Commit 1848802c authored by Tomáš Oberhuber's avatar Tomáš Oberhuber
Browse files

Merge branch 'diffusion' of ssh://geraldine.fjfi.cvut.cz:2222/local/projects/tnl/tnl into diffusion 

Conflicts:
	src/implementation/functions/tnlExpBumpFunction_impl.h
parents 382ad350 eb29b04a

.cproject

+18 −7
Original line number Diff line number Diff line
@@ -5,26 +5,37 @@ 
			<storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="cdt.managedbuild.toolchain.gnu.base.2134791445" moduleId="org.eclipse.cdt.core.settings" name="Default">

				<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">

				<configuration buildProperties="" id="cdt.managedbuild.toolchain.gnu.base.2134791445" name="Default" parent="org.eclipse.cdt.build.core.emptycfg">

				<configuration buildProperties="" description="" id="cdt.managedbuild.toolchain.gnu.base.2134791445" name="Default" parent="org.eclipse.cdt.build.core.emptycfg">

					<folderInfo id="cdt.managedbuild.toolchain.gnu.base.2134791445.1799170915" name="/" resourcePath="">

						<toolChain id="cdt.managedbuild.toolchain.gnu.base.1762402759" name="cdt.managedbuild.toolchain.gnu.base" superClass="cdt.managedbuild.toolchain.gnu.base">

							<targetPlatform archList="all" binaryParser="org.eclipse.cdt.core.ELF" id="cdt.managedbuild.target.gnu.platform.base.840154721" name="Debug Platform" osList="linux,hpux,aix,qnx" superClass="cdt.managedbuild.target.gnu.platform.base"/>

							<builder id="cdt.managedbuild.target.gnu.builder.base.573876641" managedBuildOn="false" name="Gnu Make Builder.Default" superClass="cdt.managedbuild.target.gnu.builder.base"/>

							<builder id="cdt.managedbuild.target.gnu.builder.base.573876641" keepEnvironmentInBuildfile="false" managedBuildOn="false" name="Gnu Make Builder" superClass="cdt.managedbuild.target.gnu.builder.base"/>

							<tool id="cdt.managedbuild.tool.gnu.archiver.base.958650307" name="GCC Archiver" superClass="cdt.managedbuild.tool.gnu.archiver.base"/>

							<tool id="cdt.managedbuild.tool.gnu.cpp.compiler.base.1237330740" name="GCC C++ Compiler" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.base"/>

							<tool id="cdt.managedbuild.tool.gnu.c.compiler.base.315517693" name="GCC C Compiler" superClass="cdt.managedbuild.tool.gnu.c.compiler.base"/>

							<tool id="cdt.managedbuild.tool.gnu.cpp.compiler.base.1237330740" name="GCC C++ Compiler" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.base">

								<inputType id="cdt.managedbuild.tool.gnu.cpp.compiler.input.1856262209" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.input"/>

							</tool>

							<tool id="cdt.managedbuild.tool.gnu.c.compiler.base.315517693" name="GCC C Compiler" superClass="cdt.managedbuild.tool.gnu.c.compiler.base">

								<inputType id="cdt.managedbuild.tool.gnu.c.compiler.input.950045328" superClass="cdt.managedbuild.tool.gnu.c.compiler.input"/>

							</tool>

							<tool id="cdt.managedbuild.tool.gnu.c.linker.base.1786292703" name="GCC C Linker" superClass="cdt.managedbuild.tool.gnu.c.linker.base"/>

							<tool id="cdt.managedbuild.tool.gnu.cpp.linker.base.1133414639" name="GCC C++ Linker" superClass="cdt.managedbuild.tool.gnu.cpp.linker.base"/>

							<tool id="cdt.managedbuild.tool.gnu.assembler.base.336757143" name="GCC Assembler" superClass="cdt.managedbuild.tool.gnu.assembler.base"/>

							<tool id="cdt.managedbuild.tool.gnu.cpp.linker.base.1133414639" name="GCC C++ Linker" superClass="cdt.managedbuild.tool.gnu.cpp.linker.base">

								<inputType id="cdt.managedbuild.tool.gnu.cpp.linker.input.692614544" superClass="cdt.managedbuild.tool.gnu.cpp.linker.input">

									<additionalInput kind="additionalinputdependency" paths="$(USER_OBJS)"/>

									<additionalInput kind="additionalinput" paths="$(LIBS)"/>

								</inputType>

							</tool>

							<tool id="cdt.managedbuild.tool.gnu.assembler.base.336757143" name="GCC Assembler" superClass="cdt.managedbuild.tool.gnu.assembler.base">

