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  • nektar/tutorial
  • victorballester7/tutorial
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with 2020 additions and 9 deletions
CMakeLists.txt
View file @ a20044f2
......@@ -16,35 +16,37 @@ SET(TUTORIAL_ROOT ${CMAKE_CURRENT_SOURCE_DIR})
# HTML_BREAK_LEVEL <N> Section depth to break into separate files.
# USES_INDEX Run 'makeindex'
# USES_REFS Run 'bibtex'
# ARCHIVE Make tarball of associated files
# First file is archive name, followed by included files.
#
MACRO(ADD_NEKTAR_TUTORIAL)
SET(options PDF HTML USES_INDEX USES_REFS)
SET(oneValueArgs TARGET BASE STYLING_FILE HTML_BREAK_LEVEL)
SET(multiValueArgs "")
SET(multiValueArgs ARCHIVE)
cmake_parse_arguments(NEK "${options}"
"${oneValueArgs}" "${multiValueArgs}" ${ARGN} )
SET(NEKSRC ${CMAKE_SOURCE_DIR})
SET(SRC ${CMAKE_CURRENT_SOURCE_DIR})
SET(TGT ${CMAKE_CURRENT_BINARY_DIR})
IF (NEK_PDF)
FIND_PROGRAM(PDFLATEX pdflatex)
FIND_PROGRAM(BIBTEX bibtex)
FIND_PROGRAM(MAKEINDEX makeindex)
MARK_AS_ADVANCED(PDFLATEX BIBTEX MAKEINDEX)
# Main target (Final PDFLatex)
ADD_CUSTOM_TARGET(${NEK_TARGET}-pdf
export TEXINPUTS=${NEKSRC}//: &&
TEXINPUTS=${NEKSRC}/:${TUTORIAL_ROOT}/shared//:
${PDFLATEX} --output-directory ${TGT} ${SRC}/${NEK_BASE}.tex
WORKING_DIRECTORY ${SRC}
)
# Initial PDFLATEX
ADD_CUSTOM_TARGET(${NEK_TARGET}-pdflatex
COMMAND export TEXINPUTS=${NEKSRC}//: &&
${PDFLATEX} --output-directory ${TGT} ${SRC}/${NEK_BASE}.tex
TEXINPUTS=${NEKSRC}/:${TUTORIAL_ROOT}/shared//:
${PDFLATEX} --output-directory ${TGT} ${SRC}/${NEK_BASE}.tex
WORKING_DIRECTORY ${SRC})
ADD_DEPENDENCIES(${NEK_TARGET}-pdf ${NEK_TARGET}-pdflatex)
......@@ -65,6 +67,16 @@ MACRO(ADD_NEKTAR_TUTORIAL)
ADD_DEPENDENCIES(${NEK_TARGET}-pdf ${NEK_TARGET}-index)
ADD_DEPENDENCIES(${NEK_TARGET}-index ${NEK_TARGET}-pdflatex)
ENDIF()
# Create an archive of the tutorial files
IF (NEK_ARCHIVE)
SET(TARFILE "${TGT}/${NEK_TARGET}.tar.gz")
ADD_CUSTOM_COMMAND(TARGET ${NEK_TARGET}-pdf POST_BUILD
COMMAND ${CMAKE_COMMAND} -E tar "cvfz" ${TARFILE}
${NEK_ARCHIVE}
WORKING_DIRECTORY ${SRC}
COMMENT "Generating ${TARFILE}")
ENDIF()
ENDIF ()
IF (NEK_HTML)
......@@ -82,8 +94,9 @@ MACRO(ADD_NEKTAR_TUTORIAL)
IF (NEK_STYLING_FILE)
SET(FLAGS "${NEK_STYLING_FILE},${FLAGS}")
ENDIF()
ADD_CUSTOM_TARGET(${NEK_TARGET}-html
export TEXINPUTS=${NEKSRC}//:${SRC}//: &&
TEXINPUTS=${NEKSRC}/:${SRC}//:${TUTORIAL_ROOT}/shared//:
${HTLATEX} ${SRC}/${NEK_BASE}.tex
"${FLAGS}"
WORKING_DIRECTORY ${TGT}/html
......@@ -91,7 +104,8 @@ MACRO(ADD_NEKTAR_TUTORIAL)
