Merge pull request idaholab#60 from bwspenc/neml

NEML integration

.gitignore

@@ -52,7 +52,6 @@ temp_print_trace.*
 *.poly
 *.mpx
 *.btr
-*.xml
 *.gmv
 *.plt
 *.slh

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "contrib/neml"]
+	path = contrib/neml
+	url = ../../Argonne-National-Laboratory/neml.git
+	ignore = untracked

Makefile

@@ -44,6 +44,7 @@ POROUS_FLOW         := no
 
 include $(MOOSE_DIR)/modules/modules.mk
 ###############################################################################
+BLACKBEAR_DIR      := $(CURDIR)
 
 # dep apps
 APPLICATION_DIR    := $(CURDIR)

blackbear.mk

@@ -0,0 +1 @@
+include $(BLACKBEAR_DIR)/contrib/neml.mk

contrib/neml.mk

@@ -0,0 +1,33 @@
+neml_DIR            := $(BLACKBEAR_DIR)/contrib/neml
+
+ifneq ($(wildcard $(neml_DIR)/CMakeLists.txt),)
+
+#Exclude all the files with _wrap in the name because they are drivers for testing
+#that are not needed and have additional dependencies.
+neml_srcfiles       := $(shell find $(neml_DIR)/src -name "*.cxx" | grep -v _wrap)
+neml_objects        += $(patsubst %.cxx,%.$(obj-suffix),$(neml_srcfiles))
+neml_LIB            := $(neml_DIR)/libneml-$(METHOD).la
+neml_includes       := $(neml_DIR)/src
+neml_dep_includes   := -I$(neml_DIR)/rapidxml
+
+$(APPLICATION_DIR)/lib/libblackbear-$(METHOD).la: $(neml_LIB)
+
+$(neml_LIB): $(neml_objects)
+	@echo "Linking Library "$@"..."
+	@$(libmesh_LIBTOOL) --tag=CC $(LIBTOOLFLAGS) --mode=link --quiet \
+	  $(libmesh_CC) $(libmesh_CFLAGS) -o $@ $(neml_objects) $(libmesh_LDFLAGS) $(EXTERNAL_FLAGS) -rpath $(neml_DIR)
+	@$(libmesh_LIBTOOL) --mode=install --quiet install -c $(neml_LIB) $(neml_DIR)
+
+$(neml_DIR)/src/%.$(obj-suffix) : $(neml_DIR)/src/%.cxx
+	@echo "Compiling C++ (in "$(METHOD)" mode) "$<"..."
+	@$(libmesh_LIBTOOL) --tag=CXX $(LIBTOOLFLAGS) --mode=compile --quiet \
+	  $(libmesh_CXX) $(libmesh_CPPFLAGS) $(ADDITIONAL_CPPFLAGS) $(libmesh_CXXFLAGS) $(neml_dep_includes) $(app_INCLUDES) $(libmesh_INCLUDE) -w -DHAVE_CONFIG_H -MMD -MP -MF $@.d -MT $@ -c $< -o $@
+
+ADDITIONAL_INCLUDES  += -I$(neml_includes)
+ADDITIONAL_LIBS      += -L$(neml_DIR) -lneml-$(METHOD)
+ADDITIONAL_CPPFLAGS  += -DNEML_ENABLED
+
+else
+$(info WARNING: Not building with NEML because contrib/neml submodule is not present)
+$(info See https://github.com/Argonne-National-Laboratory/neml/blob/dev/INSTALL.md)
+endif

