Merge commit 'b3c692172e5b5241b028a98e1977f9fb12eeaf42'

7 files changed, 237 insertions, 14 deletions

diff --git a/nixpkgs/pkgs/applications/science/chemistry/avogadro2/default.nix b/nixpkgs/pkgs/applications/science/chemistry/avogadro2/default.nix
new file mode 100644
index 000000000000..437123faafd8
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/chemistry/avogadro2/default.nix
@@ -0,0 +1,37 @@
+{ lib, stdenv, fetchFromGitHub, cmake, eigen, avogadrolibs, molequeue, hdf5
+, openbabel, qttools, wrapQtAppsHook
+}:
+
+stdenv.mkDerivation rec {
+  pname = "avogadro2";
+  version = "1.94.0";
+
+  src = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "avogadroapp";
+    rev = version;
+    sha256 = "6RaiX23YUMfTYAuSighcLGGlJtqeydNgi3PWGF77Jp8=";
+  };
+
+  nativeBuildInputs = [ cmake wrapQtAppsHook ];
+
+  buildInputs = [
+    avogadrolibs
+    molequeue
+    eigen
+    hdf5
+    qttools
+  ];
+
+  propagatedBuildInputs = [ openbabel ];
+
+  qtWrapperArgs = [ "--prefix PATH : ${openbabel}/bin" ];
+
+  meta = with lib; {
+    description = "Molecule editor and visualizer";
+    maintainers = with maintainers; [ sheepforce ];
+    homepage = "https://github.com/OpenChemistry/avogadroapp";
+    platforms = platforms.mesaPlatforms;
+    license = licenses.bsd3;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix b/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix
new file mode 100644
index 000000000000..6bb99ce556dd
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix
@@ -0,0 +1,117 @@
+{ lib, stdenv, fetchFromGitHub, python3, gfortran, blas, lapack
+, fftw, libint, libvori, libxc, mpi, gsl, scalapack, openssh, makeWrapper
+, libxsmm, spglib, which
+} :
+
+let
+  cp2kVersion = "psmp";
+  arch = "Linux-x86-64-gfortran";
+
+in stdenv.mkDerivation rec {
+  pname = "cp2k";
+  version = "8.2.0";
+
+  src = fetchFromGitHub {
+    owner = "cp2k";
+    repo = "cp2k";
+    rev = "v${version}";
+    sha256 = "0kykq5p318hxjzd4gzqjwv9gqshbdvbg0gnjbd9bdfjx1r6jkjn3";
+    fetchSubmodules = true;
+  };
+
+  nativeBuildInputs = [ python3 which openssh makeWrapper ];
+  buildInputs = [
+    gfortran
+    fftw
+    gsl
+    libint
+    libvori
+    libxc
+    libxsmm
+    spglib
+    scalapack
+    blas
+    lapack
+  ];
+
+  propagatedBuildInputs = [ mpi ];
+  propagatedUserEnvPkgs = [ mpi ];
+
+  makeFlags = [
+    "ARCH=${arch}"
+    "VERSION=${cp2kVersion}"
+  ];
+
+  doCheck = true;
+
+  enableParallelBuilding = true;
+
+  postPatch = ''
+    patchShebangs tools exts/dbcsr/tools/build_utils exts/dbcsr/.cp2k
+    substituteInPlace exts/dbcsr/.cp2k/Makefile --replace '/usr/bin/env python3' '${python3}/bin/python'
+  '';
+
+  configurePhase = ''
+    cat > arch/${arch}.${cp2kVersion} << EOF
+    CC         = mpicc
+    CPP        =
+    FC         = mpif90
+    LD         = mpif90
+    AR         = ar -r
+    DFLAGS     = -D__FFTW3 -D__LIBXC -D__LIBINT -D__parallel -D__SCALAPACK \
+                 -D__MPI_VERSION=3 -D__F2008 -D__LIBXSMM -D__SPGLIB \
+                 -D__MAX_CONTR=4 -D__LIBVORI
+    CFLAGS    = -fopenmp
+    FCFLAGS    = \$(DFLAGS) -O2 -ffree-form -ffree-line-length-none \
+                 -ftree-vectorize -funroll-loops -msse2 \
+                 -std=f2008 \
+                 -fopenmp -ftree-vectorize -funroll-loops \
+                 -I${libxc}/include -I${libxsmm}/include \
+                 -I${libint}/include
+    LIBS       = -lfftw3 -lfftw3_threads \
+                 -lscalapack -lblas -llapack \
+                 -lxcf03 -lxc -lxsmmf -lxsmm -lsymspg \
+                 -lint2 -lstdc++ -lvori \