# Copy images across
FILE(GLOB_RECURSE imgfiles "img/*.png" "img/*.jpg" "*/img/*.png"
"*/img/*.jpg")
"*/img/*.jpg" "${TUTORIAL_ROOT}/shared/img/*.png"
"${TUTORIAL_ROOT}/shared/img/*.jpg")
ADD_CUSTOM_COMMAND(TARGET ${NEK_TARGET}-html POST_BUILD
COMMAND ${CMAKE_COMMAND} -E make_directory ${TGT}/html/img)
FOREACH(img ${imgfiles})
......@@ -101,7 +115,8 @@ MACRO(ADD_NEKTAR_TUTORIAL)
ENDFOREACH()
# Convert PDF files and copy across
FILE(GLOB_RECURSE pdffiles "img/*.pdf" "*/img/*.pdf")
FILE(GLOB_RECURSE pdffiles "img/*.pdf" "*/img/*.pdf"
"${TUTORIAL_ROOT}/shared/img/*.pdf")
FIND_PROGRAM(CONVERT convert)
MARK_AS_ADVANCED(CONVERT)
FOREACH(pdf ${pdffiles})
......@@ -110,8 +125,33 @@ MACRO(ADD_NEKTAR_TUTORIAL)
COMMAND ${CONVERT} ${pdf} ${TGT}/html/img/${BASENAME}.png
COMMENT "Converting ${pdf} to PNG...")
ENDFOREACH()
IF (NEK_ARCHIVE)
SET(TARFILE "${TGT}/html/${NEK_TARGET}.tar.gz")
ADD_CUSTOM_COMMAND(TARGET ${NEK_TARGET}-html POST_BUILD
COMMAND ${CMAKE_COMMAND} -E tar "cvfz" ${TARFILE}
${NEK_ARCHIVE}
WORKING_DIRECTORY ${SRC}
COMMENT "Generating ${TARFILE}")
FOREACH(f ${NEK_ARCHIVE})
GET_FILENAME_COMPONENT(TGTNAME ${f} NAME)
ADD_CUSTOM_COMMAND(TARGET ${NEK_TARGET}-html POST_BUILD
COMMAND ${CMAKE_COMMAND} -E copy_directory ${f}
${TGT}/html/${TGTNAME}
COMMENT "Copying file ${f} to ${TGT}/html/${TGTNAME}...")
ENDFOREACH()
ENDIF()
ENDIF()
ENDMACRO()
MACRO(ADD_NEKTAR_TUTORIAL_TEST solver testname)
GET_FILENAME_COMPONENT(dir ${CMAKE_CURRENT_SOURCE_DIR} NAME)
ADD_TEST(NAME tutorial_${testname}
COMMAND $<TARGET_FILE:Tester> -e $<TARGET_FILE:${solver}>
${CMAKE_CURRENT_SOURCE_DIR}/tests/${testname}.tst)
ENDMACRO()
ADD_SUBDIRECTORY(basics)
ADD_SUBDIRECTORY(events)
ADD_SUBDIRECTORY(fundamentals)
ADD_SUBDIRECTORY(flow-stability)
basics/CMakeLists.txt 0 → 100644
View file @ a20044f2
ADD_SUBDIRECTORY(advection-diffusion)
ADD_SUBDIRECTORY(helmholtz)
basics/advection-diffusion/CMakeLists.txt 0 → 100644
View file @ a20044f2
ADD_NEKTAR_TUTORIAL(PDF HTML TARGET basics-advection-diffusion
HTML_BREAK_LEVEL 2
BASE basics-advection-diffusion
STYLING_FILE styling.cfg
ARCHIVE basics-advection-diffusion)
# Add tests only if we are building from within the Nektar++ tree
IF (DEFINED NEKTAR_BUILD_TESTS)
ADD_NEKTAR_TUTORIAL_TEST(NekMesh basics-advection-diffusion-msh)
ADD_NEKTAR_TUTORIAL_TEST(NekMesh basics-advection-diffusion-msh-align)
ADD_NEKTAR_TUTORIAL_TEST(FieldConvert basics-advection-diffusion-post)
ADD_NEKTAR_TUTORIAL_TEST(ADRSolver basics-advection-diffusion-slv)
ENDIF()
basics/advection-diffusion/basics-advection-diffusion.tex 0 → 100644
View file @ a20044f2
This diff is collapsed.
