diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/chemistry')
10 files changed, 30 insertions, 26 deletions
diff --git a/nixpkgs/pkgs/applications/science/chemistry/avogadro/default.nix b/nixpkgs/pkgs/applications/science/chemistry/avogadro/default.nix index 6aca678480da..96dea10333b3 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/avogadro/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/avogadro/default.nix @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { patches = [ (fetchurl { - url = https://data.gpo.zugaina.org/fusion809/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch; + url = "https://data.gpo.zugaina.org/fusion809/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch"; sha256 = "1p113v19z3zwr9gxj2k599f8p97a8rwm93pa4amqvd0snn31mw0k"; }) ]; diff --git a/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix b/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix index cd8b93c9aac7..dec63910f709 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix @@ -12,7 +12,7 @@ zlibSupport ? true, zlib ? null, libuniqueSupport ? true, libunique ? null, libpngSupport ? true, libpng ? null, - openglSupport ? true + openglSupport ? !stdenv.isDarwin }: assert openexrSupport -> openexr != null; @@ -45,7 +45,7 @@ stdenv.mkDerivation rec { buildInputs = with stdenv.lib; [ gtk2 fftw ] ++ - optionals openglSupport [gnome2.gtkglext] ++ + optional openglSupport gnome2.gtkglext ++ optional openexrSupport openexr ++ optional libXmuSupport xorg.libXmu ++ optional fitsSupport cfitsio ++ @@ -65,7 +65,7 @@ stdenv.mkDerivation rec { # it is disabled. patches = [ ./codegen.patch ]; meta = { - homepage = http://gwyddion.net/; + homepage = "http://gwyddion.net/"; description = "Scanning probe microscopy data visualization and analysis"; @@ -80,7 +80,7 @@ stdenv.mkDerivation rec { spectrophotometry. ''; license = stdenv.lib.licenses.gpl2; - platforms = stdenv.lib.platforms.linux; + platforms = with stdenv.lib.platforms; linux ++ darwin; maintainers = [ stdenv.lib.maintainers.cge ]; }; } diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix index 7259705bc804..f52621dd71af 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix @@ -45,7 +45,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "A Java 3D viewer for chemical structures"; - homepage = https://sourceforge.net/projects/jmol; + homepage = "https://sourceforge.net/projects/jmol"; license = licenses.lgpl2; platforms = platforms.all; maintainers = with maintainers; [ timokau mounium ]; diff --git a/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix b/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix index 2c155e4e848f..c54fb3444bb0 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix @@ -4,12 +4,12 @@ with stdenv.lib; stdenv.mkDerivation rec { pname = "marvin"; - version = "20.6.0"; + version = "20.9.0"; src = fetchurl { name = "marvin-${version}.deb"; url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb"; - sha256 = "1vd1hsj36wzghpn6xnppjmva35kdcin7h0xdj3xmi4w5l3qw7fl6"; + sha256 = "1c6q1vb96jsb37g5qbhzcnasd5pdqjyc190yg3caw3gwrd97889q"; }; nativeBuildInputs = [ dpkg makeWrapper ]; @@ -40,7 +40,7 @@ stdenv.mkDerivation rec { meta = { description = "A chemical modelling, analysis and structure drawing program"; - homepage = https://chemaxon.com/products/marvin; + homepage = "https://chemaxon.com/products/marvin"; maintainers = with maintainers; [ fusion809 ]; license = licenses.unfree; platforms = platforms.linux; diff --git a/nixpkgs/pkgs/applications/science/chemistry/molden/default.nix b/nixpkgs/pkgs/applications/science/chemistry/molden/default.nix index 87dae3b14d9e..5e5df85a5279 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/molden/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/molden/default.nix @@ -31,10 +31,10 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Display and manipulate molecular structures"; - homepage = http://www.cmbi.ru.nl/molden/; + homepage = "http://www.cmbi.ru.nl/molden/"; license = { fullName = "Free for academic/non-profit use"; - url = http://www.cmbi.ru.nl/molden/CopyRight.html; + url = "http://www.cmbi.ru.nl/molden/CopyRight.html"; free = false; }; platforms = platforms.linux; diff --git a/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix b/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix index a5abbe2d1de6..f30954367cf7 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix @@ -1,7 +1,9 @@ { stdenv, fetchFromGitLab, symlinkJoin, gfortran, perl, procps -, libyaml, libxc, fftw, openblas, gsl, netcdf, arpack, autoreconfHook +, libyaml, libxc, fftw, blas, lapack, gsl, netcdf, arpack, autoreconfHook }: +assert (!blas.is64bit) && (!lapack.is64bit); + stdenv.mkDerivation rec { pname = "octopus"; version = "9.2"; @@ -14,12 +16,12 @@ stdenv.mkDerivation rec { }; nativeBuildInputs = [ perl procps autoreconfHook ]; - buildInputs = [ libyaml gfortran libxc openblas gsl fftw netcdf arpack ]; + buildInputs = [ libyaml gfortran libxc blas lapack gsl fftw netcdf arpack ]; configureFlags = [ "--with-yaml-prefix=${libyaml}" - "--with-blas=-lopenblas" - "--with-lapack=-lopenblas" + "--with-blas=-lblas" + "--with-lapack=-llapack" "--with-fftw-prefix=${fftw.dev}" "--with-gsl-prefix=${gsl}" "--with-libxc-prefix=${libxc}" @@ -40,7 +42,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Real-space time dependent density-functional theory code"; - homepage = https://octopus-code.org; + homepage = "https://octopus-code.org"; maintainers = with maintainers; [ markuskowa ]; license = licenses.gpl2; platforms = [ "x86_64-linux" ]; diff --git a/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix b/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix index d73e86d2f577..0d74e784d772 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix @@ -1,9 +1,11 @@ { stdenv, fetchFromGitLab, cmake, gfortran, perl -, openblas, hdf5-cpp, python3, texlive +, openblas, blas, lapack, hdf5-cpp, python3, texlive , armadillo, openmpi, globalarrays, openssh , makeWrapper, fetchpatch } : +assert blas.implementation == "openblas" && lapack.implementation == "openblas"; + let version = "19.11"; gitLabRev = "v${version}"; @@ -74,7 +76,7 @@ in stdenv.mkDerivation { meta = with stdenv.lib; { description = "Advanced quantum chemistry software package"; - homepage = https://gitlab.com/Molcas/OpenMolcas; + homepage = "https://gitlab.com/Molcas/OpenMolcas"; maintainers = [ maintainers.markuskowa ]; license = licenses.lgpl21; platforms = platforms.linux; diff --git a/nixpkgs/pkgs/applications/science/chemistry/pymol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/pymol/default.nix index e8b3b23ddd9d..474986901225 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/pymol/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/pymol/default.nix @@ -50,7 +50,7 @@ python3Packages.buildPythonApplication rec { meta = with lib; { description = description; - homepage = https://www.pymol.org/; + homepage = "https://www.pymol.org/"; license = licenses.mit; maintainers = with maintainers; [ samlich ]; }; diff --git a/nixpkgs/pkgs/applications/science/chemistry/quantum-espresso/default.nix b/nixpkgs/pkgs/applications/science/chemistry/quantum-espresso/default.nix index bd420519ce01..2443e6b23aba 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/quantum-espresso/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/quantum-espresso/default.nix @@ -1,5 +1,5 @@ { stdenv, fetchurl -, gfortran, fftw, openblas +, gfortran, fftw, blas, lapack , mpi ? null }: @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { patchShebangs configure ''; - buildInputs = [ fftw openblas gfortran ] + buildInputs = [ fftw blas lapack gfortran ] ++ (stdenv.lib.optionals (mpi != null) [ mpi ]); configureFlags = if (mpi != null) then [ "LD=${mpi}/bin/mpif90" ] else [ "LD=${gfortran}/bin/gfortran" ]; diff --git a/nixpkgs/pkgs/applications/science/chemistry/siesta/default.nix b/nixpkgs/pkgs/applications/science/chemistry/siesta/default.nix index 9d7880f57df5..c053c0a09cdf 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/siesta/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/siesta/default.nix @@ -1,5 +1,5 @@ { stdenv, fetchurl -, gfortran, openblas +, gfortran, blas, lapack , mpi ? null, scalapack }: @@ -16,7 +16,7 @@ stdenv.mkDerivation { inherit mpi; }; - buildInputs = [ openblas gfortran ] + buildInputs = [ blas lapack gfortran ] ++ (stdenv.lib.optionals (mpi != null) [ mpi scalapack ]); enableParallelBuilding = true; @@ -33,11 +33,11 @@ stdenv.mkDerivation { makeFlagsArray=( CC="mpicc" FC="mpifort" FPPFLAGS="-DMPI" MPI_INTERFACE="libmpi_f90.a" MPI_INCLUDE="." - COMP_LIBS="" LIBS="-lopenblas -lscalapack" + COMP_LIBS="" LIBS="-lblas -llapack -lscalapack" ); '' else '' makeFlagsArray=( - COMP_LIBS="" LIBS="-lopenblas" + COMP_LIBS="" LIBS="-lblas -llapack" ); ''; @@ -61,7 +61,7 @@ stdenv.mkDerivation { matching the quality of other approaches, such as plane-wave and all-electron methods. ''; - homepage = https://www.quantum-espresso.org/; + homepage = "https://www.quantum-espresso.org/"; license = licenses.gpl2; platforms = [ "x86_64-linux" ]; maintainers = [ maintainers.costrouc ]; |