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-rw-r--r--gnu/packages/chemistry.scm126
1 files changed, 126 insertions, 0 deletions
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 855ae2df22..0540dfceb6 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -4,6 +4,7 @@
;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
+;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -29,15 +30,20 @@
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages boost)
+ #:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages documentation)
#:use-module (gnu packages gl)
+ #:use-module (gnu packages graphviz)
#:use-module (gnu packages gv)
#:use-module (gnu packages maths)
+ #:use-module (gnu packages mpi)
+ #:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages qt)
+ #:use-module (gnu packages sphinx)
#:use-module (gnu packages xml)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
@@ -300,6 +306,126 @@ is currently not actively maintained and works only with Python 2 and
NumPy < 1.9.")
(license license:cecill)))
+(define-public tng
+ (package
+ (name "tng")
+ (version "1.8.2")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/gromacs/tng.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q"))))
+ (build-system cmake-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'remove-bundled-zlib
+ (lambda _
+ (delete-file-recursively "external")
+ #t))
+ (replace 'check
+ (lambda _
+ (invoke "../build/bin/tests/tng_testing")
+ #t)))))
+ (home-page "https://github.com/gromacs/tng")
+ (synopsis "Trajectory Next Generation binary format manipulation library")
+ (description "TRAJNG (Trajectory next generation) is a program library for
+handling molecular dynamics (MD) trajectories. It can store coordinates, and
+optionally velocities and the H-matrix. Coordinates and velocities are
+stored with user-specified precision.")
+ (license license:bsd-3)))
+
+(define-public gromacs
+ (package
+ (name "gromacs")
+ (version "2020.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl"))
+ ;; Our version of tinyxml2 is far newer than the bundled one and
+ ;; require fixing `testutils' code. See patch header for more info
+ (patches (search-patches "gromacs-tinyxml2.patch"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:configure-flags
+ (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
+ ;; Unbundling
+ "-DGMX_USE_LMFIT=EXTERNAL"
+ "-DGMX_BUILD_OWN_FFTW=off"
+ "-DGMX_EXTERNAL_BLAS=on"
+ "-DGMX_EXTERNAL_LAPACK=on"
+ "-DGMX_EXTERNAL_TNG=on"
+ "-DGMX_EXTERNAL_ZLIB=on"
+ "-DGMX_EXTERNAL_TINYXML2=on"
+ (string-append "-DTinyXML2_DIR="
+ (assoc-ref %build-inputs "tinyxml2"))
+ ;; Workaround for cmake/FindSphinx.cmake version parsing that does
+ ;; not understand the guix-wrapped `sphinx-build --version' answer
+ (string-append "-DSPHINX_EXECUTABLE_VERSION="
+ ,(package-version python-sphinx)))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fixes
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; Still bundled: part of gromacs, source behind registration
+ ;; but free software anyways
+ ;;(delete-file-recursively "src/external/vmd_molfile")
+ ;; Still bundled: threads-based OpenMPI-compatible fallback
+ ;; designed to be bundled like that
+ ;;(delete-file-recursively "src/external/thread_mpi")
+ ;; Unbundling
+ (delete-file-recursively "src/external/lmfit")
+ (delete-file-recursively "src/external/clFFT")
+ (delete-file-recursively "src/external/fftpack")
+ (delete-file-recursively "src/external/build-fftw")
+ (delete-file-recursively "src/external/tng_io")
+ (delete-file-recursively "src/external/tinyxml2")
+ (delete-file-recursively "src/external/googletest")
+ (copy-recursively (assoc-ref inputs "googletest-source")
+ "src/external/googletest")
+ ;; This test warns about the build host hardware, disable
+ (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
+ (("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
+ "void __guix_disabled()"))
+ #t)))))
+ (native-inputs
+ `(("doxygen" ,doxygen)
+ ("googletest-source" ,(package-source googletest))
+ ("graphviz" ,graphviz)
+ ("pkg-config" ,pkg-config)
+ ("python" ,python)
+ ("python-pygments" ,python-pygments)
+ ("python-sphinx" ,python-sphinx)))
+ (inputs
+ `(("fftwf" ,fftwf)
+ ("hwloc" ,hwloc-2 "lib")
+ ("lmfit" ,lmfit)
+ ("openblas" ,openblas)
+ ("perl" ,perl)
+ ("tinyxml2" ,tinyxml2)
+ ("tng" ,tng)))
+ (home-page "http://www.gromacs.org/")
+ (synopsis "Molecular dynamics software package")
+ (description "GROMACS is a versatile package to perform molecular dynamics,
+i.e. simulate the Newtonian equations of motion for systems with hundreds to
+millions of particles. It is primarily designed for biochemical molecules like
+proteins, lipids and nucleic acids that have a lot of complicated bonded
+interactions, but since GROMACS is extremely fast at calculating the nonbonded
+interactions (that usually dominate simulations) many groups are also using it
+for research on non-biological systems, e.g. polymers. GROMACS supports all the
+usual algorithms you expect from a modern molecular dynamics implementation.")
+ (license license:lgpl2.1+)))
+
(define-public openbabel
(package
(name "openbabel")