grinsfem · pbauman · Jun 3, 2016 · May 26, 2016 · May 26, 2016 · May 26, 2016
diff --git a/AUTHORS b/AUTHORS
@@ -6,6 +6,7 @@ Timo van Opstal
 Timothy R. Adowski
 Vikram Garg
 Chris Haynes
+Nicholas Malaya
 
 Early contributions from:
 Onkar Sahni
diff --git a/CHANGES b/CHANGES
@@ -1,6 +1,50 @@
-Version 0.7.0 (In progress)
+Version 0.7.0
+   * Complete refactoring of material property parsing. Old
+     style is deprecated. See examples, master input file for
+     a description of the new style.
+   * Complete refactoring of Variable parsing and internal
+     object construction. Old style is deprecated. See examples,
+     master input file for a description of new style. Expect
+     the old style to be unsupported soon after 0.7.0 release.
+   * Refactoring in progress for SolverOptions. Except further
+     changes to input parsing for SolverOptions.
+   * Refactoring ErrorEstimation parsing and construction. See
+     examples  master input file for a description of new style.
+   * Complete refactoring of BoundaryCondition parsing and construction.
+     Old input style is deprecated. See examples, master input file
+     for a description of new style. In particular, for Neumann
+     boundary conditions, all fluxes are assumed to *positive outward*
+     in the new format.
+   * Added support for using multiple instances of the same Physics.
+     See examples, master input file for a description.
+   * Added support for second order-in-time problems, including
+     Physics::damping_residual and libMesh::NewmarkSolver.
+   * Minimum version of Antioch is now 0.4.0
+   * Added support for Antioch's MixturedAveraged, KineticsTheory
+     models. This is still experimental.
+   * Further developments on parameter management/parsing for
+     sensitivity calculations.
+   * Better error checking for PressurePinning.
+   * Support for varying numerical Jacobian h values from input.
+   * Boost is now *optional*. If your compiler supports C++11,
+     that will be preferred. If it does not, then we will fallback
+     to Boost. This is specifically for shared_ptr.
+   * Updated testing infrastructure, including support for CppUnit.
    * Added support for output of 'base_velocity' in averaged_fan
-   * Added scalar parsed qoi regression test case
+   * Added scalar parsed qoi regression test case.
+   * Complete refactoring of Physics construction.
+   * Use libMesh::UniquePtr instead of libMesh::AutoPtr
+   * Much internal refactoring.
+   * Increased error checking, testing throughout.
+   * New Physics include:
+     - RayleighDamping
+     - ConvectionDiffusion
+   * New QoIs include:
+     - WeightedFlux
+     - ParsedBoundary
+   * New examples include:
+     - SpalartAllmaras Airfoil
+     - Time-dependent AMR (ConvectionDiffusion Physics)
 
 Version 0.6.1
 https://github.com/grinsfem/grins/releases/tag/v0.6.1

diff --git a/LICENSE b/LICENSE
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/Makefile.am b/Makefile.am
@@ -1,8 +1,6 @@
 include $(top_srcdir)/doxygen/aminclude.am
 
-BUILT_SOURCES   = .license.stamp
 
-CLEANFILES = .license.stamp
 
 AUTOMAKE_OPTIONS = foreign
 ACLOCAL_AMFLAGS  = -I m4 -I m4/common
@@ -28,23 +26,9 @@ EXTRA_DIST += $(GRINS_TEST_SH_FILES) $(GRINS_TEST_INPUT_FILES) $(GRINS_TEST_DATA
 #doxygen_DATA = $(top_srcdir)/docs/doxygen/GRINS.tag
 
 includedir = $(prefix)/include
+BUILT_SOURCES = grins_config.h
 include_HEADERS = $(top_builddir)/grins_config.h
 
-# Eliminate .svn directories in dist tarball
-dist-hook:
-	rm -rf `find $(distdir)/ -name .svn`
-
-#if SVN_CHECKOUT
-#  EXTRA_DIST     += dist_version
-#
-#TODO: check if dist_version is needed in BUILT_SOURCES (in addition to EXTRA_DIST)
-#  BUILT_SOURCES   = dist_version
-#
-#dist_version: FORCE
-#	@SVN_REVISION@ > $(top_srcdir)/dist_version
-#
-#FORCE:
-#endif
 
 # Tools in the auxiliary directory
 
@@ -89,10 +73,18 @@ MOSTLYCLEANFILES     = $(DX_CLEANFILES) \
 #     works.
 #STAMPED_FILES  = $(shell find $(top_srcdir)/src -name '*.h' -or -name '*.C')
 
+# Since we don't distribute the lic_utils, check and make sure it's there.
+# This way, we won't run this on distributed tarballs, only on the repos clones
+
+if GRINS_LICENSESTAMPEXISTS
+BUILT_SOURCES += .license.stamp
 .license.stamp: $(top_srcdir)/LICENSE
 	@$(top_srcdir)/src/common/lic_utils/update_license.pl $(top_srcdir)/LICENSE $(GRINS_STAMPED_FILES)
 	echo 'updated source license headers' >$@
 
+CLEANFILES = .license.stamp
+endif
+
 # -------------------------------------------
 # Optional support for code coverage analysis
 # -------------------------------------------

diff --git a/configure.ac b/configure.ac
@@ -465,6 +465,11 @@ _AC_SRCDIRS(.)
 ABS_TOP_SRC_DIR=$ac_abs_top_srcdir
 TOP_SRC_DIR=$ac_srcdir
 