								<inputType id="cdt.managedbuild.tool.gnu.assembler.input.1329383797" superClass="cdt.managedbuild.tool.gnu.assembler.input"/>

							</tool>

						</toolChain>

					</folderInfo>

				</configuration>

CMakeLists.txt

+6 −5
Original line number Diff line number Diff line
@@ -105,11 +105,11 @@ endif() 
####

# Check for MPI

#

find_package( MPI )

if( MPI_CXX_FOUND )

    set( BUILD_MPI TRUE )

    message( "MPI headers found -- ${MPI_CXX_INCLUDE_PATH}")

endif()

#find_package( MPI )

#if( MPI_CXX_FOUND )

#    set( BUILD_MPI TRUE )

#    message( "MPI headers found -- ${MPI_CXX_INCLUDE_PATH}")

#endif()



####

# Check for some system header
@@ -227,6 +227,7 @@ INSTALL( FILES ${PROJECT_BUILD_PATH}/tnlConfig.h DESTINATION include/tnl-${tnlVe 


#Nastavime cesty k hlavickovym souborum a knihovnam

INCLUDE_DIRECTORIES( src )

INCLUDE_DIRECTORIES( tests )

INCLUDE_DIRECTORIES( ${PROJECT_BUILD_PATH} )

LINK_DIRECTORIES( ${LIBRARY_OUTPUT_PATH} )

examples/heat-equation/CMakeLists.txt

+14 −24
Original line number Diff line number Diff line 
set( tnl_heat_equation_SOURCES

               tnlZeroRightHandSide_impl.h

               tnlZeroRightHandSide.h

               tnlTimeFunction_impl.h

               tnlTimeFunction.h

     tnlHeatEquationEocRhs.h

               tnlRightHandSide_impl.h

               tnlRightHandSide.h

               tnlNeumannBoundaryConditions_impl.h

               tnlNeumannBoundaryConditions.h

               tnlDirichletBoundaryConditions_impl.h

               tnlDirichletBoundaryConditions.h

               tnlAnalyticSolution_impl.h

               tnlAnalyticSolution.h

               main.cpp

               tnl-heat-equation.cpp

               tnl-heat-equation-eoc.cpp

               heatEquationSolver_impl.h

               heatEquationSolver.h

               heatEquationSetter_impl.h

               heatEquationSetter.h

               heatEquationConfig.h )

               heatEquationEocRhs.h )

               

ADD_EXECUTABLE(tnl-heat-equation${debugExt} ${tnl_heat_equation_SOURCES})

target_link_libraries (tnl-heat-equation${debugExt} tnl${debugExt}-${tnlVersion} )

#ADD_EXECUTABLE(tnl-heat-equation${debugExt} tnl-heat-equation.cpp)

#target_link_libraries (tnl-heat-equation${debugExt} tnl${debugExt}-${tnlVersion} )



INSTALL( TARGETS tnl-heat-equation${debugExt}

ADD_EXECUTABLE(tnl-heat-equation-eoc-test${debugExt} tnl-heat-equation-eoc.cpp)

target_link_libraries (tnl-heat-equation-eoc-test${debugExt} tnl${debugExt}-${tnlVersion} )



INSTALL( TARGETS #tnl-heat-equation${debugExt}

                 tnl-heat-equation-eoc-test${debugExt}

         RUNTIME DESTINATION bin

         PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE )

        

INSTALL( FILES #Makefile

               run-init-mesh

               run-heat-equation-testy-laplace-konvergence

               run-heat-equation-testy-konvergence

               run-heat-equation

               heat-equation.cfg.desc

					debugging_parameters

					EOCtest

					EOCtest-adaptivity-cycle



INSTALL( FILES tnl-run-heat-equation-eoc-test

               tnl-run-heat-equation

         DESTINATION share/tnl-${tnlVersion}/examples/heat-equation )

examples/heat-equation/EOCtest

deleted100755 → 0
+0 −185
Original line number Diff line number Diff line 
#!/bin/bash



