branch master updated: gnu: Add lammps.

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The following commit(s) were added to refs/heads/master by this push:
     new 95879674c2 gnu: Add lammps.
95879674c2 is described below

commit 95879674c2312432f778383c2979fd0c9c098721
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Mon Dec 25 16:37:46 2023 +0100

    gnu: Add lammps.
    
    * gnu/packages/bioinformatics.scm (lammps): New variable.
    
    Change-Id: Ic9745a623300b82b7fb1417437220415305e7332
---
 gnu/packages/bioinformatics.scm | 71 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 71 insertions(+)

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")