diff --git a/bin/doc/compareparameters.sh b/bin/doc/compareparameters.sh
index f788e42c586f276a2d6d37a82889aaedbbb80ad0..920c910db6b9e3a857a635dc7487fd5715645ebf 100755
--- a/bin/doc/compareparameters.sh
+++ b/bin/doc/compareparameters.sh
@@ -2,51 +2,72 @@
# 1. obtain a list new_parameters.csv of all current parameters
# retrieve all occurrences of GET_PARAM and GET_RUNTIME_PARAM
-find dumux/ -name '*.[ch][ch]' -exec grep 'GET_PARAM' {} \; | sort -u >new_parameters.csv
-find dumux/ -name '*.[ch][ch]' -exec grep 'GET_RUNTIME_PARAM' {} \; | sort -u >>new_parameters.csv
-# remove all lines containing CSTRING
-sed -i '/CSTRING/d' new_parameters.csv
+find dumux/ -name '*.[ch][ch]' -exec awk '/getParam</,/;/' {} \; >new_parameters.csv
+find dumux/ -name '*.[ch][ch]' -exec awk '/getParamFromGroup</,/;/' {} \; >>new_parameters.csv
+#add \ to lines not ending with ;
+sed -i '/\;$/!s/$/\\/' new_parameters.csv
+# move lines with \ to previous line
+sed -i ':x; /\\$/ { N; s/\\\n//; tx }' new_parameters.csv
# remove #define's
sed -i '/#define/d' new_parameters.csv
# remove everything before GET_PARAM and GET_RUNTIME_PARAM
-sed -i 's/^.*GET_PARAM/GET_PARAM/' new_parameters.csv
-sed -i 's/^.*GET_RUNTIME_PARAM/GET_RUNTIME_PARAM/' new_parameters.csv
-# remove everything before and including first comma
-awk '{print substr($0,index($0,",")+1)}' new_parameters.csv >tmp.txt
+sed -i 's/^.*getParam/getParam/' new_parameters.csv
+# remove everything before and including first <
+awk '{print substr($0,index($0,"<")+1)}' new_parameters.csv >tmp.txt
mv tmp.txt new_parameters.csv
-# remove leading whitespace
-sed -i 's/^[ \t]*//' new_parameters.csv
-# remove everything after and including paranthesis
-sed -i 's/).*//' new_parameters.csv
+# remove all blanks
+sed -i 's/ //g' new_parameters.csv
+#change unsigned to int
+sed -i 's/unsigned int/int/' new_parameters.csv
+sed -i 's/unsignedint/int/' new_parameters.csv
+sed -i 's/unsigned/int/' new_parameters.csv
+#remove everything after last )
+sed -i 's/\(.*\)).*/\1 /' new_parameters.csv
+#remove everything after last {
+sed -i 's/{.*$//' new_parameters.csv
# sort uniquely
sort -u new_parameters.csv -o new_parameters.csv
-# keep only the lines containing two commas
-sed -i '/,.*,/!d' new_parameters.csv
# append types to the end of the lines
-sed -i '/^bool,/ s/$/, bool/' new_parameters.csv
-sed -i '/^double,/ s/$/, double/' new_parameters.csv
-sed -i 's/unsigned int/int/' new_parameters.csv
-sed -i 's/unsigned/int/' new_parameters.csv
-sed -i '/^int,/ s/$/, int/' new_parameters.csv
-sed -i '/^Scalar,/ s/$/, Scalar/' new_parameters.csv
-sed -i '/^std::string,/ s/$/, std::string/' new_parameters.csv
-# remove types from the beginning of the lines
-sed -i 's/bool,//' new_parameters.csv
-sed -i 's/double,//' new_parameters.csv
-sed -i 's/int,//' new_parameters.csv
-sed -i 's/Scalar,//' new_parameters.csv
-sed -i 's/std::string,//' new_parameters.csv
-# remove all blanks
-sed -i 's/ //g' new_parameters.csv
-# add blanks after every comma
-sed -i 's/,/, /g' new_parameters.csv
+sed -i 's/\(bool.*\)\(>.*\)/\2 \1/' new_parameters.csv
+sed -i 's/\(double.*\)\(>.*\)/\2 \1/' new_parameters.csv
+sed -i 's/\(int.*\)\(>.*\)/\2 \1/' new_parameters.csv
+sed -i 's/\(Scalar.*\)\(>.*\)/\2 \1/' new_parameters.csv
+sed -i 's/\(GlobalPosition.*\)\(>.*\)/\2 \1/' new_parameters.csv
+sed -i 's/\(CoordinateType.*\)\(>.*\)/\2 \1/' new_parameters.csv
+sed -i 's/\(CellArray.*\)\(>.*\)/\2 \1/' new_parameters.csv
+sed -i 's/\(Dune::.*\)\(>.*\)/\2 \1/' new_parameters.csv
+sed -i 's/\(std::.*\)\(>.*\)/\2 \1/' new_parameters.csv
+#remove everything until first "
+sed -i 's/[^"]*"//' new_parameters.csv
+# move everything between , and BLANK to end of the lines
+sed -i 's/\(,.*\)\( .*\)/\2 \1/' new_parameters.csv
+# remove all "))
+sed -i 's/"))//g' new_parameters.csv
+# remove all ")
+sed -i 's/")//g' new_parameters.csv
+# remove all "
+sed -i 's/"//g' new_parameters.csv
+#remove all ,
+sed -i 's/,//g' new_parameters.csv
+#remove frist . in every line
+sed -i 's/\./\ /' new_parameters.csv
+#replace double blank by single blank
+sed -i 's/ */ /g' new_parameters.csv
# sort uniquely
sort -u new_parameters.csv -o new_parameters.csv
-# remove lines containing no parameter names
-sed -i '/, , /d' new_parameters.csv
-#adapt to doxygen format
+#adapt to doxygen format:
+#add final blank
+sed -i '/\ $/!s/$/ /' new_parameters.csv
+#replace blank with |
+sed -i 's/ / | /g' new_parameters.csv
+#add starting * |
sed -i 's/^/ * | /' new_parameters.csv
-sed -i 's/, / | /g' new_parameters.csv
+#add final | if not there 4th to 6th |)
+sed -i '/\ |$/!s/$/|/' new_parameters.csv
+#add 5th | if still missing
+sed -i '/\ |.*|.*|.*|.*|$/!s/$/ |/' new_parameters.csv
+#add 6th | if still missing
+sed -i '/\ |.*|.*|.*|.*|.*|$/!s/$/ |/' new_parameters.csv
# 2. obtain a list old_parameters.csv of all old parameters
cp -v doc/doxygen/extradoc/parameterlist.txt old_parameters.csv
diff --git a/doc/doxygen/DoxygenDumuxLayout.xml b/doc/doxygen/DoxygenDumuxLayout.xml
new file mode 100644
index 0000000000000000000000000000000000000000..3cfe34c877d9e8546d0bb6917fc5d309eb2dbb60
--- /dev/null
+++ b/doc/doxygen/DoxygenDumuxLayout.xml
@@ -0,0 +1,194 @@
+<doxygenlayout version="1.0">
+ <!-- Generated by doxygen 1.8.13 -->
+ <!-- Navigation index tabs for HTML output -->
+ <navindex>
+ <tab type="mainpage" visible="yes" title=""/>
+ <tab type="pages" visible="yes" title="" intro=""/>
+ <tab type="modules" visible="yes" title="" intro=""/>
+ <tab type="namespaces" visible="yes" title="">
+ <tab type="namespacelist" visible="yes" title="" intro=""/>
+ <tab type="namespacemembers" visible="yes" title="" intro=""/>
+ </tab>
+ <tab type="classes" visible="yes" title="">
+ <tab type="classlist" visible="yes" title="" intro=""/>
+ <tab type="classindex" visible="$ALPHABETICAL_INDEX" title=""/>
+ <tab type="hierarchy" visible="yes" title="" intro=""/>
+ <tab type="classmembers" visible="yes" title="" intro=""/>
+ </tab>
+ <tab type="files" visible="yes" title="">
+ <tab type="filelist" visible="yes" title="" intro=""/>
+ <tab type="globals" visible="yes" title="" intro=""/>
+ </tab>
+ <tab type="examples" visible="yes" title="" intro=""/>
+ </navindex>
+
+ <!-- Layout definition for a class page -->
+ <class>
+ <briefdescription visible="yes"/>
+ <includes visible="$SHOW_INCLUDE_FILES"/>
+ <inheritancegraph visible="$CLASS_GRAPH"/>
+ <collaborationgraph visible="$COLLABORATION_GRAPH"/>
+ <detaileddescription title="Description"/>
+ <memberdecl>
+ <nestedclasses visible="yes" title=""/>
+ <publictypes title=""/>
+ <services title=""/>
+ <interfaces title=""/>
+ <publicslots title=""/>
+ <signals title=""/>
+ <publicmethods title=""/>
+ <publicstaticmethods title=""/>
+ <publicattributes title=""/>
+ <publicstaticattributes title=""/>
+ <protectedtypes title=""/>
+ <protectedslots title=""/>
+ <protectedmethods title=""/>
+ <protectedstaticmethods title=""/>
+ <protectedattributes title=""/>
+ <protectedstaticattributes title=""/>
+ <packagetypes title=""/>
+ <packagemethods title=""/>
+ <packagestaticmethods title=""/>
+ <packageattributes title=""/>
+ <packagestaticattributes title=""/>
+ <properties title=""/>
+ <events title=""/>
+ <privatetypes title=""/>
+ <privateslots title=""/>
+ <privatemethods title=""/>
+ <privatestaticmethods title=""/>
+ <privateattributes title=""/>
+ <privatestaticattributes title=""/>
+ <friends title=""/>
+ <related title="" subtitle=""/>
+ <membergroups visible="yes"/>
+ </memberdecl>
+ <memberdef>
+ <inlineclasses title=""/>
+ <typedefs title=""/>
+ <enums title=""/>
+ <services title=""/>
+ <interfaces title=""/>
+ <constructors title=""/>
+ <functions title=""/>
+ <related title=""/>
+ <variables title=""/>
+ <properties title=""/>
+ <events title=""/>
+ </memberdef>
+ <allmemberslink visible="yes"/>
+ <usedfiles visible="$SHOW_USED_FILES"/>
+ <authorsection visible="yes"/>
+ </class>
+
+ <!-- Layout definition for a namespace page -->
+ <namespace>
+ <briefdescription visible="yes"/>
+ <detaileddescription title="Description"/>
+ <memberdecl>
+ <nestednamespaces visible="yes" title=""/>
+ <constantgroups visible="yes" title=""/>
+ <classes visible="yes" title=""/>
+ <typedefs title=""/>
+ <enums title=""/>
+ <functions title=""/>
+ <variables title=""/>
+ <membergroups visible="yes"/>
+ </memberdecl>
+ <memberdef>
+ <inlineclasses title=""/>
+ <typedefs title=""/>
+ <enums title=""/>
+ <functions title=""/>
+ <variables title=""/>
+ </memberdef>
+ <authorsection visible="yes"/>
+ </namespace>
+
+ <!-- Layout definition for a file page -->
+ <file>
+ <briefdescription visible="yes"/>
+ <includes visible="$SHOW_INCLUDE_FILES"/>
+ <sourcelink visible="yes"/>
+ <detaileddescription title="Description"/>
+ <memberdecl>
+ <classes visible="yes" title=""/>
+ <namespaces visible="yes" title=""/>
+ <constantgroups visible="yes" title=""/>
+ <defines title=""/>
+ <typedefs title=""/>
+ <enums title=""/>
+ <functions title=""/>
+ <variables title=""/>
+ <membergroups visible="yes"/>
+ </memberdecl>
+ <memberdef>
+ <inlineclasses title=""/>