basics/advection-diffusion/basics-advection-diffusion/completed/ADR_conditions.xml 0 → 100644
View file @ a20044f2
<?xml version="1.0" encoding="utf-8" ?>
<NEKTAR>
<EXPANSIONS>
<E COMPOSITE="C[1]" NUMMODES="5" TYPE="MODIFIED" FIELDS="u" />
<E COMPOSITE="C[2]" NUMMODES="5" TYPE="MODIFIED" FIELDS="u" />
<E COMPOSITE="C[3]" NUMMODES="5" TYPE="MODIFIED" FIELDS="u" />
</EXPANSIONS>
<CONDITIONS>
<PARAMETERS>
<P> FinTime = 1.0 </P>
<P> TimeStep = 0.001 </P>
<P> NumSteps = FinTime/TimeStep </P>
<P> IO_CheckSteps = 100 </P>
<P> IO_InfoSteps = 100 </P>
<P> advx = 2.0 </P>
<P> advy = 0.0 </P>
<P> k = 2*PI </P>
</PARAMETERS>
<SOLVERINFO>
<I PROPERTY="EQTYPE" VALUE="UnsteadyAdvection" />
<I PROPERTY="Projection" VALUE="DisContinuous" />
<I PROPERTY="AdvectionType" VALUE="WeakDG" />
<I PROPERTY="UpwindType" VALUE="Upwind" />
<I PROPERTY="TimeIntegrationMethod" VALUE="ClassicalRungeKutta4"/>
</SOLVERINFO>
<VARIABLES>
<V ID="0"> u </V>
</VARIABLES>
<BOUNDARYREGIONS>
<B ID="0"> C[100] </B>
<B ID="1"> C[200] </B>
<B ID="2"> C[300] </B>
<B ID="3"> C[400] </B>
</BOUNDARYREGIONS>
<BOUNDARYCONDITIONS>
<REGION REF="0">
<D VAR="u" USERDEFINEDTYPE="TimeDependent"
VALUE="sin(k*(x-advx*t))*cos(k*(y-advy*t))" />
</REGION>
<REGION REF="1">
<P VAR="u" VALUE="[3]" />
</REGION>
<REGION REF="2">
<D VAR="u" USERDEFINEDTYPE="TimeDependent"
VALUE="sin(k*(x-advx*t))*cos(k*(y-advy*t))" />
</REGION>
<REGION REF="3">
<P VAR="u" VALUE="[1]" />
</REGION>
</BOUNDARYCONDITIONS>
<FUNCTION NAME="AdvectionVelocity">
<E VAR="Vx" VALUE="advx" />
<E VAR="Vy" VALUE="advy" />
</FUNCTION>
<FUNCTION NAME="ExactSolution">
<E VAR="u" VALUE="sin(k*(x-advx*t))*cos(k*(y-advy*t))" />
</FUNCTION>
<FUNCTION NAME="InitialConditions">
<E VAR="u" VALUE="sin(k*x)*cos(k*y)" />
</FUNCTION>
</CONDITIONS>
</NEKTAR>
basics/advection-diffusion/basics-advection-diffusion/completed/ADR_mesh.geo 0 → 100644
View file @ a20044f2
// Bigger square points
Point(1) = {-1.00, -1.00, 0.00, 0.4};
Point(2) = { 1.00, -1.00, 0.00, 0.4};
Point(3) = { 1.00, 1.00, 0.00, 0.4};
Point(4) = {-1.00, 1.00, 0.00, 0.4};
// Refinement region points
Point(5) = { 1.00, -0.25, 0.00, 0.4};
Point(6) = { 1.00, 0.25, 0.00, 0.4};
Point(7) = {-1.00, 0.25, 0.00, 0.4};
Point(8) = {-1.00, -0.25, 0.00, 0.4};
// Lines of the square
Line(1) = {1, 2};
Line(2) = {2, 5};
Line(3) = {5, 6};
Line(4) = {6, 3};
Line(5) = {3, 4};
Line(6) = {4, 7};
Line(7) = {7, 8};
Line(8) = {8, 1};
// Two central lines for mesh generation purposes
Line(9) = {5, 8};
Line(10) = {6, 7};
//Line Loops to create physical surfaces
Line Loop(1) = {1, 2, 9, 8};
Plane Surface(1) = {1};
Physical Surface(1) = {1};
Line Loop(2) = {-9, 3, 10, 7};
Plane Surface(2) = {2};
Physical Surface(2) = {2};
Line Loop(3) = {-10, 4, 5, 6};
Plane Surface(3) = {3};
Physical Surface(3) = {3};
// Making a structured mesh in the central region
Transfinite Line {7, -3} = 5 Using Progression 1;
Transfinite Surface{2};
Recombine Surface{2};
