Merge pull request #53 from openworm/development

Development

.cproject

@@ -1,20 +1,18 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<?fileVersion 4.0.0?>
-
-<cproject storage_type_id="org.eclipse.cdt.core.XmlProjectDescriptionStorage">
+<?fileVersion 4.0.0?><cproject storage_type_id="org.eclipse.cdt.core.XmlProjectDescriptionStorage">
 	<storageModule moduleId="org.eclipse.cdt.core.settings">
 		<cconfiguration id="cdt.managedbuild.config.gnu.exe.release.2025909945">
 			<storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="cdt.managedbuild.config.gnu.exe.release.2025909945" moduleId="org.eclipse.cdt.core.settings" name="Build">
 				<externalSettings>
 					<externalSetting/>
 				</externalSettings>
 				<extensions>
-					<extension id="org.eclipse.cdt.core.ELF" point="org.eclipse.cdt.core.BinaryParser"/>
 					<extension id="org.eclipse.cdt.core.GCCErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
 					<extension id="org.eclipse.cdt.core.GASErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
 					<extension id="org.eclipse.cdt.core.GLDErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
 					<extension id="org.eclipse.cdt.core.GmakeErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
 					<extension id="org.eclipse.cdt.core.CWDLocator" point="org.eclipse.cdt.core.ErrorParser"/>
+					<extension id="org.eclipse.cdt.core.ELF" point="org.eclipse.cdt.core.BinaryParser"/>
 				</extensions>
 			</storageModule>
 			<storageModule moduleId="cdtBuildSystem" version="4.0.0">
@@ -29,6 +27,7 @@
 								<option id="gnu.cpp.compiler.exe.release.option.debugging.level.1679425131" name="Debug Level" superClass="gnu.cpp.compiler.exe.release.option.debugging.level" value="gnu.cpp.compiler.debugging.level.none" valueType="enumerated"/>
 								<option id="gnu.cpp.compiler.option.include.paths.997000422" name="Include paths (-I)" superClass="gnu.cpp.compiler.option.include.paths" valueType="includePath">
 									<listOptionValue builtIn="false" value="/usr/include/python2.7"/>
+									<listOptionValue builtIn="false" value="&quot;${workspace_loc:/${ProjName}/inc}&quot;"/>
 								</option>
 								<inputType id="cdt.managedbuild.tool.gnu.cpp.compiler.input.1448416343" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.input"/>
 							</tool>
@@ -54,6 +53,9 @@
 								</inputType>
 							</tool>
 							<tool id="cdt.managedbuild.tool.gnu.assembler.exe.release.1756360065" name="GCC Assembler" superClass="cdt.managedbuild.tool.gnu.assembler.exe.release">
+								<option id="gnu.both.asm.option.include.paths.1804308571" name="Include paths (-I)" superClass="gnu.both.asm.option.include.paths" valueType="includePath">
+									<listOptionValue builtIn="false" value="&quot;${workspace_loc:/Smoothed-Particle-Hydrodynamics/inc}&quot;"/>
+								</option>
 								<inputType id="cdt.managedbuild.tool.gnu.assembler.input.612136578" superClass="cdt.managedbuild.tool.gnu.assembler.input"/>
 							</tool>
 						</toolChain>
@@ -66,12 +68,12 @@
 			<storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="cdt.managedbuild.config.gnu.exe.debug.333205532" moduleId="org.eclipse.cdt.core.settings" name="debug">
 				<externalSettings/>
 				<extensions>
-					<extension id="org.eclipse.cdt.core.ELF" point="org.eclipse.cdt.core.BinaryParser"/>
 					<extension id="org.eclipse.cdt.core.GmakeErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
 					<extension id="org.eclipse.cdt.core.CWDLocator" point="org.eclipse.cdt.core.ErrorParser"/>
 					<extension id="org.eclipse.cdt.core.GCCErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
 					<extension id="org.eclipse.cdt.core.GASErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
 					<extension id="org.eclipse.cdt.core.GLDErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
+					<extension id="org.eclipse.cdt.core.ELF" point="org.eclipse.cdt.core.BinaryParser"/>
 				</extensions>
 			</storageModule>
 			<storageModule moduleId="cdtBuildSystem" version="4.0.0">
@@ -81,11 +83,12 @@
 							<targetPlatform id="cdt.managedbuild.target.gnu.platform.exe.debug.884686243" name="Debug Platform" superClass="cdt.managedbuild.target.gnu.platform.exe.debug"/>