+ <defines title=""/>
+ <typedefs title=""/>
+ <enums title=""/>
+ <functions title=""/>
+ <variables title=""/>
+ </memberdef>
+ <includegraph visible="yes"/>
+ <includedbygraph visible="yes"/>
+ <authorsection/>
+ </file>
+
+ <!-- Layout definition for a group page -->
+ <group>
+ <briefdescription visible="yes"/>
+ <groupgraph visible="no"/>
+ <detaileddescription title="Description"/>
+ <memberdecl>
+ <nestedgroups visible="yes" title=""/>
+ <dirs visible="yes" title=""/>
+ <files visible="yes" title=""/>
+ <namespaces visible="yes" title=""/>
+ <classes visible="yes" title=""/>
+ <defines title=""/>
+ <typedefs title=""/>
+ <enums title=""/>
+ <enumvalues title=""/>
+ <functions title=""/>
+ <variables title=""/>
+ <signals title=""/>
+ <publicslots title=""/>
+ <protectedslots title=""/>
+ <privateslots title=""/>
+ <events title=""/>
+ <properties title=""/>
+ <friends title=""/>
+ <membergroups visible="yes"/>
+ </memberdecl>
+ <memberdef>
+ <pagedocs/>
+ <inlineclasses title=""/>
+ <defines title=""/>
+ <typedefs title=""/>
+ <enums title=""/>
+ <enumvalues title=""/>
+ <functions title=""/>
+ <variables title=""/>
+ <signals title=""/>
+ <publicslots title=""/>
+ <protectedslots title=""/>
+ <privateslots title=""/>
+ <events title=""/>
+ <properties title=""/>
+ <friends title=""/>
+ </memberdef>
+ <authorsection visible="yes"/>
+ </group>
+
+ <!-- Layout definition for a directory page -->
+ <directory>
+ <briefdescription visible="yes"/>
+ <directorygraph visible="no"/>
+ <detaileddescription title="Description"/>
+ <memberdecl>
+ <dirs visible="yes"/>
+ <files visible="yes"/>
+ </memberdecl>
+ </directory>
+</doxygenlayout>
diff --git a/doc/doxygen/Doxylocal b/doc/doxygen/Doxylocal
index b45d87babb0442b42f01e48e74a0a31e22bd4eba..578d304befd7b6ae2242e3508d92593f68533a0c 100644
--- a/doc/doxygen/Doxylocal
+++ b/doc/doxygen/Doxylocal
@@ -19,19 +19,27 @@ IMAGE_PATH = @srcdir@/images
EXTRA_PACKAGES += amsmath,amssymb,units
-EXCLUDE_PATTERNS =
+LAYOUT_FILE = @srcdir@/DoxygenDumuxLayout.xml
-ALIASES += "warning=\xrefitem warning \"Warning List\" \"Warning List\""
+HTML_EXTRA_STYLESHEET = @srcdir@/customdoxygendumux.css
+
+HTML_COLORSTYLE_HUE = 37
+
+HTML_COLORSTYLE_SAT = 206
+
+EXCLUDE_PATTERNS =
+
+ALIASES += "warning=\xrefitem warning \"Warning List\" \"Warning List\""
# enable client side searching
SEARCHENGINE = YES
SERVER_BASED_SEARCH = NO
# the bibliography file used for the doxygen documentation
-CITE_BIB_FILES = @top_srcdir@/doc/handbook/dumux-handbook.bib
+CITE_BIB_FILES = @top_srcdir@/doc/handbook/dumux-handbook.bib
# enable macro expansion only for specified macros
MACRO_EXPANSION = YES
EXPAND_ONLY_PREDEF = YES
-PREDEFINED += "DUNE_DEPRECATED:=/** \deprecated */" \
+PREDEFINED += "DUNE_DEPRECATED:=/** \deprecated */" \
"DUNE_DEPRECATED_MSG(A):=/** \deprecated A */"
diff --git a/doc/doxygen/customdoxygendumux.css b/doc/doxygen/customdoxygendumux.css
new file mode 100644
index 0000000000000000000000000000000000000000..3cd19f7d80bb465e684312550be401652ed1b07e
--- /dev/null
+++ b/doc/doxygen/customdoxygendumux.css
@@ -0,0 +1,1596 @@
+/* The standard CSS for doxygen 1.8.13 */
+
+body, table, div, p, dl {
+ font: 400 14px/22px Roboto,sans-serif;
+}
+
+p.reference, p.definition {
+ font: 400 14px/22px Roboto,sans-serif;
+}
+
+/* @group Heading Levels */
+
+h1.groupheader {
+ font-size: 150%;
+}
+
+.title {
+ font: 400 14px/28px Roboto,sans-serif;
+ font-size: 150%;
+ font-weight: bold;
+ margin: 10px 2px;
+}
+
+h2.groupheader {
+ border-bottom: 1px solid #879ECB;
+ color: #354C7B;
+ font-size: 150%;
+ font-weight: normal;
+ margin-top: 1.75em;
+ padding-top: 8px;
+ padding-bottom: 4px;
+ width: 100%;
+}
+
+h3.groupheader {
+ font-size: 100%;
+}
+
+h1, h2, h3, h4, h5, h6 {
+ -webkit-transition: text-shadow 0.5s linear;
+ -moz-transition: text-shadow 0.5s linear;
+ -ms-transition: text-shadow 0.5s linear;
+ -o-transition: text-shadow 0.5s linear;
+ transition: text-shadow 0.5s linear;
+ margin-right: 15px;
+}
+
+h1.glow, h2.glow, h3.glow, h4.glow, h5.glow, h6.glow {
+ text-shadow: 0 0 15px cyan;
+}
+
+dt {
+ font-weight: bold;
+}
+
+div.multicol {
+ -moz-column-gap: 1em;
+ -webkit-column-gap: 1em;
+ -moz-column-count: 3;
+ -webkit-column-count: 3;
+}
+
+p.startli, p.startdd {
+ margin-top: 2px;
+}
+
+p.starttd {
+ margin-top: 0px;
+}
+
+p.endli {
+ margin-bottom: 0px;
+}
+
+p.enddd {
+ margin-bottom: 4px;
+}
+
+p.endtd {
+ margin-bottom: 2px;
+}
+
+/* @end */
+
+caption {
+ font-weight: bold;
+}
+
+span.legend {
+ font-size: 70%;
+ text-align: center;
+}
+
+h3.version {
+ font-size: 90%;
+ text-align: center;
+}
+
+div.qindex, div.navtab{
+ background-color: #EBEFF6;
+ border: 1px solid #A3B4D7;
+ text-align: center;
+}
+
+div.qindex, div.navpath {
+ width: 100%;
+ line-height: 140%;
+}
+
+div.navtab {
+ margin-right: 15px;
+}
+
+/* @group Link Styling */
+
+a {
+ color: #3D578C;
+ font-weight: normal;
+ text-decoration: none;
+}
+
+.contents a:visited {
+ color: #4665A2;
+}
+
+a:hover {
+ text-decoration: underline;
+}
+
+a.qindex {
+ font-weight: bold;
+}
+
+a.qindexHL {
+ font-weight: bold;
+ background-color: #ffcd78;
+ color: #ffffff;
+ border: 1px double #f5bf5b;
+}
+
+.contents a.qindexHL:visited {
+ color: #ffffff;
+}
+
+a.el {
+ font-weight: bold;
+}
+
+a.elRef {
+}
+
+a.code, a.code:visited, a.line, a.line:visited {
+ color: #4665A2;
+}
+
+a.codeRef, a.codeRef:visited, a.lineRef, a.lineRef:visited {
+ color: #4665A2;
+}
+
+/* @end */
+
+dl.el {
+ margin-left: -1cm;
+}
+
+pre.fragment {
+ border: 1px solid #C4CFE5;
+ background-color: #FBFCFD;
+ padding: 4px 6px;
+ margin: 4px 8px 4px 2px;
+ overflow: auto;
+ word-wrap: break-word;
+ font-size: 9pt;
+ line-height: 125%;
+ font-family: monospace, fixed;
+ font-size: 105%;
+}
+
+div.fragment {
+ padding: 0px;
+ margin: 4px 8px 4px 2px;
+ background-color: #FBFCFD;
+ border: 1px solid #C4CFE5;
+}
+
+div.line {
+ font-family: monospace, fixed;
+ font-size: 13px;
+ min-height: 13px;
+ line-height: 1.0;
+ text-wrap: unrestricted;
+ white-space: -moz-pre-wrap; /* Moz */
+ white-space: -pre-wrap; /* Opera 4-6 */
+ white-space: -o-pre-wrap; /* Opera 7 */
+ white-space: pre-wrap; /* CSS3 */
+ word-wrap: break-word; /* IE 5.5+ */
+ text-indent: -53px;
+ padding-left: 53px;
+ padding-bottom: 0px;
+ margin: 0px;
+ -webkit-transition-property: background-color, box-shadow;
+ -webkit-transition-duration: 0.5s;
+ -moz-transition-property: background-color, box-shadow;
+ -moz-transition-duration: 0.5s;
+ -ms-transition-property: background-color, box-shadow;
+ -ms-transition-duration: 0.5s;
+ -o-transition-property: background-color, box-shadow;
+ -o-transition-duration: 0.5s;
+ transition-property: background-color, box-shadow;
+ transition-duration: 0.5s;
+}
+
+div.line:after {
+ content:"\000A";
+ white-space: pre;
+}
+
+div.line.glow {
+ background-color: cyan;
+ box-shadow: 0 0 10px cyan;
+}
+
+
+span.lineno {
+ padding-right: 4px;
+ text-align: right;
+ border-right: 2px solid #0F0;
+ background-color: #E8E8E8;
+ white-space: pre;
+}
+span.lineno a {
+ background-color: #D8D8D8;
+}
+
+span.lineno a:hover {
+ background-color: #C8C8C8;
+}
+
+.lineno {
+ -webkit-touch-callout: none;
+ -webkit-user-select: none;
+ -khtml-user-select: none;
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+ -ms-user-select: none;
+ user-select: none;
+}
+
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+ font-weight: bold;
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+}
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+}
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+}
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+}
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+ margin-left: 16px;
+ font-style: italic;
+}
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+}
+
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+ margin-top: 10px;
+ margin-left: 12px;
+ margin-right: 8px;
+}
+
+td.indexkey {
+ background-color: #EBEFF6;
+ font-weight: bold;
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+ margin: 2px 0px 2px 0;
+ padding: 2px 10px;
+ white-space: nowrap;
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+}
+
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+ border: 1px solid #C4CFE5;
+ padding: 2px 10px;
+ margin: 2px 0px;
+}
+
+tr.memlist {
+ background-color: #EEF1F7;
+}
+
+p.formulaDsp {
+ text-align: center;
+}
+
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+
+}
+
+img.formulaInl {
+ vertical-align: middle;
+}
+
+div.center {
+ text-align: center;
+ margin-top: 0px;
+ margin-bottom: 0px;
+ padding: 0px;
+}
+
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+ border: 0px;
+}
+
+address.footer {
+ text-align: right;
+ padding-right: 12px;
+}
+
+img.footer {
+ border: 0px;
+ vertical-align: middle;
+}
+
+/* @group Code Colorization */
+
+span.keyword {
+ color: #008000
+}
+
+span.keywordtype {
+ color: #604020
+}
+
+span.keywordflow {
+ color: #e08000
+}
+
+span.comment {
+ color: #800000
+}
+
+span.preprocessor {
+ color: #806020
+}
+
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+ color: #002080
