push sheeet

pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix

@@ -0,0 +1,99 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  cmake,
+  zlib,
+  eigen,
+  libGL,
+  spglib,
+  mmtf-cpp,
+  glew,
+  python3,
+  libarchive,
+  libmsym,
+  qttools,
+  wrapQtAppsHook,
+}:
+
+let
+  pythonWP = python3.withPackages (
+    p: with p; [
+      openbabel
+      numpy
+    ]
+  );
+
+  # Pure data repositories
+  moleculesRepo = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "molecules";
+    tag = "1.101.0";
+    hash = "sha256-hMLf0gYYnQpjSGKcPy4tihNbmpRR7UxnXF/hyhforgI=";
+  };
+  crystalsRepo = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "crystals";
+    tag = "1.101.0";
+    hash = "sha256-WhzFldaOt/wJy1kk+ypOkw1OYFT3hqD7j5qGdq9g+IY=";
+  };
+  fragmentsRepo = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "fragments";
+    tag = "1.101.0";
+    hash = "sha256-x10jGl3lAEfm8OxUZJnjXRJCQg8RLQZTstjwnt5B2bw=";
+  };
+
+in
+stdenv.mkDerivation rec {
+  pname = "avogadrolibs";
+  version = "1.101.0";
+
+  src = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "avogadrolibs";
+    tag = version;
+    hash = "sha256-0DJU40Etse90rdX8xByjQeUiBsJtEQozZQQsWsc4vxk=";
+  };
+
+  postUnpack = ''
+    cp -r ${moleculesRepo} molecules
+    cp -r ${crystalsRepo} crystals
+    cp -r ${fragmentsRepo} fragments
+  '';
+
+  nativeBuildInputs = [
+    cmake
+    wrapQtAppsHook
+    pythonWP
+  ];
+
+  buildInputs = [
+    eigen
+    zlib
+    libGL
+    spglib
+    mmtf-cpp
+    glew
+    libarchive
+    libmsym
+    qttools
+  ];
+
+  # Fix the broken CMake files to use the correct paths
+  postInstall = ''
+    substituteInPlace $out/lib/cmake/avogadrolibs/AvogadroLibsConfig.cmake \
+      --replace "$out/" ""
+
+    substituteInPlace $out/lib/cmake/avogadrolibs/AvogadroLibsTargets.cmake \
+      --replace "_IMPORT_PREFIX}/$out" "_IMPORT_PREFIX}/"
+  '';
+
+  meta = with lib; {
+    description = "Molecule editor and visualizer";
+    maintainers = with maintainers; [ sheepforce ];
+    homepage = "https://github.com/OpenChemistry/avogadrolibs";
+    platforms = platforms.linux;
+    license = licenses.gpl2Only;
+  };
+}

pkgs/development/libraries/science/chemistry/molequeue/default.nix

@@ -0,0 +1,42 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  cmake,
+  qttools,
+  wrapQtAppsHook,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "molequeue";
+  version = "0.9.0";
+
+  src = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "molequeue";
+    rev = version;
+    hash = "sha256-+NoY8YVseFyBbxc3ttFWiQuHQyy1GN8zvV1jGFjmvLg=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    wrapQtAppsHook
+  ];
+
+  buildInputs = [ qttools ];
+
+  # Fix the broken CMake files to use the correct paths
+  postInstall = ''
+    substituteInPlace $out/lib/cmake/molequeue/MoleQueueConfig.cmake \
+      --replace "$out/" ""
+  '';
+
+  meta = with lib; {
+    description = "Desktop integration of high performance computing resources";
+    mainProgram = "molequeue";
+    maintainers = with maintainers; [ sheepforce ];
+    homepage = "https://github.com/OpenChemistry/molequeue";
+    platforms = platforms.linux;
+    license = licenses.bsd3;
+  };
+}

pkgs/development/libraries/science/chemistry/simple-dftd3/cmake.patch

@@ -0,0 +1,13 @@
+diff --git a/config/template.pc b/config/template.pc
+index 3d6efbb..e338a42 100644
+--- a/config/template.pc
++++ b/config/template.pc
+@@ -1,6 +1,6 @@
+ prefix=@CMAKE_INSTALL_PREFIX@
+-libdir=${prefix}/@CMAKE_INSTALL_LIBDIR@
+-includedir=${prefix}/@CMAKE_INSTALL_INCLUDEDIR@
++libdir=@CMAKE_INSTALL_FULL_LIBDIR@
++includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
+ 
+ Name: @PROJECT_NAME@
+ Description: @PROJECT_DESCRIPTION@

