initial commit

.gitignore

@@ -0,0 +1,19 @@
+CMakeCache.txt
+CMakeFiles/
+doc/doxygen/
+Makefile
+pu-dwr-diffusion
+cmake_install.cmake
+output*/
+build/
+*.h5
+*.xdmf
+*.log
+*.aux
+*.tex
+*.pdf
+*.png
+.cproject
+.settings/
+.project
+/my-convergence-table.synctex.gz

CMakeLists.txt

@@ -0,0 +1,81 @@
+# Copyright (C) 2012-2023 by Jan Philipp Thiele and Uwe Koecher
+# 
+# This file is part of pu-dwr-diffusion.
+# 
+# pu-dwr-diffusion is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as
+# published by the Free Software Foundation, either
+# version 3 of the License, or (at your option) any later version.
+# 
+# pu-dwr-diffusion is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+# 
+# You should have received a copy of the GNU Lesser General Public License
+# along with pu-dwr-diffusion. If not, see <http://www.gnu.org/licenses/>.
+
+
+## ---------------------------------------------------------------------
+##
+## Copyright (C) 2012 - 2014 by the deal.II authors
+##
+## This file is part of the deal.II library.
+##
+## The deal.II library is free software; you can use it, redistribute
+## it, and/or modify it under the terms of the GNU Lesser General
+## Public License as published by the Free Software Foundation; either
+## version 2.1 of the License, or (at your option) any later version.
+## The full text of the license can be found in the file LICENSE at
+## the top level of the deal.II distribution.
+##
+## ---------------------------------------------------------------------
+
+
+MESSAGE("================================================================================")
+MESSAGE("=== Configuring DTM++.Project/heat =============================================")
+MESSAGE("================================================================================")
+
+# SETs the NAME of the TARGET and PROJECT
+SET(TARGET "pu-dwr-diffusion")
+
+FILE(GLOB_RECURSE TARGET_SRC "source/*.cc")
+INCLUDE_DIRECTORIES(include)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8.12)
+
+FIND_PACKAGE(deal.II 9.0 QUIET HINTS ${DEAL_II_DIR} $ENV{DEAL_II_DIR})
+IF(NOT ${deal.II_FOUND})
+	MESSAGE(FATAL_ERROR "\n*** ERROR: Could not locate a suitably recent version of deal.II. ***\n"
+		"SOLUTION A: EITHER you pass a flag -DDEAL_II_DIR=/path/to/deal.II to cmake.\n"
+		"SOLUTION B: OR, set an environment variable \"DEAL_II_DIR\".\n"
+	)
+ENDIF()
+
+MESSAGE(STATUS "Found deal.II version ${DEAL_II_PACKAGE_VERSION} at '${deal.II_DIR}'")
+
+SET(_DEALII_GOOD ON)
+
+# IF(NOT DEAL_II_WITH_P4EST)
+# 	MESSAGE(SEND_ERROR "\n-- deal.II was build without support for p4est!\n")
+# 	SET(_DEALII_GOOD OFF)
+# ENDIF()
+
+# IF(NOT DEAL_II_WITH_TRILINOS)
+# 	MESSAGE(SEND_ERROR "\n-- deal.II was build without support for Trilinos!\n")
+# 	SET(_DEALII_GOOD OFF)
+# ENDIF()
+
+DEAL_II_INITIALIZE_CACHED_VARIABLES()
+PROJECT(${TARGET})
+
+MESSAGE("================================================================================")
+
+INCLUDE(cmake/InvokeAutopilot.cmake)
+INCLUDE(cmake/AddAdditionalCompilerWarnings.cmake)
+INVOKE_AUTOPILOT()
+
+MESSAGE(STATUS "NOTE: Writing configuration into ./detailed.log")
+LIST(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR})
+
+INCLUDE(cmake/CreateDetailedLog.cmake)

LICENSE

@@ -0,0 +1,165 @@
+GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
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+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
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+   b) under the GNU GPL, with none of the additional permissions of
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+
+  3. Object Code Incorporating Material from Library Header Files.
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+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
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+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
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+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
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+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
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+   the Library is used in it and that the Library and its use are
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+   document.
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+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