+}
+
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+}
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+}
+
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+}
+
+span.vhdlkeyword {
+ color: #700070
+}
+
+span.vhdllogic {
+ color: #ff0000
+}
+
+blockquote {
+ background-color: #fefaf5;
+ border-left: 2px solid #f7cb78;
+ margin: 0 24px 0 4px;
+ padding: 0 12px 0 16px;
+}
+
+/* @end */
+
+/*
+.search {
+ color: #003399;
+ font-weight: bold;
+}
+
+form.search {
+ margin-bottom: 0px;
+ margin-top: 0px;
+}
+
+input.search {
+ font-size: 75%;
+ color: #000080;
+ font-weight: normal;
+ background-color: #e8eef2;
+}
+*/
+
+td.tiny {
+ font-size: 75%;
+}
+
+.dirtab {
+ padding: 4px;
+ border-collapse: collapse;
+ border: 1px solid #A3B4D7;
+}
+
+th.dirtab {
+ background: #EBEFF6;
+ font-weight: bold;
+}
+
+hr {
+ height: 0px;
+ border: none;
+ border-top: 1px solid #4A6AAA;
+}
+
+hr.footer {
+ height: 1px;
+}
+
+/* @group Member Descriptions */
+
+table.memberdecls {
+ border-spacing: 0px;
+ padding: 0px;
+}
+
+.memberdecls td, .fieldtable tr {
+ -webkit-transition-property: background-color, box-shadow;
+ -webkit-transition-duration: 0.5s;
+ -moz-transition-property: background-color, box-shadow;
+ -moz-transition-duration: 0.5s;
+ -ms-transition-property: background-color, box-shadow;
+ -ms-transition-duration: 0.5s;
+ -o-transition-property: background-color, box-shadow;
+ -o-transition-duration: 0.5s;
+ transition-property: background-color, box-shadow;
+ transition-duration: 0.5s;
+}
+
+.memberdecls td.glow, .fieldtable tr.glow {
+ background-color: cyan;
+ box-shadow: 0 0 15px cyan;
+}
+
+.mdescLeft, .mdescRight,
+.memItemLeft, .memItemRight,
+.memTemplItemLeft, .memTemplItemRight, .memTemplParams {
+ background-color: #fefbf5;
+ border: none;
+ margin: 4px;
+ padding: 1px 0 0 8px;
+}
+
+.mdescLeft, .mdescRight {
+ padding: 0px 8px 4px 8px;
+ color: #555;
+}
+
+.memSeparator {
+ border-bottom: 1px solid #DEE4F0;
+ line-height: 1px;
+ margin: 0px;
+ padding: 0px;
+}
+
+.memItemLeft, .memTemplItemLeft {
+ white-space: nowrap;
+}
+
+.memItemRight {
+ width: 100%;
+}
+
+.memTemplParams {
+ color: #4665A2;
+ white-space: nowrap;
+ font-size: 80%;
+}
+
+/* @end */
+
+/* @group Member Details */
+
+/* Styles for detailed member documentation */
+
+.memtitle {
+ padding: 8px;
+ border-top: 1px solid #A8B8D9;
+ border-left: 1px solid #A8B8D9;
+ border-right: 1px solid #A8B8D9;
+ border-top-right-radius: 4px;
+ border-top-left-radius: 4px;
+ margin-bottom: -1px;
+ background-image: url('nav_f.png');
+ background-repeat: repeat-x;
+ background-color: #fdf0d8;
+ line-height: 1.25;
+ font-weight: 300;
+ float:left;
+}
+
+.permalink
+{
+ font-size: 65%;
+ display: inline-block;
+ vertical-align: middle;
+}
+
+.memtemplate {
+ font-size: 80%;
+ color: #4665A2;
+ font-weight: normal;
+ margin-left: 9px;
+}
+
+.memnav {
+ background-color: #EBEFF6;
+ border: 1px solid #A3B4D7;
+ text-align: center;
+ margin: 2px;
+ margin-right: 15px;
+ padding: 2px;
+}
+
+.mempage {
+ width: 100%;
+}
+
+.memitem {
+ padding: 0;
+ margin-bottom: 10px;
+ margin-right: 5px;
+ -webkit-transition: box-shadow 0.5s linear;
+ -moz-transition: box-shadow 0.5s linear;
+ -ms-transition: box-shadow 0.5s linear;
+ -o-transition: box-shadow 0.5s linear;
+ transition: box-shadow 0.5s linear;
+ display: table !important;
+ width: 100%;
+}
+
+.memitem.glow {
+ box-shadow: 0 0 15px cyan;
+}
+
+.memname {
+ font-weight: 400;
+ margin-left: 6px;
+}
+
+.memname td {
+ vertical-align: bottom;
+}
+
+.memproto, dl.reflist dt {
+ border-top: 1px solid #A8B8D9;
+ border-left: 1px solid #A8B8D9;
+ border-right: 1px solid #A8B8D9;
+ padding: 6px 0px 6px 0px;
+ color: #253555;
+ font-weight: bold;
+ text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9);
+ background-color: #fceed4;
+ /* opera specific markup */
+ box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+ border-top-right-radius: 4px;
+ /* firefox specific markup */
+ -moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px;
+ -moz-border-radius-topright: 4px;
+ /* webkit specific markup */
+ -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+ -webkit-border-top-right-radius: 4px;
+
+}
+
+.overload {
+ font-family: "courier new",courier,monospace;
+ font-size: 65%;
+}
+
+.memdoc, dl.reflist dd {
+ border-bottom: 1px solid #f8d087;
+ border-left: 1px solid #f8d087;
+ border-right: 1px solid #f8d087;
+ padding: 6px 10px 2px 10px;
+ background-color: #FBFCFD;
+ border-top-width: 0;
+ background-image:url('nav_g.png');
+ background-repeat:repeat-x;
+ background-color: #FFFFFF;
+ /* opera specific markup */
+ border-bottom-left-radius: 4px;
+ border-bottom-right-radius: 4px;
+ box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+ /* firefox specific markup */
+ -moz-border-radius-bottomleft: 4px;
+ -moz-border-radius-bottomright: 4px;
+ -moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px;
+ /* webkit specific markup */
+ -webkit-border-bottom-left-radius: 4px;
+ -webkit-border-bottom-right-radius: 4px;
+ -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+}
+
+dl.reflist dt {
+ padding: 5px;
+}
+
+dl.reflist dd {
+ margin: 0px 0px 10px 0px;
+ padding: 5px;
+}
+
+.paramkey {
+ text-align: right;
+}
+
+.paramtype {
+ white-space: nowrap;
+}
+
+.paramname {
+ color: #602020;
+ white-space: nowrap;
+}
+.paramname em {
+ font-style: normal;
+}
+.paramname code {
+ line-height: 14px;
+}
+
+.params, .retval, .exception, .tparams {
+ margin-left: 0px;
+ padding-left: 0px;
+}
+
+.params .paramname, .retval .paramname {
+ font-weight: bold;
+ vertical-align: top;
+}
+
+.params .paramtype {
+ font-style: italic;
+ vertical-align: top;
+}
+
+.params .paramdir {
+ font-family: "courier new",courier,monospace;
+ vertical-align: top;
+}
+
+table.mlabels {
+ border-spacing: 0px;
+}
+
+td.mlabels-left {
+ width: 100%;
+ padding: 0px;
+}
+
+td.mlabels-right {
+ vertical-align: bottom;
+ padding: 0px;
+ white-space: nowrap;
+}
+
+span.mlabels {
+ margin-left: 8px;
+}
+
+span.mlabel {
+ background-color: #728DC1;
+ border-top:1px solid #5373B4;
+ border-left:1px solid #5373B4;
+ border-right:1px solid #C4CFE5;
+ border-bottom:1px solid #C4CFE5;
+ text-shadow: none;
+ color: white;
+ margin-right: 4px;
+ padding: 2px 3px;
+ border-radius: 3px;
+ font-size: 7pt;
+ white-space: nowrap;
+ vertical-align: middle;
+}
+
+
+
+/* @end */
+
+/* these are for tree view inside a (index) page */
+
+div.directory {
+ margin: 10px 0px;
+ border-top: 1px solid #98ABD2;
+ border-bottom: 1px solid #98ABD2;
+ width: 100%;
+}
+
+.directory table {
+ border-collapse:collapse;
+}
+
+.directory td {
+ margin: 0px;
+ padding: 0px;
+ vertical-align: top;
+}
+
+.directory td.entry {
+ white-space: nowrap;
+ padding-right: 6px;
+ padding-top: 3px;
+}
+
+.directory td.entry a {
+ outline:none;
+}
+
+.directory td.entry a img {
+ border: none;
+}
+
+.directory td.desc {
+ width: 100%;
+ padding-left: 6px;
+ padding-right: 6px;
+ padding-top: 3px;
+ border-left: 1px solid rgba(0,0,0,0.05);
+}
+
+.directory tr.even {
+ padding-left: 6px;
+ background-color: #fef8ec;
+}
+
+.directory img {
+ vertical-align: -30%;
+}
+
+.directory .levels {
+ white-space: nowrap;
+ width: 100%;
+ text-align: right;
+ font-size: 9pt;
+}
+
+.directory .levels span {
+ cursor: pointer;
+ padding-left: 2px;
+ padding-right: 2px;
+ color: #3D578C;
+}
+
+.arrow {
+ color: #98ABD2;
+ -webkit-user-select: none;
+ -khtml-user-select: none;
+ -moz-user-select: none;
+ -ms-user-select: none;
+ user-select: none;
+ cursor: pointer;
+ font-size: 80%;
+ display: inline-block;
+ width: 16px;
+ height: 22px;
+}
+
+.icon {
+ font-family: Arial, Helvetica;
+ font-weight: bold;
+ font-size: 12px;
+ height: 14px;
+ width: 16px;
+ display: inline-block;
+ background-color: #728DC1;
+ color: white;
+ text-align: center;
+ border-radius: 4px;
+ margin-left: 2px;
+ margin-right: 2px;
+}
+
+.icona {
+ width: 24px;
+ height: 22px;
+ display: inline-block;
+}
+
+.iconfopen {
+ width: 24px;
+ height: 18px;
+ margin-bottom: 4px;
+ background-image:url('folderopen.png');
+ background-position: 0px -4px;
+ background-repeat: repeat-y;
+ vertical-align:top;
+ display: inline-block;
+}
+
+.iconfclosed {
+ width: 24px;
+ height: 18px;
+ margin-bottom: 4px;
+ background-image:url('folderclosed.png');
+ background-position: 0px -4px;
+ background-repeat: repeat-y;
+ vertical-align:top;
+ display: inline-block;
+}
+
+.icondoc {
+ width: 24px;
+ height: 18px;
+ margin-bottom: 4px;
+ background-image:url('doc.png');
+ background-position: 0px -4px;
+ background-repeat: repeat-y;
+ vertical-align:top;
+ display: inline-block;
+}
+
+table.directory {
+ font: 400 14px Roboto,sans-serif;
+}
+
+/* @end */
+
+div.dynheader {
+ margin-top: 8px;
+ -webkit-touch-callout: none;
+ -webkit-user-select: none;
+ -khtml-user-select: none;
+ -moz-user-select: none;
+ -ms-user-select: none;
+ user-select: none;
+}
+
+address {
+ font-style: normal;
+ color: #2A3D61;
+}
+
+table.doxtable caption {
+ caption-side: top;
+}
+
+table.doxtable {
+ border-collapse:collapse;
