Shared Voronoi functionality between baseplate and powder init (#372)

* Shared Voronoi functionality between baseplate and powder init

* Updated deprecation notices and log file print

examples/Inp_Finch.json

@@ -18,7 +18,7 @@
       "TrimUnmeltedRegion": true
    },
    "Substrate": {
-      "MeanSize": 50
+      "MeanBaseplateGrainSize": 50
    },
    "Printing": {
       "PathToOutput": "./",

examples/Inp_FinchTranslate.json

@@ -15,7 +15,7 @@
       "StDev": 0.5
    },
    "Substrate": {
-      "MeanSize": 50
+      "MeanBaseplateGrainSize": 50
    },
    "TemperatureData": {
        "TranslationCount": 2,

examples/Inp_SingleLine.json

@@ -19,8 +19,8 @@
        "TemperatureFiles": ["examples/Temperatures/Line.txt"]
    },
    "Substrate": {
-      "MeanSize": 25,
-      "PowderDensity": 64000,
+      "MeanBaseplateGrainSize": 25,
+      "MeanPowderGrainSize": 2.5,
       "BaseplateTopZ": -0.000020
    },
    "Printing": {

examples/Inp_SingleLineTranslate.json

@@ -25,8 +25,8 @@
        "AlternatingDirection": true
    },
    "Substrate": {
-      "MeanSize": 25,
-      "PowderDensity": 64000,
+      "MeanBaseplateGrainSize": 25,
+      "MeanPowderGrainSize": 2.5,
       "BaseplateTopZ": -0.000020
    },
    "Printing": {

examples/Inp_SmallFinch.json

@@ -15,7 +15,7 @@
       "StDev": 0.5
    },
    "Substrate": {
-      "MeanSize": 75
+      "MeanBaseplateGrainSize": 75
    },
    "Printing": {
       "PathToOutput": "./",

examples/Inp_SmallSpotMelt.json

@@ -18,8 +18,8 @@
       "R": 300000
    },
    "Substrate": {
-      "MeanSize": 25,
-      "PowderDensity": 1000000
+      "MeanBaseplateGrainSize": 25,
+      "MeanPowderGrainSize": 1000000
    },
    "Printing": {
        "PathToOutput": "./",

examples/Inp_SpotMelt.json

@@ -18,8 +18,8 @@
       "R": 300000
    },
    "Substrate": {
-      "MeanSize": 25,
-      "PowderDensity": 1000000
+      "MeanBaseplateGrainSize": 25,
+      "MeanPowderGrainSize": 1
    },
    "Printing": {
       "PathToOutput": "./",

examples/Inp_TwoLineTwoLayer.json

@@ -19,8 +19,8 @@
        "TemperatureFiles": ["examples/Temperatures/TwoLine.txt"]
    },
    "Substrate": {
-      "MeanSize": 25,
-      "PowderDensity": 64000
+      "MeanBaseplateGrainSize": 25,
+      "MeanPowderGrainSize": 2.5
    },
    "Printing": {
       "PathToOutput": "./",

examples/README.md

@@ -106,9 +106,9 @@ The .json files in the examples subdirectory are provided on the command line to
 |GrainLocationsY     | Directional      | List of grain locations in Y on the bottom surface of the domain (see note (b-iii))
 |GrainIDs            | Directional      | GrainID values for each grain in (X,Y) (see note (b3))
 |FillBottomSurface   | Directional      | Optionally assign all cells on the bottom surface the grain ID of the closest grain (defaults to false)
-|MeanSize            | Spot, FromFile, FromFinch       | Mean spacing between grain centers in the baseplate/substrate (in microns) (see note (a))
+|MeanBaseplateGrainSize | Spot, FromFile, FromFinch       | Mean spacing between grain centers in the baseplate/substrate (in microns) (see note (a))
 |SubstrateFilename   |  Spot, FromFile, FromFinch  | Path to and filename for substrate data in vtk format (see note (a))
-|PowderDensity       | Spot, FromFile, FromFinch       | Density of sites in the powder layer to be assigned as the home of a unique grain, normalized by 1 x 10^12 m^-3 (default value is 1/(CA cell size ^3) (see note (a))
+|MeanPowderGrainSize | Spot, FromFile, FromFinch    | Mean spacing between grain centers in the powder layer (in microns). Defaults to one grain per cell
 |ExtendSubstrateThroughPowder| FromFile, FromFinch  | true/false value: Whether to use the baseplate microstructure as the boundary condition for the entire height of the simulation (defaults to false) (see note (a))
 | BaseplateTopZ      | FromFile, FromFinch          | The Z coordinate that marks the top of the baseplate/boundary of the baseplate with the powder. If not given, Z = 0 microns will be assumed to be the baseplate top if ExtendSubstrateThroughPowder = false (If ExtendSubstrateThroughPowder = true, the entire domain will be initialized with the baseplate grain structure)
 |GrainOrientation | SingleGrain           | Which orientation from the orientation's file is assigned to the grain (starts at 0). Default is 0 

