Merge branch 'master' into 157-cyclotron-trim-coil-has-discontinuous-derivative

CMakeLists.txt

 cmake_minimum_required (VERSION 3.1)
-project (OPAL VERSION 1.9.0)
+project (OPAL VERSION 2.0.0)
 set (PROJECT_BUGREPORT opal@lists.psi.ch)
 
 string (REGEX REPLACE "\\.([0-9])\\." ".0\\1." PACKAGE_VERSION ${PROJECT_VERSION})
@@ -41,16 +41,20 @@ set (CMAKE_CXX_STANDARD 11)
 set (CMAKE_CXX_STANDARD_REQUIRED ON)
 set (CMAKE_CXX_EXTENSIONS OFF)
 
-add_compile_options (-Wall)
 add_definitions (-DIPPL_LINUX -DIPPL_STRINGSTREAM)
-add_definitions (-DIPPL_MPI -DMPICH_SKIP_MPICXX -DIPPL_DONT_POOL -DIPPL_USE_XDIV_RNG -DPETE_BITWISE_COPY -DIPPL_HAS_TEMPLATED_COMPLEX -DIPPL_USE_PARTIAL_SPECIALIZATION -Drestrict=__restrict__ -DNOCTAssert)
+add_definitions (-DIPPL_MPI -DMPICH_SKIP_MPICXX -DIPPL_DONT_POOL)
+add_definitions (-DIPPL_USE_XDIV_RNG -DPETE_BITWISE_COPY)
+add_definitions (-DIPPL_HAS_TEMPLATED_COMPLEX)
+add_definitions (-DIPPL_USE_PARTIAL_SPECIALIZATION)
+add_definitions ( -Drestrict=__restrict__ -DNOCTAssert)
 
-add_compile_options (-ftemplate-depth=1024 -funroll-loops -fstrict-aliasing)
+add_compile_options (-Wall)
+add_compile_options (-funroll-loops -fstrict-aliasing)
 
 # compiler dependent flags
 message ("The underlying C++ compiler ID is: ${CMAKE_CXX_COMPILER_ID}")
 if ( ${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel" )
-    add_compile_options ("-diag-disable 383") 
+    add_compile_options ("-diag-disable 383")
     add_compile_options ("-diag-disable 981")
     if (ENABLE_OpenMP)
 	add_compile_options (-openmp)
@@ -160,7 +164,7 @@ IF (ENABLE_AMR)
     message ("Found AMReX libraries: ${AMREX_LIBRARIES}")
     message ("Found AMReX Fortran links: ${AMREX_EXTRA_Fortran_LINK_LINE}")
     echo_amrex_config_options()
-    
+
     add_definitions(${AMREX_DEFINES})
     add_definitions(-DENABLE_AMR)
     add_compile_options (-Wno-unused-variable -Wno-unused-but-set-variable -Wno-maybe-uninitialized)
@@ -176,7 +180,7 @@ if (ENABLE_SAAMG_SOLVER OR ENABLE_AMR_MG_SOLVER)
     #         Trilinos. Host specific should be avoided in almost any case.
     message ("Enable SAAMG_SOLVER: " ${ENABLE_SAAMG_SOLVER})
     message ("Enable AMR_MG_SOLVER: " ${ENABLE_AMR_MG_SOLVER})
-    
+
     find_package (Trilinos REQUIRED HINTS $ENV{TRILINOS_PREFIX} $ENV{TRILINOS_DIR} $ENV{TRILINOS})
 
     message ("Found Trilinos: ${Trilinos_DIR}")
@@ -265,4 +269,4 @@ install (
 # mode:cmake
 # cmake-tab-width: 4
 # indent-tabs-mode:nil
-# End:
+# End:
\ No newline at end of file

Doxyfile

@@ -51,7 +51,7 @@ PROJECT_BRIEF          = "OPAL"
 # and the maximum width should not exceed 200 pixels. Doxygen will copy the logo
 # to the output directory.
 
-PROJECT_LOGO           = 
+PROJECT_LOGO           = ./amas.png
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
 # into which the generated documentation will be written. If a relative path is
@@ -1572,7 +1572,7 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output.
 # The default value is: YES.
 