// Making a structured mesh in the other two regions
//Transfinite Line {2, -8} = 5 Using Progression 0.75;
//Transfinite Surface{1};
//Recombine Surface{1};
//Transfinite Line {4, -6} = 5 Using Progression 1.25;
//Transfinite Surface{3};
//Recombine Surface{3};
// Defining physical lines for applying the boundary
// conditions
Physical Line(100) = {1};
Physical Line(200) = {2,3,4};
Physical Line(300) = {5};
Physical Line(400) = {6,7,8};
basics/advection-diffusion/basics-advection-diffusion/completed/ADR_mesh.msh 0 → 100644
View file @ a20044f2
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$EndMeshFormat
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basics/advection-diffusion/basics-advection-diffusion/completed/ADR_mesh.xml 0 → 100644
View file @ a20044f2
<?xml version="1.0" encoding="utf-8" ?>
<NEKTAR>
<GEOMETRY DIM="2" SPACE="2">
<VERTEX>
<V ID="0">2.00000000e-01 -1.00000000e+00 0.00000000e+00</V>
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basics/advection-diffusion/basics-advection-diffusion/completed/ADR_mesh_aligned.fld 0 → 100644
View file @ a20044f2
<?xml version="1.0" encoding="utf-8" ?>
<NEKTAR>
<Metadata>
<Provenance>
<GitBranch>refs/heads/feature/hdf5</GitBranch>
<GitSHA1>34b0da287d03a983b0d9ee9cb3c33c6c5d604fff</GitSHA1>
<Hostname>Spencers-MacBook-Pro.local</Hostname>
<NektarVersion>4.3.0</NektarVersion>
<Timestamp>01-Apr-2016 16:21:55</Timestamp>
</Provenance>
<SessionName0>ADR_mesh_aligned.xml</SessionName0>
<SessionName1>ADR_conditions.xml</SessionName1>
<Time>1.0000000000000007</Time>
</Metadata>
<ELEMENTS FIELDS="u" SHAPE="Triangle" BASIS="Modified_A,Modified_B" NUMMODESPERDIR="UNIORDER:5,5" ID="0-61" COMPRESSED="B64Z-LittleEndian" 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basics/advection-diffusion/basics-advection-diffusion/completed/ADR_mesh_aligned.xml 0 → 100644
View file @ a20044f2
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basics/advection-diffusion/basics-advection-diffusion/tutorial/ADR_mesh.geo 0 → 100644
View file @ a20044f2
// Bigger square points
Point(1) = {-1.00, -1.00, 0.00, 0.4};
Point(2) = { 1.00, -1.00, 0.00, 0.4};
Point(3) = { 1.00, 1.00, 0.00, 0.4};
Point(4) = {-1.00, 1.00, 0.00, 0.4};
// Refinement region points
Point(5) = { 1.00, -0.25, 0.00, 0.4};
Point(6) = { 1.00, 0.25, 0.00, 0.4};
Point(7) = {-1.00, 0.25, 0.00, 0.4};
Point(8) = {-1.00, -0.25, 0.00, 0.4};
// Lines of the square
Line(1) = {1, 2};
Line(2) = {2, 5};
Line(3) = {5, 6};
Line(4) = {6, 3};
Line(5) = {3, 4};
Line(6) = {4, 7};
Line(7) = {7, 8};
Line(8) = {8, 1};
// Two central lines for mesh generation purposes
Line(9) = {5, 8};
Line(10) = {6, 7};
//Line Loops to create physical surfaces
Line Loop(1) = {1, 2, 9, 8};
Plane Surface(1) = {1};
Physical Surface(1) = {1};
Line Loop(2) = {-9, 3, 10, 7};
Plane Surface(2) = {2};
Physical Surface(2) = {2};
Line Loop(3) = {-10, 4, 5, 6};
Plane Surface(3) = {3};
Physical Surface(3) = {3};