doc/content/source/materials/NEMLStress.md

@@ -0,0 +1,32 @@
+# NEML Stress
+
+!syntax description /Materials/NEMLStress
+
+# Stress Calculator Based on NEML Constitutive Models
+
+This material model provides an interface to the constitutive models for structural materials provided by the [Nuclear Engineering Material model Library (NEML)](https://github.com/Argonne-National-Laboratory/neml) developed by Argonne National Laboratory. This is a general interface to all of the models provided by that library, which are documented in detail in the [NEML documentation](https://neml.readthedocs.io/en/stable/).
+
+NEML permits the definition of complex material constitutive models, the details of which are defined in an XML file that is independent of the MOOSE input file. The required inputs for this model on the MOOSE side simply provide the location of the XML file, which contains a database of potentially multiple material models, and the name of the model within that database to be used.  This model computes the stress, elasticity tensor, and material Jacobian.
+
+Using this model requires that the NEML source code is present, and that the prerequisite libraries are available. NEML is provided as a submodule in BlackBear under the directory `blackbear/contrib/neml`. The up-to-date version of the NEML submodule is obtained using:
+```
+git submodule init
+git submodule update
+```
+in the `blackbear` directory.
+
+NEML is compiled using the MOOSE build system, so no separate compilation step is required to build the library. However, NEML has dependencies on the BOOST library that is not present in the default MOOSE environment.
+
+To build with BOOST, one must simply load the `boost` module provided with MOOSE:
+```
+module load advanced_modules boost
+```
+and add the `--with-boost` option to the `update_and_rebuild_libmesh.sh` script when compiling libMesh to instruct it to use the full BOOST instalation provided by the `boost` module, rather than the subset of BOOST that is distributed with libmesh.
+
+!syntax parameters /Materials/NEMLStress
+
+!syntax inputs /Materials/NEMLStress
+
+!syntax children /Materials/NEMLStress
+
+!bibtex bibliography

doc/content/source/materials/NEMLThermalExpansionEigenstrain.md

@@ -0,0 +1,17 @@
+# NEML Thermal Expansion Eigenstrain
+
+!syntax description /Materials/NEMLThermalExpansionEigenstrain
+
+# Thermal Eigenstrain Obtained from NEML
+
+This material model provides an interface to use the [Nuclear Engineering Material model Library (NEML)](https://github.com/Argonne-National-Laboratory/neml) developed by Argonne National Laboratory to provide thermal expansion eigenstrains. This model would typically be used together with the [NEMLStress](NEMLStress.md) model, the documentation of which provides more details on integration with that library.
+
+NEML permits the definition of complex material constitutive models, the details of which are defined in an XML file that is independent of the MOOSE input file. The required inputs for this model on the MOOSE side simply provide the location of the XML file, which contains a database of potentially multiple material models, and the name of the model within that database to be used.  This model computes the eigenstrain induced by thermal expansion.
+
+!syntax parameters /Materials/NEMLThermalExpansionEigenstrain
+
+!syntax inputs /Materials/NEMLThermalExpansionEigenstrain
+
+!syntax children /Materials/NEMLThermalExpansionEigenstrain
+
+!bibtex bibliography