+ margin-top: 4px;
+ margin-bottom: 4px;
+}
+
+table.doxtable td, table.doxtable th {
+ border: 1px solid #2D4068;
+ padding: 3px 7px 2px;
+}
+
+table.doxtable th {
+ background-color: #cc8500;
+ color: #FFFFFF;
+ font-size: 110%;
+ padding-bottom: 4px;
+ padding-top: 5px;
+}
+
+table.fieldtable {
+ /*width: 100%;*/
+ margin-bottom: 10px;
+ border: 1px solid #f8d087;
+ border-spacing: 0px;
+ -moz-border-radius: 4px;
+ -webkit-border-radius: 4px;
+ border-radius: 4px;
+ -moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px;
+ -webkit-box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);
+ box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);
+}
+
+.fieldtable td, .fieldtable th {
+ padding: 3px 7px 2px;
+}
+
+.fieldtable td.fieldtype, .fieldtable td.fieldname {
+ white-space: nowrap;
+ border-right: 1px solid #f8d087;
+ border-bottom: 1px solid #f8d087;
+ vertical-align: top;
+}
+
+.fieldtable td.fieldname {
+ padding-top: 3px;
+}
+
+.fieldtable td.fielddoc {
+ border-bottom: 1px solid #f8d087;
+ /*width: 100%;*/
+}
+
+.fieldtable td.fielddoc p:first-child {
+ margin-top: 0px;
+}
+
+.fieldtable td.fielddoc p:last-child {
+ margin-bottom: 2px;
+}
+
+.fieldtable tr:last-child td {
+ border-bottom: none;
+}
+
+.fieldtable th {
+ background-image:url('nav_f.png');
+ background-repeat:repeat-x;
+ background-color: #fdf0d8;
+ font-size: 90%;
+ color: #253555;
+ padding-bottom: 4px;
+ padding-top: 5px;
+ text-align:left;
+ font-weight: 400;
+ -moz-border-radius-topleft: 4px;
+ -moz-border-radius-topright: 4px;
+ -webkit-border-top-left-radius: 4px;
+ -webkit-border-top-right-radius: 4px;
+ border-top-left-radius: 4px;
+ border-top-right-radius: 4px;
+ border-bottom: 1px solid #f8d087;
+}
+
+
+.tabsearch {
+ top: 0px;
+ left: 10px;
+ height: 36px;
+ background-image: url('tab_b.png');
+ z-index: 101;
+ overflow: hidden;
+ font-size: 13px;
+}
+
+.navpath ul
+{
+ font-size: 11px;
+ background-image:url('tab_b.png');
+ background-repeat:repeat-x;
+ background-position: 0 -5px;
+ height:30px;
+ line-height:30px;
+ color:#8AA0CC;
+ border:solid 1px #C2CDE4;
+ overflow:hidden;
+ margin:0px;
+ padding:0px;
+}
+
+.navpath li
+{
+ list-style-type:none;
+ float:left;
+ padding-left:10px;
+ padding-right:15px;
+ background-image:url('bc_s.png');
+ background-repeat:no-repeat;
+ background-position:right;
+ color:#364D7C;
+}
+
+.navpath li.navelem a
+{
+ height:32px;
+ display:block;
+ text-decoration: none;
+ outline: none;
+ color: #283A5D;
+ font-family: 'Lucida Grande',Geneva,Helvetica,Arial,sans-serif;
+ text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9);
+ text-decoration: none;
+}
+
+.navpath li.navelem a:hover
+{
+ color:#6884BD;
+}
+
+.navpath li.footer
+{
+ list-style-type:none;
+ float:right;
+ padding-left:10px;
+ padding-right:15px;
+ background-image:none;
+ background-repeat:no-repeat;
+ background-position:right;
+ color:#364D7C;
+ font-size: 8pt;
+}
+
+
+div.summary
+{
+ float: right;
+ font-size: 8pt;
+ padding-right: 5px;
+ width: 50%;
+ text-align: right;
+}
+
+div.summary a
+{
+ white-space: nowrap;
+}
+
+table.classindex
+{
+ margin: 10px;
+ white-space: nowrap;
+ margin-left: 3%;
+ margin-right: 3%;
+ width: 94%;
+ border: 0;
+ border-spacing: 0;
+ padding: 0;
+}
+
+div.ingroups
+{
+ font-size: 8pt;
+ width: 50%;
+ text-align: left;
+}
+
+div.ingroups a
+{
+ white-space: nowrap;
+}
+
+div.header
+{
+ background-image:url('nav_h.png');
+ background-repeat:repeat-x;
+ background-color: #fefbf5;
+ margin: 0px;
+ border-bottom: 1px solid #C4CFE5;
+}
+
+div.headertitle
+{
+ padding: 5px 5px 5px 10px;
+}
+
+dl
+{
+ padding: 0 0 0 10px;
+}
+
+/* dl.note, dl.warning, dl.attention, dl.pre, dl.post, dl.invariant, dl.deprecated, dl.todo, dl.test, dl.bug */
+dl.section
+{
+ margin-left: 0px;
+ padding-left: 0px;
+}
+
+dl.note
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #D0C000;
+}
+
+dl.warning, dl.attention
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #FF0000;
+}
+
+dl.pre, dl.post, dl.invariant
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #00D000;
+}
+
+dl.deprecated
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #505050;
+}
+
+dl.todo
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #00C0E0;
+}
+
+dl.test
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #3030E0;
+}
+
+dl.bug
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #C08050;
+}
+
+dl.section dd {
+ margin-bottom: 6px;
+}
+
+
+#projectlogo
+{
+ text-align: center;
+ vertical-align: bottom;
+ border-collapse: separate;
+}
+
+#projectlogo img
+{
+ border: 0px none;
+}
+
+#projectalign
+{
+ vertical-align: middle;
+}
+
+#projectname
+{
+ font: 300% Tahoma, Arial,sans-serif;
+ margin: 0px;
+ padding: 2px 0px;
+}
+
+#projectbrief
+{
+ font: 120% Tahoma, Arial,sans-serif;
+ margin: 0px;
+ padding: 0px;
+}
+
+#projectnumber
+{
+ font: 50% Tahoma, Arial,sans-serif;
+ margin: 0px;
+ padding: 0px;
+}
+
+#titlearea
+{
+ padding: 0px;
+ margin: 0px;
+ width: 100%;
+ border-bottom: 1px solid #5373B4;
+}
+
+.image
+{
+ text-align: center;
+}
+
+.dotgraph
+{
+ text-align: center;
+}
+
+.mscgraph
+{
+ text-align: center;
+}
+
+.plantumlgraph
+{
+ text-align: center;
+}
+
+.diagraph
+{
+ text-align: center;
+}
+
+.caption
+{
+ font-weight: bold;
+}
+
+div.zoom
+{
+ border: 1px solid #f6c56a;
+}
+
+dl.citelist {
+ margin-bottom:50px;
+}
+
+dl.citelist dt {
+ color:#334975;
+ float:left;
+ font-weight:bold;
+ margin-right:10px;
+ padding:5px;
+}
+
+dl.citelist dd {
+ margin:2px 0;
+ padding:5px 0;
+}
+
+div.toc {
+ padding: 14px 25px;
+ background-color: #F4F6FA;
+ border: 1px solid #D8DFEE;
+ border-radius: 7px 7px 7px 7px;
+ float: right;
+ height: auto;
+ margin: 0 8px 10px 10px;
+ width: 200px;
+}
+
+div.toc li {
+ background: url("bdwn.png") no-repeat scroll 0 5px transparent;
+ font: 10px/1.2 Verdana,DejaVu Sans,Geneva,sans-serif;
+ margin-top: 5px;
+ padding-left: 10px;
+ padding-top: 2px;
+}
+
+div.toc h3 {
+ font: bold 12px/1.2 Arial,FreeSans,sans-serif;
+ color: #4665A2;
+ border-bottom: 0 none;
+ margin: 0;
+}
+
+div.toc ul {
+ list-style: none outside none;
+ border: medium none;
+ padding: 0px;
+}
+
+div.toc li.level1 {
+ margin-left: 0px;
+}
+
+div.toc li.level2 {
+ margin-left: 15px;
+}
+
+div.toc li.level3 {
+ margin-left: 30px;
+}
+
+div.toc li.level4 {
+ margin-left: 45px;
+}
+
+.inherit_header {
+ font-weight: bold;
+ color: gray;
+ cursor: pointer;
+ -webkit-touch-callout: none;
+ -webkit-user-select: none;
+ -khtml-user-select: none;
+ -moz-user-select: none;
+ -ms-user-select: none;
+ user-select: none;
+}
+
+.inherit_header td {
+ padding: 6px 0px 2px 5px;
+}
+
+.inherit {
+ display: none;
+}
+
+tr.heading h2 {
+ margin-top: 12px;
+ margin-bottom: 4px;
+}
+
+/* tooltip related style info */
+
+.ttc {
+ position: absolute;
+ display: none;
+}
+
+#powerTip {
+ cursor: default;
+ white-space: nowrap;
+ background-color: white;
+ border: 1px solid gray;
+ border-radius: 4px 4px 4px 4px;
+ box-shadow: 1px 1px 7px gray;
+ display: none;
+ font-size: smaller;
+ max-width: 80%;
+ opacity: 0.9;
+ padding: 1ex 1em 1em;
+ position: absolute;
+ z-index: 2147483647;
+}
+
+#powerTip div.ttdoc {
+ color: grey;
+ font-style: italic;
+}
+
+#powerTip div.ttname a {
+ font-weight: bold;
+}
+
+#powerTip div.ttname {
+ font-weight: bold;
+}
+
+#powerTip div.ttdeci {
+ color: #006318;
+}
+
+#powerTip div {
+ margin: 0px;
+ padding: 0px;
+ font: 12px/16px Roboto,sans-serif;
+}
+
+#powerTip:before, #powerTip:after {
+ content: "";
+ position: absolute;
+ margin: 0px;
+}
+
+#powerTip.n:after, #powerTip.n:before,
+#powerTip.s:after, #powerTip.s:before,
+#powerTip.w:after, #powerTip.w:before,
+#powerTip.e:after, #powerTip.e:before,
+#powerTip.ne:after, #powerTip.ne:before,
+#powerTip.se:after, #powerTip.se:before,
+#powerTip.nw:after, #powerTip.nw:before,
+#powerTip.sw:after, #powerTip.sw:before {
+ border: solid transparent;
+ content: " ";
+ height: 0;
+ width: 0;
+ position: absolute;
+}
+
+#powerTip.n:after, #powerTip.s:after,
+#powerTip.w:after, #powerTip.e:after,
+#powerTip.nw:after, #powerTip.ne:after,
+#powerTip.sw:after, #powerTip.se:after {
+ border-color: rgba(255, 255, 255, 0);
+}
+
+#powerTip.n:before, #powerTip.s:before,
+#powerTip.w:before, #powerTip.e:before,
+#powerTip.nw:before, #powerTip.ne:before,
+#powerTip.sw:before, #powerTip.se:before {
+ border-color: rgba(128, 128, 128, 0);
+}
+
+#powerTip.n:after, #powerTip.n:before,
+#powerTip.ne:after, #powerTip.ne:before,
+#powerTip.nw:after, #powerTip.nw:before {
+ top: 100%;
+}
+
+#powerTip.n:after, #powerTip.ne:after, #powerTip.nw:after {
+ border-top-color: #ffffff;
+ border-width: 10px;
+ margin: 0px -10px;
+}
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diff --git a/doc/doxygen/extradoc/parameterlist.txt b/doc/doxygen/extradoc/parameterlist.txt
index 130e603aec960bbba3add9e6a8f38da93641ca3e..e53848e39bf36a05a4b2883ae02fb166df7082a5 100644
--- a/doc/doxygen/extradoc/parameterlist.txt
+++ b/doc/doxygen/extradoc/parameterlist.txt
@@ -8,138 +8,107 @@
* but we point out that a certain model might not be able
* to use every parameter!
