diff options
| author | Erik Schnetter <schnetter@cct.lsu.edu> | 2010-08-24 12:04:51 -0400 |
|---|---|---|
| committer | Barry Wardell <barry.wardell@gmail.com> | 2011-12-14 18:21:12 +0000 |
| commit | a62e8ee3f1e86100cda633f51c22ee063e28df76 (patch) | |
| tree | 96c4522bba984cfb4a1e53ce75733d6cdbf08c01 /CarpetDev/CarpetIOF5 | |
| parent | eb813afcef1be0aba7154fe41d21e4a7657371ad (diff) | |
CarpetIOF5: Rename old thorn
Diffstat (limited to 'CarpetDev/CarpetIOF5')
40 files changed, 0 insertions, 6453 deletions
diff --git a/CarpetDev/CarpetIOF5/README b/CarpetDev/CarpetIOF5/README deleted file mode 100644 index a625117a0..000000000 --- a/CarpetDev/CarpetIOF5/README +++ /dev/null @@ -1,30 +0,0 @@ -Cactus Code Thorn CarpetIOF5 -Thorn Author(s) : Erik Schnetter <schnetter@aei.mpg.de> -Thorn Maintainer(s) : Erik Schnetter <schnetter@aei.mpg.de> --------------------------------------------------------------------------- - -Purpose of the thorn: - -Input and output data using the HDF5 based F5 file format. - - - -An F5 file contains the following hierarchy: - - Bundle - Slice - Grid - Topology - Representation - Field - -We have a class hierarchy: - - file - timestep (slice) - simulation (grid) [grid hierarchy of one patch] - topology (topology) [one refinement level] - coordinate_system (representation) - physical_quantity (field) - data_region - tensor_component diff --git a/CarpetDev/CarpetIOF5/TODO b/CarpetDev/CarpetIOF5/TODO deleted file mode 100644 index 3fa9b3ca2..000000000 --- a/CarpetDev/CarpetIOF5/TODO +++ /dev/null @@ -1,4 +0,0 @@ -2008-01-19: Need to write table of contents as well. What format -should it have? - -2008-01-19: Checkpointing and recovery is not yet supported. diff --git a/CarpetDev/CarpetIOF5/configuration.ccl b/CarpetDev/CarpetIOF5/configuration.ccl deleted file mode 100644 index d5c33c995..000000000 --- a/CarpetDev/CarpetIOF5/configuration.ccl +++ /dev/null @@ -1,3 +0,0 @@ -# Configuration definitions for thorn CarpetIOF5 - -REQUIRES Carpet CarpetLib F5 HDF5 IOUtil diff --git a/CarpetDev/CarpetIOF5/doc/documentation.tex b/CarpetDev/CarpetIOF5/doc/documentation.tex deleted file mode 100644 index 9d8b3d19e..000000000 --- a/CarpetDev/CarpetIOF5/doc/documentation.tex +++ /dev/null @@ -1,144 +0,0 @@ -% *======================================================================* -% Cactus Thorn template for ThornGuide documentation -% Author: Ian Kelley -% Date: Sun Jun 02, 2002 -% $Header: /cactusdevcvs/Cactus/doc/ThornGuide/template.tex,v 1.12 2004/01/07 20:12:39 rideout Exp $ -% -% Thorn documentation in the latex file doc/documentation.tex -% will be included in ThornGuides built with the Cactus make system. -% The scripts employed by the make system automatically include -% pages about variables, parameters and scheduling parsed from the -% relevant thorn CCL files. -% -% This template contains guidelines which help to assure that your -% documentation will be correctly added to ThornGuides. More -% information is available in the Cactus UsersGuide. -% -% Guidelines: -% - Do not change anything before the line -% % START CACTUS THORNGUIDE", -% except for filling in the title, author, date, etc. fields. -% - Each of these fields should only be on ONE line. -% - Author names should be separated with a \\ or a comma. -% - You can define your own macros, but they must appear after -% the START CACTUS THORNGUIDE line, and must not redefine standard -% latex commands. -% - To avoid name clashes with other thorns, 'labels', 'citations', -% 'references', and 'image' names should conform to the following -% convention: -% ARRANGEMENT_THORN_LABEL -% For example, an image wave.eps in the arrangement CactusWave and -% thorn WaveToyC should be renamed to CactusWave_WaveToyC_wave.eps -% - Graphics should only be included using the graphicx package. -% More specifically, with the "\includegraphics" command. Do -% not specify any graphic file extensions in your .tex file. This -% will allow us to create a PDF version of the ThornGuide -% via pdflatex. -% - References should be included with the latex "\bibitem" command. -% - Use \begin{abstract}...\end{abstract} instead of \abstract{...} -% - Do not use \appendix, instead include any appendices you need as -% standard sections. -% - For the benefit of our Perl scripts, and for future extensions, -% please use simple latex. -% -% *======================================================================* -% -% Example of including a graphic image: -% \begin{figure}[ht] -% \begin{center} -% \includegraphics[width=6cm]{MyArrangement_MyThorn_MyFigure} -% \end{center} -% \caption{Illustration of this and that} -% \label{MyArrangement_MyThorn_MyLabel} -% \end{figure} -% -% Example of using a label: -% \label{MyArrangement_MyThorn_MyLabel} -% -% Example of a citation: -% \cite{MyArrangement_MyThorn_Author99} -% -% Example of including a reference -% \bibitem{MyArrangement_MyThorn_Author99} -% {J. Author, {\em The Title of the Book, Journal, or periodical}, 1 (1999), -% 1--16. {\tt http://www.nowhere.com/}} -% -% *======================================================================* - -% If you are using CVS use this line to give version information -% $Header: /cactusdevcvs/Cactus/doc/ThornGuide/template.tex,v 1.12 2004/01/07 20:12:39 rideout Exp $ - -\documentclass{article} - -% Use the Cactus ThornGuide style file -% (Automatically used from Cactus distribution, if you have a -% thorn without the Cactus Flesh download this from the Cactus -% homepage at www.cactuscode.org) -\usepackage{../../../../doc/latex/cactus} - -\begin{document} - -% The author of the documentation -\author{Erik Schnetter \textless schnetter@aei.mpg.de\textgreater} - -% The title of the document (not necessarily the name of the Thorn) -\title{} - -% the date your document was last changed, if your document is in CVS, -% please use: -% \date{$ $Date: 2004/01/07 20:12:39 $ $} -\date{April 24 2005} - -\maketitle - -% Do not delete next line -% START CACTUS THORNGUIDE - -% Add all definitions used in this documentation here -% \def\mydef etc - -% Add an abstract for this thorn's documentation -\begin{abstract} - -\end{abstract} - -% The following sections are suggestive only. -% Remove them or add your own. - -\section{Introduction} - -\section{Physical System} - -\section{Numerical Implementation} - -\section{Using This Thorn} - -\subsection{Obtaining This Thorn} - -\subsection{Basic Usage} - -\subsection{Special Behaviour} - -\subsection{Interaction With Other Thorns} - -\subsection{Examples} - -\subsection{Support and Feedback} - -\section{History} - -\subsection{Thorn Source Code} - -\subsection{Thorn Documentation} - -\subsection{Acknowledgements} - - -\begin{thebibliography}{9} - -\end{thebibliography} - -% Do not delete next line -% END CACTUS THORNGUIDE - -\end{document} diff --git a/CarpetDev/CarpetIOF5/interface.ccl b/CarpetDev/CarpetIOF5/interface.ccl deleted file mode 100644 index aa7a39fee..000000000 --- a/CarpetDev/CarpetIOF5/interface.ccl +++ /dev/null @@ -1,50 +0,0 @@ -# Interface definition for thorn CarpetIOF5 - -IMPLEMENTS: IOF5 - -USES INCLUDE: bbox.hh defs.hh dh.hh vect.hh -USES INCLUDE: carpet.hh modes.hh - - - -CCTK_INT next_output_iteration TYPE=scalar -CCTK_REAL next_output_time TYPE=scalar -CCTK_INT this_iteration TYPE=scalar - - - -CCTK_INT FUNCTION Coord_GroupSystem \ - (CCTK_POINTER_TO_CONST IN cctkGH, \ - CCTK_STRING IN groupname) -REQUIRES FUNCTION Coord_GroupSystem - -# Check whether existing output files should be truncated or not -CCTK_INT FUNCTION IO_TruncateOutputFiles \ - (CCTK_POINTER_TO_CONST IN cctkGH) -REQUIRES FUNCTION IO_TruncateOutputFiles - - - -# Return a pointer to an unmodifiable C string -# which contains a unique ID for this configuration -CCTK_POINTER_TO_CONST \ -FUNCTION UniqueConfigID (CCTK_POINTER_TO_CONST IN cctkGH) -USES FUNCTION UniqueConfigID - -# Return a pointer to an unmodifiable C string -# which contains a unique ID for this build -CCTK_POINTER_TO_CONST \ -FUNCTION UniqueBuildID (CCTK_POINTER_TO_CONST IN cctkGH) -USES FUNCTION UniqueBuildID - -# Return a pointer to an unmodifiable C string -# which contains a unique ID for this simulation -CCTK_POINTER_TO_CONST \ -FUNCTION UniqueSimulationID (CCTK_POINTER_TO_CONST IN cctkGH) -USES FUNCTION UniqueSimulationID - -# Return a pointer to an unmodifiable C string -# which contains a unique ID for this run -CCTK_POINTER_TO_CONST \ -FUNCTION UniqueRunID (CCTK_POINTER_TO_CONST IN cctkGH) -USES FUNCTION UniqueRunID diff --git a/CarpetDev/CarpetIOF5/par/wavetoy-cc-ref.par b/CarpetDev/CarpetIOF5/par/wavetoy-cc-ref.par deleted file mode 100644 index 1e8c2783d..000000000 --- a/CarpetDev/CarpetIOF5/par/wavetoy-cc-ref.par +++ /dev/null @@ -1,244 +0,0 @@ -Cactus::cctk_run_title = "WaveToy cell-centred refined" - -Cactus::cctk_full_warnings = yes -Cactus::highlight_warning_messages = no -#Cactus::cctk_timer_output = "full" - -Cactus::terminate = "time" -Cactus::cctk_final_time = 1.0 - - - -ActiveThorns = "IOUtil" - -IO::out_dir = $parfile - - - -ActiveThorns = "InitBase" - -InitBase::initial_data_setup_method = "init_single_level" - - - -ActiveThorns = "AEILocalInterp" - -ActiveThorns = "Fortran" - -ActiveThorns = "HDF5" - -ActiveThorns = "LocalInterp" - -ActiveThorns = "LoopControl" - -ActiveThorns = "NaNCatcher" - -ActiveThorns = "Slab" - - - -ActiveThorns = "Carpet CarpetLib CarpetInterp CarpetReduce CarpetSlab" - -Carpet::verbose = no -Carpet::schedule_barriers = no -Carpet::veryverbose = no -CarpetLib::output_bboxes = no - -Carpet::domain_from_coordbase = yes -Carpet::max_refinement_levels = 3 - -driver::ghost_size = 2 - -Carpet::refinement_centering = "cell" -Carpet::prolongation_order_space = 2 -Carpet::prolongation_order_time = 2 - -Carpet::convergence_level = 0 - -Carpet::init_each_timelevel = yes -Carpet::regrid_during_initialisation = no -Carpet::enable_all_storage = no - -Carpet::poison_new_timelevels = yes -CarpetLib::poison_new_memory = yes - -Carpet::grid_structure_filename = "carpet-grid-structure" -Carpet::output_timers_every = 100 -CarpetLib::print_timestats_every = 100 -CarpetLib::print_memstats_every = 100 - - - -ActiveThorns = "NaNChecker" - -NaNChecker::check_every = 100 -NaNChecker::action_if_found = "terminate" -NaNChecker::check_vars = " - WaveToy::scalarevolve -" - - - -ActiveThorns = "Boundary CartGrid3D CoordBase SymBase" - -CoordBase::domainsize = "minmax" - -CoordBase::xmin = -0.50 -CoordBase::ymin = -0.50 -CoordBase::zmin = -0.50 -CoordBase::xmax = +0.50 -CoordBase::ymax = +0.50 -CoordBase::zmax = +0.50 -CoordBase::dx = 0.05 -CoordBase::dy = 0.05 -CoordBase::dz = 0.05 - -CoordBase::boundary_staggered_x_lower = yes -CoordBase::boundary_staggered_y_lower = yes -CoordBase::boundary_staggered_z_lower = yes -CoordBase::boundary_staggered_x_upper = yes -CoordBase::boundary_staggered_y_upper = yes -CoordBase::boundary_staggered_z_upper = yes - -CartGrid3D::type = "coordbase" - - - -ActiveThorns = "CarpetRegrid2" - -CarpetRegrid2::regrid_every = 0 - -CarpetRegrid2::snap_to_coarse = yes - -CarpetRegrid2::num_centres = 1 - -CarpetRegrid2::num_levels_1 = 3 -CarpetRegrid2::radius_1[1] = 0.25 -CarpetRegrid2::radius_1[2] = 0.125 - - - -ActiveThorns = "WavetoyC" - -WaveToy::bound = "radiation" - - - -ActiveThorns = "IDScalarWaveC" - -IDScalarWave::initial_data = "gaussian" -IDScalarWave::radius = 0.0 -IDScalarWave::sigma = 0.1 -IDScalarWave::amplitude = 1.0 - - - -ActiveThorns = "Time" - -Time::dtfac = 0.5 - - - -ActiveThorns = "CarpetIOBasic" - -IOBasic::outInfo_every = 1 -IOBasic::outInfo_reductions = "norm2 minimum maximum" -IOBasic::outInfo_vars = " - WaveToy::phi -" - - - -ActiveThorns = "CarpetIOScalar" - -IOScalar::one_file_per_group = yes - -IOScalar::outScalar_every = 1 -IOScalar::outScalar_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - - - -ActiveThorns = "CarpetIOASCII" - -IOASCII::one_file_per_group = yes - -#IOASCII::output_symmetry_points = no -#IOASCII::out3D_ghosts = no - -IOASCII::out0D_every = 1 -IOASCII::out0D_vars = " - Carpet::timing - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - -IOASCII::out1D_every = 1 -IOASCII::out1D_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - -IOASCII::out2D_every = 10 -IOASCII::out2D_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - -IOASCII::out3D_every = 100 -IOASCII::out3D_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - - - -Activethorns = "CarpetIOHDF5" - -IOHDF5::out_every = 100 -IOHDF5::compression_level = 1 -IOHDF5::out_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - -IOHDF5::checkpoint = yes -IO::checkpoint_dir = $parfile -IO::checkpoint_ID = yes -IO::checkpoint_every = 100 -IO::checkpoint_on_terminate = yes - -Carpet::regrid_during_recovery = no -IOHDF5::use_grid_structure_from_checkpoint = yes - -IO::recover = "autoprobe" -IO::recover_dir = $parfile - - - -ActiveThorns = "Formaline" - -Formaline::send_as_rdf = yes -Formaline::rdf_hostname[0] = "buran.aei.mpg.de" -Formaline::rdf_port [0] = 24997 -Formaline::rdf_hostname[1] = "devportal.cct.lsu.edu" -Formaline::rdf_port [1] = 8080 - - - -ActiveThorns = "Twitter" - - - -ActiveThorns = "TimerReport" - -TimerReport::out_every = 100 -TimerReport::out_filename = "TimerReport" diff --git a/CarpetDev/CarpetIOF5/par/wavetoy-cc-uni.par b/CarpetDev/CarpetIOF5/par/wavetoy-cc-uni.par deleted file mode 100644 index d5265e3c8..000000000 --- a/CarpetDev/CarpetIOF5/par/wavetoy-cc-uni.par +++ /dev/null @@ -1,230 +0,0 @@ -Cactus::cctk_run_title = "WaveToy cell-centred unigrid" - -Cactus::cctk_full_warnings = yes -Cactus::highlight_warning_messages = no -#Cactus::cctk_timer_output = "full" - -Cactus::terminate = "time" -Cactus::cctk_final_time = 1.0 - - - -ActiveThorns = "IOUtil" - -IO::out_dir = $parfile - - - -ActiveThorns = "InitBase" - -InitBase::initial_data_setup_method = "init_single_level" - - - -ActiveThorns = "AEILocalInterp" - -ActiveThorns = "Fortran" - -ActiveThorns = "HDF5" - -ActiveThorns = "LocalInterp" - -ActiveThorns = "LoopControl" - -ActiveThorns = "NaNCatcher" - -ActiveThorns = "Slab" - - - -ActiveThorns = "Carpet CarpetLib CarpetInterp CarpetReduce CarpetSlab" - -Carpet::verbose = no -Carpet::schedule_barriers = no -Carpet::veryverbose = no -CarpetLib::output_bboxes = no - -Carpet::domain_from_coordbase = yes -Carpet::max_refinement_levels = 3 - -driver::ghost_size = 2 - -Carpet::refinement_centering = "cell" -Carpet::prolongation_order_space = 3 -Carpet::prolongation_order_time = 2 - -Carpet::convergence_level = 0 - -Carpet::init_each_timelevel = yes -Carpet::regrid_during_initialisation = no -Carpet::enable_all_storage = no - -Carpet::poison_new_timelevels = yes -CarpetLib::poison_new_memory = yes - -Carpet::grid_structure_filename = "carpet-grid-structure" -Carpet::output_timers_every = 100 -CarpetLib::print_timestats_every = 100 -CarpetLib::print_memstats_every = 100 - - - -ActiveThorns = "NaNChecker" - -NaNChecker::check_every = 100 -NaNChecker::action_if_found = "terminate" -NaNChecker::check_vars = " - WaveToy::scalarevolve -" - - - -ActiveThorns = "Boundary CartGrid3D CoordBase SymBase" - -CoordBase::domainsize = "minmax" - -CoordBase::xmin = -0.50 -CoordBase::ymin = -0.50 -CoordBase::zmin = -0.50 -CoordBase::xmax = +0.50 -CoordBase::ymax = +0.50 -CoordBase::zmax = +0.50 -CoordBase::dx = 0.0125 -CoordBase::dy = 0.0125 -CoordBase::dz = 0.0125 - -CoordBase::boundary_staggered_x_lower = yes -CoordBase::boundary_staggered_y_lower = yes -CoordBase::boundary_staggered_z_lower = yes -CoordBase::boundary_staggered_x_upper = yes -CoordBase::boundary_staggered_y_upper = yes -CoordBase::boundary_staggered_z_upper = yes - -CartGrid3D::type = "coordbase" - - - -ActiveThorns = "WavetoyC" - -WaveToy::bound = "radiation" - - - -ActiveThorns = "IDScalarWaveC" - -IDScalarWave::initial_data = "gaussian" -IDScalarWave::radius = 0.0 -IDScalarWave::sigma = 0.1 -IDScalarWave::amplitude = 1.0 - - - -ActiveThorns = "Time" - -Time::dtfac = 0.5 - - - -ActiveThorns = "CarpetIOBasic" - -IOBasic::outInfo_every = 1 -IOBasic::outInfo_reductions = "norm2 minimum maximum" -IOBasic::outInfo_vars = " - WaveToy::phi -" - - - -ActiveThorns = "CarpetIOScalar" - -IOScalar::one_file_per_group = yes - -IOScalar::outScalar_every = 1 -IOScalar::outScalar_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - - - -ActiveThorns = "CarpetIOASCII" - -IOASCII::one_file_per_group = yes - -IOASCII::output_symmetry_points = no -IOASCII::out3D_ghosts = no - -IOASCII::out0D_every = 1 -IOASCII::out0D_vars = " - Carpet::timing - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - -IOASCII::out1D_every = 1 -IOASCII::out1D_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - -IOASCII::out2D_every = 10 -IOASCII::out2D_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - -IOASCII::out3D_every = 100 -IOASCII::out3D_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - - - -Activethorns = "CarpetIOHDF5" - -IOHDF5::out_every = 100 -IOHDF5::compression_level = 1 -IOHDF5::out_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - -IOHDF5::checkpoint = yes -IO::checkpoint_dir = $parfile -IO::checkpoint_ID = yes -IO::checkpoint_every = 100 -IO::checkpoint_on_terminate = yes - -Carpet::regrid_during_recovery = no -IOHDF5::use_grid_structure_from_checkpoint = yes - -IO::recover = "autoprobe" -IO::recover_dir = $parfile - - - -ActiveThorns = "Formaline" - -Formaline::send_as_rdf = yes -Formaline::rdf_hostname[0] = "buran.aei.mpg.de" -Formaline::rdf_port [0] = 24997 -Formaline::rdf_hostname[1] = "devportal.cct.lsu.edu" -Formaline::rdf_port [1] = 8080 - - - -ActiveThorns = "Twitter" - - - -ActiveThorns = "TimerReport" - -TimerReport::out_every = 100 -TimerReport::out_filename = "TimerReport" diff --git a/CarpetDev/CarpetIOF5/par/wavetoy-vc-ref.par b/CarpetDev/CarpetIOF5/par/wavetoy-vc-ref.par deleted file mode 100644 index 46ccdd6b2..000000000 --- a/CarpetDev/CarpetIOF5/par/wavetoy-vc-ref.par +++ /dev/null @@ -1,244 +0,0 @@ -Cactus::cctk_run_title = "WaveToy vertex-centred refined" - -Cactus::cctk_full_warnings = yes -Cactus::highlight_warning_messages = no -#Cactus::cctk_timer_output = "full" - -Cactus::terminate = "time" -Cactus::cctk_final_time = 1.0 - - - -ActiveThorns = "IOUtil" - -IO::out_dir = $parfile - - - -ActiveThorns = "InitBase" - -InitBase::initial_data_setup_method = "init_single_level" - - - -ActiveThorns = "AEILocalInterp" - -ActiveThorns = "Fortran" - -ActiveThorns = "HDF5" - -ActiveThorns = "LocalInterp" - -ActiveThorns = "LoopControl" - -ActiveThorns = "NaNCatcher" - -ActiveThorns = "Slab" - - - -ActiveThorns = "Carpet CarpetLib CarpetInterp CarpetReduce CarpetSlab" - -Carpet::verbose = no -Carpet::schedule_barriers = no -Carpet::veryverbose = no -CarpetLib::output_bboxes = no - -Carpet::domain_from_coordbase = yes -Carpet::max_refinement_levels = 3 - -driver::ghost_size = 2 - -Carpet::refinement_centering = "vertex" -Carpet::prolongation_order_space = 3 -Carpet::prolongation_order_time = 2 - -Carpet::convergence_level = 0 - -Carpet::init_each_timelevel = yes -Carpet::regrid_during_initialisation = no -Carpet::enable_all_storage = no - -Carpet::poison_new_timelevels = yes -CarpetLib::poison_new_memory = yes - -Carpet::grid_structure_filename = "carpet-grid-structure" -Carpet::output_timers_every = 100 -CarpetLib::print_timestats_every = 100 -CarpetLib::print_memstats_every = 100 - - - -ActiveThorns = "NaNChecker" - -NaNChecker::check_every = 100 -NaNChecker::action_if_found = "terminate" -NaNChecker::check_vars = " - WaveToy::scalarevolve -" - - - -ActiveThorns = "Boundary CartGrid3D CoordBase SymBase" - -CoordBase::domainsize = "minmax" - -CoordBase::xmin = -0.50 -CoordBase::ymin = -0.50 -CoordBase::zmin = -0.50 -CoordBase::xmax = +0.50 -CoordBase::ymax = +0.50 -CoordBase::zmax = +0.50 -CoordBase::dx = 0.05 -CoordBase::dy = 0.05 -CoordBase::dz = 0.05 - -CoordBase::boundary_staggered_x_lower = no -CoordBase::boundary_staggered_y_lower = no -CoordBase::boundary_staggered_z_lower = no -CoordBase::boundary_staggered_x_upper = no -CoordBase::boundary_staggered_y_upper = no -CoordBase::boundary_staggered_z_upper = no - -CartGrid3D::type = "coordbase" - - - -ActiveThorns = "CarpetRegrid2" - -CarpetRegrid2::regrid_every = 0 - -CarpetRegrid2::snap_to_coarse = yes - -CarpetRegrid2::num_centres = 1 - -CarpetRegrid2::num_levels_1 = 3 -CarpetRegrid2::radius_1[1] = 0.25 -CarpetRegrid2::radius_1[2] = 0.125 - - - -ActiveThorns = "WavetoyC" - -WaveToy::bound = "radiation" - - - -ActiveThorns = "IDScalarWaveC" - -IDScalarWave::initial_data = "gaussian" -IDScalarWave::radius = 0.0 -IDScalarWave::sigma = 0.1 -IDScalarWave::amplitude = 1.0 - - - -ActiveThorns = "Time" - -Time::dtfac = 0.5 - - - -ActiveThorns = "CarpetIOBasic" - -IOBasic::outInfo_every = 1 -IOBasic::outInfo_reductions = "norm2 minimum maximum" -IOBasic::outInfo_vars = " - WaveToy::phi -" - - - -ActiveThorns = "CarpetIOScalar" - -IOScalar::one_file_per_group = yes - -IOScalar::outScalar_every = 1 -IOScalar::outScalar_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - - - -ActiveThorns = "CarpetIOASCII" - -IOASCII::one_file_per_group = yes - -#IOASCII::output_symmetry_points = no -#IOASCII::out3D_ghosts = no - -IOASCII::out0D_every = 1 -IOASCII::out0D_vars = " - Carpet::timing - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - -IOASCII::out1D_every = 1 -IOASCII::out1D_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - -IOASCII::out2D_every = 10 -IOASCII::out2D_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - -IOASCII::out3D_every = 100 -IOASCII::out3D_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - - - -Activethorns = "CarpetIOHDF5" - -IOHDF5::out_every = 100 -IOHDF5::compression_level = 1 -IOHDF5::out_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - -IOHDF5::checkpoint = yes -IO::checkpoint_dir = $parfile -IO::checkpoint_ID = yes -IO::checkpoint_every = 100 -IO::checkpoint_on_terminate = yes - -Carpet::regrid_during_recovery = no -IOHDF5::use_grid_structure_from_checkpoint = yes - -IO::recover = "autoprobe" -IO::recover_dir = $parfile - - - -ActiveThorns = "Formaline" - -Formaline::send_as_rdf = yes -Formaline::rdf_hostname[0] = "buran.aei.mpg.de" -Formaline::rdf_port [0] = 24997 -Formaline::rdf_hostname[1] = "devportal.cct.lsu.edu" -Formaline::rdf_port [1] = 8080 - - - -ActiveThorns = "Twitter" - - - -ActiveThorns = "TimerReport" - -TimerReport::out_every = 100 -TimerReport::out_filename = "TimerReport" diff --git a/CarpetDev/CarpetIOF5/par/wavetoy-vc-uni.par b/CarpetDev/CarpetIOF5/par/wavetoy-vc-uni.par deleted file mode 100644 index e2339f342..000000000 --- a/CarpetDev/CarpetIOF5/par/wavetoy-vc-uni.par +++ /dev/null @@ -1,245 +0,0 @@ -Cactus::cctk_run_title = "WaveToy vertex-centred unigrid" - -Cactus::cctk_full_warnings = yes -Cactus::highlight_warning_messages = no - -Cactus::terminate = "time" -Cactus::cctk_final_time = 1.0 - - - -ActiveThorns = "IOUtil" - -IO::out_dir = $parfile - - - -ActiveThorns = "InitBase" - -InitBase::initial_data_setup_method = "init_single_level" - - - -ActiveThorns = "AEILocalInterp" - -ActiveThorns = "Fortran" - -ActiveThorns = "HDF5" - -ActiveThorns = "LocalInterp" - -ActiveThorns = "LoopControl" - -ActiveThorns = "NaNCatcher" - -ActiveThorns = "Slab" - - - -ActiveThorns = "Carpet CarpetLib CarpetInterp CarpetReduce CarpetSlab" - -Carpet::verbose = no -Carpet::schedule_barriers = no -Carpet::veryverbose = no -CarpetLib::output_bboxes = no - -Carpet::domain_from_coordbase = yes -Carpet::max_refinement_levels = 3 - -driver::ghost_size = 2 - -Carpet::refinement_centering = "vertex" -Carpet::prolongation_order_space = 3 -Carpet::prolongation_order_time = 2 - -Carpet::convergence_level = 0 - -Carpet::init_each_timelevel = yes -Carpet::regrid_during_initialisation = no -Carpet::enable_all_storage = no - -Carpet::poison_new_timelevels = yes -CarpetLib::poison_new_memory = yes - -Carpet::grid_structure_filename = "carpet-grid-structure" -Carpet::output_timers_every = 100 -CarpetLib::print_timestats_every = 100 -CarpetLib::print_memstats_every = 100 - - - -ActiveThorns = "NaNChecker" - -NaNChecker::check_every = 100 -NaNChecker::action_if_found = "terminate" -NaNChecker::check_vars = " - WaveToy::scalarevolve -" - - - -ActiveThorns = "Boundary CartGrid3D CoordBase SymBase" - -CoordBase::domainsize = "minmax" - -CoordBase::xmin = -0.50 -CoordBase::ymin = -0.50 -CoordBase::zmin = -0.50 -CoordBase::xmax = +0.50 -CoordBase::ymax = +0.50 -CoordBase::zmax = +0.50 -CoordBase::dx = 0.0125 -CoordBase::dy = 0.0125 -CoordBase::dz = 0.0125 - -CoordBase::boundary_staggered_x_lower = no -CoordBase::boundary_staggered_y_lower = no -CoordBase::boundary_staggered_z_lower = no -CoordBase::boundary_staggered_x_upper = no -CoordBase::boundary_staggered_y_upper = no -CoordBase::boundary_staggered_z_upper = no - -CartGrid3D::type = "coordbase" - - - -ActiveThorns = "WavetoyC" - -WaveToy::bound = "radiation" - - - -ActiveThorns = "IDScalarWaveC" - -IDScalarWave::initial_data = "gaussian" -IDScalarWave::radius = 0.0 -IDScalarWave::sigma = 0.1 -IDScalarWave::amplitude = 1.0 - - - -ActiveThorns = "Time" - -Time::dtfac = 0.5 - - - -ActiveThorns = "CarpetIOBasic" - -IOBasic::outInfo_every = 1 -IOBasic::outInfo_reductions = "norm2 minimum maximum" -IOBasic::outInfo_vars = " - WaveToy::phi -" - - - -#ActiveThorns = "CarpetIOScalar" -# -#IOScalar::one_file_per_group = yes -# -#IOScalar::outScalar_every = 1 -#IOScalar::outScalar_vars = " -# grid::coordinates -# CarpetReduce::weight -# WaveToy::scalarevolve -#" - - - -ActiveThorns = "CarpetIOASCII" - -IOASCII::one_file_per_group = yes - -IOASCII::output_symmetry_points = yes # no -IOASCII::out3D_ghosts = yes # no - -#IOASCII::out0D_every = 1 -#IOASCII::out0D_vars = " -# Carpet::timing -# grid::coordinates -# CarpetReduce::weight -# WaveToy::scalarevolve -#" - -IOASCII::out1D_every = 1 -IOASCII::out1D_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - -#IOASCII::out2D_every = 10 -#IOASCII::out2D_vars = " -# grid::coordinates -# CarpetReduce::weight -# WaveToy::scalarevolve -#" -# -#IOASCII::out3D_every = 100 -#IOASCII::out3D_vars = " -# grid::coordinates -# CarpetReduce::weight -# WaveToy::scalarevolve -#" - - - -Activethorns = "CarpetIOHDF5" - -IOHDF5::out_every = 64 -IOHDF5::compression_level = 1 -IOHDF5::out_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - -#IOHDF5::checkpoint = yes -#IO::checkpoint_dir = $parfile -#IO::checkpoint_ID = yes -#IO::checkpoint_every = 100 -#IO::checkpoint_on_terminate = yes -# -#Carpet::regrid_during_recovery = no -#IOHDF5::use_grid_structure_from_checkpoint = yes -# -#IO::recover = "autoprobe" -#IO::recover_dir = $parfile - - - -Activethorns = "CarpetIOF5" - -IOF5::out_every = 64 -IOF5::chunk_size_x = 8 -IOF5::chunk_size_y = 8 -IOF5::chunk_size_z = 8 -IOF5::compression_level = 1 -IOF5::write_checksum = yes -IOF5::out_vars = " - grid::coordinates - CarpetReduce::weight - WaveToy::scalarevolve -" - - -ActiveThorns = "Formaline" - -Formaline::send_as_rdf = yes -Formaline::rdf_hostname[0] = "buran.aei.mpg.de" -Formaline::rdf_port [0] = 24997 -Formaline::rdf_hostname[1] = "devportal.cct.lsu.edu" -Formaline::rdf_port [1] = 8080 - - - -ActiveThorns = "Twitter" - - - -ActiveThorns = "TimerReport" - -TimerReport::out_every = 100 -TimerReport::output_all_timers_together = yes -TimerReport::out_filename = "TimerReport" diff --git a/CarpetDev/CarpetIOF5/param.ccl b/CarpetDev/CarpetIOF5/param.ccl deleted file mode 100644 index f9d1249bd..000000000 --- a/CarpetDev/CarpetIOF5/param.ccl +++ /dev/null @@ -1,154 +0,0 @@ -# Parameter definitions for thorn CarpetIOF5 - -BOOLEAN verbose "Produce screen output while running" -{ -} no - -BOOLEAN veryverbose "Produce much screen output while running" -{ -} no - - - -SHARES: IO - -USES KEYWORD out_mode -USES INT out_proc_every - -USES INT out_timesteps_per_file - -USES KEYWORD out_save_parameters - -USES STRING out_dir AS IO_out_dir -USES KEYWORD out_criterion AS IO_out_criterion -USES INT out_every AS IO_out_every -USES REAL out_dt AS IO_out_dt - - - -PRIVATE: - -STRING out_dir "Output directory (overrides IO::out_dir)" STEERABLE=always -{ - "^$" :: "Empty: use IO::out_dir" - ".+" :: "Not empty: directory name" -} "" - -KEYWORD file_content "Create one file for every x" STEERABLE=always -{ - "variable" :: "" - "group" :: "" - "thorn" :: "" - "everything" :: "" -} "group" - -INT iteration_digits "Minimum number of digits for iteration number" STEERABLE=always -{ - 0:* :: "" -} 10 - -STRING out_filename "File name (without extension) for file_content='everything'" STEERABLE=always -{ - "" :: "" -} "output" - -INT processor_digits "Minimum number of digits for processor number" STEERABLE=always -{ - 0:* :: "" -} 6 - -STRING out_extension "File name extension" STEERABLE=always -{ - "" :: "File extension (including a leading dot, if desired)" -} ".f5" - -BOOLEAN create_subdirs "Create subdirectories for the output files to reduce the number of files per directory" STEERABLE=always -{ -} "no" - -BOOLEAN one_dir_per_file "Create one subdirectory per output file to reduce locking overhead" STEERABLE=always -{ -} "no" - - - - -STRING out_vars "Variables and groups which should be output in the F5 file format" STEERABLE=always -{ - "" :: "List of group or variable names" -} "" - -KEYWORD out_criterion "Criterion to select CarpetIOHDF5 output intervals" STEERABLE=always -{ - "default" :: "Use IO::out_criterion" - "always" :: "Always output" - "never" :: "Never output" - "iteration" :: "Output every so many iterations" - "time" :: "Output every that much coordinate time" -} "default" - -INT out_every "How often to do CarpetIOF5 output (overrides IO::out_every)" STEERABLE=always -{ - 1:* :: "Output every so many time steps" - 0 :: "As often as possible" - -1 :: "No output" - -2 :: "Use IO::out_every" -} -2 - -REAL out_dt "How often to do CarpetIOF5 output (overrides IO::out_dt)" STEERABLE=always -{ - (0:* :: "In intervals of that much coordinate time" - 0 :: "As often as possible" - -1 :: "No output" - -2 :: "Use IO::out_dt" -} -2 - -REAL dt_fudge "Fudge factor for time comparisons" STEERABLE=always -{ - 0:* :: "" -} 1.0e-12 - - - -INT chunk_size_x "Chunk size for chunked datasets" STEERABLE=always -{ - -1 :: "no chunking (use actual dataset size)" - 1:* :: "desired chunk size" -} -1 - -INT chunk_size_y "Chunk size for chunked datasets" STEERABLE=always -{ - -1 :: "no chunking (use actual dataset size)" - 1:* :: "desired chunk size" -} -1 - -INT chunk_size_z "Chunk size for chunked datasets" STEERABLE=always -{ - -1 :: "no chunking (use actual dataset size)" - 1:* :: "desired chunk size" -} -1 - -INT compression_level "Compression level to use for writing HDF5 data" STEERABLE=always -{ - 0 :: "no compression" - 1:9 :: "higher numbers compress better" -} 0 - -BOOLEAN write_checksum "Add a checksum when writing HDF5 files" STEERABLE=always -{ -} "no" - -BOOLEAN check_checksum "Check checksum (if present) when reading HDF5 files" STEERABLE=always -{ -} "no" - - - -KEYWORD output_regions "Regions which should be output" STEERABLE=always -{ - "exterior" :: "whole region (including boundaries)" - #"communicated" :: "exterior without outer boundary" - "owned" :: "evolved in time" - # "active" :: "owned minus buffers" - "interior" :: "interior (without ghost zones)" -} "exterior" diff --git a/CarpetDev/CarpetIOF5/schedule.ccl b/CarpetDev/CarpetIOF5/schedule.ccl deleted file mode 100644 index 3f6209662..000000000 --- a/CarpetDev/CarpetIOF5/schedule.ccl +++ /dev/null @@ -1,14 +0,0 @@ -# Schedule definitions for thorn CarpetIOF5 - -STORAGE: next_output_iteration next_output_time this_iteration - -SCHEDULE CarpetIOF5_Startup AT startup AFTER IOUtil_Startup -{ - LANG: C -} "Startup routine" - -SCHEDULE CarpetIOF5_Init AT basegrid -{ - LANG: C - OPTIONS: global -} "Initialisation routine" diff --git a/CarpetDev/CarpetIOF5/src/IOF5.cc b/CarpetDev/CarpetIOF5/src/IOF5.cc deleted file mode 100644 index 1173f5228..000000000 --- a/CarpetDev/CarpetIOF5/src/IOF5.cc +++ /dev/null @@ -1,694 +0,0 @@ -#include <algorithm> -#include <cassert> -#include <cctype> -#include <cmath> -#include <cstdlib> -#include <cstring> -#include <iomanip> -#include <sstream> -#include <string> -#include <vector> - -// force HDF5 1.8.x installations to use the new API -#define H5Dcreate_vers 2 - -#include <hdf5.h> - -#include "cctk.h" -#include "cctk_Arguments.h" -#include "cctk_Parameters.h" - -#include "CactusBase/IOUtil/src/ioGH.h" -#include "CactusBase/IOUtil/src/ioutil_CheckpointRecovery.h" - -#include "carpet.hh" - -#include "defs.hh" - -#include "extending.hh" -#include "file.hh" -#include "utils.hh" -#include "writer.hh" - - - -namespace CarpetIOF5 { - - - - int const Error_none = 0; // no error - - int const Error_illegal_varname = -1; - int const Error_group_has_no_storage = -2; - - int const Error_lonely_option_string = -3; - int const Error_unterminated_option_string = -4; - int const Error_garbage_after_option_string = -5; - int const Error_invalid_variable_name = -6; - - - - extern "C" int - CarpetIOF5_Startup (); - - static void * - Setup (tFleshConfig * const fleshconfig, - int const convlevel, - cGH * const cctkGH); - - extern "C" void - CarpetIOF5_Init (CCTK_ARGUMENTS); - - - - static int - OutputGH (cGH const * cctkGH); - - static void - mark_variables (int variable, - char const * options, - void * ptr); - - - - static int - TimeToOutput (cGH const * cctkGH, - int variable); - - - - static int - TriggerOutput (cGH const * cctkGH, - int variable); - - - - static int - OutputVarAs (cGH const * cctkGH, - char const * varname, - char const * alias); - - - - static void - WriteParameters (F5::file_t & file); - - - - static string - generate_filename (cGH const * cctkGH, - int variable); - - - - int - CarpetIOF5_Startup () - { - DECLARE_CCTK_PARAMETERS; - - if (verbose) CCTK_INFO ("Startup"); - return extending_t::create (Setup); - } - - - - void * - Setup (tFleshConfig * const fleshconfig, - int const convlevel, - cGH * const cctkGH) - { - DECLARE_CCTK_PARAMETERS; - - assert (fleshconfig != 0); - if (verbose) CCTK_INFO ("Setup"); - return extending_t::setup - (cctkGH, OutputGH, TimeToOutput, TriggerOutput, OutputVarAs); - } - - - - void - CarpetIOF5_Init (CCTK_ARGUMENTS) - { - DECLARE_CCTK_ARGUMENTS; - DECLARE_CCTK_PARAMETERS; - - if (verbose) CCTK_INFO ("Init"); - - * next_output_iteration = 0; - * next_output_time = cctk_time; - * this_iteration = -1; - } - - - - int - OutputGH (cGH const * const cctkGH) - { - DECLARE_CCTK_PARAMETERS; - - assert (cctkGH != 0); - - if (verbose) CCTK_INFO ("OutputGH"); - - int ierr; - - vector<bool> want_variables (CCTK_NumVars()); - ierr - = CCTK_TraverseString (out_vars, - mark_variables, - static_cast<void *> (& want_variables), - CCTK_GROUP_OR_VAR); - switch (ierr) { - case -2: return Error_lonely_option_string; - case -3: return Error_unterminated_option_string; - case -4: return Error_garbage_after_option_string; - case -5: return Error_invalid_variable_name; - } - assert (ierr >= 0); - - ierr = Error_none; - for (int variable = 0; variable < CCTK_NumVars(); ++ variable) - { - if (want_variables.at(variable)) - { - if (TimeToOutput (cctkGH, variable)) - { - ierr = TriggerOutput (cctkGH, variable); - } - } - } - - return ierr; - } - - - - void - mark_variables (int const variable, - char const * const options, - void * const ptr) - { - vector<bool> & want_variables = * static_cast<vector<bool> *> (ptr); - want_variables.at (variable) = true; - } - - - - int - TimeToOutput (cGH const * const cctkGH, - int const variable) - { - DECLARE_CCTK_ARGUMENTS; - DECLARE_CCTK_PARAMETERS; - - assert (cctkGH != 0); - assert (variable >= 0 and variable < CCTK_NumVars()); - - assert (Carpet::is_level_mode()); - - if (verbose) - { - char * const fullname = CCTK_FullName(variable); - CCTK_VInfo (CCTK_THORNSTRING, "TimeToOutput \"%s\"", fullname); - free (fullname); - } - - bool should_output; - - char const * const my_out_criterion - = (CCTK_EQUALS (out_criterion, "default") - ? IO_out_criterion - : out_criterion); - - if (CCTK_EQUALS (my_out_criterion, "always")) - { - should_output = true; - } - else if (CCTK_EQUALS (my_out_criterion, "never")) - { - should_output = false; - } - else if (CCTK_EQUALS (my_out_criterion, "iteration")) - { - int const my_out_every = out_every == -2 ? IO_out_every : out_every; - switch (my_out_every) - { - case 0: - should_output = true; - break; - case -1: - should_output = false; - break; - default: - if (* this_iteration == cctk_iteration) - { - // we already decided to output this iteration - should_output = true; - } - else if (cctk_iteration >= * next_output_iteration) - { - // it is time for the next output - should_output = true; - * this_iteration = cctk_iteration; - * next_output_iteration = cctk_iteration + my_out_every; - } - else - { - should_output = false; - } - break; - } - } - else if (CCTK_EQUALS (my_out_criterion, "time")) - { - CCTK_REAL const my_out_dt = out_dt == -2 ? IO_out_dt : out_dt; - if (out_dt == 0) - { - should_output = true; - } - else if (out_dt == -1) - { - should_output = false; - } - else - { - if (* this_iteration == cctk_iteration) - { - // we already decided to output this iteration - should_output = true; - } - else if (cctk_time / cctk_delta_time - >= * next_output_time / cctk_delta_time - dt_fudge) - { - // it is time for the next output - should_output = true; - * this_iteration = cctk_iteration; - * next_output_time = cctk_time + my_out_dt; - } - else - { - should_output = false; - } - } - } - else - { - CCTK_WARN (1, "internal error"); - should_output = false; - } - - if (should_output) - { - extending_t extending (cctkGH); - int const last_output_iteration - = (extending.get_last_output_iteration - (Carpet::mglevel, Carpet::reflevel, variable)); - assert (last_output_iteration <= cctk_iteration); - if (last_output_iteration == cctk_iteration) - { - // Skipping output for variable, because this variable has - // already been output during the current iteration -- - // probably via a trigger during the analysis stage - should_output = false; - } - else - { - extending.set_last_output_iteration - (Carpet::mglevel, Carpet::reflevel, variable, cctk_iteration); - } - } - - return should_output; - } - - - - int - TriggerOutput (cGH const * const cctkGH, - int const variable) - { - DECLARE_CCTK_PARAMETERS; - - assert (cctkGH != 0); - assert (variable >= 0 and variable < CCTK_NumVars()); - - char * const fullname = CCTK_FullName (variable); - assert (fullname); - - if (verbose) - { - CCTK_VInfo (CCTK_THORNSTRING, "TriggerOutput \"%s\"", fullname); - } - - string const alias = generate_filename (cctkGH, variable); - - int const ierr = OutputVarAs (cctkGH, fullname, alias.c_str()); - - free (fullname); - - return ierr; - } - - - - int - OutputVarAs (cGH const * const cctkGH, - char const * const varname, - char const * const alias) - { - DECLARE_CCTK_PARAMETERS; - - assert (cctkGH != 0); - assert (varname != 0); - assert (alias != 0); - - if (verbose) - { - CCTK_VInfo (CCTK_THORNSTRING, "OutputVarAs \"%s\" \"%s\"", - varname, alias); - } - - int const variable = CCTK_VarIndex (varname); - if (variable < 0) - { - return Error_illegal_varname; - } - assert (variable >= 0 and variable < CCTK_NumVars()); - - int const group = CCTK_GroupIndexFromVarI (variable); - assert (group >= 0 and group < CCTK_NumGroups()); - - if (CCTK_ActiveTimeLevelsGI (cctkGH, group) == 0) - { - return Error_group_has_no_storage; - } - - extending_t extending (cctkGH); - - bool const use_IO_out_dir = strcmp (out_dir, "") == 0; - string const path = use_IO_out_dir ? IO_out_dir : out_dir; - string const basename = alias; - - bool const did_truncate = extending.get_did_truncate (basename); - bool const do_truncate - = not did_truncate and IO_TruncateOutputFiles (cctkGH); - extending.set_did_truncate (basename); - - int const proc = CCTK_MyProc (cctkGH); - bool have_metafile; // whether there is a metadata file - int metadata_processor; // the processor which outputs the metadata file - int output_processor; // the processor which outputs our data - if (CCTK_EQUALS (out_mode, "proc")) - { - have_metafile = true; - metadata_processor = 0; - output_processor = proc; - } - else if (CCTK_EQUALS (out_mode, "np")) - { - have_metafile = true; - metadata_processor = 0; - output_processor = proc / out_proc_every * out_proc_every; - } - else if (CCTK_EQUALS (out_mode, "onefile")) - { - have_metafile = false; - metadata_processor = 0; - output_processor = 0; - } - else - { - assert (0); - } - - F5::file_t * metafile = NULL; - if (have_metafile and proc == metadata_processor) - { - metafile - = new F5::file_t (cctkGH, path, basename, string (out_extension), - do_truncate, true, false); - } - - F5::file_t * file = NULL; - if (proc == output_processor) - { - file = new F5::file_t (cctkGH, path, basename, string (out_extension), - do_truncate, not have_metafile, true); - } - - if (do_truncate) - { - // Output parameters once after the output file has been created - if (proc == metadata_processor) - { - if (CCTK_EQUALS (out_save_parameters, "all") or - CCTK_EQUALS (out_save_parameters, "only set")) - { - WriteParameters (have_metafile ? * metafile : * file); - } - else if (CCTK_EQUALS (out_save_parameters, "no")) - { - // do nothing - } - else - { - assert (0); - } - } - } - - if (metafile) - { - writer_t writer (cctkGH, variable); - writer.write (* metafile); - delete metafile; - metafile = NULL; - } - { - writer_t writer (cctkGH, variable); -#warning "TODO: handle the case where not all processors are writing to their own file" - assert (proc == output_processor); - assert (file); - writer.write (* file); - delete file; - file = NULL; - } - - return Error_none; - } - - - - void - WriteParameters (F5::file_t & file) - { - DECLARE_CCTK_PARAMETERS; - - cGH const * const cctkGH = file.get_cctkGH (); - - hid_t const hdf5_file = file.get_hdf5_file(); - - hid_t const attribute_group - = F5::open_or_create_group (hdf5_file, - "Parameters and Global Attributes"); - assert (attribute_group >= 0); - - // unique configuration identifier - if (CCTK_IsFunctionAliased ("UniqueConfigID")) { - F5::write_or_check_attribute - (attribute_group, "config id", - static_cast<char const *> (UniqueConfigID (cctkGH))); - } - - // unique build identifier - if (CCTK_IsFunctionAliased ("UniqueBuildID")) { - F5::write_or_check_attribute - (attribute_group, "build id", - static_cast<char const *> (UniqueBuildID (cctkGH))); - } - - // unique simulation identifier - if (CCTK_IsFunctionAliased ("UniqueSimulationID")) { - F5::write_or_check_attribute - (attribute_group, "simulation id", - static_cast<char const *> (UniqueSimulationID (cctkGH))); - } - - // unique run identifier - if (CCTK_IsFunctionAliased ("UniqueRunID")) { - F5::write_or_check_attribute - (attribute_group, "run id", - static_cast<char const *> (UniqueRunID (cctkGH))); - } - - // Output Cactus parameters as single string - { - char * const parameters = IOUtil_GetAllParameters (cctkGH, true); - assert (parameters); - // Create a dataset, since the data may not fit into an attribute - hsize_t const size = strlen (parameters) + 1; - hid_t const dataspace = H5Screate_simple (1, & size, NULL); - assert (dataspace >= 0); - hid_t properties = H5Pcreate (H5P_DATASET_CREATE); - assert (properties >= 0); - check (not H5Pset_chunk (properties, 1, & size)); - if (compression_level > 0) - { - check (not H5Pset_deflate (properties, compression_level)); - } - if (write_checksum) - { - check (not H5Pset_fletcher32 (properties)); - } - hid_t const dataset - = H5Dcreate (attribute_group, "All Parameters", H5T_NATIVE_CHAR, - dataspace, H5P_DEFAULT, - properties, H5P_DEFAULT); - assert (dataset >= 0); - check (not H5Dwrite (dataset, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, - H5P_DEFAULT, parameters)); - check (not H5Dclose (dataset)); - check (not H5Pclose (properties)); - check (not H5Sclose (dataspace)); - free (parameters); - } - - check (not H5Gclose (attribute_group)); - - // This is far too slow to be useful -#if 0 - hid_t const parameter_group - = F5::open_or_create_group (hdf5_file, "Cactus parameters"); - assert (parameter_group >= 0); - - int first = 1; - for (;;) - { - cParamData const * parameter_data; - char * parameter_fullname; - - int const ierr - = CCTK_ParameterWalk (first, 0, - & parameter_fullname, & parameter_data); - if (ierr > 0) break; - assert (ierr >= 0); - - int type; - void const * const parameter_value - = CCTK_ParameterGet (parameter_data->name, parameter_data->thorn, - & type); - assert (type == parameter_data->type); - assert (parameter_value != 0); - - switch (type) - { - case PARAMETER_BOOLEAN: - case PARAMETER_INT: - { - CCTK_INT const value - = * static_cast<CCTK_INT const *> (parameter_value); - F5::write_or_check_attribute - (parameter_group, parameter_fullname, value); - } - break; - case PARAMETER_REAL: - { - CCTK_REAL const value - = * static_cast<CCTK_REAL const *> (parameter_value); - F5::write_or_check_attribute - (parameter_group, parameter_fullname, value); - } - break; - case PARAMETER_KEYWORD: - case PARAMETER_STRING: - { - char const * const value - = * static_cast<char const * const *> (parameter_value); - F5::write_or_check_attribute - (parameter_group, parameter_fullname, value); - } - break; - default: - assert (0); - } - - free (parameter_fullname); - - first = 0; - } - - check (not H5Gclose (parameter_group)); -#endif - } - - - - string - generate_filename (cGH const * const cctkGH, - int const variable) - { - DECLARE_CCTK_PARAMETERS; - - assert (variable >= 0); - - ostringstream filename_buf; - - if (CCTK_EQUALS (file_content, "variable")) - { - char * const varname = CCTK_FullName (variable); - assert (varname); - for (char * p = varname; * p; ++ p) - { - *p = tolower (* p); - } - filename_buf << varname; - free (varname); - } - else if (CCTK_EQUALS (file_content, "group")) - { - char * const groupname = CCTK_GroupNameFromVarI (variable); - assert (groupname); - for (char * p = groupname; * p; ++ p) - { - *p = tolower (* p); - } - filename_buf << groupname; - free (groupname); - } - else if (CCTK_EQUALS (file_content, "thorn")) - { - char const * const impname = CCTK_ImpFromVarI (variable); - char * const thornname = strdup (impname); - assert (thornname); - char * const colon = strchr (thornname, ':'); - assert (colon); - * colon = '\0'; - for (char * p = thornname; * p; ++ p) - { - *p = tolower (* p); - } - filename_buf << thornname; - free (thornname); - } - else if (CCTK_EQUALS (file_content, "everything")) - { - filename_buf << out_filename; - } - else - { - assert (0); - } - - if (out_timesteps_per_file > 0) - { - int const iteration = (cctkGH->cctk_iteration - / out_timesteps_per_file * out_timesteps_per_file); - filename_buf << ".it" - << setw (iteration_digits) << setfill ('0') << iteration; - } - - return filename_buf.str(); - } - -} // namespace CarpetIOF5 diff --git a/CarpetDev/CarpetIOF5/src/coordinate_system.cc b/CarpetDev/CarpetIOF5/src/coordinate_system.cc deleted file mode 100644 index e030c08a9..000000000 --- a/CarpetDev/CarpetIOF5/src/coordinate_system.cc +++ /dev/null @@ -1,166 +0,0 @@ -#include <sstream> -#include <string> - -#include <hdf5.h> - -#include "cctk.h" - -#include "coordinate_system.hh" -#include "utils.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - coordinate_system_t:: - coordinate_system_t (topology_t & topology) - : m_topology (topology) - { - } - - - - coordinate_system_t:: - ~ coordinate_system_t () - { - } - - - - topology_t & coordinate_system_t:: - get_topology () - const - { - return m_topology; - } - - - - hid_t coordinate_system_t:: - get_hdf5_coordinate_system () - const - { - return m_hdf5_coordinate_system; - } - - - - bool coordinate_system_t:: - invariant () - const - { - return true; - } - - - - Cartesian_coordinate_system_t:: - Cartesian_coordinate_system_t (topology_t & topology, - vect<CCTK_REAL, dim> const & level_origin, - vect<CCTK_REAL, dim> const & level_delta) - : coordinate_system_t (topology), - m_level_origin (level_origin), - m_level_delta (level_delta) - { - assert (all (m_level_delta > (CCTK_REAL) 0)); - - init(); - - assert (invariant()); - } - - - - Cartesian_coordinate_system_t:: - Cartesian_coordinate_system_t (topology_t & topology, - vect<CCTK_REAL, dim> const & coarse_origin, - vect<CCTK_REAL, dim> const & coarse_delta, - vect<int, dim> const & level_offset, - vect<int, dim> const & level_offset_denominator) - : coordinate_system_t (topology) - { - assert (all (coarse_delta > (CCTK_REAL) 0)); - assert (all (level_offset_denominator > 0)); - - mesh_refinement_topology_t * mesh_refinement_topology - = dynamic_cast<mesh_refinement_topology_t *> (& topology); - assert (mesh_refinement_topology != 0); - mesh_refinement_topology - ->calculate_level_origin_delta (coarse_origin, coarse_delta, - level_offset, level_offset_denominator, - m_level_origin, m_level_delta); - - init(); - - assert (invariant()); - } - - - - Cartesian_coordinate_system_t:: - ~ Cartesian_coordinate_system_t () - { - check (not H5Gclose (m_hdf5_coordinate_system)); - } - - - - void Cartesian_coordinate_system_t:: - init () - { - assert (all (m_level_delta > (CCTK_REAL) 0)); - - ostringstream namebuf; - namebuf << "Cartesian3D-" - << name_from_ivect (m_level_origin) - << "-" - << name_from_ivect (m_level_delta); - string const namestr = namebuf.str(); - m_name = namestr; - char const * const name = namestr.c_str(); - - m_hdf5_coordinate_system - = open_or_create_group (m_topology.get_hdf5_topology(), name); - assert (m_hdf5_coordinate_system >= 0); - -#warning "TODO: don't output coordinates as attributes" - write_or_check_attribute - (m_hdf5_coordinate_system, "origin", m_level_origin); - write_or_check_attribute - (m_hdf5_coordinate_system, "delta", m_level_delta); - } - - - - void coordinate_system_t:: - get_link_destination (int const proc, - string & filename, - string & objectname) - const - { - get_topology().get_link_destination (proc, filename, objectname); - if (objectname.empty()) - { - objectname = m_name; - } - else - { - objectname += string ("/") + m_name; - } - } - - - - bool Cartesian_coordinate_system_t:: - invariant () - const - { - return (coordinate_system_t::invariant() - and all (m_level_delta > (CCTK_REAL) 0)); - } - - } // namespace F5 - -} // namespace CarpetIOF5 diff --git a/CarpetDev/CarpetIOF5/src/coordinate_system.hh b/CarpetDev/CarpetIOF5/src/coordinate_system.hh deleted file mode 100644 index 2b67b4561..000000000 --- a/CarpetDev/CarpetIOF5/src/coordinate_system.hh +++ /dev/null @@ -1,104 +0,0 @@ -#ifndef COORDINATE_SYSTEM_HH -#define COORDINATE_SYSTEM_HH - -#include <hdf5.h> - -#include "cctk.h" - -#include "defs.hh" -#include "vect.hh" - -#include "topology.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - class coordinate_system_t { - - coordinate_system_t (); - coordinate_system_t (coordinate_system_t const &); - coordinate_system_t operator= (coordinate_system_t const &); - - protected: - - topology_t & m_topology; - - string m_name; - - hid_t m_hdf5_coordinate_system; - - coordinate_system_t (topology_t & topology); - - public: - - virtual - ~ coordinate_system_t (); - - topology_t & - get_topology () - const; - - hid_t - get_hdf5_coordinate_system () - const; - - void - get_link_destination (int proc, - string & filename, - string & objectname) - const; - - virtual bool - invariant () - const; - - }; - - - - class Cartesian_coordinate_system_t : public coordinate_system_t { - - vect<CCTK_REAL, dim> m_level_origin; - vect<CCTK_REAL, dim> m_level_delta; - - Cartesian_coordinate_system_t (); - Cartesian_coordinate_system_t (Cartesian_coordinate_system_t const &); - Cartesian_coordinate_system_t - operator= (Cartesian_coordinate_system_t const &); - - public: - - Cartesian_coordinate_system_t (topology_t & topology, - vect<CCTK_REAL, dim> const & level_origin, - vect<CCTK_REAL, dim> const & level_delta); - - Cartesian_coordinate_system_t (topology_t & topology, - vect<CCTK_REAL, dim> const & coarse_origin, - vect<CCTK_REAL, dim> const & coarse_delta, - vect<int, dim> const & level_offset, - vect<int, dim> const & level_offset_denominator); - - private: - - void - init (); - - public: - - virtual - ~ Cartesian_coordinate_system_t (); - - virtual bool - invariant () - const; - - }; - - } // namespace F5 - -} // namespace CarpetIOF5 - -#endif // #ifndef COORDINATE_SYSTEM_HH diff --git a/CarpetDev/CarpetIOF5/src/data_region.cc b/CarpetDev/CarpetIOF5/src/data_region.cc deleted file mode 100644 index 99b188323..000000000 --- a/CarpetDev/CarpetIOF5/src/data_region.cc +++ /dev/null @@ -1,91 +0,0 @@ -#include <cassert> -#include <cstdlib> -#include <sstream> -#include <string> - -#include <hdf5.h> - -#include "cctk.h" - -#include "carpet.hh" - -#include "data_region.hh" -#include "utils.