Add PorosityAux (idaholab#367)

include/auxkernels/MDGranularPorosityAux.h

@@ -0,0 +1,39 @@
+/**********************************************************************/
+/*                     DO NOT MODIFY THIS HEADER                      */
+/* MAGPIE - Mesoscale Atomistic Glue Program for Integrated Execution */
+/*                                                                    */
+/*            Copyright 2017 Battelle Energy Alliance, LLC            */
+/*                        ALL RIGHTS RESERVED                         */
+/**********************************************************************/
+
+#ifndef MDGRANULARPOROSITYAUX_H
+#define MDGRANULARPOROSITYAUX_H
+
+#include "AuxKernel.h"
+
+// forward declarations
+class MDRunBase;
+class MDGranularPorosityAux;
+
+template <>
+InputParameters validParams<MDGranularPorosityAux>();
+
+class MDGranularPorosityAux : public AuxKernel
+{
+public:
+  MDGranularPorosityAux(const InputParameters & params);
+  virtual ~MDGranularPorosityAux() {}
+
+  virtual Real computeValue();
+
+protected:
+  /// referene to the MDRunBase user object
+  const MDRunBase & _md_uo;
+
+  const bool _compute_packing;
+
+  /// property value that is computed only on qp = 0
+  Real _packing_fraction;
+};
+
+#endif // MDGRANULARPOROSITYAUXx_H

src/auxkernels/MDGranularPorosityAux.C

@@ -0,0 +1,61 @@
+/**********************************************************************/
+/*                     DO NOT MODIFY THIS HEADER                      */
+/* MAGPIE - Mesoscale Atomistic Glue Program for Integrated Execution */
+/*                                                                    */
+/*            Copyright 2017 Battelle Energy Alliance, LLC            */
+/*                        ALL RIGHTS RESERVED                         */
+/**********************************************************************/
+
+#include "MDGranularPorosityAux.h"
+#include "MDRunBase.h"
+
+registerMooseObject("MagpieApp", MDGranularPorosityAux);
+
+template <>
+InputParameters
+validParams<MDGranularPorosityAux>()
+{
+  InputParameters params = validParams<AuxKernel>();
+  params.addRequiredParam<UserObjectName>("user_object", "Name of MD runner UserObject");
+  params.addParam<bool>("compute_packing_fraction", false, "Whether to compute porosity or packing fraction.");
+  params.addClassDescription(
+      "Computes porosity or packing fraction (1 - porosity) and injects it into and aux variable.");
+  return params;
+}
+
+MDGranularPorosityAux::MDGranularPorosityAux(const InputParameters & parameters)
+  : AuxKernel(parameters),
+    _md_uo(getUserObject<MDRunBase>("user_object")),
+    _compute_packing(getParam<bool>("compute_packing_fraction"))
+{
+  // ensure MD particles are granular
+  if (!_md_uo.isGranular())
+    mooseError("user_object stores non-granular particles.");
+
+  // ensure variable is elemental
+  if (isNodal())
+    mooseError("MDGranularPorosityAux only permits elemental variables.");
+}
+
+Real
+MDGranularPorosityAux::computeValue()
+{
+  if (_qp == 0)
+  {
+    _packing_fraction = 0.0;
+
+    // get the overlapping MD particles
+    std::vector<std::pair<unsigned int, Real>> gran_vol;
+    _md_uo.granularElementVolumes(_current_elem->unique_id(), gran_vol);
+
+    // add the overlapping volumes
+    for (auto & p : gran_vol)
+      _packing_fraction += p.second;
+
+    // divide by element volume
+    _packing_fraction /= _current_elem->volume();
+  }
+  if (_compute_packing)
+    return _packing_fraction;
+  return 1 - _packing_fraction;
+}

src/userobjects/LAMMPSFileRunner.C

@@ -336,7 +336,7 @@ LAMMPSFileRunner::readLAMMPSFileHistory(std::pair<FileName, FileName> filenames,
         largest_column = _prop_columns[i];
 
     if (largest_column >= elements.size())
-      mooseError("Error reading ", filename, " on line ", line);
+      mooseError("Error reading ", filenames.first, " on line ", line_before);
 #endif
 
     Point pos_before;
@@ -364,7 +364,7 @@ LAMMPSFileRunner::readLAMMPSFileHistory(std::pair<FileName, FileName> filenames,
 
     // we have determined largest_column in DEBUG so we can use it in mooseAssert
     mooseAssert(largest_column < elements.size(),
-                "Error reading " << filename << " on line " << line);
+                "Error reading " << filenames.second << " on line " << line_after);
 
     Point pos_after;
     for (unsigned int i = 0; i < _dim; ++i)