src/CAinputdata.hpp

@@ -95,9 +95,8 @@ struct SubstrateInputs {
     bool use_substrate_file = false;
     bool baseplate_through_powder = false;
     std::string substrate_filename = "";
-    double substrate_grain_spacing = 0.0;
-    // defaults to all sites in powder layer initialized with a new grain
-    double powder_active_fraction = 1.0;
+    double baseplate_grain_spacing = 0.0;
+    double powder_grain_spacing = 1.0;
     // Top of baseplate assumed at Z = 0 if not otherwise given
     double baseplate_top_z = 0.0;
     // Initial size of octahedra during initialization of an active cell

src/CAinputs.hpp

@@ -311,19 +311,43 @@ struct Inputs {
         else {
             // Substrate data - should data come from an initial size or a file?
             if ((input_data["Substrate"].contains("SubstrateFilename")) &&
-                (input_data["Substrate"].contains("MeanSize")))
+                ((input_data["Substrate"].contains("MeanSize")) ||
+                 (input_data["Substrate"].contains("MeanBaseplateGrainSize"))))
                 throw std::runtime_error(
-                    "Error: only one of substrate grain size and substrate structure filename should "
+                    "Error: only one of baseplate grain size and substrate structure filename should "
                     "be provided in the input file");
             else if (input_data["Substrate"].contains("SubstrateFilename")) {
                 substrate.substrate_filename = input_data["Substrate"]["SubstrateFilename"];
                 if (substrate.substrate_filename.substr(substrate.substrate_filename.length() - 4) != ".vtk")
                     throw std::runtime_error("Error: Substrate filename must be a vtk file");
                 substrate.use_substrate_file = true;
             }
-            else if (input_data["Substrate"].contains("MeanSize")) {
-                substrate.substrate_grain_spacing = input_data["Substrate"]["MeanSize"];
-                substrate.use_substrate_file = false;
+            else if (input_data["Substrate"].contains("MeanSize") ||
+                     (input_data["Substrate"].contains("MeanBaseplateGrainSize"))) {
+                // Case where only the deprecated input MeanSize was given
+                if (!input_data["Substrate"].contains("MeanBaseplateGrainSize")) {
+                    substrate.baseplate_grain_spacing = input_data["Substrate"]["MeanSize"];
+                    substrate.use_substrate_file = false;
+                    if (id == 0)
+                        std::cout
+                            << "Warning: deprecated input MeanSize has been replaced with MeanBaseplateGrainSize, "
+                               "compatibility with MeanSize input will be removed in a future release"
+                            << std::endl;
+                }
+                else {
+                    // Case were the new input MeanBaseplateGrainSize was given
+                    substrate.baseplate_grain_spacing = input_data["Substrate"]["MeanBaseplateGrainSize"];
+                    substrate.use_substrate_file = false;
+                    // Warning for case where both the deprecated and new input were given
+                    if ((input_data["Substrate"].contains("MeanSize")) && (id == 0))
+                        std::cout << "Warning: redundant inputs MeanSize and MeanBaseplateGrainSize were given - "
+                                     "deprecated input MeanSize will be ignored"
+                                  << std::endl;
+                }
+                // Check that baseplate_grain_spacing is valid
+                if ((id == 0) && (substrate.baseplate_grain_spacing < domain.deltax))
+                    throw std::runtime_error(
+                        "Error: Input MeanBaseplateGrainSize must be no smaller than the CA cell size");
             }
             if (simulation_type == "Spot") {
                 // No powder for this problem type, baseplate top at Z = 0
@@ -337,14 +361,45 @@ struct Inputs {
                 // defaults to a unique grain at each site in the powder layers if not given
                 if (input_data["Substrate"].contains("PowderDensity")) {
                     // powder density is given as a density per unit volume, normalized by 10^12 m^-3 --> convert this
-                    // into a density of sites active on the CA grid (0 to 1)
-                    substrate.powder_active_fraction = input_data["Substrate"]["PowderDensity"];
-                    substrate.powder_active_fraction =
-                        substrate.powder_active_fraction * pow(10, 12) * pow(domain.deltax, 3);
-                    if ((substrate.powder_active_fraction < 0.0) || (substrate.powder_active_fraction > 1.0))
+                    // into a powder grain spacing
+                    if (id == 0)
+                        std::cout << "Warning: PowderDensity input has been deprecated and will be removed in a future "
+                                     "release, please specify MeanPowderGrainSpacing in microns"
+                                  << std::endl;
+                    // Warning for a case where the old input PowderDensity and new input MeanPowderGrainSize are both
+                    // given
+                    if (input_data["Substrate"].contains("MeanPowderGrainSize")) {
+                        if (id == 0)
+                            std::cout << "Warning: Redundant inputs PowderDensity and MeanPowderGrainSize were given - "
+                                         "deprecated input PowderDensity will be ignored"
+                                      << std::endl;
+                    }
+                    else {
+                        double powder_density_input = input_data["Substrate"]["PowderDensity"];
+                        double powder_active_fraction = powder_density_input * pow(10, 12) * pow(domain.deltax, 3);
+                        if ((powder_active_fraction < 0.0) || (powder_active_fraction > 1.0))
+                            throw std::runtime_error(
+                                "Error: Density of powder surface sites active must be larger than 0 and less "
+                                "than 1/(CA cell volume)");
+                        // convert powder density into a powder grain spacing, in microns
+                        substrate.powder_grain_spacing =
+                            pow((1.0 / (powder_density_input * pow(10, 12))), 1.0 / 3.0) * pow(10, 6);
+                        if (id == 0)
+                            std::cout << "Calculated powder layer grain spacing using PowderDensity is "
+                                      << substrate.powder_grain_spacing << " microns" << std::endl;
+                    }
+                }
+                if (input_data["Substrate"].contains("MeanPowderGrainSize")) {
+                    substrate.powder_grain_spacing = input_data["Substrate"]["MeanPowderGrainSize"];
+                    if ((id == 0) && (substrate.powder_grain_spacing < domain.deltax))
                         throw std::runtime_error(
-                            "Error: Density of powder surface sites active must be larger than 0 and less "
-                            "than 1/(CA cell volume)");
+                            "Error: Input MeanPowderGrainSize must be no smaller than the CA cell size");
+                }
+                else if ((!input_data["Substrate"].contains("PowderDensity")) &&
+                         (!input_data["Substrate"].contains("MeanPowderGrainSize"))) {
+                    // Case where neither PowderDensity nor MeanPowderGrainSize inputs are given - defaults to powder
+                    // active fraction of 1, mean powder grain size equal to the cell size
+                    substrate.powder_grain_spacing = domain.deltax;
                 }
                 if ((input_data["Substrate"].contains("PowderFirstLayer")) && (id == 0))
                     std::cout
@@ -355,10 +410,11 @@ struct Inputs {
                 // file)
                 if (input_data["Substrate"].contains("BaseplateTopZ"))
                     substrate.baseplate_top_z = input_data["Substrate"]["BaseplateTopZ"];
-                if ((substrate.baseplate_through_powder) && (input_data["Substrate"].contains("PowderDensity")))
+                if ((substrate.baseplate_through_powder) && ((input_data["Substrate"].contains("PowderDensity")) ||
+                                                             (input_data["Substrate"].contains("MeanPowderGrainSize"))))
                     throw std::runtime_error(
                         "Error: if the option to extend the baseplate through the powder layers is "
-                        "toggled, a powder layer density cannot be given");
+                        "toggled, a powder layer density or powder grain size cannot be given");
             }
             // Optional input for initial size of octhedra when a cell begins solidification (in units of CA cells)
             if (input_data["Substrate"].contains("InitOctahedronSize")) {
@@ -633,25 +689,6 @@ struct Inputs {
             std::cout << "Successfully parsed data printing options from input file" << std::endl;
     }
 