pkgs/development/libraries/science/chemistry/simple-dftd3/default.nix

@@ -0,0 +1,82 @@
+{
+  stdenv,
+  lib,
+  fetchFromGitHub,
+  gfortran,
+  meson,
+  ninja,
+  cmake,
+  pkg-config,
+  mctc-lib,
+  mstore,
+  toml-f,
+  blas,
+  buildType ? "meson",
+}:
+
+assert !blas.isILP64;
+assert (
+  builtins.elem buildType [
+    "meson"
+    "cmake"
+  ]
+);
+
+stdenv.mkDerivation rec {
+  pname = "simple-dftd3";
+  version = "1.2.1";
+
+  src = fetchFromGitHub {
+    owner = "dftd3";
+    repo = "simple-dftd3";
+    tag = "v${version}";
+    hash = "sha256-c4xctcMcPQ70ippqbwtinygmnZ5en6ZGF5/v0ZWtzys=";
+  };
+
+  patches = [
+    ./cmake.patch
+  ];
+
+  nativeBuildInputs = [
+    gfortran
+    pkg-config
+  ]
+  ++ lib.optionals (buildType == "meson") [
+    meson
+    ninja
+  ]
+  ++ lib.optional (buildType == "cmake") cmake;
+
+  buildInputs = [
+    mctc-lib
+    mstore
+    toml-f
+    blas
+  ];
+
+  outputs = [
+    "out"
+    "dev"
+  ];
+
+  cmakeFlags = [
+    (lib.strings.cmakeBool "BUILD_SHARED_LIBS" (!stdenv.hostPlatform.isStatic))
+  ];
+
+  doCheck = true;
+  preCheck = ''
+    export OMP_NUM_THREADS=2
+  '';
+
+  meta = with lib; {
+    description = "Reimplementation of the DFT-D3 program";
+    mainProgram = "s-dftd3";
+    license = with licenses; [
+      lgpl3Only
+      gpl3Only
+    ];
+    homepage = "https://github.com/dftd3/simple-dftd3";
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}

pkgs/development/libraries/science/chemistry/simple-dftd3/python.nix

@@ -0,0 +1,58 @@
+{
+  buildPythonPackage,
+  python,
+  simple-dftd3,
+  cffi,
+  numpy,
+  toml,
+  qcengine,
+  pyscf,
+  ase,
+  pytestCheckHook,
+}:
+
+buildPythonPackage {
+  format = "setuptools";
+  inherit (simple-dftd3)
+    pname
+    version
+    src
+    meta
+    ;
+
+  # pytest is also required for installation, not only testing
+  nativeBuildInputs = [ pytestCheckHook ];
+
+  buildInputs = [ simple-dftd3 ];
+
+  propagatedBuildInputs = [
+    cffi
+    numpy
+    toml
+  ];
+
+  checkInputs = [
+    ase
+    qcengine
+    pyscf
+  ];
+
+  preConfigure = ''
+    cd python
+  '';
+
+  # The compiled CFFI is not placed correctly before pytest invocation
+  preCheck = ''
+    find . -name "_libdftd3*" -exec cp {} ./dftd3/. \;
+  '';
+
+  pythonImportsCheck = [ "dftd3" ];
+  doCheck = true;
+
+  # Parameters need to be present in the python site packages directory, but they
+  # are originally only present in the fortran package. This is a consequence of
+  # building the python bindings separately from the fortran library.
+  postInstall = ''
+    ln -s ${simple-dftd3}/share/s-dftd3/parameters.toml $out/${python.sitePackages}/dftd3/.
+  '';
+}

pkgs/development/libraries/science/chemistry/tblite/0001-fix-multicharge-dep-needed-for-static-compilation.patch

@@ -0,0 +1,31 @@
+From 1885a2349102742e33c5c97a8ab4bcacc032fc70 Mon Sep 17 00:00:00 2001
+From: Ryan Swart <ryan@talosystems.com>
+Date: Thu, 30 Mar 2023 15:50:23 +0800
+Subject: [PATCH] fix: multicharge dep needed for static compilation
+
+---
+ config/meson.build | 8 ++++++++
+ 1 file changed, 8 insertions(+)
+
+diff --git a/config/meson.build b/config/meson.build
+index 4f76160..629fa5e 100644
+--- a/config/meson.build
++++ b/config/meson.build
+@@ -136,6 +136,14 @@ sdftd3_dep = dependency(
+ )
+ lib_deps += sdftd3_dep
+ 
++# Create multicharge library as subproject
++multicharge_dep = dependency(
++  'multicharge',
++  fallback: ['multicharge'],
++  default_options: ['default_library=static', 'api=false', 'python=false'],
++)
++lib_deps += multicharge_dep
++
+ # Create TOML Fortran as subproject
+ tomlf_dep = dependency(
+   'toml-f',
+-- 
+2.39.2
+

