RePrimAnd Version 1.3

-Added experimental Einstein Toolkit thorn for building ReprimAnd library
-Fixed minor bug affecting some EOS sanity checks

ET_interface/thorns/RePrimAnd/README

@@ -0,0 +1,22 @@
+Cactus Code Thorn RePrimAnd
+Author(s)    : Wolfgang Kastaun
+Maintainer(s): Wolfgang Kastaun
+Licence      : GPL
+--------------------------------------------------------------------------
+
+1. Purpose
+
+Distribute the RePrimAnd Library; see
+<https://github.com/wokast/RePrimAnd>.
+
+
+The RePrimAnd library is a support library for general relativistic
+magnetohydrodynamics, providing:
+An extensible, modular EOS framework (thermal + barotropic)
+An algorithm for primitive variable recovery in ideal GRMHD
+
+A link to the library documentation can be found at
+https://github.com/wokast/RePrimAnd
+
+The article describing the algorithm is
+https://doi.org/10.1103/PhysRevD.103.023018

ET_interface/thorns/RePrimAnd/configuration.ccl

@@ -0,0 +1,11 @@
+# Configuration definitions for thorn RePrimAnd
+
+PROVIDES RePrimAnd
+{
+  SCRIPT src/detect.sh
+  LANG bash
+  OPTIONS REPRIMAND_DIR REPRIMAND_INSTALL_DIR REPRIMAND_LIBS
+}
+
+# Pass configuration options to build script
+REQUIRES GSL BOOST HDF5 RePrimAnd

ET_interface/thorns/RePrimAnd/interface.ccl

@@ -0,0 +1,3 @@
+# Interface definition for thorn RePrimAnd
+
+IMPLEMENTS: RePrimAnd

ET_interface/thorns/RePrimAnd/param.ccl

@@ -0,0 +1 @@
+# Parameter definitions for thorn RePrimAnd

ET_interface/thorns/RePrimAnd/schedule.ccl

@@ -0,0 +1 @@
+# Schedule definitions for thorn RePrimAnd

ET_interface/thorns/RePrimAnd/src/build.sh

@@ -0,0 +1,62 @@
+#! /bin/bash
+
+################################################################################
+# Build
+################################################################################
+
+# Set up shell
+if [ "$(echo ${VERBOSE} | tr '[:upper:]' '[:lower:]')" = 'yes' ]; then
+    set -x                      # Output commands
+fi
+set -e                          # Abort on errors
+
+
+
+# Set locations
+THORN=RePrimAnd
+NAME=RePrimAnd-1.3
+SRCDIR="$(dirname $0)"
+BUILD_DIR=${SCRATCH_BUILD}/build/${THORN}
+if [ -z "${REPRIMAND_INSTALL_DIR}" ]; then
+    INSTALL_DIR=${SCRATCH_BUILD}/external/${THORN}
+else
+    echo "BEGIN MESSAGE"
+    echo "Installing REPRIMAND into ${REPRIMAND_INSTALL_DIR} "
+    echo "END MESSAGE"
+    INSTALL_DIR=${REPRIMAND_INSTALL_DIR}
+fi
+DONE_FILE=${SCRATCH_BUILD}/done/${THORN}
+REPRIMAND_DIR=${INSTALL_DIR}
+
+# Set up environment
+#unset LIBS
+#if echo '' ${ARFLAGS} | grep 64 > /dev/null 2>&1; then
+#    export OBJECT_MODE=64
+#fi
+
+echo "REPRIMAND: Preparing directory structure..."
+cd ${SCRATCH_BUILD}
+mkdir build external done 2> /dev/null || true
+rm -rf ${BUILD_DIR} ${INSTALL_DIR}
+mkdir ${BUILD_DIR} ${INSTALL_DIR}
+
+echo "REPRIMAND: Unpacking archive..."
+pushd ${BUILD_DIR}
+${TAR?} xJf ${SRCDIR}/../dist/${NAME}.tar.xz
+
+echo "REPRIMAND: Configuring..."
+cd ${NAME}
+meson setup mesonbuild --prefix=${REPRIMAND_DIR} --default-library=static --buildtype=debugoptimized -Dbuild_documentation=false -Dbuild_benchmarks=false -Dbuild_tests=false
+
+echo "REPRIMAND: Building..."
+ninja -C mesonbuild
+
+echo "REPRIMAND: Installing..."
+meson install -C mesonbuild
+popd
+
+echo "REPRIMAND: Cleaning up..."
+rm -rf ${BUILD_DIR}
+
+date > ${DONE_FILE}
+echo "REPRIMAND: Done."

