Merge pull request #4 from MikeHeiber/development

Development Update 3 to be included with v4.0-alpha.1

Author: MikeHeiber

Morphology.cpp

@@ -36,8 +36,15 @@ struct NeighborInfo{
     char total3;
 };
 
+struct CorrelationCalcParams {
+	int N_sampling_max;
+	bool Enable_mix_frac_method;
+	bool Enable_e_method;
+	bool Enable_extended_correlation_calc;
+	int Correlation_cutoff_distance;
+};
+
 struct TomogramImportParams {
-	// Tomogram Import Options
 	bool Enable_cutoff_analysis;
 	int Mixed_greyscale_width;
 	double Mixed_conc;
@@ -54,10 +61,10 @@ class Morphology {
 	Morphology(const Lattice& input_lattice, const int id);
     virtual ~Morphology();
     bool calculateAnisotropies(const int N_sampling_max);
-	void calculateCorrelationDistances(const bool enable_extended_calc, const int N_sampling_max);
+	void calculateCorrelationDistances(const CorrelationCalcParams& parameters);
+	void calculateDepthDependentData(const CorrelationCalcParams& correlation_params);
     double calculateInterfacialAreaVolumeRatio() const;
     bool calculateInterfacialDistance();
-    //bool calculateInterfacialDistanceOld();
     double calculateInterfacialVolumeFraction() const;
 	void calculateMixFractions();
     bool calculateTortuosity(const bool enable_reduced_memory);
@@ -68,6 +75,8 @@ class Morphology {
     void executeMixing(const double width, const double interfacial_conc);
     void executeSmoothing(const double smoothing_threshold, const int rescale_factor);
     std::vector<double> getCorrelationData(const char site_type) const;
+	std::vector<double> getDepthCompositionData(const char site_type) const;
+	std::vector<double> getDepthDomainSizeData(const char site_type) const;
     double getDomainSize(const char site_type) const;
     double getDomainAnisotropy(const char site_type) const;
     int getHeight() const;
@@ -108,7 +117,7 @@ class Morphology {
     };
     // properties
     int ID;
-    std::vector<double> Mix_fractions; // Fraction of each component to total
+    std::vector<double> Mix_fractions; // Volume fraction of each component to total
     bool Enable_third_neighbor_interaction;
 	Lattice lattice;
 	std::vector<char> Site_types;
@@ -117,13 +126,13 @@ class Morphology {
 	std::vector<std::vector<float>> Tortuosity_data;
 	std::vector<std::vector<double>> InterfacialHistogram_data;
 	std::vector<std::vector<double>> TortuosityHistogram_data;
-    std::vector<bool> Domain_size_updated;
+	std::vector<std::vector<double>> Depth_composition_data;
+	std::vector<std::vector<double>> Depth_domain_size_data;
     std::vector<bool> Domain_anisotropy_updated;
-    std::vector<double> Domain_size;
-    std::vector<double> Domain_anisotropy;
+    std::vector<double> Domain_sizes;
+    std::vector<double> Domain_anisotropies;
     std::vector<int> Island_volume;
 	std::vector<long int> Interfacial_sites;
-	std::vector<std::vector<long int>> Correlation_sites_data;
 	std::vector<NeighborCounts> Neighbor_counts;
 	std::vector<NeighborInfo> Neighbor_info;
     NeighborCounts Temp_counts1;
@@ -132,8 +141,8 @@ class Morphology {
     // functions
 	void addSiteType(const char site_type);
     double calculateAdditionalEnergyChange(const long int site_index_main, const long int site_index_neighbor,const int growth_direction,const double additional_interaction) const;
-    bool calculateAnisotropy(const char site_type,const int cutoff_distance,const int N_sampling_max);
-	bool calculateCorrelationDistance(const char site_type, const int cutoff_distance, const bool enable_extended_calc, const int N_sampling_max);
+    bool calculateAnisotropy(const std::vector<long int>& correlation_sites, const char site_type,const int cutoff_distance);
+	double calculateCorrelationDistance(const std::vector<long int>& correlation_sites, std::vector<double>& correlation_data, const char site_type, const int cutoff_distance, const CorrelationCalcParams& params);
     double calculateDissimilarFraction(const Coords& coords, const int rescale_factor) const;
     double calculateEnergyChangeSimple(const long int site_index1, const long int site_index2, const double interaction_energy1, const double interaction_energy2);
     double calculateEnergyChange(const Coords& coords1, const Coords& coords2,const double interaction_energy1,const double interaction_energy2) const;
@@ -142,6 +151,7 @@ class Morphology {
     bool calculatePathDistances_ReducedMemory(std::vector<float>& path_distances);
     void createNode(Node& node,const Coords& coords);
     void getSiteSampling(std::vector<long int>& sites, const char site_type, const int N_sites);
+	void getSiteSamplingZ(std::vector<long int>& sites, const char site_type, const int N_sites, const int z);
 	int getSiteTypeIndex(const char site_type) const;
     void initializeNeighborInfo();
 	bool isNearInterface(const Coords& coords, const double distance) const;

Morphology.h

@@ -20,7 +20,8 @@ namespace Utils {
 
 	vector<pair<double, double>> calculateProbabilityHist(const vector<double>& data, int num_bins) {
 		// Determine data range
-		double min_val, max_val;
+		double min_val = 0;
+		double max_val = 0;
 		auto min_it = min_element(data.begin(), data.end());
 		if (min_it != data.end()) {
 			min_val = *min_it;
@@ -46,7 +47,8 @@ namespace Utils {
 
 	vector<pair<double, double>> calculateProbabilityHist(const vector<double>& data, double bin_size) {
 		// Determine data range
-		double min_val, max_val;
+		double min_val = 0;
+		double max_val = 0;
 		auto min_it = min_element(data.begin(), data.end());
 		if (min_it != data.end()) {
 			min_val = *min_it;
@@ -73,7 +75,7 @@ namespace Utils {
 
 	vector<pair<double, double>> calculateProbabilityHist(const vector<double>& data, const double bin_size, const int num_bins) {
 		// Determine number of bins
-		double min_val;
+		double min_val = 0;
 		auto min_it = min_element(data.begin(), data.end());
 		if (min_it != data.end()) {
 			min_val = *min_it;

Utils.cpp

@@ -12,6 +12,7 @@
 #include <iostream>
 #include <memory>
 #include <mpi.h>
+#include <fstream>
 #include <random>
 #include <set>
 #include <string>
@@ -187,8 +188,7 @@ namespace Utils {
 
 	template<typename T>
 	T array_median(const T data[], const int array_size) {
-		T element;
-		std::vector<T> data_vect(array_size, element);
+		std::vector<T> data_vect(array_size);
 		for (int i = 0; i<array_size; i++) {
 			data_vect[i] = data[i];
 		}
@@ -244,7 +244,7 @@ namespace Utils {
 	//! \param filename is the input file name.
 	template<typename T>
 	void outputVectorToFile(std::vector<T>& vec, std::string filename) {
-		ofstream outfile;
+		std::ofstream outfile;
 		outfile.open(filename);
 		for (int i = 0; i < (int)vec.size(); i++) {
 			outfile << vec[i] << "\n";
@@ -258,7 +258,7 @@ namespace Utils {
 	//! \param filename is the input file name.
 	template<typename T>
 	void outputVectorToFile(std::vector<std::pair<T,T>>& vec, std::string filename) {
-		ofstream outfile;
+		std::ofstream outfile;
 		outfile.open(filename);
 		for (int i = 0; i < (int)vec.size(); i++) {
 			outfile << vec[i].first << "," << vec[i].second << "\n";