diff options
Diffstat (limited to 'pkgs/applications/science/chemistry')
8 files changed, 41 insertions, 37 deletions
diff --git a/pkgs/applications/science/chemistry/avogadro2/default.nix b/pkgs/applications/science/chemistry/avogadro2/default.nix index 7ee42c1a793c..f69f10164cc1 100644 --- a/pkgs/applications/science/chemistry/avogadro2/default.nix +++ b/pkgs/applications/science/chemistry/avogadro2/default.nix @@ -1,5 +1,5 @@ { lib, stdenv, fetchFromGitHub, cmake, eigen, avogadrolibs, molequeue, hdf5 -, openbabel, qttools, wrapQtAppsHook +, openbabel, qttools, wrapQtAppsHook, mesa }: let @@ -44,7 +44,7 @@ in stdenv.mkDerivation rec { mainProgram = "avogadro2"; maintainers = with maintainers; [ sheepforce ]; homepage = "https://github.com/OpenChemistry/avogadroapp"; - platforms = platforms.mesaPlatforms; + inherit (mesa.meta) platforms; license = licenses.bsd3; }; } diff --git a/pkgs/applications/science/chemistry/cp2k/default.nix b/pkgs/applications/science/chemistry/cp2k/default.nix index 8a831fe23b74..f12dfda5d2c1 100644 --- a/pkgs/applications/science/chemistry/cp2k/default.nix +++ b/pkgs/applications/science/chemistry/cp2k/default.nix @@ -10,6 +10,10 @@ , libint , libvori , libxc +, dftd4 +, mctc-lib +, mstore +, multicharge , mpi , gsl , scalapack @@ -54,13 +58,13 @@ let in stdenv.mkDerivation rec { pname = "cp2k"; - version = "2024.1"; + version = "2024.2"; src = fetchFromGitHub { owner = "cp2k"; repo = "cp2k"; rev = "v${version}"; - hash = "sha256-6PB6wjdTOa55dXV7QIsjxI77hhc95WFEjNePfupBUJQ="; + hash = "sha256-KXxqzapdPZggFlxX1rkNcxEYb2+aQIPFclFspxII7aE="; fetchSubmodules = true; }; @@ -80,6 +84,10 @@ stdenv.mkDerivation rec { libint libvori libxc + dftd4 + mctc-lib + mstore + multicharge libxsmm mpi spglib @@ -154,6 +162,7 @@ stdenv.mkDerivation rec { -D__MPI_VERSION=3 -D__F2008 -D__LIBXSMM -D__SPGLIB \ -D__MAX_CONTR=4 -D__LIBVORI ${lib.optionalString enableElpa "-D__ELPA"} \ -D__PLUMED2 -D__HDF5 -D__GSL -D__SIRIUS -D__LIBVDWXC -D__SPFFT -D__SPLA \ + -D__DFTD4 \ ${lib.strings.optionalString (gpuBackend == "cuda") "-D__OFFLOAD_CUDA -D__ACC -D__DBCSR_ACC -D__NO_OFFLOAD_PW"} \ ${lib.strings.optionalString (gpuBackend == "rocm") "-D__OFFLOAD_HIP -D__DBCSR_ACC -D__NO_OFFLOAD_PW"} CFLAGS = -fopenmp @@ -165,6 +174,7 @@ stdenv.mkDerivation rec { -I${lib.getDev libint}/include \ -I${lib.getDev sirius}/include/sirius \ -I${lib.getDev libxc}/include \ + -I${lib.getDev dftd4}/include/dftd4 \ -I${lib.getDev libxsmm}/include \ -I${lib.getDev hdf5-fortran}/include \ -fallow-argument-mismatch @@ -176,6 +186,7 @@ stdenv.mkDerivation rec { -fopenmp ${lib.optionalString enableElpa "$(pkg-config --libs elpa)"} \ -lz -ldl ${lib.optionalString (mpi.pname == "openmpi") "$(mpicxx --showme:link)"} \ -lplumed -lhdf5_fortran -lhdf5_hl -lhdf5 -lgsl -lsirius -lspla -lspfft -lvdwxc \ + -ldftd4 -lmstore -lmulticharge -lmctc-lib \ ${lib.strings.optionalString (gpuBackend == "cuda") '' -L${cudaPackages.cuda_cudart}/lib/stubs/ \ -lcudart -lnvrtc -lcuda -lcublas diff --git a/pkgs/applications/science/chemistry/gwyddion/default.nix b/pkgs/applications/science/chemistry/gwyddion/default.nix index b7f06898504f..9e64ee7afe4d 100644 --- a/pkgs/applications/science/chemistry/gwyddion/default.nix +++ b/pkgs/applications/science/chemistry/gwyddion/default.nix @@ -24,19 +24,18 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ pkg-config file ]; - buildInputs = with lib; - [ gtk2 fftw ] ++ - optionals openglSupport [ gnome2.gtkglext libGL ] ++ - optional openexrSupport openexr ++ - optional libXmuSupport xorg.libXmu ++ - optional fitsSupport cfitsio ++ - optional libpngSupport libpng ++ - optional libxsltSupport libxslt ++ - optional libxml2Support libxml2 ++ - optional libwebpSupport libwebp ++ - optional zlibSupport zlib ++ - optional libuniqueSupport libunique ++ - optional libzipSupport libzip; + buildInputs = [ gtk2 fftw ] ++ + lib.optionals openglSupport [ gnome2.gtkglext libGL ] ++ + lib.optional openexrSupport openexr ++ + lib.optional libXmuSupport xorg.libXmu ++ + lib.optional fitsSupport cfitsio ++ + lib.optional libpngSupport libpng ++ + lib.optional libxsltSupport libxslt ++ + lib.optional libxml2Support libxml2 ++ + lib.optional libwebpSupport libwebp ++ + lib.optional zlibSupport zlib ++ + lib.optional libuniqueSupport libunique ++ + lib.optional libzipSupport libzip; # This patch corrects problems with python support, but should apply cleanly # regardless of whether python support is enabled, and have no effects if diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix index cba6a40b5992..a48019febb1d 100644 --- a/pkgs/applications/science/chemistry/jmol/default.nix +++ b/pkgs/applications/science/chemistry/jmol/default.nix @@ -25,14 +25,14 @@ let }; in stdenv.mkDerivation rec { - version = "16.2.17"; + version = "16.2.21"; pname = "jmol"; src = let baseVersion = "${lib.versions.major version}.${lib.versions.minor version}"; in fetchurl { url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz"; - hash = "sha256-1iBLLfaoztbphhrG3NVWH+PVSbCZd+HQqvCYF3H9S/E="; + hash = "sha256-9gIOrHoy0JyoPXaHOfBDHCL+ykmmHNam+Um12sHqZsE="; }; patchPhase = '' diff --git a/pkgs/applications/science/chemistry/marvin/default.nix b/pkgs/applications/science/chemistry/marvin/default.nix index 4228e818e488..e1e911e2d4df 100644 --- a/pkgs/applications/science/chemistry/marvin/default.nix +++ b/pkgs/applications/science/chemistry/marvin/default.nix @@ -1,14 +1,12 @@ { lib, stdenv, fetchurl, dpkg, makeWrapper, coreutils, gawk, gnugrep, gnused, openjdk17 }: -with lib; - stdenv.mkDerivation rec { pname = "marvin"; version = "23.17.0"; src = fetchurl { name = "marvin-${version}.deb"; - url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb"; + url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${lib.versions.majorMinor version}.deb"; hash = "sha256-zE/9EaOsNJwzE4Doasm9N8QG4t7wDOxqpV/Nhc4p7Ws="; }; @@ -22,7 +20,7 @@ stdenv.mkDerivation rec { wrapBin() { makeWrapper $1 $out/bin/$(basename $1) \ --set INSTALL4J_JAVA_HOME "${openjdk17}" \ - --prefix PATH : ${makeBinPath [ coreutils gawk gnugrep gnused ]} + --prefix PATH : ${lib.makeBinPath [ coreutils gawk gnugrep gnused ]} } cp -r opt $out mkdir -p $out/bin $out/share/pixmaps $out/share/applications @@ -33,12 +31,12 @@ stdenv.mkDerivation rec { for name in cxcalc cxtrain evaluate molconvert mview msketch; do wrapBin $out/opt/chemaxon/marvinsuite/bin/$name done - ${concatStrings (map (name: '' + ${lib.concatStrings (map (name: '' substitute ${./. + "/${name}.desktop"} $out/share/applications/${name}.desktop --subst-var out '') [ "LicenseManager" "MarvinSketch" "MarvinView" ])} ''; - meta = { + meta = with lib; { description = "Chemical modelling, analysis and structure