*
- * | Group | Parameter | Type | Default Value | Explanation |
- * | :- | :- | :- | :- | :-
- * | - | ParameterFile | std::string | executable.input | name of the parameter file |
- * | \b BoundaryLayer | Model | int | 0 | 0 for none, 1 Blasius, 2 and 3 turbulent BL, 9 constant thickness |
- * | | ConstThickness | Scalar | - | constant BL thickness (BL model 9) |
- * | | Offset | Scalar | - | virtual run-up distance for BL models |
- * | | RoughnessLength | Scalar | - | Equivalent sand grain roughness [m] |
- * | | YPlus | Scalar | - | Conversion factor between dimensionless wall distance y^+ and actual wall distance |
- * | \b FreeFlow | RefMassfrac | Scalar | - | free stream water vapor mass fraction |
- * | | RefTemperature | Scalar | - | free stream temperature |
- * | | RefVelocity | Scalar | - | free stream velocity |
- * | \b Grid | File | std::string | - | name of the grid file, if a corresponding GridCreator is used |
- * | | InterfacePosX | Scalar | 0.0 | x-coordinate of the refinement point/line (only Interface-GridCreator) |
- * | | InterfacePosY | Scalar | 0.0 | y-coordinate of the refinement point/line (only Interface-GridCreator) |
- * | | LowerLeft | globalPosition | - | coordinates of the lower front left corner for the Cube/Simplex/Interface-GridCreator |
- * | | Cells | globalPosition | - | number of cells in respective coordinate directions for the Cube/SimplexGridCreator |
- * | | RefineTopX | bool | false | Refine to the right of the domain (only Interface-GridCreator) |
- * | | RefineTopY | bool | false | Refine to the top of the domain (only Interface-GridCreator) |
- * | | UpperRight | globalPosition | - | coordinates of the upper back right corner for the Cube/Simplex/Interface-GridCreator |
- * | \b GridAdapt | AdaptionInterval | int | 1 | time step interval for adaption |
- * | | CoarsenPercentileFlux | Scalar | 0.2 | percentile of cells coarsened because of flux criterion |
- * | | CoarsenPercentileSat | Scalar | 0.2 | percentile of cells coarsened because of saturation criterion |
- * | | CoarsenThresholdFlux | Scalar | 0.2 | flux threshold for coarsening cells |
- * | | CoarsenThresholdSat | Scalar | 0.2 | saturation threshold for coarsening cells |
- * | | CoarsenTolerance | Scalar | 0.001 | tolerance for coarsening |
- * | | EnableInitializationIndicator | bool | false | switch the use of initial grid adaption on/off |
- * | | EnableMultiPointFluxApproximation | bool | true | hangingNode: Two-point flux approximation (false) or MPFA (true) |
- * | | MaxInteractionVolumes | int | 4 | maximum number of interaction regions used |
- * | | MaxLevel | int | 1 | maximum allowed level |
- * | | MinLevel | int | 0 | mimimum allowed level |
- * | | RefineAtDirichletBC | bool | false | switch for refinement at Dirichlet BC's -> not used by all indicators! |
- * | | RefineAtFluxBC | bool | false | switch for refinement at Neumann BC's -> not used by all indicators! |
- * | | RefineAtSource | bool | false | switch for refinement at sources -> not used by all indicators! |
- * | | RefinePercentileFlux | Scalar | 0.8 | percentile of cells refined because of flux criterion |
- * | | RefinePercentileSat | Scalar | 0.8 | percentile of cells refined because of saturation criterion |
- * | | RefineThresholdFlux | Scalar | 0.8 | flux threshold for refining cells |
- * | | RefineThresholdSat | Scalar | 0.8 | saturation threshold for refining cells |
- * | | RefineTolerance | Scalar | 0.05 | tolerance for refinement |
- * | \b Impet | CFLFactor | Scalar | 1 | scalar factor for additional scaling of the time step |
- * | | DtVariationRestrictionFactor | Scalar | std::numeric_limits<double>::max() | |
- * | | EnableVolumeIntegral | bool | true | enables volume integral in the pressure equation (volume balance formulation) |
- * | | ErrorTermFactor | Scalar | 0.5 | scaling factor for the error term |
- * | | ErrorTermLowerBound | Scalar | 0.1 (2p), 0.2 (2p2c) | lower threshold used for the error term evaluation |
- * | | ErrorTermUpperBound | Scalar | 0.9 | upper threshold used for the error term evaluation |
- * | | IterationFlag | int | 0 | 0 = no iterations, 1 = iterate IterationNumber iterations, 2 = iterate until converged or IterationNumber is reached |
- * | | IterationNumber | int | 2 | number of iterations if IMPET iterations are enabled by the IterationFlags |
- * | | MaximumDefect | Scalar | 1.00E-005 | maximum Defect if IMPET iterations are enabled by the IterationFlags |
- * | | PorosityThreshold | Scalar | 1e-6 | |
- * | | RelaxationFactor | Scalar | 1 | 1 = new solution is new solution, 0 = old solution is new solution |
- * | | RestrictFluxInTransport | int | 0 | restrict flux if direction reverses after pressure equation |
- * | | SubCFLFactor | Scalar | 1 | CFL factor for local time-stepping |
- * | | SwitchNormals | bool | false | |
- * | \b Implicit | EnableHints | bool | false | use the already calculated solutions as starting values of the volume variables |
- * | | EnableJacobianRecycling | bool | false | specify whether the jacobian matrix of the last iteration of a time step should be reused |
- * | | EnablePartialReassemble | bool | false | specify whether the jacobian matrix should be only reassembled for elements where at least one vertex is above the specified tolerance |
- * | | EnableSmoothUpwinding | bool | false | use the smooth upwinding method (MPNC only) |
- * | | MassUpwindWeight | Scalar | 1 (0.5 for 1p) | value of the weight of the upwind direction in the mass conservation equations |
- * | | MaxTimeStepDivisions | int | 10 | |
- * | | MobilityUpwindWeight | Scalar | 1 (0.5 for 1p) | weight for the upwind mobility in the velocity calculation |
- * | | NumericDifferenceMethod | int | 1 | which kind of method should be used to numerically calculate the partial derivatives of the residual (1: forward, 0: central, -1: backward) |
- * | | UseTwoPointFlux | bool | false | indicates whether two-point flux should be used |
- * | | WithStabilization | bool | true | |
- * | \b LinearSolver | GMResRestart | int | 10 | restart parameter for GMRes |
- * | | MaxIterations | double | 250 (imp), 500 (dec) | maximum number of iterations of solver |
- * | | PreconditionerIterations | int | 1 | number of preconditioner iterations per solver iteration |
- * | | PreconditionerRelaxation | double | 1 | relaxation parameter for the preconditioner |
- * | | ResidualReduction | double | 1e-6 (imp), 1e-13 (dec) | target reduction of the initial residual |
- * | | Verbosity | int | 0 | specifies the verbosity of the linear solver |
- * | \b MassTransfer | Model | int | 0 | 0 for none, 1 power law, 2 Schluender model |
- * | | CharPoreRadius | Scalar | - | parameter for Schluender mass-transfer model |
- * | | Coefficient | Scalar | - | mass transfer coefficient for S^MTC |
- * | \b MPFA | CalcVelocityInTransport | bool | false | enable facewise velocity calculation in the transport step (less efficient!) |
- * | | EnableComplexLStencil | bool | true | enable use of the two more complex (non-centered) L-shapes (3-d) |
- * | | EnableSimpleLStencil | bool | true | enable use of the two simpler (centered) L-shapes (3-d) |
- * | | EnableTPFA | bool | false | enable use of TPFA (3-d) if neighboring cells are of the same grid level |
- * | | TransmissibilityCriterion | int | 0 | 0 = default criterion, 1 = accumulative criterion |
- * | | TransmissibilityCriterionThreshold | Scalar | 1e-8 | threshold for transmissibility choice |
- * | \b Newton | EnableChop | bool | true | chop the Newton update at the beginning of the non-linear solver (MPNC only) |
- * | | EnableResidualCriterion | bool | false | declare convergence if the initial residual is reduced by the factor ResidualReduction |
- * | | EnableShiftCriterion | bool | true | declare convergence if the primary variables differ by a maximum of MaxRelativeShift |
- * | | MaxRelativeShift | Scalar | 1e-8 | tolerance for the shift criterion |
- * | | MaxSteps | int | 18 | number of maximum iterations for the Newton method |
- * | | MaxTimeStepDivisions | int | 10 | |
- * | | ResidualReduction | Scalar | 1e-5 | tolerance for the residual criterion |
- * | | SatisfyResidualAndShiftCriterion | bool | false | declare convergence only if both criteria are met |
- * | | TargetSteps | int | 10 | number of iterations at which the Newton method should aim at |
- * | | UseLineSearch | bool | false | specifies whether the update should be done using line search |
- * | | WriteConvergence | bool | false | specifies whether the convergence rate and the global residual gets written out to disk for every Newton iteration |
- * | \b Pardiso | NumProcessors | int | - | |
- * | \b Problem | EnableGravity | bool | true | returns whether gravity is considered in the problem |
- * | | GasDensity | Scalar | - | The density of the gas (only components/constant.hh) |
- * | | GasKinematicViscosity | Scalar | - | The kinematic viscosity of the gas (only components/constant.hh) |
- * | | LiquidDensity | Scalar | - | The density of the liquid (only components/constant.hh) |
- * | | LiquidKinematicViscosity | Scalar | - | The kinematic viscosity of the liquid (only components/constant.hh) |
- * | | Name | std::string | - | The name of the current problem, used for output |
- * | | Salinity | Scalar | 1e-3 | |
- * | \b SpatialParams | ForchCoeff | Scalar | 0.55 | property for the forchheimer coefficient |
- * | \b Stokes | StabilizationAlpha | Scalar | 0 | parameter for the stabilization |
- * | | StabilizationBeta | Scalar | 0 | parameter for the stabilization at boundaries |
- * | \b TimeManager | DtInitial | Scalar | - | initial time step size |
- * | | MaxTimeStepSize | Scalar | 1.00E+100 | maximum time step size |
- * | | PrintParameters | bool | true | print used and unused parameters and their values at the end of the simulation |
- * | | PrintProperties | bool | false | print used properties and their values at the end of the simulation |
- * | | Restart | Scalar | false | use the restart mechanism |
- * | | SubTimestepVerbosity | int | 0 | |
- * | | TEnd | Scalar | - | the final time until the simulation should run |
- * | \b Vtk | AddAverageMolarMass | bool | false | add average molar mass to output (MPNC only) |
- * | | AddBoundaryTypes | bool | false | add boundary types to output (MPNC only) |
- * | | AddDeltaP | bool | false | output of pressure minus a fixed value |
- * | | AddDensities | bool | true | add densities to output (MPNC only) |
- * | | AddEnthalpies | bool | true | add enthalpies to output (MPNC only) |
- * | | AddFugacities | bool | false | add fugacities to output (MPNC only) |
- * | | AddInternalEnergies | bool | false | add internal energies to output (MPNC only) |