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - using std::ostringstream; - - - - data_region_t:: - data_region_t (physical_quantity_t & physical_quantity, - bbox<int, dim> const & region) - : m_physical_quantity (physical_quantity), - m_region (region), - m_name (string ("region-") + F5::name_from_ibbox (region)) - { - assert (not region.empty()); - - m_hdf5_data_region - = open_or_create_group (m_physical_quantity - .get_hdf5_physical_quantity(), - m_name.c_str()); - assert (m_hdf5_data_region >= 0); - - assert (invariant()); - } - - - - data_region_t:: - ~ data_region_t () - { - herr_t const herr = H5Gclose (m_hdf5_data_region); - assert (not herr); - } - - - - physical_quantity_t & data_region_t:: - get_physical_quantity () - const - { - return m_physical_quantity; - } - - - - bbox<int, dim> const & data_region_t:: - get_region () - const - { - return m_region; - } - - - - hid_t data_region_t:: - get_hdf5_data_region () - const - { - return m_hdf5_data_region; - } - - - - bool data_region_t:: - invariant () - const - { - return (not m_region.empty() - and m_hdf5_data_region >= 0); - } - - } // namespace F5 - -} // namespace CarpetIOF5 diff --git a/CarpetDev/CarpetIOF5/src/data_region.hh b/CarpetDev/CarpetIOF5/src/data_region.hh deleted file mode 100644 index 35e5ecc79..000000000 --- a/CarpetDev/CarpetIOF5/src/data_region.hh +++ /dev/null @@ -1,64 +0,0 @@ -#ifndef DATA_REGION_HH -#define DATA_REGION_HH - -#include <string> - -#include <hdf5.h> - -#include "bbox.hh" -#include "defs.hh" - -#include "physical_quantity.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - using std::string; - - class data_region_t { - - physical_quantity_t & m_physical_quantity; - - bbox<int, dim> const m_region; - string const m_name; - - hid_t m_hdf5_data_region; - - data_region_t (); - data_region_t (data_region_t const &); - data_region_t operator= (data_region_t const &); - - public: - - data_region_t (physical_quantity_t & physical_quantity, - bbox<int, dim> const & region); - - virtual - ~ data_region_t (); - - physical_quantity_t & - get_physical_quantity () - const; - - bbox<int, dim> const & - get_region () - const; - - hid_t - get_hdf5_data_region () - const; - - virtual bool - invariant () - const; - - }; - - } // namespace F5 - -} // namespace CarpetIOF5 - -#endif // #ifndef DATA_REGION_HH diff --git a/CarpetDev/CarpetIOF5/src/extending.cc b/CarpetDev/CarpetIOF5/src/extending.cc deleted file mode 100644 index 26d63cb60..000000000 --- a/CarpetDev/CarpetIOF5/src/extending.cc +++ /dev/null @@ -1,113 +0,0 @@ -#include <cassert> -#include <cstring> - -#include "cctk.h" - -#include "extending.hh" - - - -namespace CarpetIOF5 { - - char const * const extending_t:: - extension_name = "CarpetIOF5"; - - int extending_t:: - create (void * (* const Setup) (tFleshConfig * config, - int convlevel, - cGH * cctkGH)) - { - int const handle = CCTK_RegisterGHExtension (extension_name); - assert (handle >= 0); - int const iflag = CCTK_RegisterGHExtensionSetupGH (handle, Setup); - assert (iflag); - return 0; // no error - } - - void * extending_t:: - setup (cGH * const cctkGH, - int (* const OutputGH) (cGH const * cctkGH), - int (* const TimeToOutput) (cGH const * cctkGH, - int variable), - int (* const TriggerOutput) (cGH const * cctkGH, - int variable), - int (* const OutputVarAs) (cGH const * cctkGH, - char const * varname, - char const * alias)) - { - assert (cctkGH != 0); - - int ierr; - int const io_method = CCTK_RegisterIOMethod (extension_name); - ierr = CCTK_RegisterIOMethodOutputGH (io_method, OutputGH); - assert (not ierr); - ierr = CCTK_RegisterIOMethodTimeToOutput (io_method, TimeToOutput); - assert (not ierr); - ierr = CCTK_RegisterIOMethodTriggerOutput (io_method, TriggerOutput); - assert (not ierr); - ierr = CCTK_RegisterIOMethodOutputVarAs (io_method, OutputVarAs); - assert (not ierr); - - return new extension_t; - } - - extending_t:: - extending_t (cGH const * cctkGH) - { - assert (cctkGH); - void * const ext = CCTK_GHExtension (cctkGH, extension_name); - assert (ext != 0); - m_extension = static_cast<extension_t *> (ext); - } - - bool extending_t:: - get_did_truncate (string const name) - const - { - return (m_extension->did_truncate.find (name) - != m_extension->did_truncate.end()); - } - - void extending_t:: - set_did_truncate (string const name) - { - m_extension->did_truncate.insert (name); - } - - int extending_t:: - get_last_output_iteration (int const ml, int const rl, int const vi) - const - { - resize_last_output_iteration (ml, rl, vi); - return m_extension->last_output_iteration.at(ml).at(rl).at(vi); - } - - void extending_t:: - set_last_output_iteration (int const ml, int const rl, int const vi, - int const iteration) - { - resize_last_output_iteration (ml, rl, vi); - m_extension->last_output_iteration.at(ml).at(rl).at(vi) = iteration; - } - - void extending_t:: - resize_last_output_iteration (int ml, int rl, int vi) - const - { - assert (ml >= 0); - if (size_t (ml) >= m_extension->last_output_iteration.size()) - { - m_extension->last_output_iteration.resize (ml+1); - } - assert (rl >= 0); - if (size_t (rl) >= m_extension->last_output_iteration.at(ml).size()) - { - m_extension->last_output_iteration.at(ml).resize (rl+1); - } - if (size_t (vi) >= m_extension->last_output_iteration.at(ml).at(rl).size()) - { - m_extension->last_output_iteration.at(ml).at(rl).resize (vi+1, -1); - } - } - -} // namespace CarpetIOF5 diff --git a/CarpetDev/CarpetIOF5/src/extending.hh b/CarpetDev/CarpetIOF5/src/extending.hh deleted file mode 100644 index 4f9bc9cc1..000000000 --- a/CarpetDev/CarpetIOF5/src/extending.hh +++ /dev/null @@ -1,76 +0,0 @@ -#ifndef EXTENDING_HH -#define EXTENDING_HH - -#include <set> -#include <string> -#include <vector> - -#include "cctk.h" - - - -namespace CarpetIOF5 { - - using std::set; - using std::string; - using std::vector; - - - - class extending_t { - - static char const * const extension_name; - - struct extension_t { - set<string> did_truncate; - // [mglevel][reflevel][variable]; - vector<vector<vector<int> > > last_output_iteration; - }; - - extension_t * m_extension; - - public: - - static int - create (void * (* Setup) (tFleshConfig * config, - int convlevel, - cGH * cctkGH)); - - static void * - setup (cGH * cctkGH, - int (* OutputGH) (cGH const * cctkGH), - int (* TimeToOutput) (cGH const * cctkGH, - int variable), - int (* TriggerOutput) (cGH const * cctkGH, - int variable), - int (* OutputVarAs) (cGH const * cctkGH, - char const * varname, - char const * alias)); - - extending_t (cGH const * cctkGH); - - bool - get_did_truncate (string name) - const; - - void - set_did_truncate (string name); - - int - get_last_output_iteration (int ml, int rl, int vi) - const; - - void - set_last_output_iteration (int ml, int rl, int vi, int iteration); - - private: - - void - resize_last_output_iteration (int ml, int rl, int vi) - const; - - }; - -} // namespace CarpetIOF5 - -#endif // #ifndef EXDENDING_HH diff --git a/CarpetDev/CarpetIOF5/src/f5writer.cc b/CarpetDev/CarpetIOF5/src/f5writer.cc deleted file mode 100644 index b351c7391..000000000 --- a/CarpetDev/CarpetIOF5/src/f5writer.cc +++ /dev/null @@ -1,445 +0,0 @@ -#include <sstream> -#include <string> - -#include <hdf5.h> - -#include "cctk.h" -#include "cctk_Arguments.h" -#include "cctk_Parameters.h" - -#include "carpet.hh" - -#include "data_region.hh" -#include "f5writer.hh" -#include "file.hh" -#include "meta_data_region.hh" -#include "physical_quantity.hh" -#include "simulation.hh" -#include "tensor_component.hh" -#include "timestep.hh" -#include "topology.hh" - - - -namespace CarpetIOF5 { - - f5writer_t:: - f5writer_t (cGH const * const cctkGH, - int const variable) - : m_cctkGH (cctkGH), - m_variable (variable) - { - } - - - - void f5writer_t:: - write (F5::file_t & file) - const - { - write_meta (file, file.get_have_metafile()); - } - - - - void f5writer_t:: - write_meta (F5::file_t & file, - bool const have_metafile) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "OutputVarAs/write_meta"); - } - - if (Carpet::is_meta_mode()) - { - for (Carpet::mglevel_iterator mglevel_iter (m_cctkGH); - not mglevel_iter.done(); - mglevel_iter.step()) - { - write_one_mglevel (file, have_metafile); - } - } - else - { - write_one_mglevel (file, have_metafile); - } - } - - - - void f5writer_t:: - write_one_mglevel (F5::file_t & file, - bool const have_metafile) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "OutputVarAs/write_one_mglevel mglevel=%d", - Carpet::mglevel); - } - - // ostringstream namebuf; - // namebuf << "convlevel=" << m_cctkGH->cctk_convlevel; - // string const namestr = namebuf.str(); - // char const * const name = namestr.c_str(); - - int const grouptype = CCTK_GroupTypeFromVarI (m_variable); - assert (grouptype >= 0); - switch (grouptype) - { - case CCTK_ARRAY: - case CCTK_SCALAR: - { - if (Carpet::do_global_mode) - { - write_global (file, have_metafile); - } - } - break; - case CCTK_GF: - { - if (Carpet::is_global_mode()) - { - for (Carpet::reflevel_iterator reflevel_iter (m_cctkGH); - not reflevel_iter.done(); - reflevel_iter.step()) - { - write_one_reflevel (file, have_metafile); - } - } - else - { - write_one_reflevel (simulation, have_metafile); - } - } - break; - default: - assert (0); - } - } - - - - void f5writer_t:: - write_global (F5::simulation_t & simulation, - bool const have_metafile) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_INFO ("OutputVarAs/write_global"); - } - - F5::unigrid_topology_t topology (simulation); - - int const grouptype = CCTK_GroupTypeFromVarI (m_variable); - assert (grouptype >= 0); - assert (grouptype == CCTK_SCALAR or grouptype == CCTK_ARRAY); - - vect<CCTK_REAL, dim> level_origin, level_delta; - for (int d=0; d<dim; ++d) - { - level_origin[d] = 0.0; - level_delta[d] = 1.0; - } - F5::Cartesian_coordinate_system_t coordinate_system - (topology, level_origin, level_delta); - - int const group = CCTK_GroupIndexFromVarI (m_variable); - assert (group >= 0 and group < CCTK_NumGroups()); - F5::physical_quantity_t physical_quantity (coordinate_system, group); - - int const map = 0; - int const reflevel = 0; - int const myproc = CCTK_MyProc (m_cctkGH); - dh * const dd = Carpet::arrdata.at(group).at(map).dd; - dh::dboxes const & boxes - = dd->boxes.at(Carpet::mglevel).at(reflevel).at(myproc); - bbox<int, dim> const & region = determine_region (boxes); - - if (have_metafile) - { - F5::meta_data_region_t meta_data_region (physical_quantity, region); - gh * const hh = Carpet::vhh.at(Carpet::map); - int const proc = hh->processor (Carpet::reflevel, Carpet::component); - meta_data_region.write (proc); - } - - F5::data_region_t data_region (physical_quantity, region); - - F5::tensor_component_t tensor_component (data_region, m_variable); - int const timelevel = 0; - void const * const varptr - = CCTK_VarDataPtrI (m_cctkGH, timelevel, m_variable); - assert (varptr != 0); - int const vartype = CCTK_VarTypeI (m_variable); - assert (vartype >= 0); - tensor_component.write (varptr, vartype); - } - - - - void f5writer_t:: - write_one_reflevel (F5::file_t & file, - bool const have_metafile) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "OutputVarAs/write_one_reflevel reflevel=%d", - Carpet::reflevel); - } - - // int const grouptype = CCTK_GroupTypeFromVarI (m_variable); - // assert (grouptype >= 0); - // assert (grouptype == CCTK_GF); - - // A name for the simulation - string sim_id; - if (CCTK_IsFunctionAliased ("UniqueSimulationID")) - { - sim_id = static_cast<char const *> (UniqueSimulationID (m_cctkGH)); - } - else { - char parfilename[10000]; - int const len = CCTK_ParameterFilename (sizeof parfilename, parfilename); - assert (len >= 0 and len < sizeof parfilename); - sim_id = parfilename; - if (sim_id.length() >= 4 - and sim_id.substr (sim_id.length() - 4) == ".par") - { - sim_id = sim_id.substr (0, sim_id.length() - 4); - } - } - - // Refinement factor of current refinement level - vect <hsize_t, dim> const current_refinement - = vect <int, dim>::ref (m_cctkGH->cctk_levfac); - - // Refinement factor of root refinement level - vect <hsize_t, dim> const rootlevel_refinement (1); - - // Remember time when the root level was output the last time - static CCTK_REAL rootlevel_time = 0.0; - if (all (current_refinement == 1)) - { - rootlevel_time = m_cctkGH->cctk_time; - } - - F5Path * refinement_path = NULL; - if (any (current_refinement != 1)) - { - refinement_path - = F5Rcreate_relative_vertex_Qrefinement3D (file, - m_cctkGH->cctk_time, - sim_id.c_str(), - current_refinement, - rootlevel_time, - rootlevel_refinement); - } - -#warning "TODO: what is this doing?" - F5T_REFINEMENT3D_POINT = refinement_path->myChart->Point_hid_t; - - if (Carpet::is_level_mode()) - { - for (Carpet::map_iterator map_iter (m_cctkGH, grouptype); - not map_iter.done(); - map_iter.step()) - { - write_one_map (simulation, have_metafile); - } - } - else - { - write_one_map (simulation, have_metafile); - } - } - - - - void f5writer_t:: - write_one_map (F5::simulation_t & simulation, - bool const have_metafile) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "OutputVarAs/write_one_map map=%d", Carpet::map); - } - - // F5::mesh_refinement_topology_t topology - // (simulation, Carpet::map, Carpet::reflevel, Carpet::maxreflevels, - // Carpet::spacereflevelfact, Carpet::maxspacereflevelfact); - - // vect<CCTK_REAL, dim> level_origin, level_delta; - // for (int d=0; d<dim; ++d) - // { - // cGH const * const cctkGH = m_cctkGH; - // DECLARE_CCTK_ARGUMENTS; - // level_origin[d] = CCTK_ORIGIN_SPACE(d); - // level_delta[d] = CCTK_DELTA_SPACE(d); - // } - // F5::Cartesian_coordinate_system_t coordinate_system - // (topology, level_origin, level_delta); - // - // int const group = CCTK_GroupIndexFromVarI (m_variable); - // assert (group >= 0 and group < CCTK_NumGroups()); - // F5::physical_quantity_t physical_quantity (coordinate_system, group); - -#warning "TODO: this should depend on the patch number" - char const * const coordinate_system = NULL; - - // Depends on the refinement level - string const gridname = sim_id + "-" + current_refinement; - - F5Path * const myPath - = F5Rcreate_vertex_refinement3D (file, - m_cctkGH->cctk_time, - sim_id.c_str(), - refinement, - coordinate_system); - - if (not refinement_path) - { - // Make root level appear as unigrid topology as well, just to - // be nice to tools that do not understand AMR - F5Rlink_default_vertex_topology (myPath, current_refinement); - } - - // Global information for this refinement level - vect <hsize_t, dim> const level_dims - = vect <int, dim>::ref (m_cctkGH->cctk_gsh); -#warning "TODO: switch to double precision" - vect <float, dim> const level_min - (CCTK_ORIGIN_SPACE(0), CCTK_ORIGIN_SPACE(1), CCTK_ORIGIN_SPACE(2)); - vect <float, dim> const level_spacing - (CCTK_DELTA_SPACE(0), CCTK_DELTA_SPACE(1), CCTK_DELTA_SPACE(2)); - vect <float, dim> const level_max - = level_min + level_spacing * (level_dims - 1); - - // Output geometric information for an entire level; it is - // uniformely covered in coordinate space - assert (dim == 3); - F5Fwrite_linear (myPath, FIBER_HDF5_POSITIONS_STRING, - dim, & level_dims [0], - F5T_COORD3_FLOAT, & level_min [0], & level_spacing [0]); - - F5Fset_range (myPath, & level_min [0], & level_max [0]); - -#error "CONTINUE HERE" - - if (Carpet::is_singlemap_mode()) - { - int const grouptype = CCTK_GroupTypeI (group); - assert (grouptype >= 0); - - for (Carpet::component_iterator component_iter (m_cctkGH, grouptype); - not component_iter.done(); - component_iter.step()) - { - write_one_component (physical_quantity, have_metafile); - } - } - else - { - write_one_component (physical_quantity, have_metafile); - } - } - - - - void f5writer_t:: - write_one_component (F5::physical_quantity_t & physical_quantity, - bool const have_metafile) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "OutputVarAs/write_one_component component=%d", - Carpet::component); - } - - gh * const hh = Carpet::vhh.at(Carpet::map); - bool const is_local = hh->is_local (Carpet::reflevel, Carpet::component); - if (have_metafile or is_local) - { - dh * const dd = Carpet::vdd.at(Carpet::map); - bbox<int, dim> const & region - = (dd->boxes.at(Carpet::mglevel).at(Carpet::reflevel) - .at(Carpet::component).exterior); - - if (have_metafile) - { - F5::meta_data_region_t meta_data_region (physical_quantity, region); - int const proc = hh->processor (Carpet::reflevel, Carpet::component); - meta_data_region.write (proc); - } - - if (is_local) - { - F5::data_region_t data_region (physical_quantity, region); - - F5::tensor_component_t tensor_component (data_region, m_variable); - int const timelevel = 0; - void const * const varptr - = CCTK_VarDataPtrI (m_cctkGH, timelevel, m_variable); - assert (varptr != 0); - int const vartype = CCTK_VarTypeI (m_variable); - assert (vartype >= 0); - tensor_component.write (varptr, vartype); - } - } - } - - - - bbox<int,dim> const & f5writer_t:: - determine_region (dh::dboxes const & boxes) - const - { - DECLARE_CCTK_PARAMETERS; - -#warning "TODO: use superregions instead of regions (? only if the regions are on the same processor?); use HDF5 chunks as well" - - bbox<int,dim> dh::dboxes::* boxptr; - if (CCTK_EQUALS (output_regions, "exterior")) - { - boxptr = & dh::dboxes::exterior; - } - else if (CCTK_EQUALS (output_regions, "owned")) - { - boxptr = & dh::dboxes::owned; - } - else if (CCTK_EQUALS (output_regions, "interior")) - { - boxptr = & dh::dboxes::interior; - } - else - { - assert (0); - } - - return boxes.