+                 -lgomp -lpthread -lm \
+                 -fopenmp
+    LDFLAGS    = \$(FCFLAGS) \$(LIBS)
+    EOF
+  '';
+
+  checkPhase = ''
+    export OMP_NUM_THREADS=1
+
+    export HYDRA_IFACE=lo  # Fix to make mpich run in a sandbox
+    export OMPI_MCA_rmaps_base_oversubscribe=1
+    export CP2K_DATA_DIR=data
+
+    mpirun -np 2 exe/${arch}/libcp2k_unittest.${cp2kVersion}
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin $out/share/cp2k
+
+    cp exe/${arch}/* $out/bin
+
+    for i in cp2k cp2k_shell graph; do
+      wrapProgram $out/bin/$i.${cp2kVersion} \
+        --set-default CP2K_DATA_DIR $out/share/cp2k
+    done
+
+    wrapProgram $out/bin/cp2k.popt \
+      --set-default CP2K_DATA_DIR $out/share/cp2k \
+      --set OMP_NUM_THREADS 1
+
+    cp -r data/* $out/share/cp2k
+  '';
+
+  passthru = { inherit mpi; };
+
+  meta = with lib; {
+    description = "Quantum chemistry and solid state physics program";
+    homepage = "https://www.cp2k.org";
+    license = licenses.gpl2Plus;
+    maintainers = [ maintainers.sheepforce ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/chemistry/ergoscf/default.nix b/nixpkgs/pkgs/applications/science/chemistry/ergoscf/default.nix
new file mode 100644
index 000000000000..b7d61848134e
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/chemistry/ergoscf/default.nix
@@ -0,0 +1,40 @@
+{ lib, stdenv, fetchurl, blas, lapack } :
+
+stdenv.mkDerivation rec {
+  pname = "ergoscf";
+  version = "3.8";
+
+  src = fetchurl {
+    url = "http://www.ergoscf.org/source/tarfiles/ergo-${version}.tar.gz";
+    sha256 = "1s50k2gfs3y6r5kddifn4p0wmj0yk85wm5vf9v3swm1c0h43riix";
+  };
+
+  buildInputs = [ blas lapack ];
+
+  patches = [ ./math-constants.patch ];
+
+  postPatch = ''
+    patchShebangs ./test
+  '';
+
+  configureFlags = [
+    "--enable-linalgebra-templates"
+    "--enable-performance"
+  ] ++ lib.optional stdenv.isx86_64 "--enable-sse-intrinsics";
+
+  LDFLAGS = "-lblas -llapack";
+
+  enableParallelBuilding = true;
+
+  OMP_NUM_THREADS = 2; # required for check phase
+
+  doCheck = true;
+
+  meta = with lib; {
+    description = "Quantum chemistry program for large-scale self-consistent field calculations";
+    homepage = "http://www.ergoscf.org";
+    license = licenses.gpl3Plus;
+    maintainers = [ maintainers.markuskowa ];
+    platforms = platforms.linux;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/chemistry/ergoscf/math-constants.patch b/nixpkgs/pkgs/applications/science/chemistry/ergoscf/math-constants.patch
new file mode 100644
index 000000000000..62209f1a3d84
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/chemistry/ergoscf/math-constants.patch
@@ -0,0 +1,19 @@
+diff --git a/source/dft/functionals.h b/source/dft/functionals.h
+index fde49ba..f7a61fc 100644
+--- a/source/dft/functionals.h
++++ b/source/dft/functionals.h
+@@ -59,6 +59,14 @@
+ #define EXTERN_C
+ #endif
+ 
++#ifndef M_PI
++#define M_PI 3.14159265358979323846
++#endif
++
++#ifndef M_SQRT2
++#define M_SQRT2        1.41421356237309504880
++#endif
++
+ typedef ergo_real real;
+ 
+ #if defined(FUNC_PRECISION) && FUNC_PRECISION == 1
diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
index 5d2158843ede..a3add93c8f70 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
@@ -17,14 +17,14 @@ let
   };
 in
 stdenv.mkDerivation rec {
-  version = "14.31.44";
+  version = "14.31.49";
   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";
-    sha256 = "sha256-MHfqoQzUEL7nje7Y/hbaA8iktxfN7464TJXum5B6OCc=";
+    sha256 = "sha256-P+bzimBVammX5LxE6Yd6CmvmBeG8WdyA1T9bHXd+ifI=";
   };
 
