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Enable COLVARS_LEPTON for make, update build doc for USER-COLVARS

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This commit is contained in:
Giacomo Fiorin
2019-10-17 22:48:57 -04:00
parent 27d3d44297
commit c578e4e7fc
5 changed files with 109 additions and 75 deletions
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60
doc/src/Build_extras.txt
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@ -642,33 +642,61 @@ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre
USER-COLVARS package :h4,link(user-colvars) 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]: [CMake build]:
The USER-COLVARS package requires the use of a C++11 compiler to compile This is the recommended build recipe: no additional settings are normally
the included Lepton library. You can set the flag "-D COLVARS_LEPTON=no" needed besides "-D PKG_USER-COLVARS=yes".
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. 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]: [Traditional make]:
Before building LAMMPS, you must build the COLVARS library in Before building LAMMPS, one must build the Colvars library in lib/colvars.
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 This can be done manually in the same folder by using or adapting one of the
from the lammps/src dir, using a command like these, which simply provided Makefiles: for example, Makefile.g++ for the GNU compiler.
invoke the lib/colvars/Install.py script with the specified args:
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 # print help message
make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial") 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 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 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 The "machine" argument of the "-m" flag is used to find a Makefile.machine to
lib/colvars/Makefile.lammps. The latter is copied from an existing use as build recipe. If it does not already exist in lib/colvars, it will be
Makefile.lammps.* and has settings needed to build LAMMPS with the auto-generated by using compiler flags consistent with those parsed from the
COLVARS library (though typically the settings are just blank). If core LAMMPS makefiles.
necessary, you can edit/create a new lib/colvars/Makefile.machine file
for your system, which should define an EXTRAMAKE variable to specify Optional flags may be specified as environment variables:
a corresponding Makefile.lammps.machine file.
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 :line

2
lib/colvars/Makefile.common
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@ -54,7 +54,7 @@ LEPTON_SRCS = \
# Allow to selectively turn off Lepton # Allow to selectively turn off Lepton
ifeq ($(ENABLE_LEPTON),no) ifeq ($(COLVARS_LEPTON),no)
LEPTON_INCFLAGS = LEPTON_INCFLAGS =
COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o) COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o)
else else

2
lib/colvars/Makefile.g++-debug
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@ -1,5 +1,5 @@
# -*- makefile -*- to build Colvars module with GNU compiler # -*- makefile -*- to build Colvars module with GNU compiler
COLVARS_DEBUG = "YES" COLVARS_DEBUG = yes
include Makefile.g++ include Makefile.g++

5
lib/colvars/Makefile.g++-no-lepton Normal file
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@ -0,0 +1,5 @@
# -*- makefile -*- to build Colvars module with GNU compiler
COLVARS_LEPTON = no
include Makefile.g++

115
lib/colvars/README
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@ -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 free-energy estimators based on thermodynamic forces, non-equilibrium work and
probability distributions. probability distributions.
For a brief description see:
http://colvars.github.io/
https://github.com/colvars/colvars/
## How to build
This directory has source files to build a library that LAMMPS
links against when using the USER-COLVARS package.
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:
cd src
make yes-user-colvars
cd ../lib/colvars
make -f Makefile.g++
where Makefile.g++ uses the GNU C++ compiler and is a good template to start.
**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*.
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
IMPORTANT: You must examine the final Makefile.lammps to insure it is
correct for your system, else the LAMMPS build will likely fail.
If you want to set a debug flag recognized by the library, the
settings in Makefile.common should work.
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
## Documentation ## Documentation
For a brief description see:
https://colvars.github.io/
https://github.com/Colvars/colvars/
For the reference manual see: For the reference manual see:
http://colvars.github.io/colvars-refman-lammps http://colvars.github.io/colvars-refman-lammps
A copy of the reference manual is also in: A PDF copy is also at:
doc/PDF/colvars-refman-lammps.pdf doc/PDF/colvars-refman-lammps.pdf
Also available is a Doxygen-based developer documentation: Also available is a Doxygen-based developer documentation:
http://colvars.github.io/doxygen/html/ http://colvars.github.io/doxygen/html/
The reference article is: The reference article is:
G. Fiorin, M. L. Klein, and J. Henin, G. Fiorin, M. L. Klein, and J. Hénin,
Molecular Physics 111, 3345 (2013). Molecular Physics 111, 3345 (2013).
http://dx.doi.org/10.1080/00268976.2013.813594 http://dx.doi.org/10.1080/00268976.2013.813594
## Updating to the latest version ## Requirements
To recompile LAMMPS with the most recent version of this module, the `master` The Colvars library can be built for the most part with all major versions of
branch of this repository from GitHub, or clone it via git: the C++ language.
git clone https://github.com/colvars/colvars.git 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.
and run the provided `update-colvars-code.sh` script against the unpacked See "here"_https://colvars.github.io/README-c++11.html for a detailed list of
LAMMPS source tree: C++11-only features.
./update-colvars-code.sh /path/to/lammps/folder
Please report bugs and request new features at: ## How to build (CMake)
https://github.com/colvars/colvars/issues
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".
## How to build (traditional make)
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 "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.