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authorRicardo Wurmus <rekado@elephly.net>2023-12-25 16:37:46 +0100
committerRicardo Wurmus <rekado@elephly.net>2023-12-25 19:52:13 +0100
commit95879674c2312432f778383c2979fd0c9c098721 (patch)
tree9b7c1f39d72925849aa20dfd2bf21727f7cb1744 /gnu/packages/bioinformatics.scm
parent103dc351111d7aff82b7b7883f79084faaa54abc (diff)
gnu: Add lammps.
* gnu/packages/bioinformatics.scm (lammps): New variable. Change-Id: Ic9745a623300b82b7fb1417437220415305e7332
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm71
1 files changed, 71 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3e7b99ee61..01718426ee 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -161,6 +161,7 @@
#:use-module (gnu packages time)
#:use-module (gnu packages tls)
#:use-module (gnu packages uglifyjs)
+ #:use-module (gnu packages video)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
#:use-module (gnu packages wget)
@@ -4287,6 +4288,76 @@ annotations of the genome.")
other types of unwanted sequence from high-throughput sequencing reads.")
(license license:expat)))
+(define-public lammps
+ (let ((commit "stable_2Aug2023_update2"))
+ (package
+ (name "lammps")
+ (version (string-append "0." commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/lammps/lammps.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "11xagacgxgldkx34qdzyjrjvn8x3hpl0kgzhh9zh7skpq79pwycz"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:tests? #f ; no check target
+ #:make-flags
+ '(list "CC=mpicc" "mpi"
+ "LMP_INC=-DLAMMPS_GZIP \
+-DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG -DLAMMPS_MEMALIGN=64"
+ "LIB=-gz -ljpeg -lpng -lavcodec")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _ (chdir "src")))
+ (replace 'configure
+ (lambda _
+ (substitute* "MAKE/Makefile.mpi"
+ (("SHELL =.*")
+ (string-append "SHELL=" (which "bash") "\n"))
+ (("cc ") "mpicc "))
+ (substitute* "Makefile"
+ (("SHELL =.*")
+ (string-append "SHELL=" (which "bash") "\n")))))
+ (add-after 'configure 'configure-modules
+ (lambda _
+ (invoke "make"
+ "yes-molecule"
+ "yes-misc"
+ "yes-granular"
+ (string-append "HDF5_PATH="
+ #$(this-package-input "hdf5")))))
+ (replace 'install
+ (lambda _
+ (let ((bin (string-append #$output "/bin")))
+ (mkdir-p bin)
+ (install-file "lmp_mpi" bin)))))))
+ (inputs
+ (list ffmpeg
+ gfortran
+ gzip
+ hdf5
+ libjpeg-turbo
+ libpng
+ openmpi
+ python-wrapper))
+ (native-inputs (list bc))
+ (home-page "https://www.lammps.org/")
+ (synopsis "Classical molecular dynamics simulator")
+ (description "LAMMPS is a classical molecular dynamics simulator
+designed to run efficiently on parallel computers. LAMMPS has potentials for
+solid-state materials (metals, semiconductors), soft matter (biomolecules,
+polymers), and coarse-grained or mesoscopic systems. It can be used to model
+atoms or, more generically, as a parallel particle simulator at the atomic,
+meso, or continuum scale.")
+ (license license:gpl2+))))
+
(define-public libbigwig
(package
(name "libbigwig")