diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/chemistry')
10 files changed, 57 insertions, 47 deletions
diff --git a/nixpkgs/pkgs/applications/science/chemistry/avogadro/default.nix b/nixpkgs/pkgs/applications/science/chemistry/avogadro/default.nix index 96dea10333b3..f5c6d79e28aa 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/avogadro/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/avogadro/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, cmake, qt4, zlib, eigen, openbabel, pkgconfig, libGLU, libGL, libX11, doxygen }: +{ lib, stdenv, fetchurl, cmake, qt4, zlib, eigen, openbabel, pkg-config, libGLU, libGL, libX11, doxygen }: stdenv.mkDerivation rec { name = "avogadro-1.1.1"; @@ -10,7 +10,7 @@ stdenv.mkDerivation rec { buildInputs = [ qt4 eigen zlib openbabel libGL libGLU libX11 ]; - nativeBuildInputs = [ cmake pkgconfig doxygen ]; + nativeBuildInputs = [ cmake pkg-config doxygen ]; NIX_CFLAGS_COMPILE = "-include ${libGLU.dev}/include/GL/glu.h"; @@ -21,9 +21,9 @@ stdenv.mkDerivation rec { }) ]; - meta = { + meta = with lib; { description = "Molecule editor and visualizer"; - maintainers = [ ]; - platforms = stdenv.lib.platforms.mesaPlatforms; + maintainers = with maintainers; [ danielbarter ]; + platforms = platforms.mesaPlatforms; }; } diff --git a/nixpkgs/pkgs/applications/science/chemistry/d-seams/default.nix b/nixpkgs/pkgs/applications/science/chemistry/d-seams/default.nix index 1c6395637573..cbe73bb7edc2 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/d-seams/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/d-seams/default.nix @@ -12,11 +12,10 @@ clangStdenv.mkDerivation rec { sha256 = "03zhhl9vhi3rhc3qz1g3zb89jksgpdlrk15fcr8xcz8pkj6r5b1i"; }; - enableParallelBuilding = true; nativeBuildInputs = [ cmake lua luaPackages.luafilesystem ]; buildInputs = [ fmt rang libyamlcpp eigen catch2 boost gsl liblapack blas ]; - meta = with stdenv.lib; { + meta = with lib; { description = "d-SEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations"; longDescription = '' diff --git a/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix b/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix index bdebfc72e471..8d9ea7a3917b 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, gtk2, pkg-config, fftw, file, +{ lib, stdenv, fetchurl, gtk2, pkg-config, fftw, file, pythonSupport ? false, pythonPackages ? null, gnome2 ? null, openexrSupport ? true, openexr ? null, @@ -40,10 +40,10 @@ stdenv.mkDerivation rec { url = "mirror://sourceforge/gwyddion/gwyddion-${version}.tar.xz"; sha256 = "0z83p3ifdkv5dds8s6fqqbycql1zmgppdc7ygqmm12z5zlrl9p12"; }; - + nativeBuildInputs = [ pkg-config file ]; - - buildInputs = with stdenv.lib; + + buildInputs = with lib; [ gtk2 fftw ] ++ optional openglSupport gnome2.gtkglext ++ optional openexrSupport openexr ++ @@ -57,7 +57,7 @@ stdenv.mkDerivation rec { optional libuniqueSupport libunique ++ optional libzipSupport libzip; - propagatedBuildInputs = with stdenv.lib; + propagatedBuildInputs = with lib; optionals pythonSupport [ pygtk pygobject2 python gnome2.gtksourceview ]; # This patch corrects problems with python support, but should apply cleanly @@ -79,8 +79,8 @@ stdenv.mkDerivation rec { analysis of profilometry data or thickness maps from imaging spectrophotometry. ''; - license = stdenv.lib.licenses.gpl2; - platforms = with stdenv.lib.platforms; linux ++ darwin; - maintainers = [ stdenv.lib.maintainers.cge ]; + license = lib.licenses.gpl2; + platforms = with lib.platforms; linux ++ darwin; + maintainers = [ lib.maintainers.cge ]; }; } diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix index e09abccad121..aa52fee0890d 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix @@ -43,7 +43,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; - meta = with stdenv.lib; { + meta = with lib; { description = "A Java 3D viewer for chemical structures"; homepage = "https://sourceforge.net/projects/jmol"; license = licenses.lgpl2; diff --git a/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix b/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix index ddab526ebe79..d90c55466f85 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix @@ -1,15 +1,15 @@ -{ stdenv, fetchurl, dpkg, makeWrapper, coreutils, gawk, gnugrep, gnused, jre }: +{ lib, stdenv, fetchurl, dpkg, makeWrapper, coreutils, gawk, gnugrep, gnused, jre }: -with stdenv.lib; +with lib; stdenv.mkDerivation rec { pname = "marvin"; - version = "20.20.0"; + version = "20.21.0"; src = fetchurl { name = "marvin-${version}.deb"; url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb"; - sha256 = "1a8b0drb0c95c8arm3aa0z0sbdm9ilj4h1g90i0qyn4g2wk2xsal"; + sha256 = "sha256-OMT6t8bNeFRWFlpyg0iKt2SMNfAmIUvVKiW+cfjfBuI="; }; nativeBuildInputs = [ dpkg makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/chemistry/molden/default.nix b/nixpkgs/pkgs/applications/science/chemistry/molden/default.nix index 0d7e81cd9dab..32e8f6ee56e2 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/molden/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/molden/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, which, gfortran, libGLU, xorg } : +{ lib, stdenv, fetchurl, which, gfortran, libGLU, xorg } : stdenv.mkDerivation rec { version = "6.3"; @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { --replace '-I/usr/X11R6/include' "" \ --replace '/usr/local/' $out/ \ --replace 'sudo' "" \ - --replace '-C surf depend' '-C surf' + --replace '-C surf depend' '-C surf' sed -in '/^# DO NOT DELETE THIS LINE/q;' surf/Makefile ''; @@ -29,7 +29,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; - meta = with stdenv.lib; { + meta = with lib; { description = "Display and manipulate molecular structures"; homepage = "http://www.cmbi.ru.nl/molden/"; license = { @@ -41,4 +41,3 @@ stdenv.mkDerivation rec { maintainers = with maintainers; [ markuskowa ]; }; } - diff --git a/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix b/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix index f8eb064e1fd7..74ed1873efed 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix @@ -1,22 +1,34 @@ -{ stdenv, fetchFromGitLab, symlinkJoin, gfortran, perl, procps +{ lib, stdenv, fetchFromGitLab, symlinkJoin, gfortran, perl, procps , libyaml, libxc, fftw, blas, lapack, gsl, netcdf, arpack, autoreconfHook +, python3 }: assert (!blas.isILP64) && (!lapack.isILP64); stdenv.mkDerivation rec { pname = "octopus"; - version = "10.0"; + version = "10.3"; src = fetchFromGitLab { owner = "octopus-code"; repo = "octopus"; rev = version; - sha256 = "1c6q20y0x9aacwa7vp6gj3yvfzain7hnk6skxmvg3wazp02l91kn"; + sha256 = "1axr3j53mi30gm3f645ga5jkhxbc7rbx432w2k2lgg6g9dv3fcs4"; }; nativeBuildInputs = [ perl procps autoreconfHook ]; - buildInputs = [ libyaml gfortran libxc blas lapack gsl fftw netcdf arpack ]; + buildInputs = [ + libyaml + gfortran + libxc + blas + lapack + gsl + fftw + netcdf + arpack + (python3.withPackages (ps: [ ps.pyyaml ])) + ]; configureFlags = [ "--with-yaml-prefix=${libyaml}" @@ -40,11 +52,11 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; - meta = with