Enable COLVARS_LEPTON for make, update build doc for USER-COLVARS
This commit is contained in:
Giacomo Fiorin
@ -642,33 +642,61 @@ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre
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USER-COLVARS package :h4,link(user-colvars)
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This package includes into the LAMMPS distribution the Colvars library, which
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can be built for the most part with all major versions of the C++ language.
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A few of the most recent features require C++11 support. In particular, the
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library is optionally built together with the
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"Lepton"_https://simtk.org/projects/lepton library, a copy of which is also
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included in the LAMMPS distribution. Lepton implements the
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"customFunction"_http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction
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feature, and requires C++11 support.
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See "here"_https://colvars.github.io/README-c++11.html for a detailed list of
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C++11-only features.
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[CMake build]:
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The USER-COLVARS package requires the use of a C++11 compiler to compile
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the included Lepton library. You can set the flag "-D COLVARS_LEPTON=no"
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in addition to "-D PKG_USER-COLVARS=yes" in order to instruct CMake to
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skip building and including the Lepton library into the USER-COLVARS code.
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This is the recommended build recipe: no additional settings are normally
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needed besides "-D PKG_USER-COLVARS=yes".
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Building and linking of Lepton (or other C++11-only features) is enabled
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automatically when compilation is carried out with C++11 support, and disabled
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otherwise. Optionally, Lepton build may be manually controlled with the flag
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"-D COLVARS_LEPTON=yes|no".
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[Traditional make]:
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Before building LAMMPS, you must build the COLVARS library in
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lib/colvars. You can do this manually if you prefer; follow the
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instructions in lib/colvars/README. You can also do it in one step
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from the lammps/src dir, using a command like these, which simply
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invoke the lib/colvars/Install.py script with the specified args:
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Before building LAMMPS, one must build the Colvars library in lib/colvars.
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This can be done manually in the same folder by using or adapting one of the
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provided Makefiles: for example, Makefile.g++ for the GNU compiler.
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In general, it is safer to use build setting consistent with the rest of
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LAMMPS. This is best carried out from the LAMMPS src directory using a
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command like these, which simply invoke the lib/colvars/Install.py script with
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the specified args:
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make lib-colvars # print help message
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make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
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make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
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make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled :pre
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The build should produce two files: lib/colvars/libcolvars.a and
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lib/colvars/Makefile.lammps. The latter is copied from an existing
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Makefile.lammps.* and has settings needed to build LAMMPS with the
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COLVARS library (though typically the settings are just blank). If
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necessary, you can edit/create a new lib/colvars/Makefile.machine file
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for your system, which should define an EXTRAMAKE variable to specify
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a corresponding Makefile.lammps.machine file.
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The "machine" argument of the "-m" flag is used to find a Makefile.machine to
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use as build recipe. If it does not already exist in lib/colvars, it will be
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auto-generated by using compiler flags consistent with those parsed from the
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core LAMMPS makefiles.
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Optional flags may be specified as environment variables:
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COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower)
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COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise)
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The build should produce two files: the library lib/colvars/libcolvars.a
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(which also includes Lepton objects if enabled) and the specification file
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lib/colvars/Makefile.lammps. The latter is auto-generated, and normally does
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not need to be edited.
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:line
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@ -54,7 +54,7 @@ LEPTON_SRCS = \
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# Allow to selectively turn off Lepton
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ifeq ($(ENABLE_LEPTON),no)
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ifeq ($(COLVARS_LEPTON),no)
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LEPTON_INCFLAGS =
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COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o)
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else
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@ -1,5 +1,5 @@
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# -*- makefile -*- to build Colvars module with GNU compiler
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COLVARS_DEBUG = "YES"
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COLVARS_DEBUG = yes
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include Makefile.g++
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5
lib/colvars/Makefile.g++-no-lepton
Normal file
5
lib/colvars/Makefile.g++-no-lepton
Normal file
@ -0,0 +1,5 @@
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# -*- makefile -*- to build Colvars module with GNU compiler
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COLVARS_LEPTON = no
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include Makefile.g++
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@ -8,82 +8,83 @@ The module itself implements a variety of functions and algorithms, including
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free-energy estimators based on thermodynamic forces, non-equilibrium work and
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probability distributions.
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For a brief description see:
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http://colvars.github.io/
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https://github.com/colvars/colvars/
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## How to build
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This directory has source files to build a library that LAMMPS
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links against when using the USER-COLVARS package.