-GENERATE_LATEX         = NO
+GENERATE_LATEX         = YES
 
 # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
@@ -1675,7 +1675,7 @@ PDF_HYPERLINKS         = YES
 # The default value is: YES.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
-USE_PDFLATEX           = NO
+USE_PDFLATEX           = YES
 
 # If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
 # command to the generated LaTeX files. This will instruct LaTeX to keep running
@@ -2328,4 +2328,4 @@ GENERATE_LEGEND        = YES
 # The default value is: YES.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-DOT_CLEANUP            = YES
\ No newline at end of file
+DOT_CLEANUP            = YES

LICENSES/H5hut

+*** Copyright Notice ***
+
+H5hut  Copyright (c) 2006-2016, The Regents of the University of California,
+through Lawrence Berkeley National Laboratory (subject to receipt of any
+required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
+Institut (Switzerland).  All rights reserved.
+
+If you have questions about your rights to use or distribute this
+software, please contact Berkeley Lab's Technology Transfer Department
+at  TTD@lbl.gov referring to "H5Part (LBNL Ref CR-2255)"
+
+NOTICE.  This software was developed under partial funding from the U.S.
+Department of Energy.  As such, the U.S. Government has been granted for
+itself and others acting on its behalf a paid-up, nonexclusive,
+irrevocable, worldwide license in the Software to reproduce, prepare
+derivative works, and perform publicly and display publicly.  Beginning
+five (5) years after the date permission to assert copyright is obtained
+from the U.S. Department of Energy, and subject to any subsequent five
+(5) year renewals, the U.S. Government is granted for itself and others
+acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide
+license in the Software to reproduce, prepare derivative works,
+distribute copies to the public, perform publicly and display publicly,
+and to permit others to do so.
+
+
+*** License agreement ***
+
+H5hut  Copyright (c) 2006-2016, The Regents of the University of California,
+through Lawrence Berkeley National Laboratory (subject to receipt of any
+required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
+Institut (Switzerland).  All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+(1) Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+
+(2) Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+(3) Neither the name of the University of California, Lawrence Berkeley
+National Laboratory, U.S. Dept. of Energy, Paul Scherrer Institut
+(Switzerland) nor the names of its contributors may be used to endorse
+or promote products derived from this software without specific prior
+written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+You are under no obligation whatsoever to provide any bug fixes,
+patches, or upgrades to the features, functionality or performance of
+the source code ("Enhancements") to anyone; however, if you choose to
+make your Enhancements available either publicly, or directly to
+Lawrence Berkeley National Laboratory, without imposing a separate
+written license agreement for such Enhancements, then you hereby grant
+the following license: a  non-exclusive, royalty-free perpetual license
+to install, use, modify, prepare derivative works, incorporate into
+other computer software, distribute, and sublicense such enhancements or
+derivative works thereof, in binary and source code form.
+