LD_LIBRARY_PATH=/home/szekely/local/lib

export LD_LIBRARY_PATH



dimension=2

proportions=1

initDofSize=8

analyticFunction="sin-wave"

timeFunction="cosinus"

snapshotPeriod=0.05

finalTime=1

mersonAdaptivity=1.0e-5

numberOfIterations=8

#{8..1024dofs}

scale=2

origin=0



amplitude=1.0

waveLength=1.0

waveLengthX=1.0

waveLengthY=1.0

waveLengthZ=1.0

wavesNumber=0.0

wavesNumberX=0.0

wavesNumberY=0.0

wavesNumberZ=0.0

phase=0.0

phaseX=0.0

phaseY=0.0

phaseZ=0.0

sigma=1.0



dofs=${initDofSize}



for ((i=1;i<=${numberOfIterations};i++))

do



tnl-grid-setup --dimensions ${dimension} \

               --proportions-x ${proportions} \

               --proportions-y ${proportions} \

               --proportions-z ${proportions} \

               --origin-x ${origin} \

               --origin-y ${origin} \

               --origin-z ${origin} \

               --size-x ${dofs} \

               --size-y ${dofs} \

               --size-z ${dofs} \



tnl-discrete --mesh mesh.tnl \

             --function ${analyticFunction} \

             --output-file u-ini.tnl \

             --amplitude ${amplitude} \

             --wave-length ${waveLength} \

             --wave-length-x ${waveLengthX} \

             --wave-length-y ${waveLengthY} \

             --wave-length-z ${waveLengthZ} \

             --waves-number ${wavesNumber} \

             --waves-number-x ${wavesNumberX} \

             --waves-number-y ${wavesNumberY} \

             --waves-number-z ${wavesNumberZ} \

             --phase ${phase} \

             --phase-x ${phaseX} \

             --phase-y ${phaseY} \

             --phase-z ${phaseZ} \

             --sigma ${sigma} \



./heat-equation_AV --dimensions ${dimension} \

                --time-discretisation explicit \

                --discrete-solver merson \

		--merson-adaptivity ${mersonAdaptivity}\

                --time-function ${timeFunction}\

                --analytic-space-function ${analyticFunction}\

                --amplitude ${amplitude} \

                --wave-length ${waveLength} \

                --wave-length-x ${waveLengthX} \

                --wave-length-y ${waveLengthY} \

                --wave-length-z ${waveLengthZ} \

                --waves-number ${wavesNumber} \

                --waves-number-x ${wavesNumberX} \

                --waves-number-y ${wavesNumberY} \

                --waves-number-z ${wavesNumberZ} \

                --phase ${phase} \

                --phase-x ${phaseX} \

                --phase-y ${phaseY} \

                --phase-z ${phaseZ} \

                --sigma ${sigma} \

                --sigma ${sigma} \

                --snapshot-period ${snapshotPeriod} \

                --final-time ${finalTime} \

                --solution-convergence-test 1 \



rm u-ini.tnl



tnl-diff --mesh mesh.tnl \

         --input-files numericalSolution-*.tnl analyticSolution-*.tnl \

         --mode halves \

         --output-file ${dofs} \



rm *.tnl



dofs=$((${scale} * $dofs))



done



file="EOC-${analyticFunction}-${timeFunction}-${dimension}D-${finalTime}T-adaptivity${mersonAdaptivity}"



rm ${file}

echo -e "#\tL1 diff.\t\tEOC\t\tL2 diff.\t\tEOC\t\tLmax diff.\t\tEOC" >> ${file}



echo -e -n "${initDofSize}\t" >> ${file}

nactenyRadek=$( tail -1 ${initDofSize})

for zaznam  in ${nactenyRadek}

do



hodnota=$(echo $zaznam | sed 's/e/\*10\^/' | bc -l)

if [[ ${hodnota} =~ ^\. ]]; then

echo -e -n "0${hodnota}\t\t   \t\t" >> ${file}

else

echo -e -n "${hodnota}\t\t   \t\t" >> ${file}

fi



done

echo -e -n "\n" >> ${file}





${radek} >>  ${file}



soubor1=$((${initDofSize}/${scale}))

soubor2=${initDofSize}



for ((i=1;i<${numberOfIterations};i++))

do



soubor1=$((2 * $soubor1))

soubor2=$((2 * $soubor2))



IFS=' ' read -a posledniRadek1 <<< $(tail -1 $soubor1)

IFS=' ' read -a posledniRadek2 <<< $(tail -1 $soubor2)

#{pres specialni promenou IFS utvorime pole z retezce}



echo -e -n "${soubor2}\t" >> ${file}



for j in {0..2}

do



echo -e -n "${posledniRadek2[j]}\t\t" >> ${file}



prevedenyVyraz=$(echo "l((${posledniRadek2[$j]})/(${posledniRadek1[$j]}))/l(0.5)" | sed 's/e/\*10\^/g')

hodnota=$(echo "${prevedenyVyraz}" | bc -l)

hodnota=$(echo "scale=3; ${hodnota}/1" | bc)

#hodnota =$(echo "${prevedenyVyraz}" | bc -l)