*boxptr; - } - -} // namespace CarpetIOF5 diff --git a/CarpetDev/CarpetIOF5/src/f5writer.hh b/CarpetDev/CarpetIOF5/src/f5writer.hh deleted file mode 100644 index ae016721e..000000000 --- a/CarpetDev/CarpetIOF5/src/f5writer.hh +++ /dev/null @@ -1,74 +0,0 @@ -#ifndef F5WRITER_HH -#define F5WRITER_HH - -#include "cctk.h" - -#include "bbox.hh" -#include "defs.hh" -#include "dh.hh" - -#include "file.hh" -#include "physical_quantity.hh" -#include "simulation.hh" -#include "timestep.hh" -#include "topology.hh" - - - -namespace CarpetIOF5 { - - class f5writer_t { - - cGH const * const m_cctkGH; - int const m_variable; - - public: - - f5writer_t (cGH const * cctkGH, - int variable); - - void - write (F5::file_t & file) - const; - - private: - - void - write_meta (F5::file_t & file, - bool have_metafile) - const; - - void - write_one_mglevel (F5::timestep_t & timestep, - bool have_metafile) - const; - - void - write_global (F5::simulation_t & simulation, - bool have_metafile) - const; - - void - write_one_reflevel (F5::simulation_t & simulation, - bool have_metafile) - const; - - void - write_one_map (F5::simulation_t & simulation, - bool have_metafile) - const; - - void - write_one_component (F5::physical_quantity_t & physical_quantity, - bool have_metafile) - const; - - bbox<int,dim> const & - determine_region (dh::dboxes const & boxes) - const; - - }; - -} // namespace CarpetIOF5 - -#endif // #ifndef F5WRITER_HH diff --git a/CarpetDev/CarpetIOF5/src/file.cc b/CarpetDev/CarpetIOF5/src/file.cc deleted file mode 100644 index d78dcb001..000000000 --- a/CarpetDev/CarpetIOF5/src/file.cc +++ /dev/null @@ -1,272 +0,0 @@ -#include <algorithm> -#include <cassert> -#include <iomanip> -#include <sstream> -#include <string> -#include <vector> - -#include <hdf5.h> - -#include "cctk.h" -#include "cctk_Parameters.h" - -#include "defs.hh" - -#include "file.hh" -#include "utils.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - using namespace std; - - file_t:: - file_t (cGH const * const cctkGH, - string const path, - string const basename, - string const extension, - bool const do_truncate, - bool const is_metafile, - bool const is_datafile) - : m_cctkGH (cctkGH), - m_path (path), - m_basename (basename), - m_extension (extension), - m_is_metafile (is_metafile), - m_is_datafile (is_datafile) - { - DECLARE_CCTK_PARAMETERS; - - assert (cctkGH); - - // Create file names, creating subdirectories to avoid placing - // too many files into the same directory - check (CCTK_CreateDirectory (mode, path.c_str()) >= 0); - if (is_metafile) - { - m_filename = basename + extension; - } - else - { - int const myproc = CCTK_MyProc (cctkGH); - m_filename = create_filename (myproc, true); - } - string const filepath = m_path + "/" + m_filename; - - htri_t is_hdf5; - H5E_BEGIN_TRY { - is_hdf5 = H5Fis_hdf5 (filepath.c_str()); - } H5E_END_TRY; - bool const file_exists = is_hdf5 > 0; - - if (do_truncate or not file_exists) - { - if (veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "H5Fcreate (name=\"%s\")", filepath.c_str()); - } - m_hdf5_file - = H5Fcreate (filepath.c_str(), - H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - } - else - { - if (veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "H5Fopen (name=\"%s\")", filepath.c_str()); - } - m_hdf5_file = H5Fopen (filepath.c_str(), H5F_ACC_RDWR, H5P_DEFAULT); - } - assert (m_hdf5_file >= 0); - - m_hdf5_fiber_contents = -1; - m_hdf5_fiber_global_charts = -1; - m_hdf5_fiber_parameter_space = -1; - if (m_is_metafile) - { - create_or_check_version (m_hdf5_file); - m_hdf5_fiber_contents - = open_or_create_group (m_hdf5_file, "TableOfContents"); - assert (m_hdf5_fiber_contents >= 0); - m_hdf5_fiber_global_charts - = open_or_create_group (m_hdf5_file, "Charts"); - assert (m_hdf5_fiber_global_charts >= 0); - m_hdf5_fiber_parameter_space - = open_or_create_group (m_hdf5_fiber_contents, "Parameters"); - assert (m_hdf5_fiber_parameter_space >= 0); - - hid_t const hdf5_time_group - = open_or_create_group (m_hdf5_fiber_parameter_space, "Time"); - assert (hdf5_time_group >= 0); - check (not H5Gclose (hdf5_time_group)); - } - - assert (invariant()); - } - - - - file_t:: - ~ file_t() - { - if (m_is_metafile) - { - check (not H5Gclose (m_hdf5_fiber_parameter_space)); - check (not H5Gclose (m_hdf5_fiber_contents)); - check (not H5Gclose (m_hdf5_fiber_global_charts)); - } - check (not H5Fclose (m_hdf5_file)); - } - - - - string file_t:: - create_filename (int const proc, bool const create_directories) - const - { - DECLARE_CCTK_PARAMETERS; - - int const nprocs = CCTK_nProcs (m_cctkGH); - string extrapath; - if (create_subdirs) - { - if (nprocs >= 10000) - { - ostringstream buf; - buf << extrapath - << m_basename - << ".p" << setw (max (0, processor_digits - 4)) << setfill ('0') - << proc / 10000 - << "nnnn/"; - extrapath = buf.str(); - if (create_directories) - { - string const filepath = m_path + "/" + extrapath; - check (CCTK_CreateDirectory (mode, filepath.c_str()) >= 0); - } - } - if (nprocs >= 100) - { - ostringstream buf; - buf << extrapath - << m_basename - << ".p" << setw (max (0, processor_digits - 2)) << setfill ('0') - << proc / 100 - << "nn/"; - extrapath = buf.str(); - if (create_directories) - { - string const filepath = m_path + "/" + extrapath; - check (CCTK_CreateDirectory (mode, filepath.c_str()) >= 0); - } - } - } - if (one_dir_per_file and nprocs >= 1) - { - ostringstream buf; - buf << extrapath - << m_basename - << ".p" << setw (processor_digits) << setfill ('0') - << proc - << "/"; - extrapath = buf.str(); - if (create_directories) - { - string const filepath = m_path + "/" + extrapath; - check (CCTK_CreateDirectory (mode, filepath.c_str()) >= 0); - } - } - ostringstream buf; - buf << extrapath - << m_basename - << ".p" << setw (processor_digits) << setfill ('0') << proc - << m_extension; - return buf.str(); - } - - - - void file_t:: - create_or_check_version (hid_t const hdf5_file) - { - hid_t const hdf5_group = open_or_create_group (hdf5_file, "version"); - assert (hdf5_group >= 0); - string const version ("http://www.zib.de/visual/F5-0.1.2/"); - write_or_check_attribute (hdf5_group, "version", version.c_str()); - check (not H5Gclose (hdf5_group)); - } - - - - cGH const * file_t:: - get_cctkGH () - const - { - return m_cctkGH; - } - - - - hid_t file_t:: - get_hdf5_file () - const - { - return m_hdf5_file; - } - - - - hid_t file_t:: - get_hdf5_fiber_parameter_space () - const - { - return m_hdf5_fiber_parameter_space; - } - - - - bool file_t:: - get_is_metafile () - const - { - return m_is_metafile; - } - - - - bool file_t:: - get_is_datafile () - const - { - return m_is_datafile; - } - - - - void file_t:: - get_link_destination (int const proc, - string & filename, - string & objectname) - const - { - filename = create_filename (proc); - objectname = ""; - } - - - - bool file_t:: - invariant() - const - { - return m_cctkGH != 0 and m_hdf5_file >= 0; - } - - } // namespace F5 - -} // namespace CarpetIOF5 diff --git a/CarpetDev/CarpetIOF5/src/file.hh b/CarpetDev/CarpetIOF5/src/file.hh deleted file mode 100644 index 44d8ce00c..000000000 --- a/CarpetDev/CarpetIOF5/src/file.hh +++ /dev/null @@ -1,103 +0,0 @@ -#ifndef FILE_HH -#define FILE_HH - -#include <string> -#include <vector> - -#include <hdf5.h> - -#include "cctk.h" - -#include "extending.hh" - - - -namespace CarpetIOF5 { - - using std::string; - using std::vector; - - - - namespace F5 { - - class file_t { - - // File mode for creating directories - static int const mode = 0755; - - cGH const * const m_cctkGH; - - string const m_path; - string const m_basename; - string const m_extension; - string m_filename; - - bool const m_is_metafile; - bool const m_is_datafile; - - hid_t m_hdf5_file; - - hid_t m_hdf5_fiber_contents; - hid_t m_hdf5_fiber_global_charts; - hid_t m_hdf5_fiber_parameter_space; - - file_t (); - file_t (file_t const &); - file_t operator= (file_t const &); - - string - create_filename (int proc, - bool create_directories = false) - const; - - static void - create_or_check_version (hid_t const hdf5_file); - - public: - - file_t (cGH const * cctkGH, - string path, - string basename, - string extension, - bool do_truncate, - bool is_metafile, - bool is_datafile); - - virtual - ~ file_t (); - - cGH const * - get_cctkGH () - const; - - hid_t - get_hdf5_file () - const; - - hid_t - get_hdf5_fiber_parameter_space () - const; - - bool get_is_metafile () - const; - - bool get_is_datafile () - const; - - void - get_link_destination (int proc, - string & filename, - string & objectname) - const; - - virtual bool - invariant () - const; - }; - - } // namespace F5 - -} // namespace CarpetIOF5 - -#endif // #ifndef FILE_HH diff --git a/CarpetDev/CarpetIOF5/src/make.code.defn b/CarpetDev/CarpetIOF5/src/make.code.defn deleted file mode 100644 index d0350d235..000000000 --- a/CarpetDev/CarpetIOF5/src/make.code.defn +++ /dev/null @@ -1,19 +0,0 @@ -# Main make.code.defn file for thorn CarpetIOF5 - -# Source files in this directory -SRCS = IOF5.cc \ - coordinate_system.cc \ - data_region.cc \ - extending.cc \ - file.cc \ - meta_data_region.cc \ - physical_quantity.cc \ - simulation.cc \ - tensor_component.cc \ - timestep.cc \ - topology.cc \ - utils.cc \ - writer.cc - -# Subdirectories containing source files -SUBDIRS = diff --git a/CarpetDev/CarpetIOF5/src/meta_data_region.cc b/CarpetDev/CarpetIOF5/src/meta_data_region.cc deleted file mode 100644 index 88963ec34..000000000 --- a/CarpetDev/CarpetIOF5/src/meta_data_region.cc +++ /dev/null @@ -1,116 +0,0 @@ -#include <cassert> -#include <cstdlib> -#include <sstream> -#include <string> - -#include <hdf5.h> - -#include "cctk.h" - -#include "carpet.hh" - -#include "defs.hh" - -#include "meta_data_region.hh" -#include "utils.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - using std::ostringstream; - - - - meta_data_region_t:: - meta_data_region_t (physical_quantity_t & physical_quantity, - bbox<int, dim> const & region) - : m_physical_quantity (physical_quantity), - m_region (region), - m_name (string ("region-") + F5::name_from_ibbox (region)) - { - assert (not region.empty()); - - assert (invariant()); - } - - - - meta_data_region_t:: - ~ meta_data_region_t () - { - } - - - - physical_quantity_t & meta_data_region_t:: - get_physical_quantity () - const - { - return m_physical_quantity; - } - - - - void meta_data_region_t:: - write (int const proc) - const - { - DECLARE_CCTK_PARAMETERS; - - string filename; - string objectname; - get_physical_quantity().get_link_destination (proc, filename, objectname); - - hid_t const hdf5_physical_quantity - = m_physical_quantity.get_hdf5_physical_quantity(); - - bool link_exists; - H5E_BEGIN_TRY { - H5L_info_t linkbuf; - herr_t const herr - = H5Lget_info (hdf5_physical_quantity, m_name.c_str(), - & linkbuf, H5P_DEFAULT); - link_exists = herr == 0; - } H5E_END_TRY; - if (veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "Link \"%s\" %s", - m_name.c_str(), - link_exists ? "exists" : "does not exist"); - } - - if (not link_exists) - { - if (veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "H5Lcreate_external " - "(filename=\"%s\", objectname=\"%s\", linkname=\"%s\")", - filename.c_str(), - objectname.c_str(), - m_name.c_str()); - } - check (not H5Lcreate_external (filename.c_str(), - objectname.c_str(), - hdf5_physical_quantity, - m_name.c_str(), - H5P_DEFAULT, H5P_DEFAULT)); - } - } - - - - bool meta_data_region_t:: - invariant () - const - { - return not m_region.empty(); - } - - } // namespace F5 - -} // namespace CarpetIOF5 diff --git a/CarpetDev/CarpetIOF5/src/meta_data_region.hh b/CarpetDev/CarpetIOF5/src/meta_data_region.hh deleted file mode 100644 index ac59c18e2..000000000 --- a/CarpetDev/CarpetIOF5/src/meta_data_region.hh +++ /dev/null @@ -1,62 +0,0 @@ -#ifndef META_DATA_REGION_HH -#define META_DATA_REGION_HH - -#include <string> - -#include <hdf5.h> - -#include "bbox.hh" -#include "defs.hh" - -#include "physical_quantity.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - using std::string; - - class meta_data_region_t { - - physical_quantity_t & m_physical_quantity; - - bbox<int, dim> const m_region; - string const m_name; - - hid_t m_properties; - hid_t m_dataset; - hid_t m_dataspace; - - meta_data_region_t (); - meta_data_region_t (meta_data_region_t const &); - meta_data_region_t operator= (meta_data_region_t const &); - - public: - - meta_data_region_t (physical_quantity_t & physical_quantity, - bbox<int, dim> const & region); - - virtual - ~ meta_data_region_t (); - - physical_quantity_t & - get_physical_quantity () - const; - - void - write (int proc) - const; - - virtual bool - invariant () - const; - - }; - - } // namespace F5 - -} // namespace CarpetIOF5 - -#endif // #ifndef META_DATA_REGION_HH diff --git a/CarpetDev/CarpetIOF5/src/physical_quantity.cc b/CarpetDev/CarpetIOF5/src/physical_quantity.cc deleted file mode 100644 index d0cb78dcd..000000000 --- a/CarpetDev/CarpetIOF5/src/physical_quantity.cc +++ /dev/null @@ -1,119 +0,0 @@ -#include <cassert> -#include <cstdlib> - -#include <hdf5.h> - -#include "cctk.h" - -#include "physical_quantity.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - physical_quantity_t:: - physical_quantity_t (coordinate_system_t & coordinate_system, - int const group) - : m_coordinate_system (coordinate_system), - m_group (group) - { - assert (group >= 0 and group < CCTK_NumGroups()); - - char * const name = CCTK_GroupName (group); - assert (name != 0); - for (char * p = name; * p; ++ p) - { - * p = static_cast<char> (tolower (* p)); - } - m_name = string (name); - - m_hdf5_physical_quantity - = open_or_create_group (m_coordinate_system - .get_hdf5_coordinate_system(), - name); - assert (m_hdf5_physical_quantity >= 0); - - free (name); - - assert (invariant()); - } - - - - physical_quantity_t:: - ~ physical_quantity_t () - { - herr_t const herr = H5Gclose (m_hdf5_physical_quantity); - assert (not herr); - } - - - - coordinate_system_t & physical_quantity_t:: - get_coordinate_system () - const - { - return m_coordinate_system; - } - - - - int physical_quantity_t:: - get_group () - const - { - return m_group; - } - - - - string physical_quantity_t:: - get_name () - const - { - return m_name; - } - - - - hid_t physical_quantity_t:: - get_hdf5_physical_quantity () - const - { - return m_hdf5_physical_quantity; - } - - - - void physical_quantity_t:: - get_link_destination (int const proc, - string & filename, - string & objectname) - const - { - get_coordinate_system().get_link_destination (proc, filename, objectname); - if (objectname.empty()) - { - objectname = m_name; - } - else - { - objectname += string ("/") + m_name; - } - } - - - - bool physical_quantity_t:: - invariant () - const - { - return (m_group >= 0 and m_group < CCTK_NumGroups() - and m_hdf5_physical_quantity >= 0); - } - - } // namespace F5 - -} // namespace CarpetIOF5 diff --git a/CarpetDev/CarpetIOF5/src/physical_quantity.hh b/CarpetDev/CarpetIOF5/src/physical_quantity.hh deleted file mode 100644 index e2b025b81..000000000 --- a/CarpetDev/CarpetIOF5/src/physical_quantity.hh +++ /dev/null @@ -1,67 +0,0 @@ -#ifndef PHYSICAL_QUANTITY_HH -#define PHYSICAL_QUANTITY_HH - -#include <hdf5.h> - -#include "coordinate_system.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - class physical_quantity_t { - - coordinate_system_t & m_coordinate_system; - - int const m_group; - string m_name; - - hid_t m_hdf5_physical_quantity; - - physical_quantity_t (); - physical_quantity_t (physical_quantity_t const &); - physical_quantity_t operator= (physical_quantity_t const &); - - public: - - physical_quantity_t (coordinate_system_t & coordinate_system, - int group); - - virtual - ~ physical_quantity_t (); - - coordinate_system_t & - get_coordinate_system () - const; - - int - get_group () - const; - - string - get_name () - const; - - hid_t - get_hdf5_physical_quantity () - const; - - void - get_link_destination (int proc, - string & filename, - string & objectname) - const; - - virtual bool - invariant () - const; - - }; - - } // namespace F5 - -} // namespace CarpetIOF5 - -#endif // #ifndef PHYSICAL_QUANTITY_HH diff --git a/CarpetDev/CarpetIOF5/src/simulation.cc b/CarpetDev/CarpetIOF5/src/simulation.cc deleted file mode 100644 index 1adde5e5a..000000000 --- a/CarpetDev/CarpetIOF5/src/simulation.cc +++ /dev/null @@ -1,96 +0,0 @@ -#include <cassert> - -#include <hdf5.h> - -#include "cctk.h" - -#include "defs.hh" - -#include "simulation.hh" -#include "utils.