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This library must be built with a C++ compiler, *before* LAMMPS is built and
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*after* packages are configured, so that LAMMPS can link against it.
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You can use the provided Makefile.* files or create your own, specific to your
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compiler and system. For example:
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cd src
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make yes-user-colvars
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cd ../lib/colvars
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make -f Makefile.g++
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where Makefile.g++ uses the GNU C++ compiler and is a good template to start.
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**Optional**: if you use the Install.py script provided in this folder, you
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can give the machine name as the '-m' argument. This can be the suffix of one
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of the files from either this folder, or from src/MAKE/MACHINES.
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*This is only supported by the Install.py within the lib/colvars folder*.
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When you are done building this library, two files should
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exist in this directory:
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libcolvars.a the library LAMMPS will link against
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Makefile.lammps settings the LAMMPS Makefile will import
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IMPORTANT: You must examine the final Makefile.lammps to insure it is
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correct for your system, else the LAMMPS build will likely fail.
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If you want to set a debug flag recognized by the library, the
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settings in Makefile.common should work.
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Note: some Colvars functions use the Lepton mathematical expression parser,
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which is here included (no additional steps required). For more details, see:
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https://simtk.org/projects/lepton
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Starting from 2019-06-02, Lepton requires C++11. Please see:
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https://colvars.github.io/README-c++11.html
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https://lammps.sandia.gov/doc/Build_settings.html#cxx11
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## Documentation
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For a brief description see:
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https://colvars.github.io/
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https://github.com/Colvars/colvars/
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For the reference manual see:
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http://colvars.github.io/colvars-refman-lammps
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A copy of the reference manual is also in:
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A PDF copy is also at:
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doc/PDF/colvars-refman-lammps.pdf
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Also available is a Doxygen-based developer documentation:
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http://colvars.github.io/doxygen/html/
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The reference article is:
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G. Fiorin, M. L. Klein, and J. Henin,
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G. Fiorin, M. L. Klein, and J. Hénin,
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Molecular Physics 111, 3345 (2013).
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http://dx.doi.org/10.1080/00268976.2013.813594
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## Updating to the latest version
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## Requirements
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To recompile LAMMPS with the most recent version of this module, the `master`
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branch of this repository from GitHub, or clone it via git:
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The Colvars library can be built for the most part with all major versions of
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the C++ language.
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git clone https://github.com/colvars/colvars.git
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A few of the most recent features require C++11 support. In particular, the
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library is optionally built together with the
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"Lepton"_https://simtk.org/projects/lepton library, a copy of which is also
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included in the LAMMPS distribution. Lepton implements the
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"customFunction"_http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction
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feature, and requires C++11 support.
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and run the provided `update-colvars-code.sh` script against the unpacked
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LAMMPS source tree:
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See "here"_https://colvars.github.io/README-c++11.html for a detailed list of
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C++11-only features.
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./update-colvars-code.sh /path/to/lammps/folder
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Please report bugs and request new features at:
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https://github.com/colvars/colvars/issues
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## How to build (CMake)
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This is the recommended build recipe: no additional settings are normally
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needed besides "-D PKG_USER-COLVARS=yes".
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Building and linking of Lepton (or other C++11-only features) is enabled
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automatically when compilation is carried out with C++11 support, and disabled
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otherwise. Optionally, Lepton build may be manually controlled with the flag
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"-D COLVARS_LEPTON=yes|no".
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## How to build (traditional make)
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Before building LAMMPS, one must build the Colvars library in lib/colvars.
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This can be done manually in the same folder by using or adapting one of the
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provided Makefiles: for example, Makefile.g++ for the GNU compiler.
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In general, it is safer to use build setting consistent with the rest of
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LAMMPS. This is best carried out from the LAMMPS src directory using a
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command like these, which simply invoke the lib/colvars/Install.py script with
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the specified args:
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make lib-colvars # print help message
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make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
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make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
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make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled :pre
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The "machine" argument of the "-m" flag is used to find a Makefile.machine to
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use as build recipe. If it does not already exist in lib/colvars, it will be
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auto-generated by using compiler flags consistent with those parsed from the
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core LAMMPS makefiles.
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Optional flags may be specified as environment variables:
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COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower)
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COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise)
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The build should produce two files: the library lib/colvars/libcolvars.a
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(which also includes Lepton objects if enabled) and the specification file
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lib/colvars/Makefile.lammps. The latter is auto-generated, and normally does
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not need to be edited.
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Block a user