-    // Ensure that input powder layer init options are compatible with this domain size, if needed for this problem type
-    // TODO: Expand check that inputs are valid for the problem type
-    void checkPowderOverflow(const int nx, const int ny, const int layer_height, const int number_of_layers) {
-        // Check to make sure powder grain density is compatible with the number of powder sites
-        // If this problem type includes a powder layer of some grain density, ensure that integer overflow won't occur
-        // when assigning powder layer GrainIDs
-        if (!(substrate.baseplate_through_powder)) {
-            long int num_cells_powder_layers = static_cast<long int>(nx) * static_cast<long int>(ny) *
-                                               static_cast<long int>(layer_height) *
-                                               static_cast<long int>(number_of_layers - 1);
-            long int num_assigned_cells_powder_layers = std::lround(
-                Kokkos::round(static_cast<double>(num_cells_powder_layers) * substrate.powder_active_fraction));
-            if (num_assigned_cells_powder_layers > INT_MAX)
-                throw std::runtime_error(
-                    "Error: A smaller value for powder density is required to avoid potential integer "
-                    "overflow when assigning powder layer GrainID");
-        }
-    }
-
     // Print a log file for this ExaCA run in json file format, containing information about the run parameters used
     // from the input file as well as the decomposition scheme
     void printExaCALog(const int id, const int np, const int cycle, const Grid grid, Timers timers,
@@ -723,8 +760,12 @@ struct Inputs {
                 if (substrate.use_substrate_file)
                     exaca_log << "       \"SubstrateFilename\": "
                               << "\"" << substrate.substrate_filename << "\"" << std::endl;
-                else
-                    exaca_log << "       \"MeanSize\": " << substrate.substrate_grain_spacing << std::endl;
+                else {
+                    exaca_log << "       \"MeanSize\": " << substrate.baseplate_grain_spacing << "," << std::endl;
+                    exaca_log << "       \"MeanBaseplateGrainSize\": " << substrate.baseplate_grain_spacing << ","
+                              << std::endl;
+                    exaca_log << "       \"MeanPowderGrainSize\": " << substrate.powder_grain_spacing << std::endl;
+                }
             }
             exaca_log << "   }," << std::endl;
             exaca_log << "   \"InterfacialResponse\": {" << std::endl;