LICENSES/HDF5

+Copyright Notice and License Terms for 
+HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+-----------------------------------------------------------------------------
+
+HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+Copyright (c) 2006, The HDF Group. 
+
+NCSA HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+Copyright (c) 1998-2006, The Board of Trustees of the University of Illinois. 
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted for any purpose (including commercial purposes) 
+provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, 
+   this list of conditions, and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, 
+   this list of conditions, and the following disclaimer in the documentation 
+   and/or materials provided with the distribution.
+
+3. In addition, redistributions of modified forms of the source or binary 
+   code must carry prominent notices stating that the original code was 
+   changed and the date of the change.
+
+4. All publications or advertising materials mentioning features or use of 
+   this software are asked, but not required, to acknowledge that it was 
+   developed by The HDF Group and by the National Center for Supercomputing 
+   Applications at the University of Illinois at Urbana-Champaign and 
+   credit the contributors.
+
+5. Neither the name of The HDF Group, the name of the University, nor the 
+   name of any Contributor may be used to endorse or promote products derived 
+   from this software without specific prior written permission from 
+   The HDF Group, the University, or the Contributor, respectively.
+
+DISCLAIMER: 
+THIS SOFTWARE IS PROVIDED BY THE HDF GROUP AND THE CONTRIBUTORS 
+"AS IS" WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED.  In no 
+event shall The HDF Group or the Contributors be liable for any damages 
+suffered by the users arising out of the use of this software, even if 
+advised of the possibility of such damage. 
+
+-----------------------------------------------------------------------------
+-----------------------------------------------------------------------------
+
+Limited portions of HDF5 were developed by Lawrence Berkeley National 
+Laboratory (LBNL). LBNL's Copyright Notice and Licensing Terms can be
+found here: COPYING_LBNL_HDF5 file in this directory or at 
+https://support.hdfgroup.org/ftp/HDF5/releases/COPYING_LBNL_HDF5. 
+
+-----------------------------------------------------------------------------
+-----------------------------------------------------------------------------
+
+Contributors:   National Center for Supercomputing Applications (NCSA) at 
+the University of Illinois, Fortner Software, Unidata Program Center (netCDF), 
+The Independent JPEG Group (JPEG), Jean-loup Gailly and Mark Adler (gzip), 
+and Digital Equipment Corporation (DEC).
+
+-----------------------------------------------------------------------------
+ 
+Portions of HDF5 were developed with support from the Lawrence Berkeley 
+National Laboratory (LBNL) and the United States Department of Energy 
+under Prime Contract No. DE-AC02-05CH11231.
+
+-----------------------------------------------------------------------------
+
+Portions of HDF5 were developed with support from the University of 
+California, Lawrence Livermore National Laboratory (UC LLNL).  
+The following statement applies to those portions of the product and must 
+be retained in any redistribution of source code, binaries, documentation, 
+and/or accompanying materials:
+
+   This work was partially produced at the University of California, 
+   Lawrence Livermore National Laboratory (UC LLNL) under contract 
+   no. W-7405-ENG-48 (Contract 48) between the U.S. Department of Energy 
+   (DOE) and The Regents of the University of California (University) 
+   for the operation of UC LLNL.
+
+   DISCLAIMER: 
+   This work was prepared as an account of work sponsored by an agency of 
+   the United States Government. Neither the United States Government nor 
+   the University of California nor any of their employees, makes any 
+   warranty, express or implied, or assumes any liability or responsibility 
+   for the accuracy, completeness, or usefulness of any information, 
+   apparatus, product, or process disclosed, or represents that its use 
+   would not infringe privately- owned rights. Reference herein to any 
+   specific commercial products, process, or service by trade name, 
+   trademark, manufacturer, or otherwise, does not necessarily constitute 
+   or imply its endorsement, recommendation, or favoring by the United 
+   States Government or the University of California. The views and 
+   opinions of authors expressed herein do not necessarily state or reflect 
+   those of the United States Government or the University of California, 
+   and shall not be used for advertising or product endorsement purposes.
+
+-----------------------------------------------------------------------------
+
+HDF5 is available with the SZIP compression library but SZIP is not part 
+of HDF5 and has separate copyright and license terms. See “Szip Compression 
+in HDF Products” (https://support.hdfgroup.org/doc_resource/SZIP/) for 
+further details.
+
+-----------------------------------------------------------------------------
+

LICENSES/HDF5_LBNL

+Copyright Notice and License Terms for
+HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+-----------------------------------------------------------------------------
+
+HDF5 (Hierarchical Data Format 5)
+Copyright (c) 2016, The Regents of the University of California, through 
+Lawrence Berkeley National Laboratory (subject to receipt of any required 
+approvals from the U.S. Dept. of Energy).
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, 
+   this list of conditions, and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, 
+   this list of conditions, and the following disclaimer in the documentation 
+   and/or materials provided with the distribution.
+
+3. Neither the name of the University of California, Lawrence Berkeley 
+National Laboratory, U.S. Dept. of Energy nor the names of its contributors 
+may be used to endorse or promote products derived from this software without 
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF 
+THE POSSIBILITY OF SUCH DAMAGE.
+
+You are under no obligation whatsoever to provide any bug fixes, patches, 
+or upgrades to the features, functionality or performance of the source 
+code ("Enhancements") to anyone; however, if you choose to make your 
+Enhancements available either publicly, or directly to Lawrence Berkeley 
+National Laboratory, without imposing a separate written license agreement 
+for such Enhancements, then you hereby grant the following license: 
+a non-exclusive, royalty-free perpetual license to install, use, modify, 
+prepare derivative works, incorporate into other computer software, 
+distribute, and sublicense such enhancements or derivative works thereof, 
+in binary and source code form.
+

LICENSES/OPAL

+TBD

LICENSES/OpenBLAS

+Copyright (c) 2011-2014, The OpenBLAS Project
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   1. Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in
+      the documentation and/or other materials provided with the
+      distribution.
+   3. Neither the name of the OpenBLAS project nor the names of 
+      its contributors may be used to endorse or promote products 
+      derived from this software without specific prior written 
+      permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
+USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