ET_interface/thorns/RePrimAnd/src/detect.sh

@@ -0,0 +1,85 @@
+#! /bin/bash
+
+################################################################################
+# Prepare
+################################################################################
+
+# Set up shell
+if [ "$(echo ${VERBOSE} | tr '[:upper:]' '[:lower:]')" = 'yes' ]; then
+    set -x                      # Output commands
+fi
+set -e                          # Abort on errors
+
+. $CCTK_HOME/lib/make/bash_utils.sh
+
+# Take care of requests to build the library in any case
+REPRIMAND_DIR_INPUT=$REPRIMAND_DIR
+if [ "$(echo "${REPRIMAND_DIR}" | tr '[a-z]' '[A-Z]')" = 'BUILD' ]; then
+    REPRIMAND_BUILD=yes
+    REPRIMAND_DIR=
+else
+    REPRIMAND_BUILD=
+fi
+
+
+THORN=RePrimAnd
+
+################################################################################
+# Build
+################################################################################
+
+if [ -n "$REPRIMAND_BUILD" -o -z "${REPRIMAND_DIR}" ]; then
+    echo "BEGIN MESSAGE"
+    echo "Using bundled REPRIMAND..."
+    echo "END MESSAGE"
+
+    check_tools "tar"
+
+    # Set locations
+    BUILD_DIR=${SCRATCH_BUILD}/build/${THORN}
+    if [ -z "${REPRIMAND_INSTALL_DIR}" ]; then
+        INSTALL_DIR=${SCRATCH_BUILD}/external/${THORN}
+    else
+        echo "BEGIN MESSAGE"
+        echo "Installing REPRIMAND into ${REPRIMAND_INSTALL_DIR} "
+        echo "END MESSAGE"
+        INSTALL_DIR=${REPRIMAND_INSTALL_DIR}
+    fi
+    REPRIMAND_BUILD=1
+    REPRIMAND_DIR=${INSTALL_DIR}
+    REPRIMAND_INC_DIRS="$REPRIMAND_DIR/include"
+    REPRIMAND_LIB_DIRS="$REPRIMAND_DIR/lib"
+    REPRIMAND_LIBS="RePrimAnd"
+else
+    REPRIMAND_BUILD=
+    DONE_FILE=${SCRATCH_BUILD}/done/${THORN}
+    if [ ! -e ${DONE_FILE} ]; then
+        mkdir ${SCRATCH_BUILD}/done 2> /dev/null || true
+        date > ${DONE_FILE}
+    fi
+fi
+
+################################################################################
+# Configure Cactus
+################################################################################
+
+# Pass configuration options to build script
+echo "BEGIN MAKE_DEFINITION"
+echo "REPRIMAND_BUILD       = ${REPRIMAND_BUILD}"
+echo "REPRIMAND_INSTALL_DIR = ${REPRIMAND_INSTALL_DIR}"
+echo "END MAKE_DEFINITION"
+
+
+set_make_vars "REPRIMAND" "$REPRIMAND_LIBS" "$REPRIMAND_LIB_DIRS" "$REPRIMAND_INC_DIRS"
+
+# Pass options to Cactus
+echo "BEGIN MAKE_DEFINITION"
+echo "REPRIMAND_DIR      = ${REPRIMAND_DIR}"
+echo "REPRIMAND_INC_DIRS = ${REPRIMAND_INC_DIRS}"
+echo "REPRIMAND_LIB_DIRS = ${REPRIMAND_LIB_DIRS}"
+echo "REPRIMAND_LIBS     = ${REPRIMAND_LIBS}"
+echo "END MAKE_DEFINITION"
+
+echo 'INCLUDE_DIRECTORY $(REPRIMAND_INC_DIRS)'
+echo 'LIBRARY_DIRECTORY $(REPRIMAND_LIB_DIRS)'
+echo 'LIBRARY           $(REPRIMAND_LIBS)'

ET_interface/thorns/RePrimAnd/src/make.code.defn

@@ -0,0 +1,7 @@
+# Main make.code.defn file for thorn REPRIMAND
+
+# Source files in this directory
+SRCS = 
+
+# Subdirectories containing source files
+SUBDIRS = 

ET_interface/thorns/RePrimAnd/src/make.code.deps

@@ -0,0 +1,10 @@
+# Main make.code.deps file for thorn RePrimAnd
+
+export REPRIMAND_INSTALL_DIR
+
+$(CCTK_TARGET) $(OBJS) $(SRCS:%=%.d): $(SCRATCH_BUILD)/done/$(THORN)
+
+ifneq ($(REPRIMAND_BUILD),)
+$(SCRATCH_BUILD)/done/$(THORN): $(SRCDIR)/build.sh
+	+$(SRCDIR)/build.sh
+endif

README.md

@@ -92,6 +92,19 @@ together with the library. The Python extension module is called
 `pyreprimand`.
 