README.md

@@ -0,0 +1,85 @@
+# README #
+
+This README documents whatever steps are necessary to get the application
+  pu-dwr-diffusion
+up and running.
+
+### What is this repository for? ###
+
+* Goal-oriented adaptivity for diffusion/heat equations
+
+* This software is a modification of DTM++/dwr-diffusion which can be found 
+  at https://github.com/dtm-project/dwr-diffusion
+
+### How do I get set up? ###
+
+* Dependencies
+deal.II v9.3.0 at least, linked to HDF5 
+
+* Configuration
+```
+   cmake -S. -Bbuild --DEAL_II_DIR=<path_to_your_deal_installation
+   cmake --build build``
+```
+* Run (single process)
+```
+    ./build/pu-dwr-diffusion input/default.prm
+```
+
+### Who do I talk to? ###
+
+* Principial Author
+    * Jan Philipp Thiele, M.Sc. ([email protected])
+
+* Contributors (original dwr-diffusion)
+    * Marius P. Bruchhaeuser ([email protected])
+    * Dr.-Ing. Dipl.-Ing. Uwe Koecher ([email protected], [email protected])
+
+
+This software is adapted to the diffusion equations and a partition-of-unity 
+localization approach for dual-weighted residuals.
+
+If you write scientific publication using results obtained by reusing parts
+of pu-dwr-diffusion, especially by reusing the partition-of-unity for your applications
+please cite the following publication:
+
+- J. P. Thiele, T. Wick: "Numerical modeling and open-source implementation
+  of variational partition-of-unity localizations of space-time dual-weighted 
+  residual estimators for parabolic problems, in preparation
+
+Furthermore, if you reuse the
+datastructures, algorithms and/or supporting parameter/data input/output
+classes, please cite the following two publications:
+
+- U. Koecher, M.P. Bruchhaeuser, M. Bause: "Efficient and scalable
+  data structures and algorithms for goal-oriented adaptivity of space-time
+  FEM codes", Software X, Vol. 10, 2019
+  https://doi.org/10.1016/j.softx.2019.100239
+
+
+- U. Koecher: "Variational space-time methods for the elastic wave equation
+  and the diffusion equation", Ph.D. thesis,
+  Department of Mechanical Engineering of the Helmut-Schmidt-University,
+  University of the German Federal Armed Forces Hamburg, Germany, p. 1-188,
+  urn:nbn:de:gbv:705-opus-31129, 2015. Open access via:
+  http://edoc.sub.uni-hamburg.de/hsu/volltexte/2015/3112/
+
+### License ###
+Copyright (C) 2012-2023 by Jan Philipp Thiele and contributors
+
+
+pu-dwr-diffusion is free software: you can redistribute it and/or modify
+it under the terms of the GNU Lesser General Public License as
+published by the Free Software Foundation, either
+version 3 of the License, or (at your option) any later version.
+
+pu-dwr-diffusion is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with pu-dwr-diffusion. If not, see <http://www.gnu.org/licenses/>.
+Please see the file
+        ./LICENSE
+for details.

cmake/AddAdditionalCompilerWarnings.cmake

@@ -0,0 +1,39 @@
+# Copyright (C) 2012-2023 by Jan Philipp Thiele and Uwe Koecher
+# 
+# This file is part of pu-dwr-diffusion.
+# 
+# pu-dwr-diffusion is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as
+# published by the Free Software Foundation, either
+# version 3 of the License, or (at your option) any later version.
+# 
+# pu-dwr-diffusion is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+# 
+# You should have received a copy of the GNU Lesser General Public License
+# along with pu-dwr-diffusion. If not, see <http://www.gnu.org/licenses/>.
+
+
+# CMAKE_MINIMUM_REQUIRED(VERSION 2.8.12)
+
+################################################################################
+# Add additional compiler options:
+# 
+ADD_DEFINITIONS(-std=c++17)
+
+ADD_DEFINITIONS(-Wall)
+ADD_DEFINITIONS(-Wextra)
+ADD_DEFINITIONS(-Wpedantic)
+
+# Unset specific warnings (that are warnings coming from the deal.II lib)
+#ADD_DEFINITIONS(-Wno-unneeded-internal-declaration)
+#ADD_DEFINITIONS(-Wno-unused-parameter)
+#ADD_DEFINITIONS(-Wno-unused-variable)
+
+# Make WARNINGS to ERRORS
+#ADD_DEFINITIONS(-Werror)        # Compilation breaks, if warnings are present
+ADD_DEFINITIONS(-Wfatal-errors) # Compilation breaks directly after first error
+################################################################################
+