Bump version number to 7.9.0 and merge recent bug fixes from main [WIP]

CMakeLists.txt

@@ -7,6 +7,7 @@ project(
   LANGUAGES C CXX Fortran)
 
 set(CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
+set(CMAKE_C_STANDARD 17)
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_EXTENSIONS OFF)
 

doc/exp.cfg

@@ -964,6 +964,8 @@ INPUT                  = ./intro.doc \
                          ../include \
                          ../src \
                          ../src/user \
+			 ../exputil \
+			 ../expui \
                          ../utils/ICs \
                          ../utils/Analysis \
                          ../utils/PhaseSpace
@@ -1788,7 +1790,7 @@ FORMULA_MACROFILE      =
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-USE_MATHJAX            = NO
+USE_MATHJAX            = YES
 
 # With MATHJAX_VERSION it is possible to specify the MathJax version to be used.
 # Note that the different versions of MathJax have different requirements with
@@ -1948,7 +1950,7 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
 # The default value is: YES.
 
-GENERATE_LATEX         = NO
+GENERATE_LATEX         = YES
 
 # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of

expui/BasisFactory.H

@@ -24,6 +24,8 @@ namespace BasisClasses
 {
   using RowMatrixXd = Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>;
 
+  using RowMatrix3d = Eigen::Matrix<double, 3, 3, Eigen::RowMajor>;
+
     //! Callback function signature for selection particles to
     //! accumulate
     using Callback =
@@ -66,7 +68,10 @@ namespace BasisClasses
     unsigned long coefindx;
 
     //! The expansion center
-    std::vector<double> coefctr;
+    Eigen::Vector3d coefctr = Eigen::Vector3d::Zero();
+
+    //! Rotation matrix
+    RowMatrix3d coefrot = Eigen::Matrix3d::Identity();
 
     //! Contains contructor and BFE parameter database
     YAML::Node node, conf;
@@ -151,8 +156,10 @@ namespace BasisClasses
     virtual ~Basis(void) {}
 
     //! Set the expansion center
-    void setCenter(std::vector<double> center)
-    { coefctr = center; }
+    void setCenter(Eigen::Vector3d center) { coefctr = center; }
+
+    //! Set the rotation matrix
+    void setRotation(RowMatrix3d rot) { coefrot = rot; }
 
     //! Evaluate basis in desired coordinates
     virtual std::vector<double>
@@ -213,11 +220,12 @@ namespace BasisClasses
 
     //! Generate coeffients from a particle reader
     virtual CoefClasses::CoefStrPtr
-    createFromReader(PR::PRptr reader, std::vector<double> ctr) = 0;
+    createFromReader(PR::PRptr reader, Eigen::Vector3d ctr,
+		     RowMatrix3d rot) = 0;
 
     //! Generate coefficients from a phase-space table
     virtual void
-    initFromArray(std::vector<double> ctr) = 0;
+    initFromArray(Eigen::Vector3d ctr, RowMatrix3d rot) = 0;
 
     //! Accumulate coefficient contributions from arrays
     virtual void
@@ -228,7 +236,8 @@ namespace BasisClasses
     //! for the expansion
     CoefClasses::CoefStrPtr createFromArray
     (Eigen::VectorXd& m, RowMatrixXd& p, double time=0.0,
-     std::vector<double> center={0.0, 0.0, 0.0},
+     Eigen::Vector3d center=Eigen::Vector3d::Zero(),
+     RowMatrix3d rot=RowMatrix3d::Identity(),
      bool roundrobin=true, bool posvelrows=false);
 
     //! Create and the coefficients from the array accumulation with the
@@ -275,7 +284,10 @@ namespace BasisClasses
     { return getFieldLabels(coordinates); }
 
     //! Get the basis expansion center
-    std::vector<double> getCenter() { return coefctr; }
+    Eigen::Vector3d getCenter() { return coefctr; }
+
+    //! Get the basis expansion center
+    RowMatrix3d getRotation() { return coefrot; }
   };
 
   using BasisPtr = std::shared_ptr<Basis>;

expui/BasisFactory.cc

@@ -137,7 +137,7 @@ namespace BasisClasses
       node = YAML::Load(conf);
     }
     catch (const std::runtime_error& error) {
-      std::cout << "Basis constructor: found a problem in the YAML config"
+      std::cout << "Basis::factory constructor: found a problem in the YAML config"
 		<< std::endl;
       throw;
     }
@@ -163,12 +163,12 @@ namespace BasisClasses
       name = conf["id"].as<std::string>();
     } 
     catch (YAML::Exception & error) {
-      if (myid==0) std::cout << "Error parsing force id in BasisFactory"
+      if (myid==0) std::cout << "Error parsing force id in Basis::factory"
 			     << std::string(60, '-') << std::endl
 			     << conf                 << std::endl
 			     << std::string(60, '-') << std::endl;
 
-      throw std::runtime_error("BasisFactory: error parsing YAML");
+      throw std::runtime_error("Basis::factory: error parsing YAML");
     }
 
     try {
@@ -202,12 +202,12 @@ namespace BasisClasses
       else {
 	std::string msg("I don't know about the basis named: ");
 	msg += name;
-	msg += ". Known types are currently 'sphereSL', 'cylinder', 'flatdisk', 'slabSL', 'field', and 'velocity'";
+	msg += ". Known types are currently 'sphereSL', 'cylinder', 'flatdisk', 'CBDisk', 'slabSL', 'cube', 'field', and 'velocity'";
 	throw std::runtime_error(msg);
       }
     }
     catch (std::exception& e) {
-      std::cout << "Error in BasisFactory constructor: " << e.what() << std::endl;
+      std::cout << "Error in Basis::factory constructor: " << e.what() << std::endl;
       throw;			// Rethrow the exception?
     }
 
@@ -275,10 +275,10 @@ namespace BasisClasses
   // Generate coefficients from a phase-space table
   //
   CoefClasses::CoefStrPtr Basis::createFromArray
-  (Eigen::VectorXd& m, RowMatrixXd& p, double time, std::vector<double> ctr,
-   bool roundrobin, bool posvelrows)
+  (Eigen::VectorXd& m, RowMatrixXd& p, double time, Eigen::Vector3d ctr,
+   RowMatrix3d rot, bool roundrobin, bool posvelrows)
   {
-    initFromArray(ctr);
+    initFromArray(ctr, rot);
     addFromArray(m, p, roundrobin, posvelrows);
     return makeFromArray(time);
   }