 
+## Einstein Toolkit Support
+
+RePrimAnd does provide an (experimental) thorn that builds the library within
+an EinsteinToolkit (ET) environment, using the ExternalLibraries mechanism. The
+thorn can be found in the folder `ET_interface/thorns/RePrimAnd/`. The thorn
+depends on the HDF5, GSL, and BOOST ExternalLibraries thorns. In addition,
+the meson build system needs to be installed on the build host.
+
+Currently there is are no thorns that provide an ET-style interface for using
+this library, although this might change in future versions. ET Thorns can of
+course use the library like any other C++ library.
+
+
 ## Creating Documentation
 
 To just build the documentation, use the target `documentation`.

docsrc/sphinx/index.rst

@@ -15,18 +15,20 @@ and velocity from the variables evolved in quasi-conservative
 formulations. Further, it provides a general framework for handling
 matter equations of state. 
 
-This version of the library was made public together with the article 
-describing the recovery scheme:
+A description of the algorithm and tests of the library is given in 
+the accompanying article:
 
 Wolfgang Kastaun, Jay Vijay Kalinani, Riccardo Ciolfi, 
 "Robust Recovery of Primitive Variables in Relativistic Ideal 
 Magnetohydrodynamics",  
-`arXiv:2005.01821 [gr-qc] <https://arxiv.org/abs/2005.01821>`_ 
-(2020).
+`Phys. Rev. D 103, 023018 (2021) <https://doi.org/10.1103/PhysRevD.103.023018>`_
+`(arXiv:2005.01821) <https://arxiv.org/abs/2005.01821>`_.
 
-Prospective users should be sure to check for updated versions
-that will likely be made available in a public repository.
+The latest public versions can be found on the 
+`github page <https://github.com/wokast/RePrimAnd>`_.
 
+Releases are also archived on Zenodo and can be cited via the   
+`DOI <https://doi.org/10.5281/zenodo.3785074>`_.
 
 Developers
 ^^^^^^^^^^
@@ -41,6 +43,10 @@ License
 
    <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License</a>.
 
+Please cite the
+`PRD article <https://doi.org/10.1103/PhysRevD.103.023018>`_ 
+and the `DOI on Zenodo <https://doi.org/10.5281/zenodo.3785074>`_
+when publishing results obtained using the library.
 
 Contents
 --------

docsrc/sphinx/installing.rst

@@ -1,7 +1,7 @@
 Installation
 ============
 
-The main target and devolpment platform is Linux, although the 
+The main target and development platform is Linux, although the 
 library code is not platform-specific and should also work on Macs.
 Windows and AIX are not supported.
 
@@ -38,7 +38,7 @@ To build the library,
    ninja
    
 This will compile with optimization and without debug symbols. Other
-possibilities are `--buildtype=debug` and `--buildtype=debugoptimized`
+possibilities are `--buildtype=debug` and `--buildtype=debugoptimized`.
 To use a different compiler, e.g. clang, prefix the meson command
 with `CC=clang CXX=clang++`.
 See `here <https://mesonbuild.com/Running-Meson.html>`_ for general 
@@ -97,6 +97,18 @@ If the Python bindings have been build, they are automatically installed
 together with the library. The Python extension module is called 
 `pyreprimand`.
 
+Einstein Toolkit Support
+------------------------
+RePrimAnd does provide an (experimental) thorn that builds the library within
+an EinsteinToolkit (ET) environment, using the ExternalLibraries mechanism. The
+thorn can be found in the folder `ET_interface/thorns/RePrimAnd/`. The thorn
+depends on the HDF5, GSL, and BOOST ExternalLibraries thorns. In addition,
+the meson build system needs to be installed on the build host.
+
+Currently there are no thorns that provide an ET-style interface for using
+this library, although this might change in future versions. ET Thorns can of
+course use the library like any other C++ library.
+
 
 Creating Documentation
 ----------------------

library/BasicStuff/interpol.cc

@@ -198,7 +198,7 @@ detail::cspline_mono_impl::cspline_mono_impl(
                 std::vector<double> x_, std::vector<double> y_)
 : x{std::move(x_)}, y{std::move(y_)}, interp{x,y}
 {  
-  auto ext = std::minmax_element(x.begin(), x.end());
+  auto ext = std::minmax_element(y.begin(), y.end());
   rgy = {*ext.first, *ext.second};
   rgx = {x.front(), x.back()};
 }

meson.build

@@ -1,6 +1,6 @@
 
 project('RePrimAnd', ['cpp','c'], default_options : ['cpp_std=c++11'],
-        version : '1.2', license : 'CC BY-NC-SA 4.0')
+        version : '1.3', license : 'CC BY-NC-SA 4.0')
 
 project_headers_dest = 'reprimand'