Merge 56ea9e9 into 61b137f

.gitignore

@@ -24,3 +24,4 @@ makefile.dep
 /config.*
 /autom4*
 /stamp-h
+build

CMakeLists.txt

@@ -0,0 +1,29 @@
+cmake_minimum_required(VERSION 3.20.2)
+
+
+
+project(Plumed2 LANGUAGES CXX)
+
+set(PLUMED_VERSION_SHORT "2.10")
+set(PLUMED_VERSION_LONG "2.10.0-dev")
+#set(PLUMED_VERSION_GIT "23e754fd4-dirty")
+execute_process(
+        COMMAND git describe --long --dirty --always
+        WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR}
+        OUTPUT_VARIABLE PLUMED_VERSION_GIT
+        OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+set(PLUMED_VERSION_MAJOR 2)
+set(PLUMED_VERSION_MINOR 10)
+set(PLUMED_VERSION_PATCH 0)
+#as now CMake is only experimental, it can be useful if you use vscode or other
+#IDE that have an interface with it, but we are not still confident that it is ready
+#for installation purposes
+set(CMAKE_SKIP_INSTALL_RULES YES)
+option(risk_accepted "CMake is experimental use at your own risk" OFF)
+if(NOT risk_accepted)
+   message(FATAL_ERROR "You must accept the risk to use the experimental cmake compilation: -Drisk_accepted=ON")
+endif(NOT risk_accepted)
+
+
+add_subdirectory(src)

src/.gitignore

@@ -55,6 +55,7 @@
 !/s2cm
 !/pytorch
 !/membranefusion
+!CMakeLists.txt
 
 # And just ignore these files
 *.xxd

src/adjmat/.gitignore

@@ -7,3 +7,4 @@
 !/Makefile
 !/README
 !/module.type
+!/CMakeLists.txt

src/adjmat/CMakeLists.txt

@@ -0,0 +1,37 @@
+#the variable module_name is set up as a sugar to reduce "copy-paste" errors
+set (module_name "adjmat")
+#Note that the macros here require this directory added as a subdir of plumed/src
+option(module_${module_name} "activate module ${module_name}" OFF)
+ADDMODULETOKERNEL(${module_name}
+ActionWithInputMatrix.cpp
+AdjacencyMatrixBase.cpp
+AdjacencyMatrixVessel.cpp
+AlignedMatrixBase.cpp
+ClusterAnalysisBase.cpp
+ClusterDiameter.cpp
+ClusterDistribution.cpp
+ClusteringBase.cpp
+ClusterProperties.cpp
+ClusterSize.cpp
+ClusterWithSurface.cpp
+ContactAlignedMatrix.cpp
+ContactMatrix.cpp
+DFSClustering.cpp
+DumpGraph.cpp
+HbondMatrix.cpp
+MatrixColumnSums.cpp
+MatrixRowSums.cpp
+OutputCluster.cpp
+SMACMatrix.cpp
+Sprint.cpp
+TopologyMatrix.cpp
+)
+ADDMODULENEEDS(${module_name}
+	core tools vesselbase multicolvar
+)
+ADDMODULEDEPENDENCIES(${module_name}
+	#core #tools depends on
+	#tools #vesselbase depends on
+	#vesselbase # multicolvar depends on
+	multicolvar
+)

src/analysis/.gitignore

@@ -7,3 +7,4 @@
 !/Makefile
 !/README
 !/module.type
+!/CMakeLists.txt

src/analysis/CMakeLists.txt

@@ -0,0 +1,35 @@
+#the variable module_name is set up as a sugar to reduce "copy-paste" errors
+set (module_name "analysis")
+#Note that the macros here require this directory added as a subdir of plumed/src
+option(module_${module_name} "activate module ${module_name}" ON)
+ADDMODULETOKERNEL(${module_name}
+AnalysisBase.cpp
+Average.cpp
+AverageVessel.cpp
+Committor.cpp
+DataCollectionObject.cpp
+EuclideanDissimilarityMatrix.cpp
+FarthestPointSampling.cpp
+Histogram.cpp
+LandmarkSelectionBase.cpp
+LandmarkStaged.cpp
+OutputColvarFile.cpp
+OutputPDBFile.cpp
+PrintDissimilarityMatrix.cpp
+ReadAnalysisFrames.cpp
+ReadDissimilarityMatrix.cpp
+ReselectLandmarks.cpp
+SelectRandomFrames.cpp
+SelectWithStride.cpp
+WhamHistogram.cpp
+WhamWeights.cpp
+)
+ADDMODULENEEDS(${module_name}
+	core tools reference vesselbase gridtools multicolvar bias
+)
+ADDMODULEDEPENDENCIES(${module_name}
+	reference #core
+	#TODO: resolve THIS circular dependency:
+	#vesselbase gridtools multicolvar# it does actually depend on them, but it is better to avid cyclic dependencies
+	bias #tools core
+)

