First design of MD capability in Magpie (idaholab#367)

doc/content/source/auxkernels/MDNParticleAux.md

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+# MDNParticleAux
+
+!syntax description /AuxKernels/MDNParticleAux
+
+Injects the number of MD particles per element computed by
+MD runner object into an auxiliary variable.
+
+!syntax parameters /AuxKernels/MDNParticleAux
+
+!syntax inputs /AuxKernels/MDNParticleAux
+
+!syntax children /AuxKernels/MDNParticleAux
+
+!bibtex bibliography

doc/content/source/userobjects/LAMMPSFileRunner.md

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+# LAMMPSFileRunner
+
+`LAMMPSFileRunner` reads in LAMMPS dumps file and maps them on an FEM mesh.
+The `time_sequence` parameter determines if a sequence of LAMMPS files is read
+or a single file is loaded and used throughout. If a sequence of files is used,
+the `lammps_file` parameter should contain the file base, e.g. `path/to/file/filebase`
+if the files are called `path/to/file/filebase.<time>.xyz`.
+
+Time conversion from FEM time to LAMMPS time is facilitated by the `time_conversion`
+parameter that accepts a MOOSE function object. Denoting FEM time by `t` and LAMMPS time
+by `T`, `time_conversion` is a function `T = F(t)`.
+
+!syntax description /UserObjects/LAMMPSFileRunner
+
+!syntax parameters /UserObjects/LAMMPSFileRunner
+
+!syntax inputs /UserObjects/LAMMPSFileRunner
+
+!syntax children /UserObjects/LAMMPSFileRunner
+
+!bibtex bibliography

include/auxkernels/MDNParticleAux.h

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+/**********************************************************************/
+/*                     DO NOT MODIFY THIS HEADER                      */
+/* MAGPIE - Mesoscale Atomistic Glue Program for Integrated Execution */
+/*                                                                    */
+/*            Copyright 2017 Battelle Energy Alliance, LLC            */
+/*                        ALL RIGHTS RESERVED                         */
+/**********************************************************************/
+
+#ifndef MDNPARTICLEAUX_H
+#define MDNPARTICLEAUX_H
+
+#include "AuxKernel.h"
+
+// forward declarations
+class MDRunBase;
+class MDNParticleAux;
+
+template <>
+InputParameters validParams<MDNParticleAux>();
+
+class MDNParticleAux : public AuxKernel
+{
+public:
+  MDNParticleAux(const InputParameters & params);
+  virtual ~MDNParticleAux() {}
+
+  virtual Real computeValue();
+
+protected:
+  const MDRunBase & _md_uo;
+};
+
+#endif // MDNPARTICLEAUX_H

include/userobjects/LAMMPSFileRunner.h

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+/**********************************************************************/
+/*                     DO NOT MODIFY THIS HEADER                      */
+/* MAGPIE - Mesoscale Atomistic Glue Program for Integrated Execution */
+/*                                                                    */
+/*            Copyright 2017 Battelle Energy Alliance, LLC            */
+/*                        ALL RIGHTS RESERVED                         */
+/**********************************************************************/
+
+#ifndef LAMMPSFILERUNNER_H
+#define LAMMPSFILERUNNER_H
+
+#include "MDRunBase.h"
+
+class LAMMPSFileRunner;
+
+template <>
+InputParameters validParams<LAMMPSFileRunner>();
+
+/**
+ * Reads lammps dump files to emulate MD simulation
+ */
+class LAMMPSFileRunner : public MDRunBase
+{
+public:
+  LAMMPSFileRunner(const InputParameters & parameters);
+
+  virtual void initialize() override {}
+  virtual void execute() override {}
+  virtual void finalize() override {}
+  virtual void initialSetup() override;
+
+  virtual void updateParticleList() override;
+
+protected:
+  /// reads a LAMMPS file
+  void readLAMMPSFile(FileName filename);
+
+  /// reads two LAMMPS files and interpolates times
+  void readLAMMPSFileHistory(std::pair<FileName, FileName> filenames,
+                             std::pair<Real, Real> timestamps,
+                             Real current_time);
+
+  /// helper function that finds two files, one right before and one right after md_time
+  void findBracketingLAMMPSFiles(Real md_time,
+                                 std::pair<std::string, std::string> & filenames,
+                                 std::pair<Real, Real> & timestamps);
+
+  /// whether a sequence of input files or a single input file is read
+  bool _time_sequence;
+
+  /// name of LAMMPS file or file base if _time_sequence == true
+  FileName _lammps_file;
+
+  /// column of x, y, z coordinate in LAMMPS files
+  std::vector<unsigned int> _pos_columns;
+
+  /// Conversion from FEM time to MD time_stamp
+  Function * _time_conversion;
+};
+
+#endif // LAMMPSFILERUNNER_H

