Merge remote-tracking branch 'origin/develop'

documentation/pestpp_users_manual.md

@@ -1,13 +1,13 @@
 
  <img src="0d3cb7750c90b712af04ea3a51c8ecb968d784cc.png" style="width:6.26806in;height:1.68194in" alt="A close up of a purple sign Description automatically generated" />
 
-# <a id='s1' />Version 5.2.4
+# <a id='s1' />Version 5.2.6
 
 <img src="0e14ec9848f78a9809081572ca785af9990c2d38.png" style="width:6.26806in;height:3.05972in" />
 
 PEST++ Development Team
 
-May 2023
+August 2023
 
 # <a id='s2' />Acknowledgements
 
@@ -70,7 +70,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 
 # Table of Contents
 
-- [Version 5.2.4](#s1)
+- [Version 5.2.6](#s1)
 - [Acknowledgements](#s2)
 - [Preface](#s3)
 - [License](#s4)

scripts/build_pestpp_linux.sh

@@ -1,6 +1,6 @@
 # this should be run from one dir level up - the repo root...
 rm -rf build
 mkdir build && cd build
-cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=g++-9 ..
+cmake -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_COMPILER=g++ ..
 make -j install
 cpack -G TGZ

src/libs/common/config_os.h

@@ -2,7 +2,7 @@
 #define CONFIG_OS_H_
 
 
-#define PESTPP_VERSION "5.2.4";
+#define PESTPP_VERSION "5.2.6";
 
 #if defined(_WIN32) || defined(_WIN64)
 #define OS_WIN

src/libs/common/system_variables.cpp

@@ -46,8 +46,6 @@ const std::string OperSys::DIR_SEP = "/";
 const std::string OperSys::COMMAND_LINE_APPEND = " & ";
 #endif
 
-const int OperSys::thread_sleep_milli_secs=1000;
-
 using namespace std;
 
 void OperSys::string2pathname(string &s)

src/libs/common/system_variables.h

@@ -25,8 +25,6 @@
 class OperSys
 {
 public:
-	//const static int thread_sleep_secs = 1;
-	static const int thread_sleep_milli_secs;
 	static const std::string DIR_SEP;
 	static const std::string COMMAND_LINE_APPEND;
 	void string2pathname(std::string &s);

src/libs/common/utilities.cpp

@@ -918,6 +918,7 @@ void read_dense_binary(const string& filename, vector<string>& row_names, vector
 			pest_utils::upper_ip(name);
 			col_names.push_back(name);
 			i++;
+			delete[] col_name;
 		}
 		i = 0;
 		double data = -1.;
@@ -956,6 +957,7 @@ void read_dense_binary(const string& filename, vector<string>& row_names, vector
 				break;
 			}
 			name = string(row_name, name_size);
+            delete[] row_name;
 			pest_utils::strip_ip(name);
 			pest_utils::upper_ip(name);
             if (!in.good())
@@ -965,10 +967,12 @@ void read_dense_binary(const string& filename, vector<string>& row_names, vector
 				cout << ss.str();
 				break;
 			}
+
 			//skip the values
 			//in.seekg(col_names.size() * sizeof(double), ios_base::cur);
-			row_name = new char[sizeof(double) * col_names.size()];
-			in.read(row_name, sizeof(double)* col_names.size());
+			char* rest_of_line = new char[sizeof(double) * col_names.size()];
+			in.read(rest_of_line, sizeof(double)* col_names.size());
+			delete[] rest_of_line;
 			if (in.eof())
 				break;
             if (!in.good())
@@ -1520,7 +1524,7 @@ void ExternalCtlFile::read_file(ofstream& f_rec)
 		throw_externalctrlfile_error("filename '" + filename + "' not found");
 	}
 	ifstream f_in(filename);
-    if (!f_in.good())
+    if (f_in.bad())
 	{
 		throw_externalctrlfile_error("error opening filename '" + filename + "' for reading");
 	}
@@ -1542,10 +1546,10 @@ void ExternalCtlFile::read_file(ofstream& f_rec)
 				cleaned = true;
 			}
 		}
-		if (cleaned)
-		{
+//		if (cleaned)
+//		{
 			strip_ip(t);
-		}
+//		}
 	}
 	int hsize = col_names.size();
 	set<string> tset;

src/libs/pestpp_common/Ensemble.cpp

@@ -3169,14 +3169,17 @@ void ParameterEnsemble::to_dense_ordered(string file_name)
 		fout.write((char*)&tmp, sizeof(tmp));
 		mx = max(tmp, mx);
 	}
+
 	for (vector<string>::const_iterator b = vnames.begin(), e = vnames.end();
 		b != e; ++b)
 	{
 		string name = pest_utils::lower_cp(*b);
 		char* par_name = new char[name.size()];
 		pest_utils::string_to_fortran_char(name, par_name, name.size());
 		fout.write(par_name, name.size());
+        delete[] par_name;
 	}
+
 