+# Since we don't distribute the lic_utils, check and make sure it's there.
+# This way, we won't run the license stamping perl script on distributed
+# tarballs, only on the repository clones
+AM_CONDITIONAL(GRINS_LICENSESTAMPEXISTS, [test -f $ABS_TOP_SRC_DIR/src/common/lic_utils/update_license.pl])
+
 # We have to do this by subdirectory because otherwise distcheck
 # breaks as we start picking up files in the directories
 # that it uses.

diff --git a/examples/cavity_benchmark/cavity.C b/examples/cavity_benchmark/cavity.C
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/examples/elastic_sheet/displacement_continuation_solver.C b/examples/elastic_sheet/displacement_continuation_solver.C
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/examples/elastic_sheet/displacement_continuation_solver.h b/examples/elastic_sheet/displacement_continuation_solver.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/examples/elastic_sheet/displacement_continuation_solver_factory.h b/examples/elastic_sheet/displacement_continuation_solver_factory.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/examples/elastic_sheet/stretching_sheet.C b/examples/elastic_sheet/stretching_sheet.C
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/examples/inflating_sheet/inflating_sheet.C b/examples/inflating_sheet/inflating_sheet.C
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/examples/inflating_sheet/inflating_sheet_solver_factory.C b/examples/inflating_sheet/inflating_sheet_solver_factory.C
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/examples/inflating_sheet/inflating_sheet_solver_factory.h b/examples/inflating_sheet/inflating_sheet_solver_factory.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/examples/inflating_sheet/pressure_continuation_solver.C b/examples/inflating_sheet/pressure_continuation_solver.C
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/examples/inflating_sheet/pressure_continuation_solver.h b/examples/inflating_sheet/pressure_continuation_solver.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/examples/suspended_cable/suspended_cable.C b/examples/suspended_cable/suspended_cable.C
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/src/Makefile.am b/src/Makefile.am
@@ -291,6 +291,7 @@ include_HEADERS += boundary_conditions/include/grins/bc_factory_abstract.h
 include_HEADERS += boundary_conditions/include/grins/dirichlet_bc_factory_abstract.h
 include_HEADERS += boundary_conditions/include/grins/dirichlet_bc_factory_function_base.h
 include_HEADERS += boundary_conditions/include/grins/dirichlet_bc_factory_function_old_style_base.h
+include_HEADERS += boundary_conditions/include/grins/parsed_function_traits.h
 include_HEADERS += boundary_conditions/include/grins/parsed_function_factory_helper.h
 include_HEADERS += boundary_conditions/include/grins/parsed_function_dirichlet_bc_factory.h
 include_HEADERS += boundary_conditions/include/grins/constant_function_dirichlet_bc_factory.h
@@ -506,6 +507,7 @@ include_HEADERS += variables/include/grins/displacement_fe_variables.h
 include_HEADERS += variables/include/grins/species_mass_fracs_fe_variables.h
 include_HEADERS += variables/include/grins/thermo_pressure_fe_variable.h
 include_HEADERS += variables/include/grins/turbulence_fe_variables.h
+include_HEADERS += variables/include/grins/generic_fe_type_variable.h
 include_HEADERS += variables/include/grins/variable_name_defaults.h
 include_HEADERS += variables/include/grins/variables_parsing.h
 include_HEADERS += variables/include/grins/variable_warehouse.h
@@ -632,7 +634,7 @@ if CODE_COVERAGE_ENABLED
   CLEANFILES += *.gcda *.gcno
 endif
 
-EXTRA_DIST  = common
+EXTRA_DIST  = common/lcov
 EXTRA_DIST += $(sfiles_DATA)
 
 # Required for AX_AM_MACROS

diff --git a/src/apps/antioch_kinetic_rates.C b/src/apps/antioch_kinetic_rates.C
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/src/apps/antioch_thermo_tables.C b/src/apps/antioch_thermo_tables.C
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/src/apps/antioch_transport_values.C b/src/apps/antioch_transport_values.C
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/src/apps/cantera_kinetic_rates.C b/src/apps/cantera_kinetic_rates.C
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/src/boundary_conditions/include/grins/arrhenius_catalycity.h b/src/boundary_conditions/include/grins/arrhenius_catalycity.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/src/boundary_conditions/include/grins/bc_builder.h b/src/boundary_conditions/include/grins/bc_builder.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/src/boundary_conditions/include/grins/bc_factory_abstract.h b/src/boundary_conditions/include/grins/bc_factory_abstract.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/src/boundary_conditions/include/grins/boundary_condition_names.h b/src/boundary_conditions/include/grins/boundary_condition_names.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/src/boundary_conditions/include/grins/catalycity_base.h b/src/boundary_conditions/include/grins/catalycity_base.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/src/boundary_conditions/include/grins/catalycity_factories.h b/src/boundary_conditions/include/grins/catalycity_factories.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/src/boundary_conditions/include/grins/catalycity_factories_old_style.h b/src/boundary_conditions/include/grins/catalycity_factories_old_style.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/src/boundary_conditions/include/grins/catalycity_factory_abstract.h b/src/boundary_conditions/include/grins/catalycity_factory_abstract.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/src/boundary_conditions/include/grins/catalycity_factory_old_style_base.h b/src/boundary_conditions/include/grins/catalycity_factory_old_style_base.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/src/boundary_conditions/include/grins/catalytic_wall_base.h b/src/boundary_conditions/include/grins/catalytic_wall_base.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or

diff --git a/src/boundary_conditions/include/grins/catalytic_wall_neumann_bc_factory_base.h b/src/boundary_conditions/include/grins/catalytic_wall_neumann_bc_factory_base.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2015 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
 // Copyright (C) 2010-2013 The PECOS Development Team
 //
 // This library is free software; you can redistribute it and/or