src/annfunc/.gitignore

@@ -2,3 +2,4 @@ core/**
 deps/**
 function/**
 *.o
+!/CMakeLists.txt

src/annfunc/CMakeLists.txt

@@ -0,0 +1,13 @@
+#the variable module_name is set up as a sugar to reduce "copy-paste" errors
+set (module_name "annfunc")
+#Note that the macros here require this directory added as a subdir of plumed/src
+option(module_${module_name} "activate module ${module_name}" OFF)
+ADDMODULETOKERNEL(${module_name}
+ANN.cpp
+)
+ADDMODULENEEDS(${module_name}
+	core function
+)
+ADDMODULEDEPENDENCIES(${module_name}
+	function #reference tools core lepton
+)

src/asmjit/CMakeLists.txt

@@ -0,0 +1,42 @@
+#the variable module_name is set up as a sugar to reduce "copy-paste" errors
+set (module_name "asmjit")
+#Note that the macros here require this directory added as a subdir of plumed/src
+set(module_${module_name} ON CACHE INTERNAL "always active module ${module_name}")
+ADDMODULETOKERNEL(${module_name}
+arch.cpp
+assembler.cpp
+codebuilder.cpp
+codecompiler.cpp
+codeemitter.cpp
+codeholder.cpp
+constpool.cpp
+cpuinfo.cpp
+func.cpp
+globals.cpp
+inst.cpp
+logging.cpp
+operand.cpp
+osutils.cpp
+regalloc.cpp
+runtime.cpp
+string.cpp
+utils.cpp
+vmem.cpp
+x86assembler.cpp
+x86builder.cpp
+x86compiler.cpp
+x86inst.cpp
+x86instimpl.cpp
+x86internal.cpp
+x86logging.cpp
+x86operand.cpp
+x86operand_regs.cpp
+x86regalloc.cpp
+zone.cpp
+)
+ADDMODULENEEDS(${module_name}
+
+)
+ADDMODULEDEPENDENCIES(${module_name}
+
+)

src/bias/.gitignore

@@ -7,3 +7,4 @@
 !/Makefile
 !/README
 !/module.type
+!/CMakeLists.txt

src/bias/CMakeLists.txt

@@ -0,0 +1,29 @@
+#the variable module_name is set up as a sugar to reduce "copy-paste" errors
+set (module_name "bias")
+#Note that the macros here require this directory added as a subdir of plumed/src
+option(module_${module_name} "activate module ${module_name}" ON)
+ADDMODULETOKERNEL(${module_name}
+ABMD.cpp
+Bias.cpp
+BiasValue.cpp
+ExtendedLagrangian.cpp
+External.cpp
+LWalls.cpp
+MaxEnt.cpp
+MetaD.cpp
+MovingRestraint.cpp
+PBMetaD.cpp
+Restraint.cpp
+ReweightBase.cpp
+ReweightBias.cpp
+ReweightMetad.cpp
+ReweightTemperaturePressure.cpp
+ReweightWham.cpp
+UWalls.cpp
+)
+ADDMODULENEEDS(${module_name}
+	core tools
+)
+ADDMODULEDEPENDENCIES(${module_name}
+	core #tools
+)