 							<builder autoBuildTarget="all" buildPath="${workspace_loc:/Smoothed-Particle-Hydrodynamics/debug}" cleanBuildTarget="clean" enableAutoBuild="false" enableCleanBuild="true" enabledIncrementalBuild="true" id="cdt.managedbuild.target.gnu.builder.exe.debug.1189096949" incrementalBuildTarget="all" keepEnvironmentInBuildfile="false" managedBuildOn="true" name="Gnu Make Builder" superClass="cdt.managedbuild.target.gnu.builder.exe.debug"/>
 							<tool id="cdt.managedbuild.tool.gnu.archiver.base.1441642354" name="GCC Archiver" superClass="cdt.managedbuild.tool.gnu.archiver.base"/>
-							<tool id="cdt.managedbuild.tool.gnu.cpp.compiler.exe.debug.1106861907" name="GCC C++ Compiler" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.exe.debug">
+							<tool command="g++" commandLinePattern="${COMMAND} ${FLAGS} ${OUTPUT_FLAG} ${OUTPUT_PREFIX}${OUTPUT} ${INPUTS}" id="cdt.managedbuild.tool.gnu.cpp.compiler.exe.debug.1106861907" name="GCC C++ Compiler" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.exe.debug">
 								<option id="gnu.cpp.compiler.exe.debug.option.optimization.level.921234671" name="Optimization Level" superClass="gnu.cpp.compiler.exe.debug.option.optimization.level" value="gnu.cpp.compiler.optimization.level.none" valueType="enumerated"/>
 								<option id="gnu.cpp.compiler.exe.debug.option.debugging.level.1358949615" name="Debug Level" superClass="gnu.cpp.compiler.exe.debug.option.debugging.level" value="gnu.cpp.compiler.debugging.level.max" valueType="enumerated"/>
 								<option id="gnu.cpp.compiler.option.include.paths.521963291" name="Include paths (-I)" superClass="gnu.cpp.compiler.option.include.paths" valueType="includePath">
 									<listOptionValue builtIn="false" value="/usr/include/python2.7"/>
+									<listOptionValue builtIn="false" value="&quot;${workspace_loc:/${ProjName}/inc}&quot;"/>
 								</option>
 								<inputType id="cdt.managedbuild.tool.gnu.cpp.compiler.input.2098511886" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.input"/>
 							</tool>
@@ -110,6 +113,7 @@
 								</inputType>
 							</tool>
 							<tool id="cdt.managedbuild.tool.gnu.assembler.exe.debug.250299533" name="GCC Assembler" superClass="cdt.managedbuild.tool.gnu.assembler.exe.debug">
+								<option id="gnu.both.asm.option.include.paths.1091188493" name="Include paths (-I)" superClass="gnu.both.asm.option.include.paths" valueType="includePath"/>
 								<inputType id="cdt.managedbuild.tool.gnu.assembler.input.95686167" superClass="cdt.managedbuild.tool.gnu.assembler.input"/>
 							</tool>
 						</toolChain>
@@ -143,12 +147,12 @@
 		<scannerConfigBuildInfo instanceId="cdt.managedbuild.config.gnu.exe.release.2025909945;cdt.managedbuild.config.gnu.exe.release.2025909945.;cdt.managedbuild.tool.gnu.cpp.compiler.exe.release.37396283;cdt.managedbuild.tool.gnu.cpp.compiler.input.1448416343">
 			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileCPP"/>
 		</scannerConfigBuildInfo>
-		<scannerConfigBuildInfo instanceId="cdt.managedbuild.config.gnu.exe.release.2025909945;cdt.managedbuild.config.gnu.exe.release.2025909945.;cdt.managedbuild.tool.gnu.c.compiler.exe.release.1665591112;cdt.managedbuild.tool.gnu.c.compiler.input.1611269568">
-			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileC"/>
-		</scannerConfigBuildInfo>
 		<scannerConfigBuildInfo instanceId="cdt.managedbuild.config.gnu.cross.exe.release.1456821005;cdt.managedbuild.config.gnu.cross.exe.release.1456821005.;cdt.managedbuild.tool.gnu.cross.cpp.compiler.1917076731;cdt.managedbuild.tool.gnu.cpp.compiler.input.1889670210">
 			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileCPP"/>
 		</scannerConfigBuildInfo>
+		<scannerConfigBuildInfo instanceId="cdt.managedbuild.config.gnu.exe.release.2025909945;cdt.managedbuild.config.gnu.exe.release.2025909945.;cdt.managedbuild.tool.gnu.c.compiler.exe.release.1665591112;cdt.managedbuild.tool.gnu.c.compiler.input.1611269568">
+			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileC"/>
+		</scannerConfigBuildInfo>
 		<scannerConfigBuildInfo instanceId="cdt.managedbuild.config.gnu.exe.debug.333205532;cdt.managedbuild.config.gnu.exe.debug.333205532.;cdt.managedbuild.tool.gnu.c.compiler.exe.debug.745142970;cdt.managedbuild.tool.gnu.c.compiler.input.1706681846">
 			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileC"/>
 		</scannerConfigBuildInfo>