include/userobjects/MDRunBase.h

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+/**********************************************************************/
+/*                     DO NOT MODIFY THIS HEADER                      */
+/* MAGPIE - Mesoscale Atomistic Glue Program for Integrated Execution */
+/*                                                                    */
+/*            Copyright 2017 Battelle Energy Alliance, LLC            */
+/*                        ALL RIGHTS RESERVED                         */
+/**********************************************************************/
+
+#ifndef MDRUNBASE_H
+#define MDRUNBASE_H
+
+#include "GeneralUserObject.h"
+#include "KDTree.h"
+#include "libmesh/bounding_box.h"
+
+class MDRunBase;
+class MooseMesh;
+
+template <>
+InputParameters validParams<MDRunBase>();
+
+/**
+ * Base class for molecular dynamics runs in Magpie
+ */
+class MDRunBase : public GeneralUserObject
+{
+public:
+  MDRunBase(const InputParameters & parameters);
+
+  void initialSetup() override;
+  void timestepSetup() override;
+
+  class MDParticles
+  {
+  public:
+    /// particle's position
+    std::vector<Point> pos;
+
+    /// particle's velocity
+    std::vector<Point> vel;
+
+    /// the id of particle in the MD calculation
+    std::vector<unsigned int> id;
+
+    /// the mesh element the particles are in
+    std::vector<unique_id_type> elem_id;
+  };
+
+  /// access to the MDParticles
+  const MDParticles & particles() const { return _md_particles; }
+
+  /// access to the element to particle map
+  const std::vector<unsigned int> elemParticles(unique_id_type elem_id) const;
+
+  /// List of quantities to get from MD simulation
+  MultiMooseEnum getMDQuantities() const;
+
+protected:
+  /// call back function to update the particle list
+  virtual void updateParticleList() = 0;
+
+  /// updates the KDTree object
+  void updateKDTree();
+
+  /// map MDParticles to elements
+  void mapMDParticles();
+
+  /// The Mesh we're using
+  MooseMesh & _mesh;
+
+  /// dimension of the mesh
+  const unsigned int _dim;
+
+  /// dimension of the mesh
+  const unsigned int _nproc;
+
+  /// stores bounding boxes of all other processors
+  std::vector<BoundingBox> _bbox;
+
+  /// total number of particles
+  unsigned int _n_particles;
+
+  /// number of local particles
+  unsigned int _n_local_particles;
+
+  /// stores the location of
+  MDParticles _md_particles;
+
+  /// a map from elem pointer to particles in this element
+  std::map<unique_id_type, std::vector<unsigned int>> _elem_particles;
+
+  /// A KDTree object to handle md_particles
+  std::unique_ptr<KDTree> _kd_tree;
+};
+
+#endif // MDRUNBASE_H

src/auxkernels/MDNParticleAux.C

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+/**********************************************************************/
+/*                     DO NOT MODIFY THIS HEADER                      */
+/* MAGPIE - Mesoscale Atomistic Glue Program for Integrated Execution */
+/*                                                                    */
+/*            Copyright 2017 Battelle Energy Alliance, LLC            */
+/*                        ALL RIGHTS RESERVED                         */
+/**********************************************************************/
+
+#include "MDNParticleAux.h"
+#include "MDRunBase.h"
+
+registerMooseObject("MagpieApp", MDNParticleAux);
+
+template <>
+InputParameters
+validParams<MDNParticleAux>()
+{
+  InputParameters params = validParams<AuxKernel>();
+  params.addRequiredParam<UserObjectName>("user_object", "Name of MD runner UserObject");
+  params.addClassDescription("Injects the number of MD particles from MDRunBase object user_object "
+                             "into auxiliary variable.");
+  return params;
+}
+
+MDNParticleAux::MDNParticleAux(const InputParameters & parameters)
+  : AuxKernel(parameters), _md_uo(getUserObject<MDRunBase>("user_object"))
+{
+}
+
+Real
+MDNParticleAux::computeValue()
+{
+  return _md_uo.elemParticles(_current_elem->unique_id()).size();
+}