pkgs/development/libraries/science/chemistry/tblite/default.nix

@@ -0,0 +1,106 @@
+{
+  stdenv,
+  lib,
+  fetchFromGitHub,
+  gfortran,
+  buildType ? "meson",
+  meson,
+  ninja,
+  cmake,
+  pkg-config,
+  blas,
+  lapack,
+  mctc-lib,
+  mstore,
+  toml-f,
+  multicharge,
+  dftd4,
+  simple-dftd3,
+  python3,
+}:
+
+assert !blas.isILP64 && !lapack.isILP64;
+assert (
+  builtins.elem buildType [
+    "meson"
+    "cmake"
+  ]
+);
+
+stdenv.mkDerivation rec {
+  pname = "tblite";
+  version = "0.5.0";
+
+  src = fetchFromGitHub {
+    owner = "tblite";
+    repo = "tblite";
+    rev = "v${version}";
+    hash = "sha256-hePy/slEeM2o1gtrAbq/nkEUILa6oQjkD2ddDstQ2Zc=";
+  };
+
+  patches = [
+    ./0001-fix-multicharge-dep-needed-for-static-compilation.patch
+
+    # Fix wrong paths in pkg-config file
+    ./pkgconfig.patch
+  ];
+
+  # Python scripts in test subdirectories to run the tests
+  postPatch = ''
+    patchShebangs ./
+  '';
+
+  nativeBuildInputs = [
+    gfortran
+    pkg-config
+  ]
+  ++ lib.optionals (buildType == "meson") [
+    meson
+    ninja
+  ]
+  ++ lib.optionals (buildType == "cmake") [
+    cmake
+  ];
+
+  buildInputs = [
+    blas
+    lapack
+    mctc-lib
+    mstore
+    toml-f
+    multicharge
+    dftd4
+    simple-dftd3
+  ];
+
+  outputs = [
+    "out"
+    "dev"
+  ];
+
+  checkInputs = [
+    python3
+  ];
+
+  checkFlags = [
+    "-j1" # Tests hang when multiple are run in parallel
+  ];
+
+  doCheck = buildType == "meson";
+
+  preCheck = ''
+    export OMP_NUM_THREADS=2
+  '';
+
+  meta = with lib; {
+    description = "Light-weight tight-binding framework";
+    mainProgram = "tblite";
+    license = with licenses; [
+      gpl3Plus
+      lgpl3Plus
+    ];
+    homepage = "https://github.com/tblite/tblite";
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}

pkgs/development/libraries/science/chemistry/tblite/pkgconfig.patch

@@ -0,0 +1,13 @@
+diff --git a/config/template.pc b/config/template.pc
+index 3d6efbb..e338a42 100644
+--- a/config/template.pc
++++ b/config/template.pc
+@@ -1,6 +1,6 @@
+ prefix=@CMAKE_INSTALL_PREFIX@
+-libdir=${prefix}/@CMAKE_INSTALL_LIBDIR@
+-includedir=${prefix}/@CMAKE_INSTALL_INCLUDEDIR@
++libdir=@CMAKE_INSTALL_FULL_LIBDIR@
++includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
+ 
+ Name: @PROJECT_NAME@
+ Description: @PROJECT_DESCRIPTION@

pkgs/development/libraries/science/chemistry/tblite/python.nix

@@ -0,0 +1,69 @@
+{
+  buildPythonPackage,
+  meson,
+  ninja,
+  pkg-config,
+  tblite,
+  numpy,
+  simple-dftd3,
+  cffi,
+  gfortran,
+  blas,
+  lapack,
+  mctc-lib,
+  mstore,
+  toml-f,
+  multicharge,
+  dftd4,
+  setuptools,
+}:
+
+buildPythonPackage {
+  inherit (tblite)
+    pname
+    version
+    src
+    meta
+    ;
+
+  nativeBuildInputs = [
+    tblite
+    meson
+    ninja
+    pkg-config
+    gfortran
+    mctc-lib
+    setuptools
+  ];
+
+  buildInputs = [
+    tblite
+    simple-dftd3
+    blas
+    lapack
+    mctc-lib
+    mstore
+    toml-f
+    multicharge
+    dftd4
+  ];
+
+  propagatedBuildInputs = [
+    tblite
+    simple-dftd3
+    cffi
+    numpy
+  ];
+
+  patches = [
+    # Add multicharge to the meson deps; otherwise we get missing mod_multicharge errors
+    ./0001-fix-multicharge-dep-needed-for-static-compilation.patch
+  ];
+
+  format = "other";
+  pythonImportsCheck = [
+    "tblite"
+    "tblite.interface"
+  ];
+  mesonFlags = [ "-Dpython=true" ];
+}