LICENSES/ParMETIS

+Copyright & License Notice
+--------------------------
+
+The ParMETIS package is copyrighted by the Regents of the 
+University of Minnesota. It can be freely used for educational and 
+research purposes by non-profit institutions and US government 
+agencies only. Other organizations are allowed to use ParMETIS 
+only for evaluation purposes, and any further uses will require prior 
+approval. The software may not be sold or redistributed without prior 
+approval. One may make copies of the software for their use provided 
+that the copies, are not sold or distributed, are used under the same 
+terms and conditions.
+
+As unestablished research software, this code is provided on an 
+``as is'' basis without warranty of any kind, either expressed or
+implied. The downloading, or executing any part of this software
+constitutes an implicit agreement to these terms. These terms and
+conditions are subject to change at any time without prior notice.
+

LICENSES/Trilinos

+The Trilinos project is a collection of open-source packages licensed
+individually under multiple open-source licenses. Licensing terms are
+available at the Trilinos website:
+
+https://trilinos.org/download/license/  
+
+For information about the software license for a particular package,
+see package-specific documentation.

LICENSES/boost

+Boost Software License - Version 1.0 - August 17th, 2003
+
+Permission is hereby granted, free of charge, to any person or organization
+obtaining a copy of the software and accompanying documentation covered by
+this license (the "Software") to use, reproduce, display, distribute,
+execute, and transmit the Software, and to prepare derivative works of the
+Software, and to permit third-parties to whom the Software is furnished to
+do so, all subject to the following:
+
+The copyright notices in the Software and this entire statement, including
+the above license grant, this restriction and the following disclaimer,
+must be included in all copies of the Software, in whole or in part, and
+all derivative works of the Software, unless such copies or derivative
+works are solely in the form of machine-executable object code generated by
+a source language processor.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.

LICENSES/license.AMReX

+AMReX Copyright (c) 2017, The Regents of the University of California,
+through Lawrence Berkeley National Laboratory and the Alliance for
+Sustainable Energy, LLC., through National Renewable Energy Laboratory
+(subject to receipt of any required approvals from the U.S. Dept. of
+Energy).  All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+(1) Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+
+(2) Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+(3) Neither the name of the University of California, Lawrence
+Berkeley National Laboratory, Alliance for Sustainable Energy, LLC.,
+National Renewable Energy Laboratory, U.S. Dept. of Energy nor the
+names of its contributors may be used to endorse or promote products
+derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+You are under no obligation whatsoever to provide any bug fixes,
+patches, or upgrades to the features, functionality or performance of
+the source code ("Enhancements") to anyone; however, if you choose to
+make your Enhancements available either publicly, or directly to
+Lawrence Berkeley National Laboratory or National Renewable Energy
+Laboratory, without imposing a separate written license agreement for
+such Enhancements, then you hereby grant the following license: a
+non-exclusive, royalty-free perpetual license to install, use, modify,
+prepare derivative works, incorporate into other computer software,
+distribute, and sublicense such enhancements or derivative works
+thereof, in binary and source code form.

