From c20b4b62b39d5d076acb1be6bb12b75a0efbe689 Mon Sep 17 00:00:00 2001
From: Phillip Seeber <phillip.seeber@uni-jena.de>
Date: Wed, 15 Mar 2023 11:31:03 +0100
Subject: [PATCH 1/2] plumed: init at 2.8.2

plumed: fix build
---
 .../science/chemistry/plumed/default.nix      | 34 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 2 files changed, 36 insertions(+)
 create mode 100644 pkgs/development/libraries/science/chemistry/plumed/default.nix

diff --git a/pkgs/development/libraries/science/chemistry/plumed/default.nix b/pkgs/development/libraries/science/chemistry/plumed/default.nix
new file mode 100644
index 000000000000..8c308cf2df5b
--- /dev/null
+++ b/pkgs/development/libraries/science/chemistry/plumed/default.nix
@@ -0,0 +1,34 @@
+{ stdenv
+, lib
+, fetchFromGitHub
+, blas
+}:
+
+assert !blas.isILP64;
+
+stdenv.mkDerivation rec {
+  pname = "plumed";
+  version = "2.8.2";
+
+  src = fetchFromGitHub {
+    owner = "plumed";
+    repo = "plumed2";
+    rev = "v${version}";
+    hash = "sha256-ugYhJq8KFjT8rkAOX/yZ9IlEklXCwRxKH49REd2QN9E=";
+  };
+
+  postPatch = ''
+    patchShebangs .
+  '';
+
+  buildInputs = [ blas ];
+
+  enableParallelBuilding = true;
+
+  meta = with lib; {
+    description = "Molecular metadynamics library";
+    homepage = "https://github.com/plumed/plumed2";
+    license = licenses.lgpl3Only;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 22049bd8762b..c814a0e31a5f 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -24224,6 +24224,8 @@ with pkgs;
     mail = callPackage ../development/libraries/gsignond/plugins/mail.nix { };
   };
 
+  plumed = callPackage ../development/libraries/science/chemistry/plumed { };
+
   ### DEVELOPMENT / LIBRARIES / AGDA
 
   agdaPackages = callPackage ./agda-packages.nix {

From 09b52c631a75aac7d68f56ec3b1e8571ece81cce Mon Sep 17 00:00:00 2001
From: Phillip Seeber <phillip.seeber@uni-jena.de>
Date: Thu, 16 Mar 2023 14:30:15 +0100
Subject: [PATCH 2/2] cp2k: enable plumed plugin

cp2k: enable plumed plugin


cp2k: use mpicxx to figure out link lines
---
 pkgs/applications/science/chemistry/cp2k/default.nix | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/pkgs/applications/science/chemistry/cp2k/default.nix b/pkgs/applications/science/chemistry/cp2k/default.nix
index 81849f675af3..a16797b955e5 100644
--- a/pkgs/applications/science/chemistry/cp2k/default.nix
+++ b/pkgs/applications/science/chemistry/cp2k/default.nix
@@ -1,6 +1,6 @@
 { lib, stdenv, fetchFromGitHub, python3, gfortran, blas, lapack
 , fftw, libint, libvori, libxc, mpi, gsl, scalapack, openssh, makeWrapper
-, libxsmm, spglib, which, pkg-config
+, libxsmm, spglib, which, pkg-config, plumed, zlib
 , enableElpa ? false
 , elpa
 } :
@@ -34,6 +34,8 @@ in stdenv.mkDerivation rec {
     scalapack
     blas
     lapack
+    plumed
+    zlib
   ] ++ lib.optional enableElpa elpa;
 
   propagatedBuildInputs = [ mpi ];
@@ -64,7 +66,8 @@ in stdenv.mkDerivation rec {
     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 ${lib.optionalString enableElpa "-D__ELPA"}
+                 -D__MAX_CONTR=4 -D__LIBVORI ${lib.optionalString enableElpa "-D__ELPA"} \
+                 -D__PLUMED2
     CFLAGS    = -fopenmp
     FCFLAGS    = \$(DFLAGS) -O2 -ffree-form -ffree-line-length-none \
                  -ftree-vectorize -funroll-loops -msse2 \
@@ -77,8 +80,11 @@ in stdenv.mkDerivation rec {
                  -lxcf03 -lxc -lxsmmf -lxsmm -lsymspg \
                  -lint2 -lstdc++ -lvori \
                  -lgomp -lpthread -lm \
-                 -fopenmp ${lib.optionalString enableElpa "$(pkg-config --libs elpa)"}
+                 -fopenmp ${lib.optionalString enableElpa "$(pkg-config --libs elpa)"} \
+                 -lz -ldl -lstdc++ ${lib.optionalString (mpi.pname == "openmpi") "$(mpicxx --showme:link)"} \
+                 -lplumed
     LDFLAGS    = \$(FCFLAGS) \$(LIBS)
+    include ${plumed}/lib/plumed/src/lib/Plumed.inc
     EOF
   '';