#{g v retezci aby nahradilo vsechny vyskyty v souboru}

if [[ ${hodnota} =~ ^\. ]]; then

echo -e -n "0${hodnota}\t\t" >> ${file}

else

if [[ ${hodnota} =~ ^\-\. ]]; then

pom=$(echo "${hodnota}" | sed 's/-\./-0\./')

echo -e -n "${pom}\t\t" >> ${file}

else

echo -e -n "${hodnota}\t\t" >> ${file}

fi

fi



done



echo -e -n "\n" >> ${file}



done



echo -e -n "\n\n\n" >> ${file}



echo -e "PARAMETERS:\n" >> ${file}

echo -e " dimensions = ${dimension}\n proportions = ${proportions}\n analytic function = ${analyticFunction}\n time function = ${timeFunction}\n snapshot period = ${snapshotPeriod}\n final time = ${finalTime}\n adaptivity = ${mersonAdaptivity}\n origin = ${origin}\n\n" >> ${file}

echo -e " amplitude = ${amplitude}\n wave length = ${waveLength}\n wave length x = ${waveLengthX}\n wave length y = ${waveLengthY}\n wave length z = ${waveLengthZ=1.0}\n wave number = ${wavesNumber}\n waves number x = ${wavesNumberX}\n waves number y = ${wavesNumberY}\n waves number z = ${wavesNumberZ}\n phase = ${phase}\n phase x = ${phaseX}\n phase y = ${phaseY}\n phase z = ${phaseZ}\n sigma = ${sigma}" >> ${file}





soubor=$((${initDofSize}/${scale}))

for ((i=1;i<=${numberOfIterations};i++))

do



soubor=$((${soubor}*${scale}))

rm ${soubor}



done

examples/heat-equation/EOCtest-adaptivity-cycle

deleted100755 → 0
+0 −194
Original line number Diff line number Diff line 
#!/bin/bash



LD_LIBRARY_PATH=/home/szekely/local/lib

export LD_LIBRARY_PATH



dimension=2

proportions=1

initDofSize=8

analyticFunction="exp-bump"

timeFunction="cosinus"

snapshotPeriod=0.01

finalTime=0.1

initMersonAdaptivity=1.0e-7

numberOfAdaptivityIter=2

adaptivityDiff=100

numberOfIterations=8

#{8..1024dofs}

scale=2

origin=0



amplitude=1.0

waveLength=1.0

waveLengthX=1.0

waveLengthY=1.0

waveLengthZ=1.0

wavesNumber=0.0

wavesNumberX=0.0

wavesNumberY=0.0

wavesNumberZ=0.0

phase=0.0

phaseX=0.0

phaseY=0.0

phaseZ=0.0

sigma=1.0



dofs=${initDofSize}

mersonAdaptivity=${initMersonAdaptivity}



for ((k=1;k<=${numberOfAdaptivityIter};k++))

do

for ((i=1;i<=${numberOfIterations};i++))

