Merge pull request #273 from ls1mardyn/code-refactor-mamico

Code refactor mamico

CMakeLists.txt

@@ -67,6 +67,9 @@ include(ALL)
 # ----- third: include autopas
 include(autopas)
 
+# ----- include mamico
+include(mamico)
+
 # ----- resilience plugin dependencies are set here
 include(compression)
 

cmake/modules/mamico.cmake

@@ -0,0 +1,18 @@
+option(MAMICO_COUPLING "Couple with MaMiCo" OFF)
+if (MAMICO_COUPLING)
+	message(STATUS "MaMiCo coupling enabled. ls1 mardyn will compile as library. No executable will be created.")
+	set(MAMICO_COMPILE_DEFINITIONS MAMICO_COUPLING MDDim3)
+	option(MAMICO_ENABLE_FPIC "Enable -fPIC flag for MaMiCo python bindings" OFF)
+	set(MAMICO_SRC_DIR CACHE PATH "Root directory of the MaMiCo codebase")
+    if(NOT MAMICO_SRC_DIR)
+		message(FATAL_ERROR "MaMiCo source directory not specified.")
+	endif()
+	if(ENABLE_MPI)
+		set(MAMICO_MPI_DEFINITIONS MDCoupledParallel TarchParallel)
+	endif()
+	if(MAMICO_ENABLE_FPIC)
+		set(MAMICO_COMPILE_OPTIONS "${MAMICO_COMPILE_OPTIONS} -fPIC")
+	endif()
+else()
+    message(STATUS "MaMiCo coupling disabled.")
+endif()

doc/Plugins_Summary.dox

@@ -38,6 +38,7 @@ SP / TemperatureProfile | temperature profile output | Outputs the average tempe
 SP / VirialProfile | virial pressure profile output | Outputs the virial/partial pressures in a spatial 1D output in y-direction or 2D output (Virial2DProfile). Requires/auto enables DensityProfile.
 LoadbalanceWriter | print, mpi, load balance, timers | Writes load balance information. Averages, min, max and a load balance is written. For more detailed output use the TimerWriter.
 LoadImbalanceThroughSleepPlugin | mpi, overlapping | Artificially introduces a load imbalance at different plugin steps. Primarily used for testing.
+MamicoCoupling | coupling, compile as library | Allows the coupling code MaMiCo to couple with ls1. Requires ls1 to be compiled as library. This is automatically done when passing MAMICO_COUPLING=ON to cmake. This plugin always switches the ls1 thermostat off.
 MaxCheck | limit, maximum values, overlaps, explosion | Limit velocity and force of individual particles to maximum values to avoid overlaps and consequently exploding systems.
 MaxWriter | sampling, maximum values, force, velocity | Sampling maximum force and velocities values occuring in the system.
 MettDeamon | particle-insertion, reservoir, replenish, stationary, evaporation | Replenish a liquid film by a particle reservoir, to attain stationary conditons in an e.g. evaporation simulation.

examples/Mamico-couette/ls1configNoCP.xml

@@ -1,5 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <mardyn version="20100525">
+    <loglevel>INFO</loglevel>
 	<refunits type="SI">
 		<length unit="nm">0.34</length>
 		<mass unit="u">39.948</mass> 
@@ -62,7 +63,8 @@
 		</ensemble>
 		<algorithm>
 			<parallelisation type="DomainDecomposition"/>
-			<datastructure type="AutoPas">
+			<datastructure type="LinkedCells">
+			<cellsInCutoffRadius>1</cellsInCutoffRadius>
 			</datastructure>
 			<cutoffs type="CenterOfMass">
 				<radiusLJ unit="reduced">2.2</radiusLJ>

src/CMakeLists.txt

@@ -46,9 +46,20 @@ else()
 endif ()
 
 # add the executable
-ADD_EXECUTABLE(MarDyn
+if (MAMICO_COUPLING)
+    ADD_LIBRARY(MarDyn STATIC
         ${MY_SRC}
-        parallel/ForceHelper.h)
+        )
+    TARGET_INCLUDE_DIRECTORIES(MarDyn SYSTEM PRIVATE "${MAMICO_SRC_DIR}")
+    TARGET_COMPILE_DEFINITIONS(MarDyn PUBLIC
+        ${MAMICO_COMPILE_DEFINITIONS} ${MAMICO_MPI_DEFINITIONS}
+        )
+    TARGET_COMPILE_OPTIONS(MarDyn PUBLIC ${MAMICO_COMPILE_OPTIONS})
+else()
+    ADD_EXECUTABLE(MarDyn
+        ${MY_SRC}
+        )
+endif()
 
 # dependencies for lz4
 if (ENABLE_LZ4)