Merge pull request #521 from pbauman/0.8.0-release-prep

0.8.0 Release Prep
grinsfem · Dec 16, 2017 · 6330423 · 6330423
2 parents fda10b6 + 6eab634
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diff --git a/CHANGES b/CHANGES
@@ -1,4 +1,26 @@
-Version 0.8.0 (in progress)
+Version 0.8.0
+   * Minimum libMesh git hash for this release is: 8be0a4e
+   * Substantial internal refactoring of Variables handling
+   * Updated parsing of Variables
+   * Now support subdomain-restricted variables; includes conjugate
+     heat transfer example illustrating usage
+   * Add SPGSM stabilization Physics for reacting low Mach Navier-Stokes
+     Include Ozone flame example illustrating usage
+   * Add RayfireMesh class 
+   * New constraint functionality to supply simple constraints on variables
+     from input file
+   * Can now override input file options from the command line
+   * Added GRINS::Runner and initializer classes to simplify construction
+     of standalone GRINS-based programs
+   * Removed GRVY
+   * Moved CachedValues interface to Physics
+   * Refactor Antioch interface to increase Antioch thermo, transport
+     feature usage 
+   * New QoIs include:
+     - IntegratedFunction
+     - SpectroscopicAbsorption
+       - Specialization of IntegratedFunction. Uses new HITRAN
+         data structures
 
 Version 0.7.0
    * Complete refactoring of material property parsing. Old

diff --git a/LICENSE b/LICENSE
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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/cavity_benchmark/cavity.C b/examples/cavity_benchmark/cavity.C
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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_kinetic_rates.C b/src/apps/antioch_kinetic_rates.C
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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/grins.C b/src/apps/grins.C
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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_factory_initializer.h b/src/boundary_conditions/include/grins/boundary_condition_factory_initializer.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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
@@ -83,7 +83,7 @@ namespace GRINS
     libMesh::Real domega_dot_dT( const libMesh::Real rho_s, const libMesh::Real T ) const;
 
     void set_catalycity_params( const std::vector<libMesh::Real>& params );
-    
+
     virtual void register_parameter(  const std::string & param_name,
                                       libMesh::ParameterMultiAccessor< libMesh::Number > & param_pointer) const;
 

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) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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_common.h b/src/boundary_conditions/include/grins/catalytic_wall_neumann_bc_factory_common.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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_old_style_factory_base.h b/src/boundary_conditions/include/grins/catalytic_wall_neumann_bc_old_style_factory_base.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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/constant_catalycity.h b/src/boundary_conditions/include/grins/constant_catalycity.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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/constant_function_dirichlet_bc_factory.h b/src/boundary_conditions/include/grins/constant_function_dirichlet_bc_factory.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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/default_bc_builder.h b/src/boundary_conditions/include/grins/default_bc_builder.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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/dirichlet_bc_factory_abstract.h b/src/boundary_conditions/include/grins/dirichlet_bc_factory_abstract.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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/dirichlet_bc_factory_function_base.h b/src/boundary_conditions/include/grins/dirichlet_bc_factory_function_base.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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/dirichlet_bc_factory_function_old_style_base.h b/src/boundary_conditions/include/grins/dirichlet_bc_factory_function_old_style_base.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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/gas_catalytic_wall_neumann_bc_factories.h b/src/boundary_conditions/include/grins/gas_catalytic_wall_neumann_bc_factories.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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/gas_catalytic_wall_neumann_bc_old_style_factories.h b/src/boundary_conditions/include/grins/gas_catalytic_wall_neumann_bc_old_style_factories.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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/gas_recombination_catalytic_wall.h b/src/boundary_conditions/include/grins/gas_recombination_catalytic_wall.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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/...ndary_conditions/include/grins/gas_recombination_catalytic_wall_neumann_bc_factory_impl.h b/...ndary_conditions/include/grins/gas_recombination_catalytic_wall_neumann_bc_factory_impl.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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/gas_solid_catalytic_wall.h b/src/boundary_conditions/include/grins/gas_solid_catalytic_wall.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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/gas_solid_catalytic_wall_neumann_bc_factory_impl.h b/src/boundary_conditions/include/grins/gas_solid_catalytic_wall_neumann_bc_factory_impl.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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/homogeneous_dirichlet_bc_factory.h b/src/boundary_conditions/include/grins/homogeneous_dirichlet_bc_factory.h
@@ -3,7 +3,7 @@
 //
 // GRINS - General Reacting Incompressible Navier-Stokes
 //
-// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
+// Copyright (C) 2014-2017 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