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - using std::ostringstream; - - - - simulation_t:: - simulation_t (timestep_t & timestep, - char const * const name) - : m_timestep (timestep), - m_name (name) - { - m_hdf5_simulation - = open_or_create_group (m_timestep.get_hdf5_timestep(), - m_name.c_str()); - assert (m_hdf5_simulation >= 0); - - cGH const * const cctkGH = m_timestep.get_file().get_cctkGH(); - write_or_check_attribute - (m_hdf5_simulation, "TimeStep", cctkGH->cctk_iteration); - - assert (invariant()); - } - - - - simulation_t:: - ~ simulation_t() - { - check (not H5Gclose (m_hdf5_simulation)); - } - - - - timestep_t & simulation_t:: - get_timestep () - const - { - return m_timestep; - } - - - - hid_t simulation_t:: - get_hdf5_simulation() - const - { - return m_hdf5_simulation; - } - - - - void simulation_t:: - get_link_destination (int const proc, - string & filename, - string & objectname) - const - { - get_timestep().get_link_destination (proc, filename, objectname); - if (objectname.empty()) - { - objectname = m_name; - } - else - { - objectname += string ("/") + m_name; - } - } - - - - bool simulation_t:: - invariant() - const - { - return m_hdf5_simulation >= 0; - } - - } // namespace F5 - -} // namespace CarpetIOF5 diff --git a/CarpetDev/CarpetIOF5/src/simulation.hh b/CarpetDev/CarpetIOF5/src/simulation.hh deleted file mode 100644 index 4c4639958..000000000 --- a/CarpetDev/CarpetIOF5/src/simulation.hh +++ /dev/null @@ -1,64 +0,0 @@ -#ifndef SIMULATION_HH -#define SIMULATION_HH - -#include <set> -#include <string> - -#include <hdf5.h> - -#include "cctk.h" - -#include "timestep.hh" - - - -namespace CarpetIOF5 { - - using std::string; - - namespace F5 { - - class simulation_t { - - timestep_t & m_timestep; - - string const m_name; - - hid_t m_hdf5_simulation; - - simulation_t (); - simulation_t (simulation_t const &); - simulation_t operator= (simulation_t const &); - - public: - - simulation_t (timestep_t & timestep, - char const * name); - - virtual - ~ simulation_t (); - - timestep_t & - get_timestep () - const; - - hid_t - get_hdf5_simulation () - const; - - void - get_link_destination (int proc, - string & filename, - string & objectname) - const; - - virtual bool - invariant () - const; - }; - - } // namespace F5 - -} // namespace CarpetIOF5 - -#endif // #ifndef SIMULATION_HH diff --git a/CarpetDev/CarpetIOF5/src/tensor_component.cc b/CarpetDev/CarpetIOF5/src/tensor_component.cc deleted file mode 100644 index 6cd2b6486..000000000 --- a/CarpetDev/CarpetIOF5/src/tensor_component.cc +++ /dev/null @@ -1,171 +0,0 @@ -#include <cassert> -#include <cstdlib> - -// force HDF5 1.8.x installations to use the new API -#define H5Dcreate_vers 2 - -#include <hdf5.h> - -#include "cctk.h" -#include "cctk_Parameters.h" - -#include "vect.hh" - -#include "tensor_component.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - tensor_component_t:: - tensor_component_t (data_region_t & data_region, - int const variable) - : m_data_region (data_region), - m_variable (variable) - { - DECLARE_CCTK_PARAMETERS; - - assert (variable >= 0 and variable < CCTK_NumVars()); - - char const * const name = CCTK_VarName (variable); - assert (name != 0); - m_name = string (name); - - int const vartype = CCTK_VarTypeI (variable); - assert (vartype >= 0); - hid_t const hdf5_datatype = hdf5_datatype_from_cactus_datatype (vartype); - assert (hdf5_datatype >= 0); - - bbox<int, dim> const & region = m_data_region.get_region(); - - vect<hsize_t, dim> const dims - = (region.shape() / region.stride()).reverse(); - m_dataspace = H5Screate_simple (dim, & dims [0], 0); - assert (m_dataspace >= 0); - - m_properties = H5Pcreate (H5P_DATASET_CREATE); - assert (m_properties >= 0); - vect<int, dim> const user_chunk_size - (chunk_size_x, chunk_size_y, chunk_size_z); - bool const need_chunks - = any (user_chunk_size > 0) or compression_level > 0 or write_checksum; - if (need_chunks) - { - vect<hsize_t, dim> const chunk_size - = either (user_chunk_size > 0, - vect<hsize_t, dim> (user_chunk_size), - dims); - herr_t const herr = H5Pset_chunk (m_properties, dim, & chunk_size [0]); - assert (not herr); - } - if (compression_level > 0) - { - herr_t const herr = H5Pset_deflate (m_properties, compression_level); - assert (not herr); - } - if (write_checksum) - { - herr_t const herr = H5Pset_fletcher32 (m_properties); - assert (not herr); - } - - m_dataset - = H5Dcreate (m_data_region.get_hdf5_data_region(), m_name.c_str(), - hdf5_datatype, m_dataspace, - H5P_DEFAULT, m_properties, H5P_DEFAULT); - assert (m_dataset >= 0); - - write_or_check_attribute - (m_dataset, "iorigin", region.lower() / region.stride()); - - assert (invariant()); - } - - - - tensor_component_t:: - ~ tensor_component_t () - { - herr_t herr; - - herr = H5Dclose (m_dataset); - assert (not herr); - - herr = H5Sclose (m_dataspace); - assert (not herr); - - herr = H5Pclose (m_properties); - assert (not herr); - } - - - - data_region_t & tensor_component_t:: - get_data_region () - const - { - return m_data_region; - } - - - - hid_t tensor_component_t:: - get_variable () - const - { - return m_variable; - } - - - -#warning "TODO: This assumes that the shape of data is the same as the shape of the region; this may not be so if not all of the data are written out" - void tensor_component_t:: - write (void const * const data, - int const cactus_datatype) - const - { - hid_t const memory_hdf5_datatype - = hdf5_datatype_from_cactus_datatype (cactus_datatype); - assert (memory_hdf5_datatype >= 0); - - bbox<int, dim> const & region = m_data_region.get_region(); - - vect<hsize_t, dim> const dims - = (region.shape() / region.stride()).reverse(); - hid_t const memory_dataspace - = H5Screate_simple (dim, & dims [0], & dims [0]); - assert (memory_dataspace >= 0); - - hid_t const transfer_properties = H5Pcreate (H5P_DATASET_XFER); - assert (transfer_properties >= 0); - - herr_t herr; - herr - = H5Dwrite (m_dataset, memory_hdf5_datatype, memory_dataspace, - m_dataspace, transfer_properties, data); - assert (not herr); - - herr = H5Pclose (transfer_properties); - assert (not herr); - - herr = H5Sclose (memory_dataspace); - assert (not herr); - } - - - - bool tensor_component_t:: - invariant () - const - { - return (m_variable >= 0 and m_variable < CCTK_NumVars() - and m_properties >= 0 - and m_dataset >= 0 - and m_dataspace >= 0); - } - - } // namespace F5 - -} // namespace CarpetIOF5 diff --git a/CarpetDev/CarpetIOF5/src/tensor_component.hh b/CarpetDev/CarpetIOF5/src/tensor_component.hh deleted file mode 100644 index 8a95d6faa..000000000 --- a/CarpetDev/CarpetIOF5/src/tensor_component.hh +++ /dev/null @@ -1,62 +0,0 @@ -#ifndef TENSOR_COMPONENT_HH -#define TENSOR_COMPONENT_HH - -#include <string> - -#include <hdf5.h> - -#include "data_region.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - class tensor_component_t { - - data_region_t & m_data_region; - - int const m_variable; - string m_name; - - hid_t m_dataspace; - hid_t m_properties; - hid_t m_dataset; - - tensor_component_t (); - tensor_component_t (tensor_component_t const &); - tensor_component_t operator= (tensor_component_t const &); - - public: - - tensor_component_t (data_region_t & data_region, - int variable); - - virtual - ~ tensor_component_t (); - - data_region_t & - get_data_region () - const; - - hid_t - get_variable () - const; - - void - write (void const * data, - int cactus_datatype) - const; - - virtual bool - invariant () - const; - - }; - - } // namespace F5 - -} // namespace CarpetIOF5 - -#endif // #ifndef TENSOR_COMPONENT_HH diff --git a/CarpetDev/CarpetIOF5/src/timestep.cc b/CarpetDev/CarpetIOF5/src/timestep.cc deleted file mode 100644 index 409f47221..000000000 --- a/CarpetDev/CarpetIOF5/src/timestep.cc +++ /dev/null @@ -1,124 +0,0 @@ -#include <cassert> -#include <iomanip> -#include <limits> -#include <string> -#include <sstream> - -#include <hdf5.h> - -#include "cctk.h" -#include "cctk_Functions.h" - -#include "defs.hh" - -#include "timestep.hh" -#include "utils.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - using std::numeric_limits; - using std::setprecision; - using std::ostringstream; - - - - timestep_t:: - timestep_t (file_t & file, - CCTK_REAL const time, - char const * const name) - : m_file (file), - m_time (time) - { - // Construct a group name from the simulation time - ostringstream buf; - if (name != 0) - { - // Use the name argument if it is present - buf << name; - } - else - { - // Create a string from the time without losing information - int const precision = numeric_limits<CCTK_REAL>::digits10 + 2; - buf << setprecision (precision) << "T=" << time; - } - m_name = buf.str(); - - m_hdf5_timestep - = open_or_create_group (m_file.get_hdf5_file(), m_name.c_str()); - assert (m_hdf5_timestep >= 0); - write_or_check_attribute (m_hdf5_timestep, "Time", time); - - assert (invariant()); - } - - - - timestep_t:: - ~ timestep_t() - { - check (not H5Gclose (m_hdf5_timestep)); - } - - - - file_t & timestep_t:: - get_file () - const - { - return m_file; - } - - - - CCTK_REAL timestep_t:: - get_time () - const - { - return m_time; - } - - - - hid_t timestep_t:: - get_hdf5_timestep() - const - { - return m_hdf5_timestep; - } - - - - void timestep_t:: - get_link_destination (int const proc, - string & filename, - string & objectname) - const - { - get_file().get_link_destination (proc, filename, objectname); - if (objectname.empty()) - { - objectname = m_name; - } - else - { - objectname += string ("/") + m_name; - } - } - - - - bool timestep_t:: - invariant() - const - { - return m_hdf5_timestep >= 0; - } - - } // namespace F5 - -} // namespace CarpetIOF5 diff --git a/CarpetDev/CarpetIOF5/src/timestep.hh b/CarpetDev/CarpetIOF5/src/timestep.hh deleted file mode 100644 index d70a00024..000000000 --- a/CarpetDev/CarpetIOF5/src/timestep.hh +++ /dev/null @@ -1,70 +0,0 @@ -#ifndef TIMESTEP_HH -#define TIMESTEP_HH - -#include <string> - -#include <hdf5.h> - -#include "cctk.h" - -#include "file.hh" - - - -namespace CarpetIOF5 { - - using std::string; - - namespace F5 { - - class timestep_t { - - file_t & m_file; - - CCTK_REAL const m_time; - - string m_name; - - hid_t m_hdf5_timestep; - - timestep_t (); - timestep_t (timestep_t const &); - timestep_t operator= (timestep_t const &); - - public: - - timestep_t (file_t & file, - CCTK_REAL time, - char const * name = 0); - - virtual - ~ timestep_t (); - - file_t & - get_file () - const; - - CCTK_REAL - get_time () - const; - - hid_t - get_hdf5_timestep () - const; - - void - get_link_destination (int proc, - string & filename, - string & objectname) - const; - - virtual bool - invariant () - const; - }; - - } // namespace F5 - -} // namespace CarpetIOF5 - -#endif // #ifndef TIMESTEP_HH diff --git a/CarpetDev/CarpetIOF5/src/topology.cc b/CarpetDev/CarpetIOF5/src/topology.cc deleted file mode 100644 index bc05c73a7..000000000 --- a/CarpetDev/CarpetIOF5/src/topology.cc +++ /dev/null @@ -1,200 +0,0 @@ -#include <cassert> -#include <sstream> - -#include <hdf5.h> - -#include "cctk.h" - -#include "defs.hh" -#include "vect.hh" - -#include "topology.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - topology_t:: - topology_t (simulation_t & simulation) - : m_simulation (simulation) - { - } - - - - topology_t:: - ~ topology_t () - { - } - - - - simulation_t & topology_t:: - get_simulation () - const - { - return m_simulation; - } - - - - hid_t topology_t:: - get_hdf5_topology() - const - { - return m_hdf5_topology; - } - - - - bool topology_t:: - invariant() - const - { - return m_hdf5_topology >= 0; - } - - - - unigrid_topology_t:: - unigrid_topology_t (simulation_t & simulation) - : topology_t (simulation) - { - char const * const name = "uniform"; - m_name = string (name); - m_hdf5_topology - = open_or_create_group (m_simulation.get_hdf5_simulation(), name); - assert (m_hdf5_topology >= 0); - - assert (invariant()); - } - - - - unigrid_topology_t:: - ~ unigrid_topology_t () - { - herr_t const herr = H5Gclose (m_hdf5_topology); - assert (not herr); - } - - - - bool unigrid_topology_t:: - invariant() - const - { - return topology_t::invariant(); - } - - - - mesh_refinement_topology_t:: - mesh_refinement_topology_t (simulation_t & simulation, - int const map, - int const maps, - int const refinement_level, - int const max_refinement_levels, - vect<int, dim> const & level_refinement_factor, - vect<int, dim> const & max_refinement_factor) - : topology_t (simulation), - m_refinement_level (refinement_level), - m_max_refinement_levels (max_refinement_levels), - m_level_refinement_factor (level_refinement_factor), - m_max_refinement_factor (max_refinement_factor) - { - assert (refinement_level >= 0); - assert (refinement_level < max_refinement_levels); - assert (all (level_refinement_factor > 0)); - assert (all (level_refinement_factor <= max_refinement_factor)); - - ostringstream namebuf; - namebuf << "Vertices"; - if (maps > 1) - { - namebuf << "-map" << map; - } - if (max_refinement_levels > 1) - { - namebuf << "-level" << refinement_level; - } - string const namestr = namebuf.str(); - m_name = namestr; - char const * const name = namestr.c_str(); - - m_hdf5_topology - = open_or_create_group (m_simulation.get_hdf5_simulation(), name); - assert (m_hdf5_topology >= 0); - - assert (invariant()); - } - - - - void mesh_refinement_topology_t:: - calculate_level_origin_delta (vect<CCTK_REAL, dim> const & coarse_origin, - vect<CCTK_REAL, dim> const & coarse_delta, - vect<int, dim> const & level_offset, - vect<int, dim> const & level_offset_denominator, - vect<CCTK_REAL, dim> & level_origin, - vect<CCTK_REAL, dim> & level_delta) - const - { - assert (all (coarse_delta > (CCTK_REAL) 0)); - assert (all (level_offset_denominator > 0)); - - level_delta - = coarse_delta / vect<CCTK_REAL, dim> (m_level_refinement_factor); - level_origin - = (coarse_origin - + (vect<CCTK_REAL, dim> (level_offset) - / vect<CCTK_REAL, dim> (level_offset_denominator) - / vect<CCTK_REAL, dim> (m_max_refinement_factor))); - } - - - - mesh_refinement_topology_t:: - ~ mesh_refinement_topology_t () - { - herr_t const herr = H5Gclose (m_hdf5_topology); - assert (not herr); - } - - - - void topology_t:: - get_link_destination (int const proc, - string & filename, - string & objectname) - const - { - get_simulation().get_link_destination (proc, filename, objectname); - if (objectname.empty()) - { - objectname = m_name; - } - else - { - objectname += string ("/") + m_name; - } - } - - - - bool mesh_refinement_topology_t:: - invariant() - const - { - return (topology_t::invariant() - and m_refinement_level >= 0 - and m_refinement_level < m_max_refinement_levels - and all (m_level_refinement_factor > 0) - and all (m_level_refinement_factor <= m_max_refinement_factor)); - } - - } // namespace F5 - -} // namespace CarpetIOF5 diff --git a/CarpetDev/CarpetIOF5/src/topology.hh b/CarpetDev/CarpetIOF5/src/topology.hh deleted file mode 100644 index e179e71db..000000000 --- a/CarpetDev/CarpetIOF5/src/topology.hh +++ /dev/null @@ -1,133 +0,0 @@ -#ifndef TOPOLOGY_HH -#define TOPOLOGY_HH - -#include <hdf5.h> - -#include "cctk.h" - -#include "defs.hh" -#include "vect.hh" - -#include "simulation.hh" -#include "utils.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - class topology_t { - - topology_t (); - topology_t (topology_t const &); - topology_t operator= (topology_t const &); - - protected: - - simulation_t & m_simulation; - - string m_name; - - hid_t m_hdf5_topology; - - topology_t (simulation_t & simulation); - - public: - - virtual - ~ topology_t (); - - public: - - simulation_t & - get_simulation () - const; - - void - get_link_destination (int proc, - string & filename, - string & objectname) - const; - - hid_t - get_hdf5_topology () - const; - - virtual bool - invariant () - const; - }; - - - - class unigrid_topology_t : public topology_t { - - unigrid_topology_t (); - unigrid_topology_t (unigrid_topology_t const &); - unigrid_topology_t operator= (unigrid_topology_t const &); - - public: - - // Create unigrid topology - unigrid_topology_t (simulation_t & simulation); - - virtual - ~ unigrid_topology_t (); - - virtual bool - invariant () - const; - }; - - - - class mesh_refinement_topology_t : public topology_t { - - int const m_refinement_level; - int const m_max_refinement_levels; - vect<int, dim> const m_level_refinement_factor; - vect<int, dim> const m_max_refinement_factor; - - mesh_refinement_topology_t (); - mesh_refinement_topology_t (mesh_refinement_topology_t const &); - mesh_refinement_topology_t - operator= (mesh_refinement_topology_t const &); - - public: - - mesh_refinement_topology_t (simulation_t & simulation, - int map, - int maps, - int refinement_level, - int max_refinement_levels, - vect<int, dim> const & level_refinement_factors, - vect<int, dim> const & max_refinement_factors); - - void - calculate_level_origin_delta (vect<CCTK_REAL, dim> const & coarse_origin, - vect<CCTK_REAL, dim> const & coarse_delta, - vect<int, dim> const & level_offset, - vect<int, dim> const & level_offset_denominator, - vect<CCTK_REAL, dim> & level_origin, - vect<CCTK_REAL, dim> & level_delta) - const; - - virtual - ~ mesh_refinement_topology_t (); - - void - get_link_destination (string & filename, - string & objectname) - const; - - virtual bool - invariant () - const; - }; - - } // namespace F5 - -} // namespace CarpetIOF5 - -#endif // #ifndef TOPOLOGY_HH diff --git a/CarpetDev/CarpetIOF5/src/utils.cc b/CarpetDev/CarpetIOF5/src/utils.cc deleted file mode 100644 index d311f0992..000000000 --- a/CarpetDev/CarpetIOF5/src/utils.cc +++ /dev/null @@ -1,512 +0,0 @@ -#include <cassert> -#include <complex> -#include <cstring> -#include <sstream> -#include <vector> - -// force HDF5 1.8.x installations to use the new API -#define H5Acreate_vers 2 -#define H5Gcreate_vers 2 -#define H5Gopen_vers 2 -#define H5Tarray_create_vers 2 - -#include <hdf5.h> - -#include "cctk.h" -#include "cctk_Parameters.h" - -#include "bbox.hh" -#include "defs.hh" -#include "vect.hh" - -#include "utils.