- * | | AddMassFractions | bool | false | add mass fractions to output (MPNC only) |
- * | | AddMobilities | bool | true | add mobilities to output (MPNC only) |
- * | | AddMolarities | bool | false | add molarities to output (MPNC only) |
- * | | AddMoleFractions | bool | true | add mole fractions to output (MPNC only) |
- * | | AddPermeability | bool | false | |
- * | | AddPorosity | bool | true | add porosity to output (MPNC only) |
- * | | AddPressures | bool | true | add pressures to output (MPNC only) |
- * | | AddSaturations | bool | true | add saturations to output (MPNC only) |
- * | | AddTemperatures | bool | false | add temperatures to output (MPNC only) |
- * | | AddVelocity | bool | false | add velocity to output (2p(ni) and 2p2c(ni) only) |
- * | | OutputLevel | int | 0 (2 for 2p2c) | Vtk output verbosity (0: only primary variables, >0 more depending on the model) |
- * | | RockMechanicsSignConvention | bool | true | Compressive stress has positive sign |
- * | \b ZeroEq | BBoxMaxSandGrainRoughness | Scalar | 0.0 | Equivalent sand grain roughness of the upper wall [m] |
- * | | BBoxMinSandGrainRoughness | Scalar | 0.0 | Equivalent sand grain roughness of the lower wall [m] |
- * | | EddyConductivityModel | int | 1 | The used eddy conductivity model (default = Reynolds analogy) |
- * | | EddyDiffusivityModel | int | 1 | The used eddy diffusivity model (default = Reynolds analogy) |
- * | | EddyViscosityModel | int | 1 | The used eddy viscosity model (default = Prandtl) |
- * | | FlowNormal | int | 0 | Coordinate axis of main velocity entry |
- * | | TurbulentPrandtlNumber | Scalar | 1.0 | Conversion between eddy viscosity and eddy conductivity |
- * | | TurbulentSchmidtNumber | Scalar | 1.0 | Conversion between eddy viscosity and eddy diffusivity |
- * | | WallNormal | int | 1 | Coordinate axis normal to the wall |
+ * | Group | Parameter | Type | Default Value | Explanation |
+ * | :- | :- | :- | :- | :- |
+ * | - | ParameterFile | std::string| executable.input | name of the parameter file |
+ * | \b Component | GasDensity | Scalar | 1.0 | |
+ * | | GasDiffusionCoefficient | Scalar | 1.0 | |
+ * | | GasKinematicViscosity | Scalar | 1.0 | |
+ * | | HenryComponentInWater | Scalar | 1.0 | |
+ * | | HenryWaterInComponent | Scalar | 1.0 | |
+ * | | LiquidDensity | Scalar | 1.0 | |
+ * | | LiquidDiffusionCoefficient | Scalar | 1.0 | |
+ * | | LiquidKinematicViscosity | Scalar | 1.0 | |
+ * | | MolarMass | Scalar | 1.0 | |
+ * | | Name | std::string | component | |
+ * | \b ElectroChemistry | ActivationBarrier | Scalar | | |
+ * | | CellVoltage | Scalar | | |
+ * | | MaxIterations | Scalar | | |
+ * | | NumElectrons | Scalar | | |
+ * | | pO2Inlet | Scalar | | |
+ * | | RefCurrentDensity | Scalar | | |
+ * | | RefO2PartialPressure | Scalar | | |
+ * | | RefTemperature | Scalar | | |
+ * | | ReversibleVoltage | Scalar | | |
+ * | | SpecificResistance | Scalar | | |
+ * | | SurfaceIncreasingFactor | Scalar | | |
+ * | | ThermoneutralVoltage | Scalar | | |
+ * | | TransferCoefficient | Scalar | | |
+ * | | TransportNumberH20 | Scalar | | |
+ * | \b Grid | Angular+std::to_string(i) | Scalar | | |
+ * | | Axial+std::to_string(i) | Scalar | | |
+ * | | BoundarySegments | bool | false | |
+ * | | Cells | CellArray | cells | |
+ * | | Cells | GlobalPosition | | |
+ * | | Cells | int | 1 | |
+ * | | Cells | intdim | cells | |
+ * | | Cellsstd::array< | | | |
+ * | | Cells+std::to_string(i) | int | cells[i] | |
+ * | | CellType | std::string | Cube | |
+ * | | ClosureType | std::string | Green | |
+ * | | Coordinates | std::vector<typenameGrid::ctype> | | |
+ * | | DomainMarkers | bool | false | |
+ * | | File | std::string | | |
+ * | | File | std::string | modelParamGroup | |
+ * | | Grading+std::to_string(i) | Scalar | grading[i] | |
+ * | | Grading+std::to_string(i) | std::vector<ctype> | grading[i] | |
+ * | | HeapSize | int | | |
+ * | | KeepPhysicalOverlap | bool | true | |
+ * | | LeftBoundary | CoordinateType | 0.0 | |
+ * | | LowerLeft | GlobalPosition | GlobalPosition(0.0) | |
+ * | | Overlap | int | 1 | |
+ * | | Partitioning | intdim | | |
+ * | | Periodicstd::bitset<dim | | | |
+ * | | Positions+std::to_string(i) | std::vector<ctype> | | |
+ * | | Radial+std::to_string(i) | Scalar | | |
+ * | | Refinement | int | | |
+ * | | RefinementType | std::string | Local | |
+ * | | RightBoundary | CoordinateType | | |
+ * | | UpperRight | Dune::FieldVector<ctdim> | | |
+ * | | UpperRight | GlobalPosition | | |
+ * | | UpperRight | GlobalPosition | GlobalPosition(0.0) | |
+ * | | Verbosity | bool | false | |
+ * | | WellRadius | Scalar | | |
+ * | \b Impet | ErrorTermFactor | Scalar | GET_PROP_VALUE(TypeTagImpetErrorTermFactor) | |
+ * | | ErrorTermLowerBound | Scalar | GET_PROP_VALUE(TypeTagImpetErrorTermLowerBound) | |
+ * | | ErrorTermUpperBound | Scalar | GET_PROP_VALUE(TypeTagImpetErrorTermUpperBound) | |
+ * | \b Implicit | NumericDifferenceMethod | int | | |
+ * | | UpwindWeight | Scalar | | |
+ * | \b LinearSolver | GMResRestart | double | | |
+ * | | GMResRestart | int | | |
+ * | | MaxIterations | int | | |
+ * | | PreconditionerIterations | int | | |
+ * | | PreconditionerRelaxation | Scalar | | |
+ * | | ResidualReduction | Scalar | | |
+ * | | ResidualReduction | Scalar | 1e-6 | |
+ * | | Verbosity | int | | |
+ * | \b Mpfa | Q | Scalar | | |
+ * | \b Newton | EnableAbsoluteResidualCriterion | bool | | |
+ * | | EnableChop | bool | | |
+ * | | EnableResidualCriterion | bool | | |
+ * | | EnableShiftCriterion | bool | | |
+ * | | MaxAbsoluteResidual | Scalar | | |
+ * | | MaxRelativeShift | Scalar | | |
+ * | | MaxSteps | int | | |
+ * | | ResidualReduction | Scalar | | |
+ * | | SatisfyResidualAndShiftCriterion | bool | | |
+ * | | TargetSteps | int | | |
+ * | | UseLineSearch | bool | | |
+ * | \b Problem | AddVelocity | bool | | |
+ * | | EnableGravity | bool | | |
+ * | | Name | std::string | | |
+ * | | Salinity | Scalar | 1e-3 | |
+ * | | UsePrimaryVariableSwitch | bool | | |
+ * | \b SpatialParams | ForchCoeff | Scalar | 0.55 | |
+ * | | Tortuosity | Scalar | 0.5 | |
+ * | \b TimeLoop | Restart | double | | |
+ * | \b TimeManager | DtInitial | Scalar | | |
+ * | | MaxTimeStepSizestd::numeric_limits<Scalar> | | | |
+ * | | Restart | Scalar | | |
+ * | | TEnd | double | | |
+ * | | TEnd | Scalar | | |
+ * | \b Vtk | AddProcessRank | bool | | |
+ * | | AddVelocity | bool | | |
+ * | | OutputLevel | int | | |
+ * | | WriteFaceData | bool | false | |
*/
diff --git a/doc/doxygen/mainpage.txt b/doc/doxygen/mainpage.txt
index f608923d87cd4dae576b8d06daf70746163839ee..bb0235b9bec4492f2245ca392e458ec97b6ec2eb 100644
--- a/doc/doxygen/mainpage.txt
+++ b/doc/doxygen/mainpage.txt
@@ -14,7 +14,7 @@ documenting C/C++ code.
\section mods Modules
-The best way to start is from the page <a href="modules.html">Modules</a> which gives
+The best way to start is from the <a href="modules.html">Modules</a> page which gives
you access to the documentation by category.
\section params Parameters
diff --git a/doc/doxygen/modules.txt b/doc/doxygen/modules.txt
index 11a3cc1fae44be0faf5da24e28ec75cfb68d7e71..c706c030929c227b53d7c0d8570685ecb5badbfe 100644
--- a/doc/doxygen/modules.txt
+++ b/doc/doxygen/modules.txt
@@ -5,345 +5,257 @@
*
*/
-/* ***************** Porousmediaflow ******************/
+/* ***************** Porousmediumflow ******************/
/*!
- * \defgroup Porousmediaflow Porous-Medium Flow (fully implicit if not denoted otherwise)
+ * \defgroup PorousmediumflowModels Porous-Medium Flow Models
*/
/*!
- * \ingroup Porousmediaflow
- * \defgroup OnePModels 1p (one-phase Darcy flow)
+ * \ingroup PorousmediumflowModels
+ * \defgroup OnePModel 1p (one-phase Darcy flow)
+ * \copydetails ./porousmediumflow/1p/model.hh
+ */
+ /*!
+ * \ingroup OnePModel
+ * \defgroup SequentialOnePModel Sequential
+ * # Pressure
+ * \copydetails ./porousmediumflow/1p/sequential/diffusion/cellcentered/pressure.hh
+ *
+ * # Velocity
+ * \copydetails ./porousmediumflow/1p/sequential/diffusion/cellcentered/velocity.hh
+ */
+ /*!
+ * \ingroup PorousmediumflowModels
+ * \defgroup OnePNCModel 1pnc (one-phase, n-component Darcy flow)
+ *
+ * \copydetails ./porousmediumflow/1pnc/model.hh
*/
- /*!
- * \ingroup OnePModels
- * \defgroup OnePModel Implicit
- *
- * \copydetails Dumux::OnePModel
- */
- /*!
- * \ingroup OnePModels
- * \defgroup OnePhase Sequential
- *
- * \copydetails Dumux::FVPressure1P
- */
/*!
- * \ingroup Porousmediaflow
- * \defgroup OnePTwoCModel 1p2c (one-phase, two-component Darcy flow)
+ * \ingroup PorousmediumflowModels
+ * \defgroup OnePNCMinModel 1pncmin (one-phase, n-component Darcy flow with mineralization)
*
- * \copydetails Dumux::OnePTwoCModel
+ * \copydetails ./porousmediumflow/1pncmin/model.hh
*/
/*!
- * \ingroup Porousmediaflow
- * \defgroup TwoPModels 2p (two-phase Darcy flow)
+ * \ingroup PorousmediumflowModels
+ * \defgroup TwoPModel 2p (two-phase Darcy flow)
+ * \copydetails ./porousmediumflow/2p/model.hh
*/
/*!
- * \ingroup TwoPModels
- * \defgroup TwoPModel Implicit
- *
- * \copydetails Dumux::TwoPModel
+ * \ingroup TwoPModel
+ * \defgroup SequentialTwoPModel Sequential
+ * # Pressure
+ * \copydetails ./porousmediumflow/2p/sequential/diffusion/cellcentered/pressure.hh
+ *
+ * # Velocity
+ * \copydetails ./porousmediumflow/2p/sequential/diffusion/cellcentered/velocity.hh
*/
/*!
- * \ingroup TwoPModels
- * \defgroup IMPES Sequential
- *
- * # Pressure
- * \copydetails Dumux::FVPressure2P
- * <br>
- * # Velocity
- * \copydetails Dumux::FVVelocity2P
- * <br>
- * # Saturation
- * \copydetails Dumux::FVSaturation2P
- */
- /*!
- * \ingroup Porousmediaflow
+ * \ingroup PorousmediumflowModels
* \defgroup TwoPOneCModel 2p1c (two-phase, one-component Darcy flow)
*
- * \copydetails Dumux::TwoPOneCModel
+ * \copydetails ./porousmediumflow/2p1c/model.hh
*/
/*!
- * \ingroup Porousmediaflow
- * \defgroup TwoPOneCModel 2p1c (two-phase, one-component Darcy flow)
- *
- * \copydetails Dumux::TwoPOneCModel
- */
- /*!
- * \ingroup Porousmediaflow
- * \defgroup TwoPTwoCModels 2p2c (two-phase, two-component Darcy flow)
+ * \ingroup PorousmediumflowModels
+ * \defgroup TwoPTwoCModel 2p2c (two-phase, two-component Darcy flow)
+ * \copydetails ./porousmediumflow/2p2c/model.hh
*/
/*!
- * \ingroup TwoPTwoCModels
- * \defgroup TwoPTwoCModel Implicit
- *
- * \copydetails Dumux::TwoPTwoCModel
+ * \ingroup TwoPTwoCModel
+ * \defgroup SequentialTwoPTwoCModel Sequential
+ * # Pressure
+ * \copydetails ./porousmediumflow/2p2c/sequential/fvpressure.hh
+ *
+ * # Velocity
+ * \copydetails ./porousmediumflow/2p2c/sequential/fvtransport.hh
*/
/*!
- * \ingroup TwoPTwoCModels
- * \defgroup IMPEC Sequential
- *
- * # Pressure
- * \copydetails Dumux::FVPressure2P2C
- * <br>
- * # Transport
- * \copydetails Dumux::FVTransport2P2C
- */
- /*!
