diff --git a/patches/gromacs-2019.1.diff/src/gromacs/CMakeLists.txt b/patches/gromacs-2019.1.diff/src/gromacs/CMakeLists.txt index 80f7d30c13f328603ca75f3b37b4d1b0e97eb22c..e010a571882d91e7e92a10e29a76328ac0f2bd0d 100644 --- a/patches/gromacs-2019.1.diff/src/gromacs/CMakeLists.txt +++ b/patches/gromacs-2019.1.diff/src/gromacs/CMakeLists.txt @@ -32,6 +32,8 @@ # To help us fund GROMACS development, we humbly ask that you cite # the research papers on the package. Check out http://www.gromacs.org. +include(${CMAKE_SOURCE_DIR}/Plumed.cmake) + set(LIBGROMACS_SOURCES) if (GMX_CLANG_CUDA) diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdlib/force.cpp b/patches/gromacs-2019.1.diff/src/gromacs/mdlib/force.cpp index 32bbd0cc08ab73c71ffa8cbfba8f0cdb32d8224e..babdf19afa341e9890590379af4bdddeb4b5ca7e 100644 --- a/patches/gromacs-2019.1.diff/src/gromacs/mdlib/force.cpp +++ b/patches/gromacs-2019.1.diff/src/gromacs/mdlib/force.cpp @@ -76,6 +76,7 @@ #include "gromacs/utility/exceptions.h" #include "gromacs/utility/fatalerror.h" #include "gromacs/utility/smalloc.h" + /* PLUMED */ #include "../../../Plumed.h" int plumedswitch=0; diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.cpp b/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.cpp index 4d9c29a1d5ad78296794ffa6fd2f8a6599aa560c..614fd9d6cc3621d86c96dc0272ce5b4115feb075 100644 --- a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.cpp +++ b/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.cpp @@ -61,13 +61,6 @@ #include "gromacs/utility/arraysize.h" #include "gromacs/utility/fatalerror.h" -/* PLUMED */ -#include "../../../Plumed.h" -extern int plumedswitch; -extern plumed plumedmain; -extern void(*plumedcmd)(plumed,const char*,const void*); -/* END PLUMED */ - namespace gmx { diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.h b/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.h index 88520e58be55f24710cedde0e53bd016d7301c35..5205b77295f2cef25cfed6a016f1b23e7e51ba23 100644 --- a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.h +++ b/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.h @@ -66,7 +66,7 @@ extern void(*plumedcmd)(plumed,const char*,const void*); /* END PLUMED */ /* PLUMED HREX */ -int plumed_hrex; +extern int plumed_hrex; /* END PLUMED HREX */ struct gmx_multisim_t; diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/replicaexchange.cpp b/patches/gromacs-2019.1.diff/src/gromacs/mdrun/replicaexchange.cpp index f0306c64f05d0c66387e05b8fe68c4c96fef437c..f9d8c88f0a8b653a3cf9d8de97ff46ff00703d54 100644 --- a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/replicaexchange.cpp +++ b/patches/gromacs-2019.1.diff/src/gromacs/mdrun/replicaexchange.cpp @@ -78,7 +78,7 @@ extern plumed plumedmain; /* END PLUMED */ /* PLUMED HREX */ -extern int plumed_hrex; +int plumed_hrex; /* END PLUMED HREX */ //! Helps cut off probability values. diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/runner.cpp b/patches/gromacs-2019.1.diff/src/gromacs/mdrun/runner.cpp index 7d206adf79a142aeb3bddc42b5e8e69c81dff63b..39608a5f8f748cace878c131e23736bed38cd75a 100644 --- a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/runner.cpp +++ b/patches/gromacs-2019.1.diff/src/gromacs/mdrun/runner.cpp @@ -147,11 +147,6 @@ #include "corewrap.h" #endif -/* PLUMED */ -#include "../../../Plumed.h" -extern int plumedswitch; -extern plumed plumedmain; -/* END PLUMED */ namespace gmx {