src/blas/.gitignore

@@ -7,3 +7,4 @@
 !/Makefile
 !/README
 !/module.type
+!/CMakeLists.txt

src/blas/CMakeLists.txt

@@ -0,0 +1,65 @@
+#the variable module_name is set up as a sugar to reduce "copy-paste" errors
+set (module_name "blas")
+string(TOUPPER ${module_name} externalLib)
+#Note that the macros here require this directory added as a subdir of plumed/src
+set(module_${module_name} ON CACHE INTERNAL "always active module ${module_name}")
+option(useExternal_${externalLib} "enable search for external ${externalLib}, default ON" ON)
+ADDMODULETOKERNEL(${module_name}
+blas.cpp
+)
+#ADDMODULENEEDS(${module_name}
+#
+#)
+
+#include(FortranCInterface)
+if (useExternal_${externalLib})
+    find_package(${externalLib})
+endif (useExternal_${externalLib})
+
+if (${externalLib}_FOUND)
+    target_compile_definitions(${module_name}
+        PUBLIC
+        __PLUMED_HAS_EXTERNAL_BLAS=1)
+    include(CheckSourceCompiles)
+    #From the manual:The check is only performed once, with the result cached in
+    #the variable named by <resultVar>. Every subsequent CMake run will re-use
+    #this cached value rather than performing the check again, even if the
+    #<code> changes. In order to force the check to be re-evaluated, the
+    #variable named by <resultVar> must be manually removed from the cache.
+    set(CMAKE_REQUIRED_LIBRARIES "BLAS::BLAS")
+    check_source_compiles(C #using C to not use extern "C"
+        "int main(void) {
+            double a,b,c,s;
+            srotg_(&a,&b,&c,&s);
+        }"
+    UnderscodeBlas)
+    check_source_compiles(C  #using C to not use extern "C"
+        "int main(void) {
+            double a,b,c,s;
+            srotg(&a,&b,&c,&s);
+        }"
+    noUnderscodeBlas
+    )
+    unset(CMAKE_REQUIRED_LIBRARIES)
+
+    if(noUnderscodeBlas AND NOT UnderscodeBlas)
+        target_compile_definitions(${module_name}
+            PUBLIC
+            F77_NO_UNDERSCORE)
+    elseif(NOT noUnderscodeBlas AND NOT UnderscodeBlas)
+        message(WARNING "both srtog_ and srtog are not linkable")
+    elseif(noUnderscodeBlas AND UnderscodeBlas)
+        message(WARNING "both srtog_ and srtog are linkable")
+    endif(noUnderscodeBlas AND NOT UnderscodeBlas)
+
+    target_link_libraries(${module_name}
+        PUBLIC
+        ${externalLib}::${externalLib})
+else()
+    set(${externalLib}_FOUND OFF)
+endif (${externalLib}_FOUND)
+set (${externalLib}_FOUND ${externalLib}_FOUND PARENT_SCOPE)
+
+# print_target_property(${module_name} COMPILE_OPTIONS)
+# print_target_property(${module_name} COMPILE_DEFINITIONS)
+# print_target_property(${module_name} INTERFACE_COMPILE_DEFINITIONS)

src/blas/blas.h

@@ -90,22 +90,22 @@ Erik Lindahl, 2008-10-07.
 
 #ifndef __PLUMED_BLAS_RETURNS_FLOAT
 #define __PLUMED_BLAS_RETURNS_FLOAT float
-#endif
+#endif //ifndef __PLUMED_BLAS_RETURNS_FLOAT
 #if ! defined (__PLUMED_HAS_EXTERNAL_BLAS)
 #include "def_internal.h"
 namespace PLMD{
 namespace blas{
 #else
 namespace PLMD{
 namespace blas{
-}
-}
+}/*PLMD*/
+}/*blas*/
 #include "def_external.h"
 extern "C"{
-#endif
+#endif //! defined (__PLUMED_HAS_EXTERNAL_BLAS)
 #if 0
 }
-#endif
+#endif //0
 
 /* Double precision versions */
 double
@@ -245,9 +245,9 @@ int
 }
 #if ! defined (__PLUMED_HAS_EXTERNAL_BLAS)
 }
-#endif
+#endif //! defined (__PLUMED_HAS_EXTERNAL_BLAS)
 
 /*! \endcond */
 
 #endif /* GMX_BLAS_H */
-#endif
+#endif //__PLUMED_blas_blas_h

src/blas/def_external.h

@@ -58,4 +58,4 @@ Erik Lindahl, 2008-10-07.
 #define plumed_blas_strmv PLUMED_BLAS_F77_FUNC(strmv,STRMV)
 #define plumed_blas_strsm PLUMED_BLAS_F77_FUNC(strsm,STRSM)
 #define plumed_blas_isamax PLUMED_BLAS_F77_FUNC(isamax,ISAMAX)
-#endif
+#endif //__PLUMED_blas_def_external_h

src/blas/def_internal.h

@@ -94,4 +94,4 @@ Erik Lindahl, 2008-10-07.
 #define plumed_blas_strsm PLMD::blas::PLUMED_BLAS_F77_FUNC(strsm,STRSM)
 /** \ingroup internal-blas */
 #define plumed_blas_isamax PLMD::blas::PLUMED_BLAS_F77_FUNC(isamax,ISAMAX)
-#endif
+#endif //__PLUMED_blas_def_internal_h

src/cltools/.gitignore

@@ -8,3 +8,4 @@
 !/README
 !/module.type
 !/*.sh
+!/CMakeLists.txt