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Added doxygen documentation and updated links in readme.md
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| # Attribution | ||
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| If you use PICLas for your publications, please cite it. | ||
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| For the general method please cite | ||
| ``` | ||
| Fasoulas, S., Munz, C.D., Pfeiffer, M., Beyer, J., Binder, T., Copplestone, S., Mirza, A., Nizenkov, P., Ortwein, P. and Reschke, W. | ||
| Combining particle-in-cell and direct simulation Monte Carlo for the simulation of reactive plasma flows. | ||
| Physics of Fluids, 31(7), (2019) p.072006. | ||
| ``` | ||
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| For the high-order Maxwell DG method please cite | ||
| ``` | ||
| Munz, C.D., Auweter-Kurtz, M., Fasoulas, S., Mirza, A., Ortwein, P., Pfeiffer, M. and Stindl, T. | ||
| Coupled particle-in-cell and direct simulation Monte Carlo method for simulating reactive plasma flows. | ||
| Comptes Rendus Mécanique, 342(10-11), (2014) pp.662-670. | ||
| ``` | ||
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| For the high-order Poisson DG method please cite | ||
| ``` | ||
| Pfeiffer, M., Hindenlang, F., Binder, T., Copplestone, S.M., Munz, C.D. and Fasoulas, S. | ||
| A particle-in-cell solver based on a high-order hybridizable discontinuous Galerkin spectral element method on unstructured curved meshes. | ||
| Computer Methods in Applied Mechanics and Engineering, 349, (2019) pp.149-166. | ||
| ``` | ||
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| or use the following Bibtex files | ||
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| @article{piclas_fasoulas, | ||
| title={Combining particle-in-cell and direct simulation Monte Carlo for the simulation of reactive plasma flows}, | ||
| author={Fasoulas, Stefanos and Munz, C-D and Pfeiffer, Marcel and Beyer, Julian and Binder, Tilman and Copplestone, Stephen and Mirza, Asim and Nizenkov, Paul and Ortwein, Philip and Reschke, Wladimir}, | ||
| journal={Physics of Fluids}, | ||
| volume={31}, | ||
| number={7}, | ||
| pages={072006}, | ||
| year={2019}, | ||
| publisher={AIP Publishing LLC} | ||
| } | ||
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| @article{piclas_munz, | ||
| title = {Coupled Particle-In-Cell and Direct Simulation Monte Carlo method for simulating reactive plasma flows}, | ||
| journal = {Comptes Rendus Mécanique}, | ||
| volume = {342}, | ||
| number = {10}, | ||
| pages = {662-670}, | ||
| year = {2014}, | ||
| note = {Theoretical and numerical approaches for Vlasov-maxwell equations}, | ||
| issn = {1631-0721}, | ||
| doi = {https://doi.org/10.1016/j.crme.2014.07.005}, | ||
| url = {https://www.sciencedirect.com/science/article/pii/S1631072114001442}, | ||
| author = {Claus-Dieter Munz and Monika Auweter-Kurtz and Stefanos Fasoulas and Asim Mirza and Philip Ortwein and Marcel Pfeiffer and Torsten Stindl}, | ||
| keywords = {Particle-In-Cell, Direct Simulation Monte Carlo, Discontinuous Galerkin, High-order, Plasma physics, Boltzmann equation}, | ||
| } | ||
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| @article{piclas_pfeiffer, | ||
| title={A particle-in-cell solver based on a high-order hybridizable discontinuous Galerkin spectral element method on unstructured curved meshes}, | ||
| author={Pfeiffer, M and Hindenlang, F and Binder, T and Copplestone, SM and Munz, C-D and Fasoulas, S}, | ||
| journal={Computer Methods in Applied Mechanics and Engineering}, | ||
| volume={349}, | ||
| pages={149--166}, | ||
| year={2019}, | ||
| publisher={Elsevier} | ||
| } | ||
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| <doxygenlayout version="1.0"> | ||
| <!-- Generated by doxygen 1.8.7 --> | ||
| <!-- 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="classmembers" visible="yes" title=""> | ||
| <tab type="classlist" visible="no" title="" intro=""/> | ||
| <tab type="classindex" visible="no" title=""/> | ||
| <tab type="hierarchy" visible="no" title="" intro=""/> | ||
| <tab type="classmembers" visible="no" title="" intro=""/> | ||
| </tab> | ||
| <tab type="files" visible="yes" title=""> | ||
