Merge branch 'upstream/develop'

documentation/tocgen.py

@@ -131,6 +131,10 @@ def clean_4_toc(docx_file,inFile,outFile,run_pandoc=True):
             math_str_pre = "<img src=\"https://latex.codecogs.com/svg.latex?\Large&space;{0}".format(eq_str)
             math_str_post = "\" title=\"\Large {0}\" />  {1}  <br>".format(eq_str,label)
             lines[i] = math_str_pre + " " + math_str_post
+        if lines[i].strip().startswith("<table>"): # and "pcf" in lines[i].lower():
+            lines[i] = "<div style=\"text-align: left\">" + lines[i] + "</div>"
+            if "comment" in lines[i].lower():
+                lines[i] = lines[i].replace("~","#")
         # elif "bmatrix" in lines[i].lower():
         #     eq_str = lines[i]
         #     lines.pop(i)

src/libs/common/config_os.h

@@ -2,7 +2,7 @@
 #define CONFIG_OS_H_
 
 
-#define PESTPP_VERSION "5.2.7";
+#define PESTPP_VERSION "5.2.8";
 
 #if defined(_WIN32) || defined(_WIN64)
 #define OS_WIN

src/libs/pestpp_common/EnsembleMethodUtils.h

@@ -106,9 +106,9 @@ class L2PhiHandler
 
 	map<string,double> get_meas_phi(ObservationEnsemble& oe, Eigen::VectorXd& q_vec);
 
-	map<string,map<string,double>> get_meas_swr_real_map(ObservationEnsemble& oe, ObservationEnsemble& weights);
+	map<string,map<string,double>> get_swr_real_map(ObservationEnsemble& oe, ObservationEnsemble& weights,phiType ptype=phiType::MEAS);
 
-    map<string,double> get_actual_swr_map(ObservationEnsemble& oe, string real_name="");
+    map<string,double> get_swr_map(ObservationEnsemble& oe, string real_name= "",phiType ptype=phiType::MEAS);
 	map<string,map<string,double>> get_meas_phi_weight_ensemble(ObservationEnsemble& oe, ObservationEnsemble& weights);
 
     vector<string> get_violating_realizations(ObservationEnsemble& oe, const vector<string>& viol_obs_names);
@@ -178,9 +178,9 @@ class ParChangeSummarizer
 	map<string, double> init_cv;
 	map<string, double> curr_cv;
 	map<string, int> num_at_ubound;
-	map<string, int> percent_at_ubound;
+	map<string, double> percent_at_ubound;
     map<string, int> num_at_lbound;
-    map<string, int> percent_at_lbound;
+    map<string, double> percent_at_lbound;
 
 	void update(ParameterEnsemble& pe);
 	void write_to_csv(string& filename);
@@ -499,5 +499,9 @@ class EnsembleMethod
 
     void prep_drop_violations();
 
+    void remove_external_pe_filenames(vector<string>& pe_filenames);
+
+    double get_lambda();
+
 };
 #endif

src/libs/pestpp_common/EnsembleSmoother.cpp

@@ -36,6 +36,8 @@ void IterEnsembleSmoother::iterate_2_solution()
 	ofstream &frec = file_manager.rec_ofstream();
 
 	bool accept;
+	int n_iter_mean = pest_scenario.get_pestpp_options().get_ies_n_iter_mean();
+
 	for (int i = 0; i < pest_scenario.get_control_info().noptmax; i++)
 	{
 		iter++;
@@ -68,8 +70,27 @@ void IterEnsembleSmoother::iterate_2_solution()
 		else
 			consec_bad_lambda_cycles++;
 
+		if (iter == n_iter_mean)
+        {
+		    double phi_lam = get_lambda();
+		    //if (phi_lam > last_best_lam)
+            //{
+            last_best_lam = phi_lam;
+            message(1,"iter = ies_n_iter_mean, resetting lambda to ",last_best_lam);
+            //}
+		    consec_bad_lambda_cycles = 0;
+        }
+
 		if (should_terminate())
-			break;
+        {
+		    if (iter > pest_scenario.get_pestpp_options().get_ies_n_iter_mean()) {
+                break;
+            }
+		    else{
+		        message(1,"continuing iterations to satisfy ies_n_iter_mean");
+		    }
+        }
+
 	}
 }
 

src/libs/pestpp_common/pest_data_structs.cpp

@@ -1177,8 +1177,12 @@ bool PestppOptions::assign_ies_value_by_key(const string& key, const string& val
         ies_phi_factors_by_real = pest_utils::parse_string_arg_to_bool(value);
         return true;
     }
-
-	return false;
+    else if (key == "IES_N_ITER_MEAN")
+    {
+        convert_ip(value,ies_n_iter_mean);
+        return true;
+    }
+    return false;
 }
 
 bool PestppOptions::assign_da_value_by_key(const string& key, const string& value, const string& org_value)
@@ -1805,6 +1809,7 @@ void PestppOptions::summary(ostream& os) const
 	os << "ies_localizer_forgive_extra: " << ies_localizer_forgive_missing << endl;
 	os << "ies_phi_factors_file: " << ies_phi_fractions_file << endl;
     os << "ies_phi_factors_by_real: " << ies_phi_factors_by_real << endl;
+    os << "ies_n_iter_mean: " << ies_n_iter_mean << endl;
 
 
 	os << endl << "pestpp-sen options: " << endl;
@@ -1945,8 +1950,8 @@ void PestppOptions::set_defaults()
 	set_ies_verbose_level(1);
 	set_ies_use_prior_scaling(false);
 	set_ies_num_reals(50);
-	set_ies_bad_phi(1.0e+300);
-	set_ies_bad_phi_sigma(1.0e+300);
+	set_ies_bad_phi(std::numeric_limits<double>::max());
+	set_ies_bad_phi_sigma(std::numeric_limits<double>::max());
 	set_ies_include_base(true);
 	set_ies_use_empirical_prior(false);
 	set_ies_group_draws(true);
@@ -1988,6 +1993,7 @@ void PestppOptions::set_defaults()
     set_ies_localizer_forgive_missing(false);
     set_ies_phi_fractions_files("");
     set_ies_phi_factors_by_real(false);
+    set_ies_n_iter_mean(0);
 
 	// DA parameters
 	//set_da_use_ies(false);

src/libs/pestpp_common/pest_data_structs.h

@@ -540,8 +540,11 @@ class PestppOptions {
     void set_ies_multimodal_alpha(double _flag) { ies_multimodal_alpha = _flag; }
     void set_ensemble_output_precision(int prec) { ensemble_output_precision = prec;}
     int get_ensemble_output_precision() const {return ensemble_output_precision;}
+    void set_ies_n_iter_mean(int _n_iter_mean)  {ies_n_iter_mean = _n_iter_mean;}
+    int get_ies_n_iter_mean() const {return ies_n_iter_mean;}
 
-	string get_gsa_method() const { return gsa_method; }
+
+    string get_gsa_method() const { return gsa_method; }
 	void set_gsa_method(string _m) { gsa_method = _m; }
 	bool get_gsa_morris_pooled_obs() const { return gsa_morris_pooled_obs; }
 	void set_gsa_morris_pooled_obs(bool _flag) {gsa_morris_pooled_obs = _flag; }
@@ -812,6 +815,7 @@ class PestppOptions {
 	bool ies_localizer_forgive_missing;
 	string ies_phi_fractions_file;
 	bool ies_phi_factors_by_real;
+	int ies_n_iter_mean;
 
 
 	// Data Assimilation parameters