start

src/libs/pestpp_common/MOEA.cpp

@@ -10,6 +10,7 @@
 #include "EnsembleMethodUtils.h"
 #include "constraints.h"
 #include "eigen_tools.h"
+#include "RedSVD-h.h"
 
 using namespace std;
 
@@ -3550,6 +3551,64 @@ ParameterEnsemble MOEA::generate_pso_population(int num_members, ParameterEnsemb
 	return new_dp;
 }
 
+ParameterEnsemble MOEA::generate_empcov_population(int num_members, ParameterEnsemble& _dp, ObservationEnsemble& _op)
+{
+
+    message(1, "generating empirical-covariance population of size", num_members);
+    vector<string> gbest_solutions = get_pso_gbest_solutions(_dp.shape().first, dp_archive, op_archive);
+    ParameterEnsemble cur_velocity = get_updated_pso_velocty(_dp, gbest_solutions);
+    Eigen::MatrixXd draws(num_members,_dp.shape().second);
+    for (int i = 0; i < num_members; i++)
+    {
+        for (int j = 0; j < _dp.shape().second; j++)
+        {
+            draws(i, j) = draw_standard_normal(rand_gen);
+        }
+    }
+    ParameterEnsemble new_dp(&pest_scenario, &rand_gen, draws, _dp.get_real_names(), _dp.get_var_names());
+    new_dp.set_fixed_info(_dp.get_fixed_info());
+    vector<string> new_real_names;
+    for (int i=0;i<num_members;i++)
+    {
+        new_real_names.push_back(get_new_member_name("empcov"));
+    }
+    new_dp.set_real_names(new_real_names);
+    new_dp.reset_org_real_names();
+
+    Eigen::MatrixXd anom,cov;
+    anom = _dp.get_eigen_anomalies();
+    cov = anom.transpose() * anom;
+
+    Covariance covmat(new_dp.get_var_names(),cov.sparseView());
+
+    new_dp.set_trans_status(_dp.get_trans_status());
+    new_dp.enforce_bounds(performance_log,false);
+    new_dp.check_for_normal("new emp-cov population");
+
+    /*if (_dp.get_fixed_info().get_map_size() > 0) {
+        vector<string> fi_fixed_names = _dp.get_fixed_info().get_fixed_names();
+        new_dp.get_fixed_info().set_fixed_names(fi_fixed_names);
+        map<string, double> fi;
+        vector<string> rnames = _dp.get_fixed_info().get_real_names();
+        set<string> sdp_rnames(rnames.begin(),rnames.end());
+        set<string>::iterator dpend = sdp_rnames.end();
+        rnames = temp.get_fixed_info().get_real_names();
+        set<string> stemp_rnames(rnames.begin(),rnames.end());
+        set<string>::iterator tend = stemp_rnames.end();
+        for (auto &p : primary_parent_map) {
+            if (sdp_rnames.find(p.second) != dpend)
+                fi = _dp.get_fixed_info().get_real_fixed_values(p.second);
+            else if (stemp_rnames.find(p.second) != tend)
+                fi = temp.get_fixed_info().get_real_fixed_values(p.second);
+            else
+                throw_moea_error("fixed info for existing realization '"+p.second+"' not found");
+            new_dp.get_fixed_info().add_realization(p.first, fi);
+        }*/
+    //}
+    return new_dp;
+}
+
+
 ParameterEnsemble MOEA::simplex_cceua_kn(ParameterEnsemble s, int k, int optbounds)
 {
 	//C++ implementation of the cceua algorithm, Duan et al. (1992) with the addition of k worst points

src/libs/pestpp_common/MOEA.h

@@ -15,6 +15,7 @@
 #include "Ensemble.h"
 #include "constraints.h"
 #include "EnsembleMethodUtils.h"
+#include "RedSVD-h.h"
 
 const string POP_SUM_TAG = "pareto.summary.csv";
 const string ARC_SUM_TAG = "pareto.archive.summary.csv";
@@ -212,13 +213,13 @@ class MOEA
 	ParameterEnsemble generate_pso_population(int num_members, ParameterEnsemble& _dp);
 	ParameterEnsemble simplex_cceua_kn(ParameterEnsemble s, int k, int optbounds);																																		
     ParameterEnsemble generate_simplex_population(int num_members, ParameterEnsemble& _dp, ObservationEnsemble& _op);
-
+    ParameterEnsemble generate_empcov_population(int num_members, ParameterEnsemble& _dp, ObservationEnsemble& _op);
 	ParameterEnsemble get_updated_pso_velocty(ParameterEnsemble& _dp, vector<string>& gbest_solutions);
 
 	vector<string> get_pso_gbest_solutions(int num_reals, ParameterEnsemble& _dp, ObservationEnsemble& _op);
 	void update_pso_pbest(ParameterEnsemble& _dp, ObservationEnsemble& _op);
 
-	map<string, string> current_pso_lineage_map;
+	map<string, string> current_pso_lineage_map, current_empcov_lineage_map;
 
 	vector<int> selection(int num_to_select, ParameterEnsemble& _dp, MouMateType& matetype);
 

src/libs/run_managers/yamr/PantherAgent.cpp

@@ -829,9 +829,6 @@ void PANTHERAgent::start_impl(const string &host, const string &port)
 			int group_id = net_pack.get_group_id();
 			int run_id = net_pack.get_run_id();
 			string info_txt = net_pack.get_info_txt();
-			//jwhite 25 may 2020 - commented this out in develop merge from Ayman's develop
-			//so that I can pull in the run mgr message passing enhancements
-			//will uncommented later when merging in pestpp-da
 			pest_utils::upper_ip(info_txt);
 			int da_cycle = NetPackage::NULL_DA_CYCLE;
 			if (info_txt.find("DA_CYCLE:") != string::npos)

src/libs/run_managers/yamr/RunManagerPanther.cpp

@@ -581,7 +581,7 @@ RunManagerAbstract::RUN_UNTIL_COND RunManagerPanther::run_until(RUN_UNTIL_COND c
         if (agent_info_set.size() == 0)
         {
             ss.str("");
-            ss << "lost comms with all agents, closing all reminaing open file transfers";
+            ss << "lost comms with all agents, closing all remaining open file transfers";
             report(ss.str(),true);
             for (auto& m : open_file_socket_map) {
                 string fname = m.second;