LICENSES/open-mpi

+Most files in this release are marked with the copyrights of the
+organizations who have edited them.  The copyrights below are in no
+particular order and generally reflect members of the Open MPI core
+team who have contributed code to this release.  The copyrights for
+code used under license from other parties are included in the
+corresponding files.
+
+Copyright (c) 2004-2010 The Trustees of Indiana University and Indiana
+                        University Research and Technology
+                        Corporation.  All rights reserved.
+Copyright (c) 2004-2010 The University of Tennessee and The University
+                        of Tennessee Research Foundation.  All rights
+                        reserved.
+Copyright (c) 2004-2010 High Performance Computing Center Stuttgart,
+                        University of Stuttgart.  All rights reserved.
+Copyright (c) 2004-2008 The Regents of the University of California.
+                        All rights reserved.
+Copyright (c) 2006-2010 Los Alamos National Security, LLC.  All rights
+                        reserved.
+Copyright (c) 2006-2010 Cisco Systems, Inc.  All rights reserved.
+Copyright (c) 2006-2010 Voltaire, Inc. All rights reserved.
+Copyright (c) 2006-2011 Sandia National Laboratories. All rights reserved.
+Copyright (c) 2006-2010 Sun Microsystems, Inc.  All rights reserved.
+                        Use is subject to license terms.
+Copyright (c) 2006-2010 The University of Houston. All rights reserved.
+Copyright (c) 2006-2009 Myricom, Inc.  All rights reserved.
+Copyright (c) 2007-2008 UT-Battelle, LLC. All rights reserved.
+Copyright (c) 2007-2010 IBM Corporation.  All rights reserved.
+Copyright (c) 1998-2005 Forschungszentrum Juelich, Juelich Supercomputing
+                        Centre, Federal Republic of Germany
+Copyright (c) 2005-2008 ZIH, TU Dresden, Federal Republic of Germany
+Copyright (c) 2007      Evergrid, Inc. All rights reserved.
+Copyright (c) 2008      Chelsio, Inc.  All rights reserved.
+Copyright (c) 2008-2009 Institut National de Recherche en
+                        Informatique.  All rights reserved.
+Copyright (c) 2007      Lawrence Livermore National Security, LLC.
+                        All rights reserved.
+Copyright (c) 2007-2009 Mellanox Technologies.  All rights reserved.
+Copyright (c) 2006-2010 QLogic Corporation.  All rights reserved.
+Copyright (c) 2008-2010 Oak Ridge National Labs.  All rights reserved.
+Copyright (c) 2006-2010 Oracle and/or its affiliates.  All rights reserved.
+Copyright (c) 2009      Bull SAS.  All rights reserved.
+Copyright (c) 2010      ARM ltd.  All rights reserved.
+Copyright (c) 2010-2011 Alex Brick <bricka@ccs.neu.edu>.  All rights reserved.
+Copyright (c) 2012      The University of Wisconsin-La Crosse. All rights
+                        reserved.
+Copyright (c) 2013-2016 Intel, Inc. All rights reserved.
+Copyright (c) 2011-2014 NVIDIA Corporation.  All rights reserved.
+Copyright (c) 2017      Amazon.com, Inc. or its affiliates.  All Rights
+                        reserved.
+
+$COPYRIGHT$
+
+Additional copyrights may follow
+
+$HEADER$
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+- Redistributions of source code must retain the above copyright
+  notice, this list of conditions and the following disclaimer.
+
+- Redistributions in binary form must reproduce the above copyright
+  notice, this list of conditions and the following disclaimer listed
+  in this license in the documentation and/or other materials
+  provided with the distribution.
+
+- Neither the name of the copyright holders nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+The copyright holders provide no reassurances that the source code
+provided does not infringe any patent, copyright, or any other
+intellectual property rights of third parties.  The copyright holders
+disclaim any liability to any recipient for claims brought against
+recipient by any third party for infringement of that parties
+intellectual property rights.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

-This is OPAL >= 1.9.9. Be aware of the fact that the documentation is not
-anymore a separate project.
+# This is OPAL 2.
 
-The documentation is in the [Wiki](https://gitlab.psi.ch/OPAL/src/wikis/home).
+The documentation has been moved to the [Wiki](https://gitlab.psi.ch/OPAL/src/wikis/home).

doc/randomnotes.txt

-
-A note on documentation etc. for collegues starting work on OPAL:
-
-1) The full documentation gor OPAL 2.x.x is on the Wiki: https://gitlab.psi.ch/OPAL/src/wikis/Manual/home 
-
-2) Also the C++ source code must be documented please read: http://en.wikipedia.org/wiki/Doxygen and document
-   your source code accordingly.
-
-3) We have to do some artwork for our paper(s) and documentation. Please use only TikZ and see the power of
-   this package (and many examples to start) at http://www.texample.net/tikz/examples/ .
-
-
-

doc/refcard/opal-ref-card-bibliography.bib

-%% objective - bibliography file for femaxx reference card
-%% author - benedikt oswald
-%% modified - 2008 jun 11, creation, benedikt oswald
-
-@Article{arbenzetal2001,
-  author = 	 {Arbenz, P. and Geus, R. and Adam, S.},
-  title = 	 {Solving Maxwell eigenvalue problems for accelerating cavities},
-  journal = 	 {Physical Review Special Topics - Accelerators and Beams},
-  year = 	 {2001},
-  volume = 	 {4},
-  pages = 	 {022001-1:022001-10},
-  annote = 	 {Abstract: we investigate algorithms for computing steady state electromagnetic waves
-                  in cavities. The Maxwell equations for the strength of the electric field are solved by
-                  a mixed method with quadratic finite edge (N{\'e}d{\'e}lec) elements for the field
-                  values and corresponding node-based finite elements for the Lagrange multiplier, This
-                  approach avoids so-called spurious modes which are introduced if the divergence-free
-                  condition for the electric field is not treated properly. To compute a few of the smalles
-                  positive eigenvalues and corresponding eigenmodes of the resulting large sparse-matrix
-                  eigenvalue problems, two algorithms have been used: the implicitly restarted Lanczos
-                  algorithm and the Jacobi-Davidson algorithm, both with shit-and-invert spectral transformation.
-                  Two-level hierarchical basis preconditioners have been employed for the iterative solution
-                  of the resulting systems of equations.}
-}
-
-
-@PhdThesis{geus2002,
-  author = 	 {Geus, R.},
-  title = 	 {The Jacobi-Davidson Algorithm for solving large sparse symmetric eigenvalue problems with application to the design of accelerator cavities},
-  school = 	 {Swiss Federal Institute of Technology Zurich},
-  year = 	 {2002},
-  OPTkey = 	 {Diss. ETH NO. 14734},
-  type = 	 {},
-  address = 	 {},
-  month = 	 {},
-  note = 	 {},
-  annote = 	 {}
-}
-
-