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - using std::complex; - using std::vector; - - - - hid_t - hdf5_datatype_from_dummy (signed char const & dummy) - { - return H5T_NATIVE_SCHAR; - } - - hid_t - hdf5_datatype_from_dummy (short const & dummy) - { - return H5T_NATIVE_SHORT; - } - - hid_t - hdf5_datatype_from_dummy (int const & dummy) - { - return H5T_NATIVE_INT; - } - - hid_t - hdf5_datatype_from_dummy (long const & dummy) - { - return H5T_NATIVE_LONG; - } - - hid_t - hdf5_datatype_from_dummy (long long const & dummy) - { - return H5T_NATIVE_LLONG; - } - - hid_t - hdf5_datatype_from_dummy (float const & dummy) - { - return H5T_NATIVE_FLOAT; - } - - hid_t - hdf5_datatype_from_dummy (double const & dummy) - { - return H5T_NATIVE_DOUBLE; - } - - hid_t - hdf5_datatype_from_dummy (long double const & dummy) - { - return H5T_NATIVE_LDOUBLE; - } - -#ifdef HAVE_CCTK_COMPLEX8 - hid_t - hdf5_datatype_from_dummy (CCTK_COMPLEX8 const & dummy) - { - CCTK_REAL4 real; - return hdf5_complex_datatype_from_dummy (dummy, real); - } -#endif - -#ifdef HAVE_CCTK_COMPLEX16 - hid_t - hdf5_datatype_from_dummy (CCTK_COMPLEX16 const & dummy) - { - CCTK_REAL8 real; - return hdf5_complex_datatype_from_dummy (dummy, real); - } -#endif - -#ifdef HAVE_CCTK_COMPLEX32 - hid_t - hdf5_datatype_from_dummy (CCTK_COMPLEX32 const & dummy) - { - CCTK_REAL16 real; - return hdf5_complex_datatype_from_dummy (dummy, real); - } -#endif - - template<typename T, typename R> - hid_t - hdf5_complex_datatype_from_dummy (T const & dummy, R const & real) - { - static bool initialised = false; - static hid_t hdf_complex_datatype; - - if (not initialised) - { - initialised = true; - - hsize_t const cdim[1] = { 2 }; - - hdf_complex_datatype - = H5Tarray_create (hdf5_datatype_from_dummy (real), 1, cdim); - assert (hdf_complex_datatype >= 0); - } - - return hdf_complex_datatype; - } - - - - hid_t - hdf5_datatype_from_cactus_datatype (int const cactus_datatype) - { - switch (cactus_datatype) { - case CCTK_VARIABLE_VOID : return H5I_INVALID_HID; -#define CASE(TYPEID, TYPE) \ - case TYPEID: \ - { \ - TYPE dummy; \ - return hdf5_datatype_from_dummy (dummy); \ - } \ - break - CASE (CCTK_VARIABLE_BYTE , CCTK_BYTE ); - CASE (CCTK_VARIABLE_INT , CCTK_INT ); -#ifdef HAVE_CCTK_INT1 - CASE (CCTK_VARIABLE_INT1 , CCTK_INT1 ); -#endif -#ifdef HAVE_CCTK_INT1 - CASE (CCTK_VARIABLE_INT2 , CCTK_INT2 ); -#endif -#ifdef HAVE_CCTK_INT2 - CASE (CCTK_VARIABLE_INT4 , CCTK_INT4 ); -#endif -#ifdef HAVE_CCTK_INT4 - CASE (CCTK_VARIABLE_INT8 , CCTK_INT8 ); -#endif - CASE (CCTK_VARIABLE_REAL , CCTK_REAL ); -#ifdef HAVE_CCTK_REAL4 - CASE (CCTK_VARIABLE_REAL4 , CCTK_REAL4 ); -#endif -#ifdef HAVE_CCTK_REAL8 - CASE (CCTK_VARIABLE_REAL8 , CCTK_REAL8 ); -#endif -#ifdef HAVE_CCTK_REAL16 - CASE (CCTK_VARIABLE_REAL16 , CCTK_REAL16 ); -#endif - CASE (CCTK_VARIABLE_COMPLEX , CCTK_COMPLEX ); -#ifdef HAVE_CCTK_COMPLEX8 - CASE (CCTK_VARIABLE_COMPLEX8 , CCTK_COMPLEX8 ); -#endif -#ifdef HAVE_CCTK_COMPLEX16 - CASE (CCTK_VARIABLE_COMPLEX16, CCTK_COMPLEX16); -#endif -#ifdef HAVE_CCTK_COMPLEX32 - CASE (CCTK_VARIABLE_COMPLEX32, CCTK_COMPLEX32); -#endif -#undef CASE - case CCTK_VARIABLE_CHAR : return H5I_INVALID_HID; - case CCTK_VARIABLE_STRING : return H5I_INVALID_HID; - case CCTK_VARIABLE_POINTER : return H5I_INVALID_HID; - case CCTK_VARIABLE_FPOINTER : return H5I_INVALID_HID; - } - return H5I_INVALID_HID; - } - - - - template <typename T, int D> - string - name_from_ivect (vect <T, D> const & ivect) - { - ostringstream buf; - for (int d = 0; d < dim; ++ d) - { - if (d > 0) - { - buf << ":"; - } - buf << ivect[d]; - } - return buf.str (); - } - - template - string - name_from_ivect (vect <int, dim> const & ivect); - - template - string - name_from_ivect (vect <CCTK_REAL, dim> const & ivect); - - - - template <typename T, int D> - string - name_from_ibbox (bbox <T, D> const & ibbox) - { - ostringstream buf; - buf << name_from_ivect (ibbox.lower ()) - << "-" - << name_from_ivect (ibbox.upper ()) - << "-" - << name_from_ivect (ibbox.stride ()); - return buf.str (); - } - - template - string - name_from_ibbox (bbox <int, dim> const & ivect); - - - - hid_t - open_or_create_group (hid_t const where, - char const * const name) - { - DECLARE_CCTK_PARAMETERS; - - assert (where >= 0); - assert (name != 0); - - // bool group_exists; - // H5E_BEGIN_TRY { - // H5G_stat_t statbuf; - // herr_t const herr = H5Gget_objinfo (where, name, true, & statbuf); - // group_exists = herr == 0; - // } H5E_END_TRY; - bool group_exists; - H5E_BEGIN_TRY { - H5G_info_t groupinfo; - herr_t const herr - = H5Gget_info_by_name (where, name, & groupinfo, H5P_DEFAULT); - group_exists = herr == 0; - } H5E_END_TRY; - if (veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "Group \"%s\" %s", - name, - group_exists ? "exists" : "does not exist"); - } - - hid_t group; - if (group_exists) - { - if (veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, "H5Gopen (name=\"%s\")", name); - } - group = H5Gopen (where, name, H5P_DEFAULT); - } - else - { - if (veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, "H5Gcreate (name=\"%s\")", name); - } - group = H5Gcreate (where, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - } - - return group; - } - - - - template<typename T> - void - write_or_check_attribute (hid_t const where, - char const * const name, - T const * const values, - int const num_values) - { - assert (where >= 0); - assert (name != 0); - assert (num_values >= 0); - assert (num_values == 0 or values != 0); - - T dummy; - hid_t const datatype = hdf5_datatype_from_dummy (dummy); - - hid_t attribute; - H5E_BEGIN_TRY { - attribute = H5Aopen_name (where, name); - } H5E_END_TRY; - - if (attribute < 0) - { - // The attribute does not yet exist; create it - hsize_t const adim = num_values; - hid_t const dataspace = H5Screate_simple (1, & adim, & adim); - assert (dataspace >= 0); - attribute = H5Acreate (where, name, datatype, dataspace, - H5P_DEFAULT, H5P_DEFAULT); - assert (attribute >= 0); - herr_t herr; - herr = H5Awrite (attribute, datatype, values); - assert (not herr); - herr = H5Aclose (attribute); - assert (not herr); - herr = H5Sclose (dataspace); - assert (not herr); - } - else - { - // The attribute already exists; read and check it - hid_t const dataspace = H5Aget_space (attribute); - htri_t const is_simple = H5Sis_simple (dataspace); - assert (is_simple >= 0); - assert (is_simple > 0); - int const ndims = H5Sget_simple_extent_ndims (dataspace); - assert (ndims == 1); - hsize_t adim; - herr_t herr; - herr = H5Sget_simple_extent_dims (dataspace, & adim, 0); - assert (adim == hsize_t (num_values)); - vector<T> buf (adim); - herr = H5Aread (attribute, datatype, & buf.front()); - assert (not herr); - herr = H5Sclose (dataspace); - assert (not herr); - herr = H5Aclose (attribute); - assert (not herr); - for (int n = 0; n < num_values; ++ n) - { - assert (values [n] == buf [n]); - } - } - } - -#if SIZEOF_INT != CCTK_INTEGER_PRECISION - template - void - write_or_check_attribute (hid_t const where, - char const * const name, - int const * const values, - int const num_values); -#endif - template - void - write_or_check_attribute (hid_t const where, - char const * const name, - CCTK_INT const * const values, - int const num_values); - template - void - write_or_check_attribute (hid_t const where, - char const * const name, - CCTK_REAL const * const values, - int const num_values); - - - - template<typename T> - void - write_or_check_attribute (hid_t const where, - char const * const name, - T const & value) - { - assert (where >= 0); - assert (name != 0); - - write_or_check_attribute (where, name, & value, 1); - } - -#if SIZEOF_INT != CCTK_INTEGER_PRECISION - template - void - write_or_check_attribute (hid_t const where, - char const * const name, - int const & value); -#endif - template - void - write_or_check_attribute (hid_t const where, - char const * const name, - CCTK_INT const & value); - template - void - write_or_check_attribute (hid_t const where, - char const * const name, - CCTK_REAL const & value); - - - - template<typename T, int D> - void - write_or_check_attribute (hid_t where, - char const * name, - vect<T,D> const & value) - { - assert (where >= 0); - assert (name != 0); - - write_or_check_attribute (where, name, & value [0], D); - } - -#if SIZEOF_INT != CCTK_INTEGER_PRECISION - template - void - write_or_check_attribute (hid_t where, - char const * name, - vect<int, dim> const & value); -#endif - template - void - write_or_check_attribute (hid_t where, - char const * name, - vect<CCTK_INT, dim> const & value); - template - void - write_or_check_attribute (hid_t where, - char const * name, - vect<CCTK_REAL, dim> const & value); - - - - template<> - void - write_or_check_attribute (hid_t const where, - char const * const name, - char const * const & value) - { - assert (where >= 0); - assert (name != 0); - assert (value != 0); - - hid_t attribute; - H5E_BEGIN_TRY { - attribute = H5Aopen_name (where, name); - } H5E_END_TRY; - - if (attribute < 0) - { - // The attribute does not yet exist; create it - hid_t const datatype = H5Tcopy (H5T_C_S1); - assert (datatype >= 0); - herr_t herr; - int const length = strlen (value) + 1; - herr = H5Tset_size (datatype, length); - assert (not herr); - hsize_t const dim = 1; - hid_t const dataspace = H5Screate_simple (1, & dim, & dim); - assert (dataspace >= 0); - attribute = H5Acreate (where, name, datatype, dataspace, - H5P_DEFAULT, H5P_DEFAULT); - assert (attribute >= 0); - herr = H5Awrite (attribute, datatype, value); - assert (not herr); - herr = H5Aclose (attribute); - assert (not herr); - herr = H5Sclose (dataspace); - assert (not herr); - herr = H5Tclose (datatype); - assert (not herr); - } - else - { - // The attribute already exists; read and check it - hid_t datatype = H5Aget_type (attribute); - assert (datatype >= 0); - hid_t typeclass = H5Tget_class (datatype); - assert (typeclass == H5T_STRING); - int const length = H5Tget_size (datatype); - assert (length >= 0); - hid_t const dataspace = H5Aget_space (attribute); - htri_t const is_simple = H5Sis_simple (dataspace); - assert (is_simple >= 0); - assert (is_simple > 0); - int const ndims = H5Sget_simple_extent_ndims (dataspace); - assert (ndims == 1); - hsize_t dim; - herr_t herr; - herr = H5Sget_simple_extent_dims (dataspace, & dim, 0); - assert (dim == 1); - vector<char> buf (length); - herr = H5Aread (attribute, datatype, & buf.front()); - assert (not herr); - herr = H5Sclose (dataspace); - assert (not herr); - herr = H5Aclose (attribute); - assert (not herr); - herr = H5Tclose (datatype); - assert (not herr); - assert (strcmp (& buf.front(), value) == 0); - } - } - - } // namespace F5 - -} // namespace CarpetIOF5 diff --git a/CarpetDev/CarpetIOF5/src/utils.hh b/CarpetDev/CarpetIOF5/src/utils.hh deleted file mode 100644 index 8d9d0a925..000000000 --- a/CarpetDev/CarpetIOF5/src/utils.hh +++ /dev/null @@ -1,93 +0,0 @@ -#ifndef UTILS_HH -#define UTILS_HH - -#include <hdf5.h> - -#include "cctk.h" - -#include "vect.hh" - - - -namespace CarpetIOF5 { - - namespace F5 { - - hid_t - hdf5_datatype_from_dummy (signed char const & dummy); - hid_t - hdf5_datatype_from_dummy (short const & dummy); - hid_t - hdf5_datatype_from_dummy (int const & dummy); - hid_t - hdf5_datatype_from_dummy (long const & dummy); - hid_t - hdf5_datatype_from_dummy (long long const & dummy); - hid_t - hdf5_datatype_from_dummy (float const & dummy); - hid_t - hdf5_datatype_from_dummy (double const & dummy); - hid_t - hdf5_datatype_from_dummy (long double const & dummy); -#ifdef HAVE_CCTK_COMPLEX8 - hid_t - hdf5_datatype_from_dummy (CCTK_COMPLEX8 const & dummy); -#endif -#ifdef HAVE_CCTK_COMPLEX16 - hid_t - hdf5_datatype_from_dummy (CCTK_COMPLEX16 const & dummy); -#endif -#ifdef HAVE_CCTK_COMPLEX32 - hid_t - hdf5_datatype_from_dummy (CCTK_COMPLEX32 const & dummy); -#endif - - template<typename T, typename R> - hid_t - hdf5_complex_datatype_from_dummy (T const & dummy, R const & real); - - hid_t - hdf5_datatype_from_cactus_datatype (int cactus_datatype); - - - - template <typename T, int D> - string - name_from_ivect (vect <T, D> const & ivect); - - template <typename T, int D> - string - name_from_ibbox (bbox <T, D> const & ibbox); - - - - hid_t - open_or_create_group (hid_t where, - char const * name); - - - - template<typename T> - void - write_or_check_attribute (hid_t where, - char const * name, - T const * values, - int num_values); - - template<typename T> - void - write_or_check_attribute (hid_t where, - char const * name, - T const & value); - - template<typename T, int D> - void - write_or_check_attribute (hid_t where, - char const * name, - vect<T,D> const & value); - - } // namespace F5 - -} // namespace CarpetIOF5 - -#endif // #ifndef UTILS_HH diff --git a/CarpetDev/CarpetIOF5/src/writer-old.cc b/CarpetDev/CarpetIOF5/src/writer-old.cc deleted file mode 100644 index 4c4f639a8..000000000 --- a/CarpetDev/CarpetIOF5/src/writer-old.cc +++ /dev/null @@ -1,511 +0,0 @@ -#include <cstdlib> -#include <sstream> -#include <string> - -#include <hdf5.h> - -#include "cctk.h" -#include "cctk_Arguments.h" -#include "cctk_Parameters.h" - -#include "carpet.hh" - -#include "data_region.hh" -#include "file.hh" -#include "meta_data_region.hh" -#include "physical_quantity.hh" -#include "simulation.hh" -#include "tensor_component.hh" -#include "timestep.hh" -#include "topology.hh" -#include "writer.hh" - - - -namespace CarpetIOF5 { - - writer_t:: - writer_t (cGH const * const cctkGH, - int const variable) - : m_cctkGH (cctkGH), - m_variable (variable) - { - } - - - - void writer_t:: - write (F5::file_t & file) - const - { - write_meta (file); - } - - - - void writer_t:: - write_meta (F5::file_t & file) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "OutputVarAs/write_meta"); - } - - F5::timestep_t timestep (file, m_cctkGH->cctk_time); - - if (Carpet::is_meta_mode()) - { - for (Carpet::mglevel_iterator mglevel_iter (m_cctkGH); - not mglevel_iter.done(); - mglevel_iter.step()) - { - write_one_mglevel (timestep); - } - } - else - { - write_one_mglevel (timestep); - } - } - - - - void writer_t:: - write_one_mglevel (F5::timestep_t & timestep) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "OutputVarAs/write_one_mglevel mglevel=%d", - Carpet::mglevel); - } - - // ostringstream namebuf; - // namebuf << sim_id; - // if (m_cctkGH->cctk_convlevel != 0) - // { - // namebuf << "-convlevel" << m_cctkGH->cctk_convlevel; - // } - // string const name = namebuf.str(); - // F5::simulation_t simulation (timestep, name.c_str()); - - int const grouptype = CCTK_GroupTypeFromVarI (m_variable); - assert (grouptype >= 0); - switch (grouptype) - { - case CCTK_ARRAY: - case CCTK_SCALAR: - { - if (Carpet::is_global_mode()) - { - int const rl = 0; - enter_level_mode (m_cctkGH, rl); - write_global_reflevel (timestep); - leave_level_mode (m_cctkGH); - } - else - { - if (Carpet::do_global_mode) - { - write_global_reflevel (timestep); - } - } - } - break; - case CCTK_GF: - { - if (Carpet::is_global_mode()) - { - for (Carpet::reflevel_iterator reflevel_iter (m_cctkGH); - not reflevel_iter.done(); - reflevel_iter.step()) - { - write_one_reflevel (timestep); - } - } - else - { - write_one_reflevel (simulation); - } - } - break; - default: - assert (0); - } - } - - - - void writer_t:: - write_global_reflevel (F5::timestep_t & timestep) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_INFO ("OutputVarAs/write_global_reflevel"); - } - - if (Carpet::is_level_mode()) - { - for (Carpet::map_iterator map_iter (m_cctkGH, grouptype); - not map_iter.done(); - map_iter.step()) - { - write_global_map (timestep); - } - } - else - { - write_global_map (timestep); - } - } - - - - void writer_t:: - write_global_map (F5::timestep_t & timestep) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_INFO ("OutputVarAs/write_global_map"); - } - - write_global_component (timestep); - } - - - - void writer_t:: - write_global_component (F5::timestep_t & timestep) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_INFO ("OutputVarAs/write_global_component"); - } - - int const group = CCTK_GroupIndexFromVarI (m_variable); - assert (group >= 0 and group < CCTK_NumGroups()); - cGroup groupdata; - check (not CCTK_GropuData (group, & groupdata)); - assert (groupdata.grouptype == CCTK_SCALAR - or groupdata.grouptype == CCTK_ARRAY); - - for (Carpet::component_iterator component_iter (m_cctkGH, grouptype); - not component_iter.done(); - component_iter.step()) - - - - int const myproc = CCTK_MyProc (m_cctkGH); - if (groupdata.disttype == CCTK_DISTRIB_CONSTANT and myproc != 0) - { - // Output DISTRIB=constant groups only on the root processor - return; - } - - // Name the grid after the variable group - char * const c_name = CCTK_GroupNameFromVarI (m_variable); - string const name = c_name; - free (c_name); - F5::simulation_t simulation (timestep, name.c_str()); - - F5::unigrid_topology_t topology (simulation); - - vect<CCTK_REAL, dim> const