do



tnl-grid-setup --dimensions ${dimension} \

               --proportions-x ${proportions} \

               --proportions-y ${proportions} \

               --proportions-z ${proportions} \

               --origin-x ${origin} \

               --origin-y ${origin} \

               --origin-z ${origin} \

               --size-x ${dofs} \

               --size-y ${dofs} \

               --size-z ${dofs} \



tnl-discrete --mesh mesh.tnl \

             --function ${analyticFunction} \

             --output-file u-ini.tnl \

             --amplitude ${amplitude} \

             --wave-length ${waveLength} \

             --wave-length-x ${waveLengthX} \

             --wave-length-y ${waveLengthY} \

             --wave-length-z ${waveLengthZ} \

             --waves-number ${wavesNumber} \

             --waves-number-x ${wavesNumberX} \

             --waves-number-y ${wavesNumberY} \

             --waves-number-z ${wavesNumberZ} \

             --phase ${phase} \

             --phase-x ${phaseX} \

             --phase-y ${phaseY} \

             --phase-z ${phaseZ} \

             --sigma ${sigma} \



./heat-equation_AV --dimensions ${dimension} \

                --time-discretisation explicit \

                --discrete-solver merson \

		--merson-adaptivity ${mersonAdaptivity}\

                --time-function ${timeFunction}\

                --analytic-space-function ${analyticFunction}\

                --amplitude ${amplitude} \

                --wave-length ${waveLength} \

                --wave-length-x ${waveLengthX} \

                --wave-length-y ${waveLengthY} \

                --wave-length-z ${waveLengthZ} \

                --waves-number ${wavesNumber} \

                --waves-number-x ${wavesNumberX} \

                --waves-number-y ${wavesNumberY} \

                --waves-number-z ${wavesNumberZ} \

                --phase ${phase} \

                --phase-x ${phaseX} \

                --phase-y ${phaseY} \

                --phase-z ${phaseZ} \

                --sigma ${sigma} \

                --sigma ${sigma} \

                --snapshot-period ${snapshotPeriod} \

                --final-time ${finalTime} \

                --solution-convergence-test 1 \



rm u-ini.tnl



tnl-diff --mesh mesh.tnl \

         --input-files numericalSolution-*.tnl analyticSolution-*.tnl \

         --mode halves \

         --output-file ${dofs} \



rm *.tnl



dofs=$((${scale} * $dofs))



done



file="EOC-${analyticFunction}-${timeFunction}-${dimension}D-${finalTime}T-adaptivity${mersonAdaptivity}"



rm ${file}

echo -e "#\tL1 diff.\t\tEOC\t\tL2 diff.\t\tEOC\t\tLmax diff.\t\tEOC" >> ${file}



echo -e -n "${initDofSize}\t" >> ${file}

nactenyRadek=$( tail -1 ${initDofSize})

for zaznam  in ${nactenyRadek}

do



hodnota=$(echo $zaznam | sed 's/e/\*10\^/' | bc -l)

if [[ ${hodnota} =~ ^\. ]]; then

echo -e -n "0${hodnota}\t\t   \t\t" >> ${file}

else

echo -e -n "${hodnota}\t\t   \t\t" >> ${file}

fi



done

echo -e -n "\n" >> ${file}





${radek} >>  ${file}



soubor1=$((${initDofSize}/${scale}))

soubor2=${initDofSize}



for ((i=1;i<${numberOfIterations};i++))

do



soubor1=$((2 * $soubor1))

soubor2=$((2 * $soubor2))



IFS=' ' read -a posledniRadek1 <<< $(tail -1 $soubor1)

IFS=' ' read -a posledniRadek2 <<< $(tail -1 $soubor2)

#{pres specialni promenou IFS utvorime pole z retezce}



echo -e -n "${soubor2}\t" >> ${file}



for j in {0..2}

do



echo -e -n "${posledniRadek2[j]}\t\t" >> ${file}



prevedenyVyraz=$(echo "l((${posledniRadek2[$j]})/(${posledniRadek1[$j]}))/l(0.5)" | sed 's/e/\*10\^/g')

hodnota=$(echo "${prevedenyVyraz}" | bc -l)

hodnota=$(echo "scale=3; ${hodnota}/1" | bc)

#hodnota =$(echo "${prevedenyVyraz}" | bc -l)

#{g v retezci aby nahradilo vsechny vyskyty v souboru}

if [[ ${hodnota} =~ ^\. ]]; then

echo -e -n "0${hodnota}\t\t" >> ${file}

else

if [[ ${hodnota} =~ ^\-\. ]]; then

pom=$(echo "${hodnota}" | sed 's/-\./-0\./')

echo -e -n "${pom}\t\t" >> ${file}

else

echo -e -n "${hodnota}\t\t" >> ${file}

fi

fi



done



echo -e -n "\n" >> ${file}



done



echo -e -n "\n\n\n" >> ${file}



echo -e "PARAMETERS:\n" >> ${file}

echo -e " dimensions = ${dimension}\n proportions = ${proportions}\n analytic function = ${analyticFunction}\n time function = ${timeFunction}\n snapshot period = ${snapshotPeriod}\n final time = ${finalTime}\n adaptivity = ${mersonAdaptivity}\n origin = ${origin}\n\n" >> ${file}

echo -e " amplitude = ${amplitude}\n wave length = ${waveLength}\n wave length x = ${waveLengthX}\n wave length y = ${waveLengthY}\n wave length z = ${waveLengthZ=1.0}\n wave number = ${wavesNumber}\n waves number x = ${wavesNumberX}\n waves number y = ${wavesNumberY}\n waves number z = ${wavesNumberZ}\n phase = ${phase}\n phase x = ${phaseX}\n phase y = ${phaseY}\n phase z = ${phaseZ}\n sigma = ${sigma}" >> ${file}





soubor=$((${initDofSize}/${scale}))

for ((i=1;i<=${numberOfIterations};i++))

do



soubor=$((${soubor}*${scale}))

rm ${soubor}



done 



mersonAdaptivity=$(echo "(${mersonAdaptivity})/(${adaptivityDiff})" | sed 's/e/\*10\^/g' | bc -l)



done