XTB updates

overlay.nix

@@ -139,6 +139,10 @@ let
 
         dftd3 = callPackage ./pkgs/apps/dft-d3 { };
 
+        dftd4 = callPackage ./pkgs/lib/dftd4 { };
+
+        dftbplus = super.python3.pkgs.toPythonApplication self.python3.pkgs.dftbplus;
+
         dirac = callPackage ./pkgs/apps/dirac {
           inherit (self) exatensor;
         };
@@ -149,6 +153,8 @@ let
 
         exciting = callPackage ./pkgs/apps/exciting { };
 
+        fypp = prev.python3.pkgs.callPackage ./pkgs/apps/fypp { };
+
         gabedit = callPackage ./pkgs/apps/gabedit { };
 
         gamess-us = callPackage ./pkgs/apps/gamess-us {
@@ -205,12 +211,18 @@ let
 
         moltemplate = super.python3.pkgs.toPythonApplication self.python3.pkgs.moltemplate;
 
+        mpifx = callPackage ./pkgs/lib/mpifx { };
+
+        mstore = callPackage ./pkgs/lib/mstore { };
+
         mrcc = callPackage ./pkgs/apps/mrcc { };
 
         mrchem = callPackage ./pkgs/apps/mrchem { };
 
         mt-dgemm = callPackage ./pkgs/apps/mt-dgemm { };
 
+        multicharge = callPackage ./pkgs/lib/multicharge { };
+
         multiwfn = callPackage ./pkgs/apps/multiwfn { };
 
         gmultiwfn = callPackage ./pkgs/apps/gmultiwfn { };
@@ -247,6 +259,8 @@ let
 
         qmcpack = callPackage ./pkgs/apps/qmcpack { };
 
+        scalapackfx = callPackage ./pkgs/lib/scalapackfx { };
+
         # blank version
         sharc = callPackage ./pkgs/apps/sharc/default.nix {
           bagel = self.bagel-serial;
@@ -275,13 +289,18 @@ let
 
         sharc-turbomole = with self; nullable turbomole (sharc.override { enableTurbomole = true; });
 
+        simple-dftd3 = callPackage ./pkgs/lib/simple-dftd3 { };
 
         stream-benchmark = callPackage ./pkgs/apps/stream { };
 
+        tblite = callPackage ./pkgs/lib/tblite { };
+
         test-drive = callPackage ./pkgs/lib/test-drive { };
 
         tinker = callPackage ./pkgs/apps/tinker { };
 
+        toml-f = callPackage ./pkgs/lib/toml-f { };
+
         travis-analyzer = callPackage ./pkgs/apps/travis-analyzer { };
 
         turbomole = callPackage ./pkgs/apps/turbomole { };

pkgs/apps/dftbplus/default.nix

@@ -0,0 +1,87 @@
+{ buildPythonPackage
+, lib
+, gfortran
+, fetchFromGitHub
+, cmake
+, blas
+, lapack
+, mpi
+, scalapack
+, test-drive
+, mctc-lib
+, mstore
+, toml-f
+, tblite
+, mpifx
+, scalapackfx
+, simple-dftd3
+, multicharge
+, dftd4
+, numpy
+}:
+
+assert !blas.isILP64 && !lapack.isILP64;
+
+buildPythonPackage rec {
+  pname = "dftbplus";
+  version = "22.2";
+
+  src = fetchFromGitHub {
+    owner = "dftbplus";
+    repo = pname;
+    rev = version;
+    hash = "sha256-bADKCee5vBH3aIhuo0Ce/GrZ//nd8j4AcWDSWYoLRY4=";
+  };
+
+  postPatch = ''
+    patchShebangs .
+
+    substituteInPlace tools/dptools/CMakeLists.txt \
+      --replace '$DESTDIR/' ""
+  '';
+
+  nativeBuildInputs = [
+    gfortran
+    cmake
+  ];
+
+  buildInputs = [
+    blas
+    lapack
+    scalapack
+    test-drive
+    mctc-lib
+    mstore
+    toml-f
+    tblite
+    mpifx
+    scalapackfx
+    simple-dftd3
+    multicharge
+    dftd4
+  ];
+
+  propagatedBuildInputs = [ numpy ];
+
+  format = "other";
+
+  cmakeFlags = [
+    "-DWITH_API=ON"
+    "-DWITH_OMP=ON"
+    "-DWITH_MPI=ON"
+    "-DWITH_TBLITE=ON"
+    "-DWITH=SDFTD3=ON"
+    "-DWITH_PYTHON=ON"
+    "-DSCALAPACK_LIBRARY=${scalapack}/lib/libscalapack.so"
+  ];
+
+  pythonImportsCheck = [ "dptools" ];
+
+  meta = with lib; {
+    description = "DFTB+ general package for performing fast atomistic simulations";
+    homepage = "https://github.com/dftbplus/dftbplus";
+    license = with licenses; [ gpl3Plus lgpl3Plus ];
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}