SimulationEnginePrototype.sln → Sibernetic.sln

@@ -1,7 +1,7 @@
 
 Microsoft Visual Studio Solution File, Format Version 10.00
 # Visual Studio 2008
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "SimulationEnginePrototype", "SimulationEnginePrototype.vcproj", "{01EA498F-06C1-4F67-8B98-E1105F9311A2}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "Sibernetic", "Sibernetic.vcproj", "{01EA498F-06C1-4F67-8B98-E1105F9311A2}"
 EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution

SimulationEnginePrototype.vcproj → Sibernetic.vcproj

@@ -267,10 +267,6 @@
 				RelativePath=".\src\owWorldSimulation.cpp"
 				>
 			</File>
-			<File
-				RelativePath=".\src\PyramidalSimulation.cpp"
-				>
-			</File>
 			<File
 				RelativePath=".\src\test\owPhysicTest.cpp"
 				>
@@ -300,39 +296,35 @@
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
 			<File
-				RelativePath=".\src\owHelper.h"
-				>
-			</File>
-			<File
-				RelativePath=".\src\owOpenCLConstant.h"
+				RelativePath=".\inc\owHelper.h"
 				>
 			</File>
 			<File
-				RelativePath=".\src\owOpenCLSolver.h"
+				RelativePath=".\inc\owOpenCLConstant.h"
 				>
 			</File>
 			<File
-				RelativePath=".\src\owPhysicsConstant.h"
+				RelativePath=".\inc\owOpenCLSolver.h"
 				>
 			</File>
 			<File
-				RelativePath=".\src\owPhysicsFluidSimulator.h"
+				RelativePath=".\inc\owPhysicsConstant.h"
 				>
 			</File>
 			<File
-				RelativePath=".\src\owWorldSimulation.h"
+				RelativePath=".\inc\owPhysicsFluidSimulator.h"
 				>
 			</File>
 			<File
-				RelativePath=".\src\PyramidalSimulation.h"
+				RelativePath=".\inc\owWorldSimulation.h"
 				>
 			</File>
 			<File
-				RelativePath=".\src\VectorMath.h"
+				RelativePath=".\inc\VectorMath.h"
 				>
 			</File>
 			<File
-				RelativePath=".\src\test\owPhysicTest.h"
+				RelativePath=".\inc\owPhysicTest.h"
 				>
 			</File>
 		</Filter>

src/owHelper.h → inc/owHelper.h

@@ -56,7 +56,6 @@ class owHelper
 public:
 	owHelper(void);
 	~owHelper(void);
-	static void generateConfiguration( int stage, float *position, float *velocity, float *& elasticConnectionsData_cpp, int *membraneData_cpp, int & numOfLiquidP, int & numOfElasticP, int & numOfBoundaryP, int & numOfElasticConnections, int & numOfMembranes, int * particleMembranesList_cpp, owConfigProrerty * config);
 	static void preLoadConfiguration( int & numOfMembranes, owConfigProrerty * config, int & numOfLiquidP, int & numOfElasticP, int & numOfBoundaryP );
 	static void loadConfiguration( float *position_cpp, float *velocity_cpp, float *& elasticConnections,int & numOfLiquidP, int & numOfElasticP, int & numOfBoundaryP, int & numOfElasticConnections, int & numOfMembranes,int * membraneData_cpp, int *& particleMembranesList_cpp, owConfigProrerty * config );
 	static void loadConfigurationFromOneFile(float * position, float  * velocity, float *& elasticConnectionsData_cpp, int & numOfLiquidP, int & numOfElasticP, int & numOfBoundaryP, int & numOfElasticConnections);

