". Also available is a Doxygen-based developer documentation: http://colvars.github.io/doxygen/html/ The reference article is: G. Fiorin, M. L. Klein, and J. Henin, Molecular Physics 111, 3345 (2013). http://dx.doi.org/10.1080/00268976.2013.813594 ## How to build (traditional make) Before building LAMMPS, one must build the Colvars library in lib/colvars. ## Updating to the latest version 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. To recompile LAMMPS with the most recent version of this module, the `master` branch of this repository from GitHub, or clone it via git: 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: git clone https://github.com/colvars/colvars.git make lib-colvars # print help message make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial") 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 :pre and run the provided `update-colvars-code.sh` script against the unpacked LAMMPS source tree: 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. ./update-colvars-code.sh /path/to/lammps/folder Optional flags may be specified as environment variables: Please report bugs and request new features at: https://github.com/colvars/colvars/issues 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.