drawing program"; homepage = "https://chemaxon.com/products/marvin"; maintainers = with maintainers; [ fusion809 ]; diff --git a/pkgs/applications/science/chemistry/nwchem/default.nix b/pkgs/applications/science/chemistry/nwchem/default.nix index 61266a9f0285..44ce15229017 100644 --- a/pkgs/applications/science/chemistry/nwchem/default.nix +++ b/pkgs/applications/science/chemistry/nwchem/default.nix @@ -1,6 +1,5 @@ { lib , stdenv -, pkgs , fetchFromGitHub , fetchurl , mpiCheckPhaseHook @@ -14,7 +13,6 @@ , lapack , python3 , tcsh -, bash , automake , autoconf , libtool @@ -34,7 +32,7 @@ let }; dftd3Src = fetchurl { - url = "https://www.chemiebn.uni-bonn.de/pctc/mulliken-center/software/dft-d3/dftd3.tgz"; + url = "https://www.chemie.uni-bonn.de/grimme/software/dft-d3/dftd3.tgz"; hash = "sha256-2Xz5dY9hqoH9hUJUSPv0pujOB8EukjZzmDGjrzKID1k="; }; @@ -47,20 +45,20 @@ let plumedSrc = fetchFromGitHub { owner = "edoapra"; repo = "plumed2"; - rev = "e7c908da50bde1c6399c9f0e445d6ea3330ddd9b"; - hash = "sha256-CNlb6MTEkD977hj3xonYqZH1/WlQ1EdVD7cvL//heRM="; + rev = "88f06db71173e7893713a582e5ada7193e8ae1c9"; + hash = "sha256-p5XNxHcE/QkJ5WdQH/xPp2EyrqCNjA/w/e1R2fkwYts="; }; in stdenv.mkDerivation rec { pname = "nwchem"; - version = "7.2.2"; + version = "7.2.3"; src = fetchFromGitHub { owner = "nwchemgit"; repo = "nwchem"; rev = "v${version}-release"; - hash = "sha256-BcYRqPaPR24OTRY0MJgBxi46HvUG4uFaY0unZmu5b9k="; + hash = "sha256-2qc4kLb/WmUJuJGonIyS7pgCfyt8yXdcpDAKU0RMY58="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/chemistry/pymol/default.nix b/pkgs/applications/science/chemistry/pymol/default.nix index 1733ba2f236c..295ac7e14cb2 100644 --- a/pkgs/applications/science/chemistry/pymol/default.nix +++ b/pkgs/applications/science/chemistry/pymol/default.nix @@ -2,7 +2,6 @@ , lib , fetchFromGitHub , makeDesktopItem -, python3 , python3Packages , netcdf , glew @@ -50,7 +49,7 @@ python3Packages.buildPythonApplication rec { postPatch = '' substituteInPlace setup.py \ - --replace-fail "self.install_libbase" '"${placeholder "out"}/${python3.sitePackages}"' + --replace-fail "self.install_libbase" '"${placeholder "out"}/${python3Packages.python.sitePackages}"' ''; build-system = [ @@ -63,10 +62,10 @@ python3Packages.buildPythonApplication rec { postInstall = with python3Packages; '' wrapProgram $out/bin/pymol \ - --prefix PYTHONPATH : ${lib.makeSearchPathOutput "lib" python3.sitePackages [ pyqt5 pyqt5.pyqt5-sip ]} + --prefix PYTHONPATH : ${lib.makeSearchPathOutput "lib" python3Packages.python.sitePackages [ pyqt5 pyqt5.pyqt5-sip ]} mkdir -p "$out/share/icons/" - ln -s $out/${python3.sitePackages}/pymol/pymol_path/data/pymol/icons/icon2.svg "$out/share/icons/pymol.svg" + ln -s $out/${python3Packages.python.sitePackages}/pymol/pymol_path/data/pymol/icons/icon2.svg "$out/share/icons/pymol.svg" '' + lib.optionalString stdenv.hostPlatform.isLinux '' cp -r "${desktopItem}/share/applications/" "$out/share/" ''; diff --git a/pkgs/applications/science/chemistry/quantum-espresso/default.nix b/pkgs/applications/science/chemistry/quantum-espresso/default.nix index 2c565cb5db9f..2156c1d26969 100644 --- a/pkgs/applications/science/chemistry/quantum-espresso/default.nix +++ b/pkgs/applications/science/chemistry/quantum-espresso/default.nix @@ -4,7 +4,6 @@ , fetchFromGitHub , git , cmake -, gnum4 , gfortran , pkg-config , fftw |