level_origin (0.0), level_delta (1.0); - F5::Cartesian_coordinate_system_t coordinate_system - (topology, level_origin, level_delta); - - F5::physical_quantity_t physical_quantity (coordinate_system, group); - - int const map = 0; - int const reflevel = 0; - dh * const dd = Carpet::arrdata.at(group).at(map).dd; - dh::dboxes const & boxes - = dd->boxes.at(Carpet::mglevel).at(reflevel).at(myproc); - bbox<int, dim> const & region = determine_region (boxes); - - F5::file_t & file = timestep.get_file(); - bool const have_metafile - = file.get_is_metafile() and not file.get_is_datafile(); - if (have_metafile) - { - F5::meta_data_region_t meta_data_region (physical_quantity, region); - gh * const hh = Carpet::vhh.at(Carpet::map); - int const proc = hh->processor (Carpet::reflevel, Carpet::component); - meta_data_region.write (proc); - } - - F5::data_region_t data_region (physical_quantity, region); - - F5::tensor_component_t tensor_component (data_region, m_variable); - int const timelevel = 0; - void const * const varptr - = CCTK_VarDataPtrI (m_cctkGH, timelevel, m_variable); - assert (varptr != 0); - int const vartype = CCTK_VarTypeI (m_variable); - assert (vartype >= 0); - tensor_component.write (varptr, vartype); - } - - - - void writer_t:: - write_global (F5::timestep_t & timestep) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_INFO ("OutputVarAs/write_global"); - } - - int const group = CCTK_GroupIndexFromVarI (m_variable); - assert (group >= 0 and group < CCTK_NumGroups()); - cGroup groupdata; - check (not CCTK_GropuData (group, & groupdata)); - assert (groupdata.grouptype == CCTK_SCALAR - or groupdata.grouptype == CCTK_ARRAY); - - for (Carpet::component_iterator component_iter (m_cctkGH, grouptype); - not component_iter.done(); - component_iter.step()) - - - - int const myproc = CCTK_MyProc (m_cctkGH); - if (groupdata.disttype == CCTK_DISTRIB_CONSTANT and myproc != 0) - { - // Output DISTRIB=constant groups only on the root processor - return; - } - - // Name the grid after the variable group - char * const c_name = CCTK_GroupNameFromVarI (m_variable); - string const name = c_name; - free (c_name); - F5::simulation_t simulation (timestep, name.c_str()); - - F5::unigrid_topology_t topology (simulation); - - vect<CCTK_REAL, dim> const level_origin (0.0), level_delta (1.0); - F5::Cartesian_coordinate_system_t coordinate_system - (topology, level_origin, level_delta); - - F5::physical_quantity_t physical_quantity (coordinate_system, group); - - int const map = 0; - int const reflevel = 0; - dh * const dd = Carpet::arrdata.at(group).at(map).dd; - dh::dboxes const & boxes - = dd->boxes.at(Carpet::mglevel).at(reflevel).at(myproc); - bbox<int, dim> const & region = determine_region (boxes); - - F5::file_t & file = timestep.get_file(); - bool const have_metafile - = file.get_is_metafile() and not file.get_is_datafile(); - if (have_metafile) - { - F5::meta_data_region_t meta_data_region (physical_quantity, region); - gh * const hh = Carpet::vhh.at(Carpet::map); - int const proc = hh->processor (Carpet::reflevel, Carpet::component); - meta_data_region.write (proc); - } - - F5::data_region_t data_region (physical_quantity, region); - - F5::tensor_component_t tensor_component (data_region, m_variable); - int const timelevel = 0; - void const * const varptr - = CCTK_VarDataPtrI (m_cctkGH, timelevel, m_variable); - assert (varptr != 0); - int const vartype = CCTK_VarTypeI (m_variable); - assert (vartype >= 0); - tensor_component.write (varptr, vartype); - } - - - - void writer_t:: - write_one_map (F5::simulation_t & simulation) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "OutputVarAs/write_one_map map=%d", Carpet::map); - } - - F5::mesh_refinement_topology_t topology - (simulation, Carpet::map, Carpet::reflevel, Carpet::maxreflevels, - Carpet::spacereflevelfact, Carpet::maxspacereflevelfact); - - vect<CCTK_REAL, dim> level_origin, level_delta; - for (int d=0; d<dim; ++d) - { - cGH const * const cctkGH = m_cctkGH; - DECLARE_CCTK_ARGUMENTS; - level_origin[d] = CCTK_ORIGIN_SPACE(d); - level_delta[d] = CCTK_DELTA_SPACE(d); - } - F5::Cartesian_coordinate_system_t coordinate_system - (topology, level_origin, level_delta); - - int const group = CCTK_GroupIndexFromVarI (m_variable); - assert (group >= 0 and group < CCTK_NumGroups()); - F5::physical_quantity_t physical_quantity (coordinate_system, group); - - if (Carpet::is_singlemap_mode()) - { - int const grouptype = CCTK_GroupTypeI (group); - assert (grouptype >= 0); - - for (Carpet::component_iterator component_iter (m_cctkGH, grouptype); - not component_iter.done(); - component_iter.step()) - { - write_one_component (physical_quantity); - } - } - else - { - write_one_component (physical_quantity); - } - } - - - - void writer_t:: - write_one_reflevel (F5::simulation_t & simulation) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "OutputVarAs/write_one_reflevel reflevel=%d", - Carpet::reflevel); - } - - int const grouptype = CCTK_GroupTypeFromVarI (m_variable); - assert (grouptype >= 0); - assert (grouptype == CCTK_GF); - - if (Carpet::is_level_mode()) - { - for (Carpet::map_iterator map_iter (m_cctkGH, grouptype); - not map_iter.done(); - map_iter.step()) - { - write_one_map (simulation); - } - } - else - { - write_one_map (simulation); - } - } - - - - void writer_t:: - write_one_component (F5::physical_quantity_t & physical_quantity) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "OutputVarAs/write_one_component component=%d", - Carpet::component); - } - - F5::file_t & file - = (physical_quantity.get_coordinate_system().get_topology() - .get_simulation().get_timestep().get_file()); - bool const have_metafile - = file.get_is_metafile() and not file.get_is_datafile(); - gh * const hh = Carpet::vhh.at(Carpet::map); - bool const is_local = hh->is_local (Carpet::reflevel, Carpet::component); - if (have_metafile or is_local) - { - dh * const dd = Carpet::vdd.at(Carpet::map); - bbox<int, dim> const & region - = (dd->boxes.at(Carpet::mglevel).at(Carpet::reflevel) - .at(Carpet::component).exterior); - - if (have_metafile) - { - F5::meta_data_region_t meta_data_region (physical_quantity, region); - int const proc = hh->processor (Carpet::reflevel, Carpet::component); - meta_data_region.write (proc); - } - - if (is_local) - { - F5::data_region_t data_region (physical_quantity, region); - - F5::tensor_component_t tensor_component (data_region, m_variable); - int const timelevel = 0; - void const * const varptr - = CCTK_VarDataPtrI (m_cctkGH, timelevel, m_variable); - assert (varptr != 0); - int const vartype = CCTK_VarTypeI (m_variable); - assert (vartype >= 0); - tensor_component.write (varptr, vartype); - } - } - } - - - - bbox<int,dim> const & writer_t:: - determine_region (dh::dboxes const & boxes) - const - { - DECLARE_CCTK_PARAMETERS; - - // TODO: use superregions instead of regions (? only if the - // regions are on the same processor?) - - bbox<int,dim> dh::dboxes::* boxptr; - if (CCTK_EQUALS (output_regions, "exterior")) - { - boxptr = & dh::dboxes::exterior; - } - else if (CCTK_EQUALS (output_regions, "owned")) - { - boxptr = & dh::dboxes::owned; - } - else if (CCTK_EQUALS (output_regions, "interior")) - { - boxptr = & dh::dboxes::interior; - } - else - { - assert (0); - } - - return boxes.*boxptr; - } - -} // namespace CarpetIOF5 diff --git a/CarpetDev/CarpetIOF5/src/writer.cc b/CarpetDev/CarpetIOF5/src/writer.cc deleted file mode 100644 index a07e1d94f..000000000 --- a/CarpetDev/CarpetIOF5/src/writer.cc +++ /dev/null @@ -1,400 +0,0 @@ -#include <cstdlib> -#include <sstream> -#include <string> - -#include <hdf5.h> - -#include "cctk.h" -#include "cctk_Arguments.h" -#include "cctk_Parameters.h" - -#include "carpet.hh" -#include "modes.hh" - -#include "data_region.hh" -#include "file.hh" -#include "meta_data_region.hh" -#include "physical_quantity.hh" -#include "simulation.hh" -#include "tensor_component.hh" -#include "timestep.hh" -#include "topology.hh" -#include "utils.hh" -#include "writer.hh" - - - -namespace CarpetIOF5 { - - writer_t:: - writer_t (cGH const * const cctkGH, - int const variable) - : m_cctkGH (cctkGH), - m_variable (variable) - { - } - - - - void writer_t:: - write (F5::file_t & file) - const - { - write_meta (file); - } - - - - void writer_t:: - write_meta (F5::file_t & file) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) { - CCTK_VInfo (CCTK_THORNSTRING, - "OutputVarAs/write_meta"); - } - - F5::timestep_t timestep (file, m_cctkGH->cctk_time); - - if (Carpet::is_meta_mode()) - { - BEGIN_MGLEVEL_LOOP (m_cctkGH) - { - write_one_mglevel (timestep); - } - END_MGLEVEL_LOOP; - } - else - { - write_one_mglevel (timestep); - } - } - - - - void writer_t:: - write_one_mglevel (F5::timestep_t & timestep) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "OutputVarAs/write_one_mglevel mglevel=%d", - Carpet::mglevel); - } - - int const grouptype = CCTK_GroupTypeFromVarI (m_variable); - assert (grouptype >= 0); - switch (grouptype) - { - case CCTK_ARRAY: - case CCTK_SCALAR: - { - if (Carpet::is_global_mode()) - { - ENTER_LEVEL_MODE (m_cctkGH, 0) - { - write_global (timestep); - } - LEAVE_LEVEL_MODE; - } - else - { - if (Carpet::do_global_mode) - { - write_global (timestep); - } - } - } - break; - case CCTK_GF: - { - if (Carpet::is_global_mode()) - { - BEGIN_REFLEVEL_LOOP (m_cctkGH) - { - write_one_reflevel (timestep); - } - END_REFLEVEL_LOOP; - } - else - { - write_one_reflevel (timestep); - } - } - break; - default: - assert (0); - } - } - - - - void writer_t:: - write_global (F5::timestep_t & timestep) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "OutputVarAs/write_global"); - } - - int const grouptype = CCTK_GroupTypeFromVarI (m_variable); - assert (grouptype == CCTK_SCALAR or grouptype == CCTK_ARRAY); - - BEGIN_MAP_LOOP (m_cctkGH, grouptype) - { - - // Name the grid after the variable group - ostringstream namebuf; - char * const c_name = CCTK_GroupNameFromVarI (m_variable); - namebuf << "Cactus-" << c_name; - free (c_name); - string const name = namebuf.str(); - F5::simulation_t simulation (timestep, name.c_str()); - - F5::unigrid_topology_t topology (simulation); - - vect<CCTK_REAL, dim> const level_origin (0.0), level_delta (1.0); - F5::Cartesian_coordinate_system_t coordinate_system - (topology, level_origin, level_delta); - - int const group = CCTK_GroupIndexFromVarI (m_variable); - assert (group >= 0 and group < CCTK_NumGroups()); - F5::physical_quantity_t physical_quantity (coordinate_system, group); - - int const myproc = CCTK_MyProc (m_cctkGH); - - F5::file_t & file = timestep.get_file(); - bool const write_metafile - = file.get_is_metafile() and not file.get_is_datafile(); - if (write_metafile) - { - - BEGIN_COMPONENT_LOOP (m_cctkGH, grouptype) - { - dh * const dd = Carpet::arrdata.at(group).at(Carpet::map).dd; - dh::light_dboxes const & light_boxes - = dd->light_boxes.at(Carpet::mglevel).at(Carpet::reflevel).at(myproc); - bbox<int, dim> const & region = determine_region (light_boxes); - F5::meta_data_region_t meta_data_region (physical_quantity, region); - - gh * const hh = Carpet::vhh.at(Carpet::map); - int const proc = hh->processor (Carpet::reflevel, Carpet::component); - meta_data_region.write (proc); - } - END_COMPONENT_LOOP; - - } - else // if not write_metafile - { - - BEGIN_LOCAL_COMPONENT_LOOP (m_cctkGH, grouptype) - { - dh * const dd = Carpet::arrdata.at(group).at(Carpet::map).dd; - dh::light_dboxes const & light_boxes - = dd->light_boxes.at(Carpet::mglevel).at(Carpet::reflevel).at(myproc); - bbox<int, dim> const & region = determine_region (light_boxes); - F5::data_region_t data_region (physical_quantity, region); - - F5::tensor_component_t tensor_component (data_region, m_variable); - int const timelevel = 0; - void const * const varptr - = CCTK_VarDataPtrI (m_cctkGH, timelevel, m_variable); - assert (varptr != 0); - int const vartype = CCTK_VarTypeI (m_variable); - assert (vartype >= 0); - tensor_component.write (varptr, vartype); - } - END_LOCAL_COMPONENT_LOOP; - - } // if not write_metafile - - } - END_MAP_LOOP; - } - - - - void writer_t:: - write_one_reflevel (F5::timestep_t & timestep) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "OutputVarAs/write_one_reflevel reflevel=%d", - Carpet::reflevel); - } - - int const grouptype = CCTK_GroupTypeFromVarI (m_variable); - assert (grouptype == CCTK_GF); - - if (Carpet::is_level_mode()) - { - BEGIN_MAP_LOOP (m_cctkGH, grouptype) - { - write_one_map (timestep); - } - END_MAP_LOOP; - } - else - { - write_one_map (timestep); - } - } - - - - void writer_t:: - write_one_map (F5::timestep_t & timestep) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "OutputVarAs/write_one_map map=%d", Carpet::map); - } - - // Name the grid after the map number - ostringstream namebuf; - namebuf << "Carpet"; - if (Carpet::maps > 1) - { - namebuf << "-map" << Carpet::map; - } - string const name = namebuf.str(); - F5::simulation_t simulation (timestep, name.c_str()); - - F5::mesh_refinement_topology_t topology - (simulation, - Carpet::map, Carpet::maps, Carpet::reflevel, Carpet::maxreflevels, - Carpet::spacereflevelfact, Carpet::maxspacereflevelfact); - - vect<CCTK_REAL, dim> level_origin, level_delta; - for (int d=0; d<dim; ++d) - { - cGH const * const cctkGH = m_cctkGH; - DECLARE_CCTK_ARGUMENTS; - level_origin[d] = CCTK_ORIGIN_SPACE(d); - level_delta[d] = CCTK_DELTA_SPACE(d); - } - F5::Cartesian_coordinate_system_t coordinate_system - (topology, level_origin, level_delta); - - int const group = CCTK_GroupIndexFromVarI (m_variable); - assert (group >= 0 and group < CCTK_NumGroups()); - F5::physical_quantity_t physical_quantity (coordinate_system, group); - - if (Carpet::is_singlemap_mode()) - { - int const grouptype = CCTK_GroupTypeI (group); - assert (grouptype >= 0); - - BEGIN_COMPONENT_LOOP (m_cctkGH, grouptype) - { - write_one_component (physical_quantity); - } - END_COMPONENT_LOOP; - } - else - { - write_one_component (physical_quantity); - } - } - - - - void writer_t:: - write_one_component (F5::physical_quantity_t & physical_quantity) - const - { - DECLARE_CCTK_PARAMETERS; - - if (verbose or veryverbose) - { - CCTK_VInfo (CCTK_THORNSTRING, - "OutputVarAs/write_one_component component=%d", - Carpet::component); - } - - gh * const hh = Carpet::vhh.at(Carpet::map); - bool const is_local = hh->is_local (Carpet::reflevel, Carpet::component); - - F5::file_t & file - = (physical_quantity.get_coordinate_system().get_topology() - .get_simulation().get_timestep().get_file()); - bool const write_metafile - = file.get_is_metafile() and not file.get_is_datafile(); - if (write_metafile or is_local) - { - dh * const dd = Carpet::vdd.at(Carpet::map); - bbox<int, dim> const & region - = (dd->light_boxes.at(Carpet::mglevel).at(Carpet::reflevel) - .at(Carpet::component).exterior); - - if (write_metafile) - { - F5::meta_data_region_t meta_data_region (physical_quantity, region); - int const proc = hh->processor (Carpet::reflevel, Carpet::component); - meta_data_region.write (proc); - } - else if (is_local) - { - F5::data_region_t data_region (physical_quantity, region); - - F5::tensor_component_t tensor_component (data_region, m_variable); - int const timelevel = 0; - void const * const varptr - = CCTK_VarDataPtrI (m_cctkGH, timelevel, m_variable); - assert (varptr != 0); - int const vartype = CCTK_VarTypeI (m_variable); - assert (vartype >= 0); - tensor_component.write (varptr, vartype); - } - } - } - - - - bbox<int,dim> const & writer_t:: - determine_region (dh::light_dboxes const & light_boxes) - { - DECLARE_CCTK_PARAMETERS; - - // TODO: use superregions instead of regions (? only if the - // regions are on the same processor?) - - bbox<int,dim> dh::light_dboxes::* boxptr; - if (CCTK_EQUALS (output_regions, "exterior")) - { - boxptr = & dh::light_dboxes::exterior; - } - else if (CCTK_EQUALS (output_regions, "owned")) - { - boxptr = & dh::light_dboxes::owned; - } - else if (CCTK_EQUALS (output_regions, "interior")) - { - boxptr = & dh::light_dboxes::interior; - } - else - { - assert (0); - } - - return light_boxes.*boxptr; - } - -} // namespace CarpetIOF5 diff --git a/CarpetDev/CarpetIOF5/src/writer.hh b/CarpetDev/CarpetIOF5/src/writer.hh deleted file mode 100644 index d3a6611aa..000000000 --- a/CarpetDev/CarpetIOF5/src/writer.hh +++ /dev/null @@ -1,70 +0,0 @@ -#ifndef WRITER_HH -#define WRITER_HH - -#include "cctk.h" - -#include "bbox.hh" -#include "defs.hh" -#include "dh.hh" -#include "vect.hh" - -#include "file.hh" -#include "physical_quantity.hh" -#include "simulation.hh" -#include "timestep.hh" -#include "topology.hh" - - - -namespace CarpetIOF5 { - - class writer_t { - - cGH const * const m_cctkGH; - int const m_variable; - - public: - - writer_t (cGH const * cctkGH, - int variable); - - void - write (F5::file_t & file) - const; - - private: - - void - write_meta (F5::file_t & file) - const; - - void - write_one_mglevel (F5::timestep_t & timestep) - const; - - void - write_global (F5::timestep_t & timestep) - const; - - void - write_one_reflevel (F5::timestep_t & timestep) - const; - - void - write_one_map (F5::timestep_t & timestep) - const; - - void - write_one_component (F5::physical_quantity_t & physical_quantity) - const; - - - - static bbox<int,dim> const & - determine_region (dh::light_dboxes const & light_boxes); - - }; - -} // namespace CarpetIOF5 - -#endif // #ifndef WRITER_HH |