include/materials/NEMLStress.h

@@ -0,0 +1,92 @@
+/****************************************************************/
+/*               DO NOT MODIFY THIS HEADER                      */
+/*                       BlackBear                              */
+/*                                                              */
+/*           (c) 2017 Battelle Energy Alliance, LLC             */
+/*                   ALL RIGHTS RESERVED                        */
+/*                                                              */
+/*          Prepared by Battelle Energy Alliance, LLC           */
+/*            Under Contract No. DE-AC07-05ID14517              */
+/*            With the U. S. Department of Energy               */
+/*                                                              */
+/*            See COPYRIGHT for full restrictions               */
+/****************************************************************/
+
+#ifndef NEMLSTRESS_H
+#define NEMLSTRESS_H
+
+#include "ComputeStressBase.h"
+
+#include "neml_interface.h"
+
+class NEMLStress;
+
+template <>
+InputParameters validParams<NEMLStress>();
+
+class NEMLStress : public ComputeStressBase
+{
+public:
+  NEMLStress(const InputParameters & parameters);
+
+  virtual void computeQpStress() override;
+  virtual void initQpStatefulProperties() override;
+
+protected:
+  /// File name of the NEML XML database
+  FileName _fname;
+  /// Model name in NEML XML database
+  std::string _mname;
+  /// NEML model
+  std::unique_ptr<neml::NEMLModel> _model;
+  /// History variables used by NEML model
+  ///@{
+  MaterialProperty<std::vector<Real>> & _hist;
+  const MaterialProperty<std::vector<Real>> & _hist_old;
+  ///@}
+  /// Old mechanical strain
+  const MaterialProperty<RankTwoTensor> & _mechanical_strain_old;
+  /// Old stress
+  const MaterialProperty<RankTwoTensor> & _stress_old;
+  /// Strain energy
+  ///@{
+  MaterialProperty<Real> & _energy;
+  const MaterialProperty<Real> & _energy_old;
+  ///@}
+  /// Dissipation
+  ///@{
+  MaterialProperty<Real> & _dissipation;
+  const MaterialProperty<Real> & _dissipation_old;
+  ///@}
+  /// Coupled temperature variable (defaults to zero if not specified)
+  ///@{
+  const VariableValue & _temperature;
+  const VariableValue & _temperature_old;
+  ///@}
+  /// Inelastic strain tensor
+  MaterialProperty<RankTwoTensor> & _inelastic_strain;
+
+  /**
+   * Translates a RankTwoTensor object to a NEML tensor stored in a vector
+   * format.
+   * @param in  RankTwoTensor to be translated
+   * @param out NEML vector output
+   **/
+  void RankTwoTensorToNeml(const RankTwoTensor & in, double * const out);
+
+  /**
+   * Translates a NEML tensor stored in vector format to a RankTwoTensor.
+   * @param in  NEML vector to be translated
+   * @param out RankTwoTensor output
+   **/
+  void NemlToRankTwoTensor(const double * const in, RankTwoTensor & out);
+
+  /**
+   * Translates a NEML elasticity tensor to a RankFourTensor.
+   * @param in  NEML elasticity tensor to be translated
+   * @param out RankFourTensor output
+   **/
+  void NemlToRankFourTensor(const double * const in, RankFourTensor & out);
+};
+
+#endif // NEMLSTRESS_H

include/materials/NEMLThermalExpansionEigenstrain.h

@@ -0,0 +1,58 @@
+/****************************************************************/
+/*               DO NOT MODIFY THIS HEADER                      */
+/*                       BlackBear                              */
+/*                                                              */
+/*           (c) 2017 Battelle Energy Alliance, LLC             */
+/*                   ALL RIGHTS RESERVED                        */
+/*                                                              */
+/*          Prepared by Battelle Energy Alliance, LLC           */
+/*            Under Contract No. DE-AC07-05ID14517              */
+/*            With the U. S. Department of Energy               */
+/*                                                              */
+/*            See COPYRIGHT for full restrictions               */
+/****************************************************************/
+
+#ifndef NEMLTHERMALEXPANSIONEIGENSTRAIN_H
+#define NEMLTHERMALEXPANSIONEIGENSTRAIN_H
+
+#include "ComputeThermalExpansionEigenstrainBase.h"
+
+#include "neml_interface.h"
+
+class NEMLThermalExpansionEigenstrain;
+
+template <>
+InputParameters validParams<NEMLThermalExpansionEigenstrain>();
+
+/**
+ *  NEMLThermalExpansionEigenstrain computes the thermal expansion
+ *  strain from the instantaneous CTE provided by a NEML model
+ */
+class NEMLThermalExpansionEigenstrain : public ComputeThermalExpansionEigenstrainBase
+{
+public:
+  NEMLThermalExpansionEigenstrain(const InputParameters & parameters);
+  virtual void initQpStatefulProperties() override;
+
+protected:
+  virtual void computeThermalStrain(Real & thermal_strain, Real & instantaneous_cte) override;
+
+protected:
+  /// File name of the NEML XML database
+  FileName _fname;
+  /// Model name in NEML XML database
+  std::string _mname;
+  /// NEML model
+  std::unique_ptr<neml::NEMLModel> _model;
+
+  /// Thermal strain
+  ///@{
+  MaterialProperty<Real> & _tstrain;
+  const MaterialProperty<Real> & _tstrain_old;
+  ///@}
+
+  /// Old state of the coupled temperature
+  const VariableValue & _temperature_old;
+};
+
+#endif // NEMLTHERMALEXPANSIONEIGENSTRAIN_H