// Making a structured mesh in the central region
Transfinite Line {7, -3} = 5 Using Progression 1;
Transfinite Surface{2};
Recombine Surface{2};
// Making a structured mesh in the other two regions
//Transfinite Line {2, -8} = 5 Using Progression 0.75;
//Transfinite Surface{1};
//Recombine Surface{1};
//Transfinite Line {4, -6} = 5 Using Progression 1.25;
//Transfinite Surface{3};
//Recombine Surface{3};
// Defining physical lines for applying the boundary
// conditions
Physical Line(100) = {1};
Physical Line(200) = {2,3,4};
Physical Line(300) = {5};
Physical Line(400) = {6,7,8};
basics/advection-diffusion/basics-advection-diffusion/tutorial/ADR_mesh.msh 0 → 100644
View file @ a20044f2
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$EndElements
basics/advection-diffusion/img/ADR_mesh.png 0 → 100644
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basics/advection-diffusion/tests/basics-advection-diffusion-msh-align.tst 0 → 100644
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<?xml version="1.0" encoding="utf-8" ?>
<test>
<description>ADR Solver, align xml to be periodic</description>
<parameters> -m peralign:surf1=200:surf2=400:dir=x -m jac:list ADR_mesh.xml ADR_mesh_aligned.xml </parameters>
<files>
<file description="Input File">../basics-advection-diffusion/completed/ADR_mesh.xml</file>
</files>
<metrics>
<metric type="regex" id="1">
<regex>^Total negative Jacobians: (\d+)</regex>
<matches>
<match>
<field id="0">0</field>
</match>
</matches>
</metric >
</metrics>
</test>
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<?xml version="1.0" encoding="utf-8" ?>
<test>
<description>ADR Solver, convert gmsh to xml</description>
<parameters> -m jac:list ADR_mesh.msh ADR_mesh.xml</parameters>
<files>
<file description="Input File">../basics-advection-diffusion/completed/ADR_mesh.msh</file>
</files>
<metrics>
<metric type="regex" id="1">
<regex>^Total negative Jacobians: (\d+)</regex>
<matches>
<match>
<field id="0">0</field>
</match>
</matches>
</metric >
</metrics>
</test>
basics/advection-diffusion/tests/basics-advection-diffusion-post.tst 0 → 100644
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<?xml version="1.0" encoding="utf-8" ?>
<test>
<description>ADR Solver, post process fld </description>
<parameters> -e ADR_mesh_aligned.xml ADR_conditions.xml ADR_mesh_aligned.fld ADR_mesh_aligned.dat</parameters>
<files>
<file description="Session File">../basics-advection-diffusion/completed/ADR_mesh_aligned.xml</file>
<file description="Session File">../basics-advection-diffusion/completed/ADR_conditions.xml</file>
<file description="Session File">../basics-advection-diffusion/completed/ADR_mesh_aligned.fld</file>
</files>
<metrics>
<metric type="L2" id="1">
<value variable="x" tolerance="1e-8">1.1547</value>
<value variable="y" tolerance="1e-8">1.1547</value>
<value variable="u" tolerance="1e-8">0.999236</value>
</metric>
</metrics>
</test>