| <tab type="filelist" visible="no" title="" intro=""/> | ||
| <tab type="globals" visible="no" title="" intro=""/> | ||
| </tab> | ||
| <tab type="examples" visible="yes" title="" intro=""/> | ||
| </navindex> | ||
|
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| <!-- Layout definition for a class page --> | ||
| <class> | ||
| <briefdescription visible="yes"/> | ||
| <includes visible="$SHOW_INCLUDE_FILES"/> | ||
| <inheritancegraph visible="$CLASS_GRAPH"/> | ||
| <collaborationgraph visible="$COLLABORATION_GRAPH"/> | ||
| <memberdecl> | ||
| <nestedclasses visible="yes" title=""/> | ||
| <publictypes title=""/> | ||
| <services title=""/> | ||
| <interfaces title=""/> | ||
| <publicslots title=""/> | ||
| <signals title=""/> | ||
| <publicmethods title=""/> | ||
| <publicstaticmethods title=""/> | ||
| <publicattributes title=""/> | ||
| <publicstaticattributes title=""/> | ||
| <protectedtypes title=""/> | ||
| <protectedslots title=""/> | ||
| <protectedmethods title=""/> | ||
| <protectedstaticmethods title=""/> | ||
| <protectedattributes title=""/> | ||
| <protectedstaticattributes title=""/> | ||
| <packagetypes title=""/> | ||
| <packagemethods title=""/> | ||
| <packagestaticmethods title=""/> | ||
| <packageattributes title=""/> | ||
| <packagestaticattributes title=""/> | ||
| <properties title=""/> | ||
| <events title=""/> | ||
| <privatetypes title=""/> | ||
| <privateslots title=""/> | ||
| <privatemethods title=""/> | ||
| <privatestaticmethods title=""/> | ||
| <privateattributes title=""/> | ||
| <privatestaticattributes title=""/> | ||
| <friends title=""/> | ||
| <related title="" subtitle=""/> | ||
| <membergroups visible="yes"/> | ||
| </memberdecl> | ||
| <detaileddescription title=""/> | ||
| <memberdef> | ||
| <inlineclasses title=""/> | ||
| <typedefs title=""/> | ||
| <enums title=""/> | ||
| <services title=""/> | ||
| <interfaces title=""/> | ||
| <constructors title=""/> | ||
| <functions title=""/> | ||
| <related title=""/> | ||
| <variables title=""/> | ||
| <properties title=""/> | ||
| <events title=""/> | ||
| </memberdef> | ||
| <allmemberslink visible="yes"/> | ||
| <usedfiles visible="$SHOW_USED_FILES"/> | ||
| <authorsection visible="yes"/> | ||
| </class> | ||
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| <!-- Layout definition for a namespace page --> | ||
| <namespace> | ||
| <briefdescription visible="yes"/> | ||
| <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> | ||
| <detaileddescription title=""/> | ||
| <memberdef> | ||
| <inlineclasses title=""/> | ||
| <typedefs title=""/> | ||
| <enums title=""/> | ||
| <functions title=""/> | ||
| <variables title=""/> | ||
| </memberdef> | ||
| <authorsection visible="yes"/> | ||
| </namespace> | ||
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| <!-- Layout definition for a file page --> | ||
| <file> | ||
| <briefdescription visible="yes"/> | ||
| <includes visible="$SHOW_INCLUDE_FILES"/> | ||
| <includegraph visible="$INCLUDE_GRAPH"/> | ||
| <includedbygraph visible="$INCLUDED_BY_GRAPH"/> | ||
| <sourcelink visible="yes"/> | ||
| <memberdecl> | ||
| <classes visible="yes" title=""/> | ||
| <namespaces visible="yes" title=""/> | ||
| <constantgroups visible="yes" title=""/> | ||
| <defines title=""/> | ||
| <typedefs title=""/> | ||
| <enums title=""/> | ||
| <functions title=""/> | ||
| <variables title=""/> | ||
| <membergroups visible="yes"/> | ||
| </memberdecl> | ||
| <detaileddescription title=""/> | ||
| <memberdef> | ||
| <inlineclasses title=""/> | ||
| <defines title=""/> | ||
| <typedefs title=""/> | ||
| <enums title=""/> | ||
| <functions title=""/> | ||
| <variables title=""/> | ||
| </memberdef> | ||
| <authorsection/> | ||
| </file> | ||
|
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| <!-- Layout definition for a group page --> | ||
| <group> | ||
| <briefdescription visible="yes"/> | ||
| <groupgraph visible="$GROUP_GRAPHS"/> | ||
| <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> | ||
| <detaileddescription title=""/> | ||
| <memberdef> | ||
| <pagedocs/> | ||
| <inlineclasses title=""/> | ||
| <defines title=""/> | ||
| <typedefs title=""/> | ||
| <enums title=""/> | ||