stdenv.lib; { + meta = with lib; { description = "Real-space time dependent density-functional theory code"; homepage = "https://octopus-code.org"; maintainers = with maintainers; [ markuskowa ]; - license = licenses.gpl2; + license = with licenses; [ gpl2Only asl20 lgpl3Plus bsd3 ]; 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 317a83371adb..4bd88456b8f6 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix @@ -1,6 +1,6 @@ -{ stdenv, fetchFromGitLab, cmake, gfortran, perl +{ lib, stdenv, fetchFromGitLab, cmake, gfortran, perl , openblas, hdf5-cpp, python3, texlive -, armadillo, openmpi, globalarrays, openssh +, armadillo, mpi, globalarrays, openssh , makeWrapper, fetchpatch } : @@ -33,13 +33,11 @@ in stdenv.mkDerivation { hdf5-cpp python armadillo - openmpi + mpi globalarrays openssh ]; - enableParallelBuilding = true; - cmakeFlags = [ "-DOPENMP=ON" "-DGA=ON" @@ -67,7 +65,7 @@ in stdenv.mkDerivation { wrapProgram $out/bin/pymolcas --set MOLCAS $out ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Advanced quantum chemistry software package"; homepage = "https://gitlab.com/Molcas/OpenMolcas"; maintainers = [ maintainers.markuskowa ]; diff --git a/nixpkgs/pkgs/applications/science/chemistry/quantum-espresso/default.nix b/nixpkgs/pkgs/applications/science/chemistry/quantum-espresso/default.nix index 071091f2ecf2..6d70e9f984f6 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/quantum-espresso/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/quantum-espresso/default.nix @@ -1,6 +1,7 @@ -{ stdenv, fetchurl +{ lib, stdenv, fetchurl , gfortran, fftw, blas, lapack -, mpi ? null +, useMpi ? false +, mpi }: stdenv.mkDerivation rec { @@ -21,13 +22,13 @@ stdenv.mkDerivation rec { ''; buildInputs = [ fftw blas lapack gfortran ] - ++ (stdenv.lib.optionals (mpi != null) [ mpi ]); + ++ (lib.optionals useMpi [ mpi ]); -configureFlags = if (mpi != null) then [ "LD=${mpi}/bin/mpif90" ] else [ "LD=${gfortran}/bin/gfortran" ]; +configureFlags = if useMpi then [ "LD=${mpi}/bin/mpif90" ] else [ "LD=${gfortran}/bin/gfortran" ]; makeFlags = [ "all" ]; - meta = with stdenv.lib; { + meta = with lib; { description = "Electronic-structure calculations and materials modeling at the nanoscale"; longDescription = '' Quantum ESPRESSO is an integrated suite of Open-Source computer codes for diff --git a/nixpkgs/pkgs/applications/science/chemistry/siesta/default.nix b/nixpkgs/pkgs/applications/science/chemistry/siesta/default.nix index c053c0a09cdf..02ff4c1ca440 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/siesta/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/siesta/default.nix @@ -1,6 +1,7 @@ -{ stdenv, fetchurl -, gfortran, blas, lapack -, mpi ? null, scalapack +{ lib, stdenv, fetchurl +, gfortran, blas, lapack, scalapack +, useMpi ? false +, mpi }: stdenv.mkDerivation { @@ -17,7 +18,7 @@ stdenv.mkDerivation { }; buildInputs = [ blas lapack gfortran ] - ++ (stdenv.lib.optionals (mpi != null) [ mpi scalapack ]); + ++ lib.optionals useMpi [ mpi scalapack ]; enableParallelBuilding = true; @@ -29,7 +30,7 @@ stdenv.mkDerivation { cp gfortran.make arch.make ''; - preBuild = if (mpi != null) then '' + preBuild = if useMpi then '' makeFlagsArray=( CC="mpicc" FC="mpifort" FPPFLAGS="-DMPI" MPI_INTERFACE="libmpi_f90.a" MPI_INCLUDE="." @@ -46,7 +47,7 @@ stdenv.mkDerivation { cp -a siesta $out/bin ''; - meta = with stdenv.lib; { + meta = with lib; { description = "A first-principles materials simulation code using DFT"; longDescription = '' SIESTA is both a method and its computer program |