src/CAnucleation.hpp

@@ -155,9 +155,9 @@ struct Nucleation {
         std::shuffle(nuclei_grain_id_whole_domain_v.begin(), nuclei_grain_id_whole_domain_v.end(), generator);
         std::shuffle(nuclei_undercooling_whole_domain_v.begin(), nuclei_undercooling_whole_domain_v.end(), generator);
         if ((id == 0) && (nuclei_this_layer > 0))
-            std::cout << "Range of Grain IDs from which layer " << layernumber
-                      << " nucleation events were selected: " << nuclei_whole_domain + 1 << " through "
-                      << nuclei_whole_domain + nuclei_this_layer << std::endl;
+            std::cout << "Range of Grain IDs from which layer " << layernumber << " nucleation events were selected: -"
+                      << nuclei_whole_domain + 1 << " through -" << nuclei_whole_domain + nuclei_this_layer
+                      << std::endl;
         // Update number of nuclei counter for whole domain based on the number of nuclei in this layer
         nuclei_whole_domain += nuclei_this_layer;
 

src/runCA.hpp

@@ -24,10 +24,6 @@ void runExaCA(int id, int np, Inputs inputs, Timers timers, Grid grid, Temperatu
     // Material response function
     InterfacialResponseFunction irf(inputs.domain.deltat, grid.deltax, inputs.irf);
 
-    // Ensure that input powder layer init options are compatible with this domain size, if needed for this problem type
-    if (simulation_type == "FromFile")
-        inputs.checkPowderOverflow(grid.nx, grid.ny, grid.layer_height, grid.number_of_layers);
-
     // Read temperature data if necessary
     if (simulation_type == "FromFile")
         temperature.readTemperatureData(id, grid, 0);

unit_test/tstCellData.hpp

@@ -270,9 +270,9 @@ void testCellDataInit(bool powder_first_layer) {
     // baseplate. This grain spacing ensures that there will be 1 grain per number of MPI ranks present (larger when
     // powder layer is present as the baseplate will only have a third as many cells)
     if (powder_first_layer)
-        inputs.substrate.substrate_grain_spacing = 2.62;
+        inputs.substrate.baseplate_grain_spacing = 2.62;
     else
-        inputs.substrate.substrate_grain_spacing = 3.0;
+        inputs.substrate.baseplate_grain_spacing = 3.0;
     inputs.rng_seed = 0.0;
 
     // Create dummy temperature data
@@ -295,10 +295,10 @@ void testCellDataInit(bool powder_first_layer) {
     CellData<memory_space> celldata(grid, inputs.substrate);
     // Check that substrate inputs were copied from inputs struct correctly
     EXPECT_DOUBLE_EQ(inputs.substrate.baseplate_top_z, celldata._inputs.baseplate_top_z);
-    EXPECT_DOUBLE_EQ(inputs.substrate.substrate_grain_spacing, celldata._inputs.substrate_grain_spacing);
+    EXPECT_DOUBLE_EQ(inputs.substrate.baseplate_grain_spacing, celldata._inputs.baseplate_grain_spacing);
     EXPECT_FALSE(celldata._inputs.use_substrate_file);
     EXPECT_FALSE(celldata._inputs.baseplate_through_powder);
-    EXPECT_DOUBLE_EQ(celldata._inputs.powder_active_fraction, 1.0);
+    EXPECT_DOUBLE_EQ(celldata._inputs.powder_grain_spacing, grid.deltax * pow(10, 6));
     // Initialize baseplate grain structure
     celldata.initSubstrate(id, grid, inputs.rng_seed, number_of_solidification_events);