Refactor finished.

pkgs/applications/lammps/default.nix

-{ src, lammps, ... }: lammps.overrideAttrs (oldAttrs: {inherit src;})
+{ lib
+, src
+, bash
+, stdenv
+, writeText
+, fetchFromGitHub
+, libpng
+, gzip
+, fftw
+, openblas
+, mpiSupport ? false, mpi ? null
+}:
+
+assert mpiSupport -> mpi != null;
+
+stdenv.mkDerivation rec {
+  # LAMMPS has weird versioning converted to ISO 8601 format
+  version = "patch_2Aug2018";
+  name = "lammps-${version}";
+
+  lammps_packages = "asphere body class2 colloid compress coreshell dipole granular kspace manybody mc misc molecule opt peri qeq replica rigid shock snap srd user-reaxc";
+  lammps_includes = "-DLAMMPS_EXCEPTIONS -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64";
+
+  inherit src;
+
+  #src = fetchFromGitHub {
+    #owner = "lammps";
+    #repo = "lammps";
+    #rev = "${version}";
+    #sha256 = "1ph9pr7s11wgmspmnhxa55bh1pq2cyl8iimfi62lbpbpl9pr1ilc";
+  #};
+
+  passthru = {
+    inherit mpi;
+  };
+
+  buildInputs = [ fftw libpng openblas gzip bash ]
+  ++ (stdenv.lib.optionals mpiSupport [ mpi ]);
+
+  # Must do manual build due to LAMMPS requiring a seperate build for
+  # the libraries and executable
+  builder = writeText "builder.sh" ''
+    source $stdenv/setup
+
+    mkdir lammps
+    cp -r $src/lib $src/src lammps
+    chmod -R 755 lammps/src/
+    cd lammps/src
+    for pack in ${lammps_packages}; do make "yes-$pack" SHELL=$SHELL; done
+    make mode=exe ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
+    make mode=shlib ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
+
+    mkdir -p $out/bin
+    cp -v lmp_* $out/bin/
+
+    mkdir -p $out/include
+    cp -v *.h $out/include/
+
+    mkdir -p $out/lib
+    cp -v liblammps* $out/lib/
+  '';
+
+  meta = {
+    description = "Classical Molecular Dynamics simulation code";
+    longDescription = ''
+      LAMMPS is a classical molecular dynamics simulation code designed to
+      run efficiently on parallel computers. It was developed at Sandia
+      National Laboratories, a US Department of Energy facility, with
+      funding from the DOE. It is an open-source code, distributed freely
+      under the terms of the GNU Public License (GPL).
+      '';
+    homepage = http://lammps.sandia.gov;
+    license = stdenv.lib.licenses.gpl2;
+    platforms = stdenv.lib.platforms.linux;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/default.nix

@@ -43,9 +43,9 @@ in rec {
   let
     paths = {
      amg = applications/amg;
-     qmcpack = applications/qmcpack;
-     openmc = applications/openmc;
-     stream = applications/stream;
+     #qmcpack = applications/qmcpack;
+     #openmc = applications/openmc;
+     #stream = applications/stream;
      lammps = applications/lammps;
     };
     rawApplication = name : path: cpDefaultPin path {};