Line data    Source code

       1             : /**********************************************************************/
       2             : /*                     DO NOT MODIFY THIS HEADER                      */
       3             : /* MAGPIE - Mesoscale Atomistic Glue Program for Integrated Execution */
       4             : /*                                                                    */
       5             : /*            Copyright 2017 Battelle Energy Alliance, LLC            */
       6             : /*                        ALL RIGHTS RESERVED                         */
       7             : /**********************************************************************/
       8             : 
       9             : #pragma once
      10             : 
      11             : #include "ElementUserObject.h"
      12             : #include "PolyatomicDisplacementFunction.h"
      13             : #include "PolyatomicDisplacementDerivativeFunction.h"
      14             : 
      15             : #include <map>
      16             : #include <array>
      17             : #include <vector>
      18             : 
      19             : #include "mytrim/ion.h"
      20             : #include "mytrim/element.h"
      21             : 
      22             : class PKAGeneratorBase;
      23             : 
      24             : /**
      25             :  * This UserObject rasterizes a simulation domain for the MyTRIM library
      26             :  */
      27             : class MyTRIMRasterizer : public ElementUserObject
      28             : {
      29             : public:
      30             :   static InputParameters validParams();
      31             : 
      32             :   MyTRIMRasterizer(const InputParameters & parameters);
      33             : 
      34             :   /// determines if a TRIM run is executed during this timestep
      35             :   virtual bool executeThisTimestep() const;
      36             : 
      37             :   virtual void initialize();
      38             :   virtual void execute();
      39             :   virtual void threadJoin(const UserObject & y);
      40             :   virtual void finalize();
      41             : 
      42             :   /// get the concentration array
      43             :   const std::vector<Real> & material(const Elem *) const;
      44             : 
      45             :   /// get the site volume
      46             :   Real siteVolume(const Elem *) const;
      47             : 
      48             :   /// get the PKA list
      49         133 :   const std::vector<MyTRIM_NS::IonBase> & getPKAList() const { return _pka_list; }
      50             : 
      51             :   /// get the variable ID of the first coupled variable (to determine the periodicity)
      52             :   int periodic() const { return _periodic; }
      53             : 
      54             :   /// returns a point with the periodic boundary conditions applied
      55             :   Point periodicPoint(const Point &) const;
      56             : 
      57             :   /// checks if species exists
      58             :   bool isTrackedSpecies(unsigned int atomic_number, Real mass_number) const;
      59             : 
      60             :   /// element averaged data
      61      455677 :   struct AveragedData
      62             :   {
      63      427146 :     AveragedData(unsigned int nvars = 0) : _elements(nvars, 0.0), _site_volume(0.0) {}
      64             : 
      65             :     std::vector<Real> _elements;
      66             :     Real _site_volume;
      67             :   };
      68             : 
      69           0 :   struct PKAParameters
      70             :   {
      71             :     /// masses, charges, and mass number tolerances (m_i, Z_i, mtol_i) of the matrix elements
      72             :     std::vector<std::tuple<Real, Real, Real>> _mass_charge_tuple;
      73             : 
      74             :     /// how many isotopes to we have for each element and which index contains the
      75             :     /// first Z match? (only support up to Z=119!)