ippl/INSTALL

-###########################################################################
-#
-# The IPPL Framework
-# 
-# Visit http://amas.web.psi.ch/tools/IPPL/index.html
-#
-###########################################################################
-
-
-
-/***************************************************************************
- * $RCSfile: INSTALL,v $   $Author: adelmann $
- * $Revision: 1.1.1.1 $   $Date: 2003/01/23 07:40:17 $
- * IPPL_VERSION_ID: $Id: INSTALL,v 1.1.1.1 2003/01/23 07:40:17 adelmann Exp $ 
- ***************************************************************************/

ippl/LICENSE

-###########################################################################
-#
-# The IPPL Framework
-# 
-#
-# http://amas.web.psi.ch/tools/IPPL/index.html
-#
-###########################################################################
-
-<License info here>
-More to come
-/***************************************************************************
- * $RCSfile: LICENSE,v $   $Author: adelmann $
- * $Revision: 1.1.1.1 $   $Date: 2003/01/23 07:40:17 $
- * IPPL_VERSION_ID: $Id: LICENSE,v 1.1.1.1 2003/01/23 07:40:17 adelmann Exp $ 
- ***************************************************************************/

ippl/README

-###########################################################################
-#
-# The IPPL Framework
-# 
-# http://amas.web.psi.ch/tools/IPPL/index.html
-#
-###########################################################################
-
-This is the main directory for version 1.0 of the IPPL FrameWork.
-The FrameWork makes heavy use of template, so, although it is
-necessary to first form libippl.a.
-
-The IPPL library is compiled using cmake, details can be found at
-
-In order to compile the FrameWork, you need to set two environment
-variables: IPPL_ROOT.
-
-Please report bugs to andreas.adelmann@psi.ch
-
-/***************************************************************************
- * $RCSfile: README,v $   $Author: adelmann $
- * $Revision: 1.1.1.1 $   $Date: 2003/01/23 07:40:17 $
- * IPPL_VERSION_ID: $Id: README,v 1.1.1.1 2003/01/23 07:40:17 adelmann Exp $ 
- ***************************************************************************/

ippl/src/CMakeLists.txt

@@ -126,7 +126,7 @@ set (MAKE_DEF
     )
 
 include_directories (
-    before ${CMAKE_CURRENT_SOURCE_DIR}
+    BEFORE ${CMAKE_CURRENT_SOURCE_DIR}
     )
 
 add_library ( ippl ${IPPL_SRCS} ${IPPL_SRCS_FORT} )

ippl/test/FFT/CMakeLists.txt

-FILE (RELATIVE_PATH _relPath "${CMAKE_SOURCE_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}")
-MESSAGE (STATUS "Adding test FFT found in ${_relPath}")
-MESSAGE (STATUS "MPI COMPILER ${MPI_UNDERLYING_COMPILER}")
-
-set (CMAKE_CXX_FLAGS
-      "-O3 ${CMAKE_CXX_FLAGS}"
-    )
+file (RELATIVE_PATH _relPath "${CMAKE_SOURCE_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}")
+message ("Adding test FFT found in ${_relPath}")
+message ("MPI CXX compiler: ${MPI_CXX_COMPILER}")
+message ("CXX compiler: ${CMAKE_CXX_COMPILER}")
 
 include_directories (
     ${CMAKE_SOURCE_DIR}/src
@@ -16,17 +13,13 @@ link_directories (
     ${CMAKE_SOURCE_DIR}/src
 )
 
-SET (IPPL_LIBS ippl)
-
-IF (ENABLE_DKS)
+set (IPPL_LIBS ippl)
 
+if (ENABLE_DKS)