 	//write matrix
 	n = 0;
@@ -3191,6 +3194,7 @@ void ParameterEnsemble::to_dense_ordered(string file_name)
 		par_transform.ctl2model_ip(org_pars);
 	else if (tstat == transStatus::NUM)
 		par_transform.ctl2numeric_ip(org_pars);
+
 	for (int irow = 0; irow < n_real; ++irow)
 	{
 		//Parameters pars(var_names, reals.row(irow));
@@ -3212,6 +3216,7 @@ void ParameterEnsemble::to_dense_ordered(string file_name)
 		fout.write((char*)&tmp, sizeof(tmp));
 		pest_utils::string_to_fortran_char(name, real_name, tmp);
 		fout.write(real_name, tmp);
+        delete[] real_name;
 		for (int jcol = 0; jcol < n_var; ++jcol)
 		{
 			data = pars[vnames[jcol]];
@@ -3296,6 +3301,7 @@ void ParameterEnsemble::to_dense_unordered(string file_name)
 		char* par_name = new char[name.size()];
 		pest_utils::string_to_fortran_char(name, par_name, name.size());
 		fout.write(par_name, name.size());
+		delete[] par_name;
 	}
 
 	//write matrix
@@ -3313,6 +3319,7 @@ void ParameterEnsemble::to_dense_unordered(string file_name)
 		fout.write((char*)&tmp, sizeof(tmp));
 		pest_utils::string_to_fortran_char(name, real_name, tmp);
 		fout.write(real_name, tmp);
+		delete[] real_name;
 		for (int jcol = 0; jcol < var_names.size(); ++jcol)
 		{
 			data = t[jcol];
@@ -4299,14 +4306,86 @@ void FixedParInfo::add_realization(string rname, Eigen::VectorXd& rvals, vector<
 	map<string, double> v;
 	for (int i = 0; i < rvals.size(); i++)
 		v[pnames[i]] = rvals[i];
+	map<string,double>::iterator  end = v.end();
 	for (auto& name : fixed_names)
 	{
-		if (v.find(name) == v.end())
+		if (v.find(name) == end)
 			throw runtime_error("FixedParInfo::add_realization(): fixed name '" + name + "' not in pnames");
 		fixed_info.at(name)[rname] = v.at(name);
 	}
 }
 
+vector<string> FixedParInfo::get_real_names()
+{
+    if (!initialized)
+    {
+        return vector<string>();
+    }
+    if (fixed_names.size() == 0)
+    {
+        return vector<string>();
+    }
+    vector<string> rnames;
+    for (auto& fi : fixed_info)
+    {
+        for (auto& ri : fi.second)
+        {
+            rnames.push_back(ri.first);
+        }
+    }
+    return rnames;
+
+}
+
+void FixedParInfo::add_realizations(map<string,map<string,double>>& other_fixed_info)
+{
+    if (!initialized)
+    {
+        throw runtime_error("FixedParInfo::update_realizations: not initialized");
+    }
+    if (fixed_names.size() == 0)
+    {
+        //this needs to be error checked..
+        fixed_info = other_fixed_info;
+        return;
+    }
+    map<string,map<string,double>>::iterator end = fixed_info.end();
+    for (auto& ofi : other_fixed_info)
+    {
+        if (fixed_info.find(ofi.first) == end)
+        {
+            throw runtime_error("FixedParInfo::add_realizations() error: pname "+ofi.first+" not in fixed_info");
+        }
+        for (auto& ori : ofi.second)
+        {
+            //probably should error check this also to make sure other_fixed_info isnt replacing things...
+            fixed_info.at(ofi.first)[ori.first] = ori.second;
+        }
+    }
+}
+
+
+void FixedParInfo::add_realization(string rname, map<string, double>& rvals)
+{
+    if (!initialized)
+    {
+        throw runtime_error("FixedParInfo::add_realization(): not initialized");
+    }
+    if (fixed_names.size() == 0)
+    {
+        return;
+    }
+    map<string,double>::iterator  end = rvals.end();
+    for (auto& name : fixed_names)
+    {
+        if (rvals.find(name) == end)
+            throw runtime_error("FixedParInfo::add_realization(): fixed name '" + name + "' not in pnames");
+        fixed_info.at(name)[rname] = rvals.at(name);
+    }
+
+
+}
+
 void FixedParInfo::keep_realizations(const vector<string>& keep)
 {
 	if (!initialized)
@@ -4342,6 +4421,7 @@ void FixedParInfo::keep_realizations(const vector<string>& keep)
 	}
 }
 
+
 void FixedParInfo::update_realizations(const vector<string>& other_var_names, const vector<string>& other_real_names, const Eigen::MatrixXd& other_mat)
 {
 	if (!initialized)

src/libs/pestpp_common/Ensemble.h

@@ -144,12 +144,18 @@ class FixedParInfo
 	vector<double> get_real_fixed_values(const string& rname, vector<string>& pnames);
 	map<string, double> get_real_fixed_values(const string& rname);
 	void add_realization(string rname, Eigen::VectorXd& rvals, vector<string>& pnames);
+    void add_realization(string rname, map<string, double>& rvals);
 	void keep_realizations(const vector<string>& keep);
 	void update_realizations(const vector<string>& other_var_names, const vector<string>& other_real_names, const Eigen::MatrixXd& other_mat);
+	void add_realizations(map<string,map<string,double>>& other_fixed_info);
 	void update_par_values(const map<string, double>& pval_map);
 	void clear() { fixed_info.clear(); fixed_names.clear(); }
 	void fill_fixed(map<string, double>& fixed_map, vector<string>& rnames);
 	int get_map_size() {return fixed_info.size();}
+	vector<string> get_real_names();
+    vector<string> get_fixed_names() {return fixed_names;}
+    map<string,map<string,double>> get_fixed_info_map() {return fixed_info;}
+
 private:
 	bool initialized;
 	vector<string> fixed_names;