- * \ingroup Porousmediaflow
- * \defgroup TwoPDFMModel 2pdfm (two-phase Darcy flow in discrete fracture-matrix)
- *
- * \copydetails Dumux::TwoPDFMModel
- */
- /*!
- * \ingroup Porousmediaflow
- * \defgroup TwoPMincModel 2pminc (two-phase Darcy flow dual continuum)
- *
- * \copydetails Dumux::TwoPMincModel
- */
- /*!
- * \ingroup Porousmediaflow
+ * \ingroup PorousmediumflowModels
* \defgroup TwoPNCModel 2pnc (two-phase, n-component Darcy flow)
*
- * \copydetails Dumux::TwoPNCModel
+ * \copydetails ./porousmediumflow/2pnc/model.hh
*/
/*!
- * \ingroup Porousmediaflow
+ * \ingroup PorousmediumflowModels
* \defgroup TwoPNCMinModel 2pncmin (two-phase, n-component Darcy flow with mineralization)
*
- * \copydetails Dumux::TwoPNCMinModel
+ * \copydetails ./porousmediumflow/2pncmin/model.hh
*/
/*!
- * \ingroup Porousmediaflow
+ * \ingroup PorousmediumflowModels
* \defgroup ThreePModel 3p (three-phase Darcy flow)
*
- * \copydetails Dumux::ThreePModel
+ * \copydetails ./porousmediumflow/3p/model.hh
*/
/*!
- * \ingroup Porousmediaflow
+ * \ingroup PorousmediumflowModels
* \defgroup ThreePThreeCModel 3p3c (three-phase, three-component Darcy flow)
*
- * \copydetails Dumux::ThreePThreeCModel
+ * \copydetails ./porousmediumflow/3p3c/model.hh
*/
/*!
- * \ingroup Porousmediaflow
+ * \ingroup PorousmediumflowModels
* \defgroup ThreePWaterOilModel 3pwateroil (three-phase, two-component Darcy flow)
*
- * \copydetails Dumux::ThreePWaterOilModel
+ * \copydetails ./porousmediumflow/3pwateroil/model.hh
*/
/*!
- * \ingroup Porousmediaflow
+ * \ingroup PorousmediumflowModels
* \defgroup CO2Model CO2 (two-phase, two-component Darcy flow)
*
- * \copydetails Dumux::CO2Model
+ * \copydetails ./porousmediumflow/co2/model.hh
*/
/*!
- * \ingroup Porousmediaflow
- * \defgroup MPNCModel MpNc (m-phase, n-component Darcy flow)
+ * \ingroup PorousmediumflowModels
+ * \defgroup MineralizationModel Mineralization (equation adding solid/mineralization-phases to a standard Darcy flow model)
*
- * \copydetails Dumux::MPNCModel
+ * \copydetails ./porousmediumflow/mineralization/model.hh
*/
/*!
- * \ingroup Porousmediaflow
- * \defgroup NIModel Non-isothermal (energy equation, to be added to an isothermal model)
+ * \ingroup PorousmediumflowModels
+ * \defgroup MPNCModel MpNc (m-phase, n-component Darcy flow)
*
- * \copydetails Dumux::NIModel
+ * \copydetails ./porousmediumflow/mpnc/model.hh
*/
/*!
- * \ingroup Porousmediaflow
- * \defgroup RichardsModel Richards (Richards flow)
+ * \ingroup PorousmediumflowModels
+ * \defgroup NIModel Non-isothermal (energy equation, to be added to an isothermal model)
*
- * \copydetails Dumux::RichardsModel
+ * \copydetails ./porousmediumflow/non-isothermal/model.hh
*/
-
-/* ***************** Geomechanics ******************/
-/*!
- * \defgroup Geomechanics Geomechanics (fully implicit)
- */
/*!
- * \ingroup Geomechanics
- * \defgroup ElOnePTwoCBoxModel El1p2c (one-phase, two-component Darcy flow, linear elastic deformation model)
+ * \ingroup PorousmediumflowModels
+ * \defgroup RichardsModel Richards (Richards flow)
*
- * \copydetails Dumux::ElOnePTwoCModel
+ * \copydetails ./porousmediumflow/richards/model.hh
*/
/*!
- * \ingroup Geomechanics
- * \defgroup ElTwoPBoxModel El2p (two-phase Darcy flow, linear elastic deformation model)
+ * \ingroup PorousmediumflowModels
+ * \defgroup RichardsNCModel RichardsNC (n-component Richards flow)
*
- * \copydetails Dumux::ElTwoPModel
+ * \copydetails ./porousmediumflow/richardsnc/model.hh
*/
/*!
- * \ingroup Geomechanics
- * \defgroup ElasticBoxModel Elastic (linear elastic deformation model)
+ * \ingroup PorousmediumflowModels
+ * \defgroup TracerModel Tracer (adds tracer transport to a model)
*
- * \copydetails Dumux::ElasticModel
+ * \copydetails ./porousmediumflow/tracer/model.hh
*/
-/* ***************** Freeflow ******************/
+/* ***************** FreeflowModels ******************/
/*!
- * \defgroup Freeflow Free Flow (fully implicit)
+ * \defgroup FreeflowModels Free Flow Models
*/
/*!
- * \ingroup Freeflow
- * \defgroup BoxStokesModel Stokes (one-phase Stokes flow)
- *
- * \copydetails Dumux::StokesModel
- */
- /*!
- * \ingroup Freeflow
- * \defgroup BoxStokesncModel Stokesnc (one-phase, n-component Stokes flow)
+ * \ingroup FreeflowModels
+ * \defgroup NavierStokesModel NavierStokes (one-phase Navier-Stokes flow)
*
- * \copydetails Dumux::StokesncModel
+ * \copydetails ./freeflow/navierstokes/model.hh
*/
/*!
- * \ingroup Freeflow
- * \defgroup BoxStokesncniModel Stokesncni (one-phase, n-component, non-isothermal Stokes flow)
+ * \ingroup FreeflowModels
+ * \defgroup NavierStokesNCModel NavierStokesnc (one-phase, n-component Navier-Stokes flow)
*
- * \copydetails Dumux::StokesncniModel
+ * \copydetails ./freeflow/navierstokesnc/model.hh
*/
/*!
- * \ingroup Freeflow
- * \defgroup BoxZeroEqModel Zeroeq (one-phase Stokes flow with zero-eq turbulence model)
+ * \ingroup FreeflowModels
+ * \defgroup NavierStokesNIModel Non-isothermal (energy equation, to be added to a isothermal NavierStokes model)
*
- * \copydetails Dumux::ZeroEqModel
- */
- /*!
- * \ingroup Freeflow
- * \defgroup BoxZeroEqncModel Zeroeqnc (one-phase, n-component Stokes flow with zero-eq turbulence model)
- *
- * \copydetails Dumux::ZeroEqncModel
- */
- /*!
- * \ingroup Freeflow
- * \defgroup BoxZeroEqncniModel Zeroeqncni (one-phase, n-component, non-isothermal Stokes flow with zero-eq turbulence model)
- *
- * \copydetails Dumux::ZeroEqncniModel
+ * \copydetails ./freeflow/non-isothermal/model.hh
*/
-/* ***************** Multidomain ******************/
+/* ***************** Benchmarks and Tests ******************/
/*!
- * \defgroup Multidomain Multidomain (fully implicit)
+ * \defgroup BenchmarksAndTests Benchmarks and Tests
+ * TODO: Doc me in modules.txt!
*/
- /*!
- * \ingroup Multidomain
- * \defgroup MultidomainModel Multidomain
- */
- /*!
- * \ingroup Multidomain
- * \defgroup TwoPTwoCStokesTwoCModel 2cstokes2p2c (1p2c Stokes flow coupled to 2p2c Darcy flow)
- *
- * # Coupling Conditions
- * \copydetails Dumux::TwoCStokesTwoPTwoCLocalOperator
- * <br>
- * # Darcy 2p2c
- * \copydetails Dumux::TwoPTwoCModel
- * <br>
- * # Stokes nc
- * \copydetails Dumux::StokesncModel
- */
- /*!
- * \ingroup Multidomain
- * \defgroup TwoPTwoCNIStokesTwoCNIModel 2cnistokes2p2cni (1p2cni Stokes flow coupled to 2p2cni Darcy flow)
- *
- * # Coupling Conditions
- * \copydetails Dumux::TwoCNIStokesTwoPTwoCNILocalOperator
- * <br>
- * # Darcy 2p2c
- * \copydetails Dumux::TwoPTwoCModel
- * <br>
- * # Darcy non-isothermal extension
- * \copydetails Dumux::NIModel
- * <br>
- * # Stokes nc
- * \copydetails Dumux::StokesncniModel
- */
- /*!
- * \ingroup Multidomain
- * \defgroup TwoPTwoCZeroEqTwoCModel 2czeroeq2p2c (1p2c Stokes flow with zero-eq turbulence model coupled to 2p2c Darcy flow)
- *
- * # Coupling Conditions
- * \copydetails Dumux::TwoCStokesTwoPTwoCLocalOperator
- * <br>
- * # Darcy 2p2c
- * \copydetails Dumux::TwoPTwoCModel
- * <br>
- * # Stokes nc
- * \copydetails Dumux::ZeroEqncModel
- */
- /*!
- * \ingroup Multidomain
- * \defgroup TwoPTwoCNIZeroEqTwoCNIModel 2cnizeroeq2p2cni (1p2cni Stokes flow with zero-eq turbulence model coupled to 2p2cni Darcy flow)
- *
- * # Coupling Conditions
- * \copydetails Dumux::TwoCNIStokesTwoPTwoCNILocalOperator
- * <br>
- * # Darcy 2p2c
- * \copydetails Dumux::TwoPTwoCModel
- * <br>
- * # Darcy non-isothermal extension
- * \copydetails Dumux::NIModel
- * <br>
- * # Stokes nc
- * \copydetails Dumux::ZeroEqncniModel
- */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup OnePTests 1p (one phase) benchmarks and tests
+ */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup OnePNCTests 1pnc (one phase, n-component) benchmarks and tests
+ */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup OnePNCMinTests 1pncmin (one phase, n-component mineralization) benchmarks and tests
+ */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup TwoPTests 2p (two phase) benchmarks and tests
+ */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup TwoPOneCTests 2p1c (two phase, one component) benchmarks and tests
+ */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup TwoPTwoCTests 2p2c (two phase, two component) benchmarks and tests
+ */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup TwoPNCTests 2pnc (two phase, n-component) benchmarks and tests
+ */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup TwoPNCMinTests 2pncmin (two phase, n-component mineralization) benchmarks and tests
+ */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup ThreePTests 3p (three phase) benchmarks and tests
+ */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup ThreePThreeCTests 3p3c (three phase, three component) benchmarks and tests
+ */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup ThreePWaterOilTests 3pwateroil (three phase, water oil) benchmarks and tests
+ */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup CO2Tests CO2 (two phase, two component) benchmarks and tests
+ */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup MPNCTests MPNC (m phase, n-component) benchmarks and tests
+ */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup MPNCTests MPNC (m phase, n-component) benchmarks and tests
+ */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup RichardsTests Richards benchmarks and tests
+ */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup RichardsNCTests Richards n-component benchmarks and tests
+ */
+ /*! \ingroup BenchmarksAndTests
+ * \defgroup TracerTests Tracer benchmarks and tests
+ */
-/* ***************** Fully Implicit ******************/
+/* ***************** Discretization ******************/
/*!
- * \defgroup ImplicitModel Fully-Coupled Fully-Implicit Scheme
+ * \defgroup Discretization Discretization schemes
*/
/*!
- * \ingroup ImplicitModel
- * \defgroup ImplicitBaseProblems Base Problems
+ * \ingroup Discretization
+ * \defgroup BoxDiscretization Box finite volume scheme
+ *
+ * \copydetails ./discretization/box/properties.hh
*/
/*!