   patchPhase = ''
diff --git a/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix b/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix
index af646b514af9..8efe537dcacd 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix
@@ -5,9 +5,9 @@
 } :
 
 let
-  version = "21.02";
+  version = "21.06";
   # The tag keeps moving, fix a hash instead
-  gitLabRev = "41cee871945ac712e86ee971425a49a8fc60a936";
+  gitLabRev = "dd982ad4bc94dec8ac1e3e99cb6a7dd249ff71de";
 
   python = python3.withPackages (ps : with ps; [ six pyparsing ]);
 
@@ -19,7 +19,7 @@ in stdenv.mkDerivation {
     owner = "Molcas";
     repo = "OpenMolcas";
     rev = gitLabRev;
-    sha256 = "0cap53gy1wds2qaxbijw09fqhvfxphfkr93nhp9xdq84yxh4wzv6";
+    sha256 = "07dm73n0s7ckif561yb3s9yqxsv39a73kb9qwny4yp39wdvv52hz";
   };
 
   patches = [
diff --git a/nixpkgs/pkgs/applications/science/chemistry/pymol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/pymol/default.nix
index 2df8b0e6d473..39bbae77a66e 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/pymol/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/pymol/default.nix
@@ -1,8 +1,18 @@
-{ lib, fetchurl, fetchFromGitHub, makeDesktopItem
-, python3, python3Packages
-, glew, glm, freeglut, libpng, libxml2, tk, freetype, msgpack }:
-
-
+{ lib
+, fetchFromGitHub
+, makeDesktopItem
+, python3
+, python3Packages
+, netcdf
+, glew
+, glm
+, freeglut
+, libpng
+, libxml2
+, tk
+, freetype
+, msgpack
+}:
 let
   pname = "pymol";
   description = "A Python-enhanced molecular graphics tool";
@@ -20,15 +30,15 @@ let
 in
 python3Packages.buildPythonApplication rec {
   inherit pname;
-  version = "2.3.0";
+  version = "2.5.0";
   src = fetchFromGitHub {
     owner = "schrodinger";
     repo = "pymol-open-source";
     rev = "v${version}";
-    sha256 = "175cqi6gfmvv49i3ws19254m7ljs53fy6y82fm1ywshq2h2c93jh";
+    sha256 = "sha256-JdsgcVF1w1xFPZxVcyS+GcWg4a1Bd4SvxFOuSdlz9SM=";
   };
 
-  buildInputs = [ python3Packages.numpy glew glm freeglut libpng libxml2 tk freetype msgpack ];
+  buildInputs = [ python3Packages.numpy glew glm freeglut libpng libxml2 tk freetype msgpack netcdf ];
   NIX_CFLAGS_COMPILE = "-I ${libxml2.dev}/include/libxml2";
   hardeningDisable = [ "format" ];
 
@@ -49,7 +59,7 @@ python3Packages.buildPythonApplication rec {
   '';
 
   meta = with lib; {
-    description = description;
+    inherit description;
     homepage = "https://www.pymol.org/";
     license = licenses.mit;
     maintainers = with maintainers; [ samlich ];