src/owOpenCLSolver.h → inc/owOpenCLSolver.h

@@ -100,7 +100,7 @@ class owOpenCLSolver
 	void read_velocity_buffer( float * velocity_cpp, owConfigProrerty * config) { copy_buffer_from_device( velocity_cpp, velocity, config->getParticleCount() * sizeof( float ) * 4 ); };
 	void read_density_buffer( float * density_cpp, owConfigProrerty * config ) { copy_buffer_from_device( density_cpp, rho, config->getParticleCount() * sizeof( float ) * 1 ); }; // This need only for visualization current density of particle (graphic effect)
 	void read_particleIndex_buffer( unsigned int * particleIndexBuffer, owConfigProrerty * config ) { copy_buffer_from_device( particleIndexBuffer, particleIndex, config->getParticleCount() * sizeof( unsigned int ) * 2 ); }; // This need only for visualization current density of particle (graphic effect)
-	void refresh(const float * position_cpp, const float * velocity_cpp, owConfigProrerty * config, const float * elasticConnectionsData_cpp = NULL, const int * membraneData_cpp = NULL, const int * particleMembranesList_cpp = NULL);
+	void reset(const float * position_cpp, const float * velocity_cpp, owConfigProrerty * config, const float * elasticConnectionsData_cpp = NULL, const int * membraneData_cpp = NULL, const int * particleMembranesList_cpp = NULL);
 private:
 	void create_ocl_kernel( const char *name, cl::Kernel &k );
 	void create_ocl_buffer(const char *name, cl::Buffer &b, const cl_mem_flags flags,const int size);

src/test/owPhysicTest.h → inc/owPhysicTest.h

@@ -8,6 +8,8 @@
 #ifndef OWPHYSICTEST_H_
 #define OWPHYSICTEST_H_
 
+#include "owPhysicsFluidSimulator.h"
+
 void test_energy_conservation();
 
 

src/owPhysicsConstant.h → inc/owPhysicsConstant.h

@@ -38,8 +38,6 @@
 
 #include "owOpenCLConstant.h"
 
-#define generateWormBodyConfiguration 0 //or load from file otherwise [0/1]
-
 #ifndef M_PI
 #define M_PI 3.1415927f
 #endif

makefile

@@ -1,8 +1,7 @@
 TARGET = Sibernetic
 RM := rm -rf
 
-SOURCES = src/PyramidalSimulation.cpp \
-src/main.cpp \
+SOURCES = src/main.cpp \
 src/owHelper.cpp \
 src/owOpenCLSolver.cpp \
 src/owPhysicsFluidSimulator.cpp \
@@ -12,6 +11,7 @@ TEST_SOURCES = src/test/owPhysicTest.cpp
 
 SRCEXT := cpp
 SRCDIR := src
+INCDIR := inc
 BUILDDIR = ./Release
 BINARYDIR = $(BUILDDIR)/obj
 BINARYTESTDIR = $(BINARYDIR)/test
@@ -32,12 +32,12 @@ $(TARGET):$(OBJECTS)
 	@echo 'Finished building target: $@'
 	@echo ' '
 
-$(BINARYDIR)/%.o: $(SRCDIR)/%.cpp
+$(BINARYDIR)/%.o: $(SRCDIR)/%.cpp 
 	@mkdir -p $(BINARYDIR)
 	@mkdir -p $(BINARYTESTDIR)
 	@echo 'Building file: $<'
 	@echo 'Invoking: GCC C++ Compiler'
-	g++ -I/usr/include/python2.7 -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
+	g++ -I/usr/include/python2.7 -I$(INCDIR) -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
 	@echo 'Finished building: $<'
 	@echo ' '
 

makefile.OSX

@@ -2,8 +2,7 @@
 RM := rm -rf
 
 # All of the sources participating in the build are defined here
-SOURCES = src/PyramidalSimulation.cpp \
-src/main.cpp \
+SOURCES = src/main.cpp \
 src/owHelper.cpp \
 src/owOpenCLSolver.cpp \
 src/owPhysicsFluidSimulator.cpp \
@@ -13,7 +12,9 @@ TEST_SOURCES = src/test/owPhysicTest.cpp
 
 SRCEXT := cpp
 SRCDIR := src
+INCDIR := inc
 BUILDDIR := build
+BINARYTESTDIR = $(BUILDDIR)/test
 OBJECTS := $(patsubst $(SRCDIR)/%,$(BUILDDIR)/%,$(SOURCES:.$(SRCEXT)=.o))
 OBJECTS += $(BINARYTESTDIR)/owPhysicTest.o 
 
@@ -45,7 +46,7 @@ $(BUILDDIR)/%.o: $(SRCDIR)/%.cpp
 	@echo 'Invoking: clang C++ Compiler'
 #### use this to compile against homebrew installed python
 #### change version number as necessary (2.7.n)
-	g++ -O1 -Wall -c -I$(PYTHONHEADERDIR) -framework OpenCL -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
+	g++ -O1 -Wall -c -I$(PYTHONHEADERDIR) -I$(INCDIR) -framework OpenCL -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
 	@echo 'Finished building: $<'
 	@echo ' '