pkgs/apps/fypp/default.nix

@@ -0,0 +1,21 @@
+{ lib, stdenv, fetchFromGitHub, buildPythonApplication }:
+
+buildPythonApplication rec {
+  pname = "fypp";
+  version = "3.1";
+
+  src = fetchFromGitHub {
+    owner = "aradi";
+    repo = pname;
+    rev = version;
+    hash = "sha256-iog5Gdcd1F230Nl4JDrKoyYr8JualVgNZQzHLzd4xe8=";
+  };
+
+  meta = with lib; {
+    description = " Python powered Fortran preprocessor ";
+    homepage = "https://github.com/gator-program/gator";
+    license = licenses.gpl3Only;
+    maintainers = [ maintainers.markuskowa ];
+  };
+}
+

pkgs/apps/pysisyphus/default.nix

@@ -70,7 +70,7 @@ let
 in
   buildPythonPackage rec {
     pname = "pysisyphus";
-    version = "0.7.6.post3";
+    version = "0.8.0a0";
 
     nativeBuildInputs = [ makeWrapper setuptools-scm ];
 
@@ -115,8 +115,8 @@ in
     src = fetchFromGitHub {
       owner = "eljost";
       repo = pname;
-      rev = "dc999130d5a0058d78ec9c19090d92656e385606";
-      hash = "sha256-KcJpDhKsB1vjPmwnNTlGsjQ6vQhFcLm8I4dfpu8r9S0=";
+      rev = version;
+      hash = "sha256-NCwhEkSTTNf2uS3BGGrl6i9dGJot/7Vqzvfr4AwwdXk=";
     };
 
     format = "pyproject";

pkgs/apps/xtb/default.nix

@@ -1,9 +1,28 @@
-{ stdenv, lib, gfortran, fetchFromGitHub, cmake, makeWrapper, blas, lapack, writeTextFile
-, mctc-lib, test-drive
-, turbomole, enableTurbomole ? false
-, orca, enableOrca ? false
+{ stdenv
+, lib
+, gfortran
+, fetchFromGitHub
+, fetchpatch
+, cmake
+, makeWrapper
+, blas
+, lapack
+, writeTextFile
+, mctc-lib
+, test-drive
+, tblite
+, toml-f
+, simple-dftd3
+, dftd4
+, multicharge
+, enableTurbomole ? false
+, turbomole
+, enableOrca ? false
+, orca
 , cefine
-} :
+}:
+
+assert !blas.isILP64 && !lapack.isILP64;
 
 let
   description = "Semiempirical extended tight-binding program package";
@@ -14,25 +33,44 @@ let
     ++ lib.optional enableTurbomole cefine
   );
 
-in stdenv.mkDerivation rec {
+in
+stdenv.mkDerivation rec {
   pname = "xtb";
-  version = "6.5.1";
+  version = "6.6.0";
 
-  src = fetchFromGitHub  {
+  src = fetchFromGitHub {
     owner = "grimme-lab";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-9DTaHsK1NgcNbPKsjrVNvoWTyLdaqilZ59sAjAudS2M=";
+    hash = "sha256-RjSxuRAddTtSXOBEBiad916w312v3PWNHDLBzRdAjJM=";
   };
 
+  patches = [
+    (# Fixes numerical hessian computation
+      fetchpatch {
+        url = "https://github.com/grimme-lab/xtb/commit/83090be673e2468c27fcd74d519548d8d51bd8df.diff";
+        hash = "sha256-EniJFAuCa58gNoyvcY2zaUcDFXtJR1/TZUNzHhuWUDA=";
+      }
+    )
+  ];
+
   nativeBuildInputs = [
     gfortran
     cmake
     makeWrapper
-    test-drive
   ];
 