- * \ingroup ImplicitModel
- * \defgroup Discretizations Discretizations
+ * \ingroup Discretization
+ * \defgroup CCDiscretization Cell-centered finite volume scheme
+ * # Tpfa
+ * \copybrief ./discretization/cellcentered/tpfa/properties.hh
+ * # Mpfa
+ * \copybrief ./discretization/cellcentered/mpfa/properties.hh
*/
/*!
- * \ingroup Discretizations
- * \defgroup CCModel Fully-implicit cell-centered discretization
+ * \ingroup CCDiscretization
+ * \defgroup CCTpfaDiscretization Cell-centered finite volume scheme with two-point flux-approximuation (Tpfa)
+ *
+ * \copydetails ./discretization/cellcentered/tpfa/properties.hh
*/
/*!
- * \ingroup Discretizations
- * \defgroup BoxModel Fully-implicit box discretization
+ * \ingroup CCDiscretization
+ * \defgroup CCMpfaDiscretization Cell-centered finite volume scheme with multi-point flux-approximuation (Mpfa)
+ *
+ * \copydetails ./discretization/cellcentered/mpfa/properties.hh
*/
/*!
- * \ingroup ImplicitModel
- * \defgroup ImplicitBoundaryTypes Boundary Types
- */
- /*!
- * \ingroup ImplicitModel
- * \defgroup ImplicitFluxVariables Flux Variables
- */
- /*!
- * \ingroup ImplicitModel
- * \defgroup ImplicitIndices Indices
- */
- /*!
- * \ingroup ImplicitModel
- * \defgroup ImplicitLocalJacobian Local Jacobian
- */
- /*!
- * \ingroup ImplicitModel
- * \defgroup ImplicitLocalResidual Local Residual
- */
- /*!
- * \ingroup ImplicitModel
- * \defgroup ImplicitProperties Properties
- */
- /*!
- * \ingroup ImplicitModel
- * \defgroup ImplicitVolumeVariables Volume Variables
- */
-
-/* ***************** Sequential ******************/
-/*!
- * \defgroup Sequential Sequential Scheme (Implicit Pressure, Explicit Transport)
- */
- /*!
- * \ingroup Sequential
- * \defgroup IMPETproblems Base Problems
- */
- /*!
- * \ingroup Sequential
- * \defgroup IMPETProperties Properties
+ * \ingroup Discretization
+ * \defgroup StaggeredDiscretization Staggered finite volume scheme
+ * \copydetails ./discretization/staggered/properties.hh
*/
/* ***************** Material ******************/
@@ -351,31 +263,15 @@
* \defgroup Material Material and Fluid Framework
* Short description of the most important concepts of the material and fluid framework:
*
- * - __Binary coefficient:__ @copydoc Binarycoefficients
- *
- *
- * - __Component:__ @copydoc Components
- *
- *
- * - __Constraint solver:__ @copydoc ConstraintSolver
- *
- *
- * - __Equation of state:__ @copydoc EOS
- *
- *
- * - __Fluid state:__ @copydoc FluidStates
- *
- *
- * - __Fluid system:__ @copydoc Fluidsystems
- *
- *
- * - __Fluid-Matrix Interactions:__ @copydoc fluidmatrixinteractions
- *
- *
- * - __Parameter cache:__ @copydoc ParameterCache
- *
- *
- * - __Spatial Parameters:__ @copydoc SpatialParameters
+ * - __Binary coefficient:__ <br> @copydoc Binarycoefficients
+ * - __Chemistry:__ <br> @copydoc Chemistry
+ * - __Component:__ <br> @copydoc Components
+ * - __Constraint solver:__ <br> @copydoc ConstraintSolver
+ * - __Equation of state:__ <br> @copydoc EOS
+ * - __Fluid-Matrix Interactions:__ <br> @copydoc fluidmatrixinteractions
+ * - __Fluid state:__ <br> @copydoc FluidStates
+ * - __Fluid system:__ <br> @copydoc Fluidsystems
+ * - __Spatial Parameters:__ <br> @copydoc SpatialParameters
*/
/*!
* \ingroup Material
@@ -386,6 +282,14 @@
* coefficients. So far, the programming interface for accessing binary
* coefficients has not been standardized in Dumux.
*/
+ /*!
+ * \ingroup Material
+ * \defgroup Chemistry Chemistry
+ * Chemical reactions can be relevant for all thermodynamic relations
+ * for the liquid and gas phase of multiple chemical species
+ * The main purpose is to provide a convenient way to access these
+ * relationships via source or sink terms.
+ */
/*!
* \ingroup Material
* \defgroup Components Components
@@ -417,13 +321,28 @@
/*!
* \ingroup Material
* \defgroup EOS Equation of State
- *
* Equations of state (EOS) are auxiliary
* classes which provide relations between a fluid phase's temperature,
* pressure, composition and density. Since these classes are only used
* internally in fluid systems, their programming interface is
* currently ad-hoc.
*/
+ /*!
+ * \ingroup Material
+ * \defgroup fluidmatrixinteractions Fluid-Matrix Interactions
+ * Some parameters are functions of the fluid state as well as parameters of
+ * the matrix. For example the capillary pressure is a function of the phase saturation
+ * and the shape parameter \f$\lambda\f$ which is dependent on the material. All such relations
+ * are gathered in this module.
+ */
+ /*!
+ * \ingroup fluidmatrixinteractions
+ * \defgroup fluidmatrixinteractionslaws Laws for Fluid-Matrix Interactions
+ */
+ /*!
+ * \ingroup fluidmatrixinteractions
+ * \defgroup fluidmatrixinteractionsparams Parameters for Fluid-Matrix Interactions
+ */
/*!
* \ingroup Material
* \defgroup FluidStates Fluid States
@@ -439,7 +358,7 @@
/*!
* \ingroup Material
* \defgroup Fluidsystems Fluid Systems
- * Fluid systems express the thermodynamic relations
+ * Fluid systems express the thermodynamic relations
* Strictly speaking, these relations are
* functions, mathematically.} between quantities. Since functions do
* not exhibit any internal state, fluid systems are stateless classes,
@@ -447,53 +366,6 @@
* decision since the thermodynamic state of the system is expressed by
* a fluid state!
*/
- /*!
- * \ingroup Material
- * \defgroup fluidmatrixinteractions Fluid-Matrix Interactions
- * Some parameters are functions of the fluid state as well as parameters of
- * the matrix. For example the capillary pressure is a function of the phase saturation
- * and the shape parameter \f$\lambda\f$ which is dependent on the material. All such relations
- * are gathered in this module.
- */
- /*!
- * \ingroup fluidmatrixinteractions
- * \defgroup fluidmatrixinteractionslaws Laws for Fluid-Matrix Interactions
- */
- /*!
- * \ingroup fluidmatrixinteractions
- * \defgroup fluidmatrixinteractionsparams Parameters for Fluid-Matrix Interactions
- */
- /*!
- * \ingroup Material
- * \defgroup ParameterCache Parameter Cache
- * Fluid systems sometimes require
- * computationally expensive parameters for multiple relations. Such
- * parameters can be cached using a so-called parameter
- * cache. Parameter cache objects are specific for each fluid system
- * but they must provide a common interface to update the internal
- * parameters depending on the quantities which changed since the last
- * update.
- * All fluid systems must export a type for their __ParameterCache__
- * objects. Parameter caches can be used to cache parameter that are
- * expensive to compute and are required in multiple thermodynamic
- * relations. For fluid systems which do need to cache parameters,
- * Dumux provides a __NullParameterCache__ class.
- * The actual quantities stored by parameter cache objects are specific
- * to the fluid system and no assumptions on what they provide should be
- * made outside of their fluid system. Parameter cache objects provide a
- * well-defined set of methods to make them coherent with a given fluid
- * state, though.
- * Note, that the parameter cache interface only guarantees that if a
- * more specialized <tt>update()</tt> method is called, it is not slower
- * than the next more-general method (e.g. calling <tt>updateSingleMoleFraction()</tt>
- * may be as expensive as <tt>updateAll()}</tt>. It is thus advisable to
- * rather use a more general <tt>update()</tt> method once than multiple
- * calls to specialized <tt>update()</tt> methods.
- * To make usage of parameter caches easier for the case where all cached
- * quantities ought to be re-calculated if a quantity of a phase was changed,
- * it is possible to only define the <tt>updatePhase()</tt> method and
- * derive the parameter cache from <tt>Dumux::ParameterCacheBase</tt>.
- */
/*!
* \ingroup Material
* \defgroup SpatialParameters Spatial Parameters
@@ -502,53 +374,50 @@
* parameters. For example permeability, porosity etc.
*
*/
-
+
+/* ***************** Adaptive ******************/
+/*!
+ * \defgroup Adaptive Adaptive
+ * TODO: Doc me in modules.txt!
+ */
+
+/* ***************** Assembly ******************/
+/*!
+ * \defgroup Assembly Assembly
+ * TODO: Doc me in modules.txt!
+ */
+
/* ***************** Common ******************/
/*!
- * \defgroup Common Common Infrastucture
+ * \defgroup Common Common
+ * TODO: Doc me in modules.txt!
+ */
+ /*!
+ * \ingroup Common
+ * \defgroup Properties Properties
+ * TODO: Doc me in modules.txt!
+ */
+
+/* ***************** InputOutput ******************/
+/*!
+ * \defgroup InputOutput Input Output
+ * TODO: Doc me in modules.txt!
+ */
+
+/* ***************** Linear ******************/
+/*!
+ * \defgroup Linear Linear
+ * TODO: Doc me in modules.txt!
+ */
+
+/* ***************** Nonlinear ******************/
+/*!
+ * \defgroup Nonlinear Nonlinear
+ * TODO: Doc me in modules.txt!
+ */
+
+/* ***************** Parallel ******************/
+/*!
+ * \defgroup Parallel Parallel
+ * TODO: Doc me in modules.txt!
*/
- /*!
- * \ingroup Common
- * \defgroup BC Boundary Conditions
- */
- /*!
- * \ingroup Common
- * \defgroup Math Elementary Math Functions
- */
- /*!
- * \ingroup Common
- * \defgroup Exception Exceptions
- */
- /*!
- * \ingroup Common
- * \defgroup Linear Linear Solver Backends
- */
- /*!
- * \ingroup Common
- * \defgroup Newton Newton Solver
- */
- /*!
- * \ingroup Common
- * \defgroup Parameter Parameters
- * See the file parameterlist for available parameters.
- */
- /*!
- * \ingroup Common
- * \defgroup Properties Property System
- */
- /*!
- * \ingroup Common
- * \defgroup Spline Splines
- */
- /*!
- * \ingroup Common
- * \defgroup Start Starting the Simulation
- */
- /*!
- * \ingroup Common
- * \defgroup SimControl Time Manager
- */
- /*!
- * \ingroup Common
- * \defgroup Valgrind Valgrind
- */
diff --git a/doc/doxygen/sanitizelinks.sh b/doc/doxygen/sanitizelinks.sh
index f23c1417bd50ac515cbdf71db756eda02913c623..52051da2fa7d8214253c7c6af94f39cb1bf70232 100755
--- a/doc/doxygen/sanitizelinks.sh
+++ b/doc/doxygen/sanitizelinks.sh
@@ -1,12 +1,2 @@
-# sanitizes the links to the given lists, because doxygen somehow links
-# to a page with a wrong index
-sanitizelinks () {
- NEW_FILE=`grep -l "\"title\">$1" html/*html | egrep -o [0-9]+`
- OLD_FILE=`awk -v a=$NEW_FILE 'BEGIN {printf("%05d", a-1)}'`
- sed -i "s/$OLD_FILE/$NEW_FILE/g" html/*html
-}
-
-sanitizelinks "Todo List"
-sanitizelinks "Bug List"
-sanitizelinks "Deprecated List"
-sanitizelinks "Bibliography"
+#make the modules page default view clearer (toggleLevel(1))
+sed -i 's/\(init_search();\)/\1 toggleLevel(1);/' html/modules.html