      76             :     std::array<std::pair<unsigned int, std::size_t>, 120> _index_Z;
      77             : 
      78             :     /// time interval over which the PKAs are added
      79             :     Real _dt;
      80             : 
      81             :     /// recoil rate scaling
      82             :     Real _recoil_rate_scaling;
      83             : 
      84             :     /// current element volume
      85             :     Real _volume;
      86             :   };
      87             : 
      88             :   enum TRIMModuleEnum
      89             :   {
      90             :     MYTRIM_CORE = 0,
      91             :     MYTRIM_ENERGY_DEPOSITION = 1
      92             :   };
      93             : 
      94             :   enum Unit
      95             :   {
      96             :     ANGSTROM = 0,
      97             :     NANOMETER,
      98             :     MICROMETER
      99             :   };
     100             : 
     101           0 :   struct TrimParameters
     102             :   {
     103             :     // Element prototype data (charge, mass, displacement and binding energies)
     104             :     std::vector<MyTRIM_NS::Element> element_prototypes;
     105             : 
     106             :     /// conversion factor from chosen length unit to Angstrom
     107             :     Real length_scale;
     108             : 
     109             :     /// the TRIM class to instantiate in the recoil loops
     110             :     TRIMModuleEnum trim_module;
     111             : 
     112             :     /// energy cutoff below which recoils are not followed explicitly but effects are calculated analytically
     113             :     Real analytical_cutoff;
     114             : 
     115             :     /// maximum acceptable distance for matching NRT objects in composition space
     116             :     Real max_nrt_distance;
     117             : 
     118             :     /// logarithmic energy spacing for NRT integration
     119             :     Real nrt_log_energy_spacing;
     120             : 
     121             :     /// enable instantaneous recombination
     122             :     bool recombination;
     123             : 
     124             :     /// recombination radius
     125             :     Real r_rec;
     126             : 
     127             :     /// target number of pkas
     128             :     unsigned int desired_npka;
     129             : 
     130             :     /// original length of pka list
     131             :     unsigned int original_npka;
     132             : 
     133             :     /// length of pka list after rejection
     134             :     unsigned int scaled_npka;
     135             : 
     136             :     /// a scaling factor for the reaction rates to avoid very large PKA lists
     137             :     Real recoil_rate_scaling;
     138             : 
     139             :     /// scaling factor for the results
     140             :     Real result_scaling_factor;
     141             : 
     142             :     /// the _dt for which mytrim was executed last
     143             :     Real last_executed_dt;
     144             : 
     145             :     /// get the number of elements in the TRIM simulation
     146         489 :     unsigned int nVars() const { return element_prototypes.size(); }
     147             :   };
     148             : 
     149             :   /// get the simulation parameters
     150         495 :   const TrimParameters & getTrimParameters() const { return _trim_parameters; }
     151             : 
     152             : protected:
     153             :   ///@{ pack/unpack the _material_map and _pka_list data into a structure suitable for parallel communication
     154             :   void serialize(std::string & serialized_buffer);
     155             :   void deserialize(std::vector<std::string> & serialized_buffers);
     156             :   ///@}
     157             : 
     158             :   /// number of coupled variables to map
     159             :   const unsigned int _nvars;
     160             : 
     161             :   /// dimension of the mesh
     162             :   const unsigned int _dim;
     163             : 
     164             :   /// Simulation parameters
     165             :   TrimParameters _trim_parameters;
     166             : 
     167             :   /// Global (non-spatial dependent) parameters required for PKA generation
     168             :   PKAParameters _pka_parameters;
     169             : 
     170             :   /// coupled variable values
     171             :   std::vector<const VariableValue *> _var;
     172             : 
     173             :   /// lattice site volume material property
     174             :   const MaterialProperty<Real> * _site_volume_prop;
     175             : 
     176             :   /// conversion of site volume if mesh units are not nm and vars are number densities
     177             :   Real _site_volume_conversion;
     178             : 
     179             :   /// @{ PKA generators
     180             :   const std::vector<UserObjectName> _pka_generator_names;
     181             :   std::vector<const PKAGeneratorBase *> _pka_generators;
     182             :   /// @}
     183             : 
     184             :   /// @{ material map for the TRIM simulation (spatial dependent)
     185             :   typedef std::map<dof_id_type, AveragedData> MaterialMap;
     186             :   MaterialMap _material_map;
     187             :   /// @}
     188             : 
     189             :   /// variable number to use for minPeriodicDistance calls (i.e. use the periodicity of this variable)
     190             :   const int _periodic;
     191             : 
     192             :   /// cumulative PKA list
     193             :   std::vector<MyTRIM_NS::IonBase> _pka_list;
     194             : 
     195             :   /// time for which the next BCMC simulation is responsible (current dt plus skipped steps)
     196             :   Real _accumulated_time;
     197             : 
     198             :   /// rollback buffer for _accumulated_time if the previous step did not converge
     199             :   Real _accumulated_time_old;
     200             : 
     201             :   /// timestep interval on which to run BCMC
     202             :   const unsigned int _interval;
     203             : 
     204             :   /// @{ periodicity data
     205             :   Point _min_dim;
     206             :   Point _max_dim;
     207             :   bool _pbc[LIBMESH_DIM];
     208             :   /// @}
     209             : 
     210             : private:
     211             :   bool _execute_this_timestep;
     212             : 
     213             :   /// timers
     214             :   PerfID _perf_finalize;
     215             : };