-  buildInputs = [ blas lapack mctc-lib ];
+  buildInputs = [
+    blas
+    lapack
+    mctc-lib
+    tblite
+    test-drive
+    toml-f
+    simple-dftd3
+    dftd4
+    multicharge
+  ];
 
   hardeningDisable = [ "format" ];
 
@@ -57,13 +95,18 @@ in stdenv.mkDerivation rec {
       --prefix PATH : "${binSearchPath}"
   '';
 
+  doCheck = true;
+  preCheck = ''
+    export OMP_NUM_THREADS=2
+  '';
+
   setupHooks = [ ./xtbHook.sh ];
 
   passthru = { inherit enableOrca enableTurbomole; };
 
   meta = with lib; {
     inherit description;
-    homepage = "https://www.chemie.uni-bonn.de/pctc/mulliken-center/grimme/software/xtb";
+    homepage = "https://github.com/grimme-lab/xtb";
     license = licenses.lgpl3Only;
     platforms = platforms.linux;
     maintainers = [ maintainers.sheepforce ];

pkgs/lib/dftd4/default.nix

@@ -0,0 +1,47 @@
+{ stdenv
+, lib
+, fetchFromGitHub
+, cmake
+, gfortran
+, blas
+, lapack
+, mctc-lib
+, mstore
+, multicharge
+}:
+
+assert !blas.isILP64 && !lapack.isILP64;
+
+stdenv.mkDerivation rec {
+  pname = "dftd4";
+  version = "3.5.0";
+
+  src = fetchFromGitHub {
+    owner = "dftd4";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-ZCoFbjTNQD7slq5sKwPRPkrHSHofsxU9C9h/bF5jmZI=";
+  };
+
+  nativeBuildInputs = [ cmake gfortran ];
+
+  buildInputs = [ blas lapack mctc-lib mstore multicharge ];
+
+  postInstall = ''
+    substituteInPlace $out/lib/pkgconfig/${pname}.pc \
+      --replace "''${prefix}" ""
+  '';
+
+  doCheck = true;
+  preCheck = ''
+    export OMP_NUM_THREADS=2
+  '';
+
+  meta = with lib; {
+    description = "Generally Applicable Atomic-Charge Dependent London Dispersion Correction";
+    license = with licenses; [ lgpl3Plus gpl3Plus ];
+    homepage = "https://github.com/grimme-lab/dftd4";
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}

pkgs/lib/mctc-lib/default.nix

@@ -1,31 +1,34 @@
-{ stdenv, lib, fetchFromGitHub, meson, ninja, gfortran, pkg-config, json-fortran, cmake }:
+{ stdenv
+, lib
+, fetchFromGitHub
+, gfortran
+, pkg-config
+, json-fortran
+, cmake
+}:
 
 stdenv.mkDerivation rec {
   pname = "mctc-lib";
-  version = "0.3.0";
+  version = "0.3.1";
 
   src = fetchFromGitHub {
     owner = "grimme-lab";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-3e89g0WkZU/HTBtGaLKzhsv2RTlFk/QK0OT24BGfcKQ=";
+    hash = "sha256-AXjg/ZsitdDf9fNoGVmVal1iZ4/sxjJb7A9W4yye/rg=";
   };
 
-  postPatch = ''
-    substituteInPlace config/template.pc \
-      --replace 'libdir=''${prefix}/@CMAKE_INSTALL_LIBDIR@' "libdir=@CMAKE_INSTALL_LIBDIR@" \
-      --replace 'includedir=''${prefix}/@CMAKE_INSTALL_INCLUDEDIR@' "includedir=@CMAKE_INSTALL_INCLUDEDIR@"
-  '';
-
-  nativeBuildInputs = [
-    ninja
-    gfortran
-    pkg-config
-    cmake
-  ];
+  nativeBuildInputs = [ gfortran pkg-config cmake ];
 
   buildInputs = [ json-fortran ];
 
+  postInstall = ''
+    substituteInPlace $out/lib/pkgconfig/${pname}.pc \
+      --replace "''${prefix}" ""
+  '';
+
+  doCheck = true;
+
   meta = with lib; {
     description = "Modular computation tool chain library";
     homepage = "https://github.com/grimme-lab/mctc-lib";