| <enumvalues title=""/> | ||
| <functions title=""/> | ||
| <variables title=""/> | ||
| <signals title=""/> | ||
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| <protectedslots title=""/> | ||
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| <events title=""/> | ||
| <properties title=""/> | ||
| <friends title=""/> | ||
| </memberdef> | ||
| <authorsection visible="yes"/> | ||
| </group> | ||
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| <!-- Layout definition for a directory page --> | ||
| <directory> | ||
| <briefdescription visible="yes"/> | ||
| <directorygraph visible="yes"/> | ||
| <memberdecl> | ||
| <dirs visible="yes"/> | ||
| <files visible="yes"/> | ||
| </memberdecl> | ||
| <detaileddescription title=""/> | ||
| </directory> | ||
| </doxygenlayout> |
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| #!/bin/bash | ||
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| EQUATION=maxwell/ | ||
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| #======================================= | ||
| # DO NOT CHANGE ANYTHING BELOW THIS LINE | ||
| #======================================= | ||
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| cd "$(dirname "$0")" # change to directory of this script | ||
| CURDIR=`readlink -f .` | ||
| cd $CURDIR | ||
| DOXYDIR=${CURDIR##*/} | ||
| if [ "$DOXYDIR" != "doxygen" ]; then | ||
| echo "Security exit:" | ||
| echo "builddoxy.sh must be placed in a directory with name 'doxygen'!" | ||
| exit 1 | ||
| fi | ||
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| function deletesrc { | ||
| cd $CURDIR | ||
| rm -rf src | ||
| rm *.md | ||
| rm logo.png | ||
| #rm doc_logo.png | ||
| } | ||
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| trap deletesrc EXIT | ||
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| #delete old files | ||
| rm -rf doxygen | ||
| cp -r ../../src . | ||
| cp -r ../../README.md . | ||
| sed -i 's\doc/logo.png\doc_logo.png\g' README.md | ||
| cp -r ../../CONTRIBUTORS.md . | ||
| cp -r ../../LICENCE.md . | ||
| cp -r ../../REFERENCE.md . | ||
| cp -r ../../REGGIE.md . | ||
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| convert -size 1769x870 ../logo.png -resize 200x55 logo.png | ||
| #cp ../logo.png doc_logo.png | ||
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| #rm -rf doc | ||
| #mkdir doc | ||
| #cp -r ../userguide doc/ | ||
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| # delete images of build status and gpl | ||
| sed -i '3,4d' README.md | ||
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| # comment INTERFACE/END INTERFACE lines and MODULE PROCEDURE lines so doxygen will create call graphs | ||
| FILELIST=`find . -name '*.f90'` | ||
| for file in $FILELIST | ||
| do | ||
| sed -i 's/END INTERFACE/!END INTERFACE/g' $file | ||
| sed -i 's/INTERFACE/!INTERFACE/g' $file | ||
| sed -i 's/MODULE PROCEDURE/!MODULE PROCEDURE/g' $file | ||
| done | ||
| # rename f90 -> F90: doxygen preprocessor is only run for these files | ||
| rename 's/\.f90$/\.F90/' $FILELIST | ||
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| # delete all equation dirs and testcase dirs except the one specified above | ||
| function cleandirs { | ||
| DIRS=`ls -d */` | ||
| for dir in $DIRS; do | ||
| if [ "$dir" != "$1" ]; then #delete all dirs except $1 | ||
| rm -r $dir | ||
| fi | ||
| done | ||
| } | ||
| cd src/equations | ||
| cleandirs $EQUATION | ||
| cd ../.. | ||
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| # run doxygen | ||
| doxygen doxyconfig > doxylog.out | ||
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| # comment in interfaces in html files | ||
| cd doxygen/html/ | ||
| FILELIST=`find . -name '*.html'` | ||
| for file in $FILELIST | ||
| do | ||
| sed -i 's/!END INTERFACE/END INTERFACE/g' $file | ||
| sed -i 's/!INTERFACE/INTERFACE/g' $file | ||
| sed -i 's/!MODULE PROCEDURE/MODULE PROCEDURE/g' $file | ||
| sed -i 's/\.F90/\.f90/g' $file | ||
| done | ||
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| cd ../.. | ||
| cp ../logo.png ./doxygen/latex/doc_logo.png | ||
| cp ../logo.png ./doxygen/html/doc_logo.png | ||
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