[oneD] Replace write_csv by save

include/cantera/oneD/Sim1D.h

@@ -142,15 +142,22 @@ class Sim1D : public OneDim
               const std::string& desc, int loglevel);
 
     /**
-     * Save the current solution to a container file.
+     * Save the current solution to a container or CSV file.
+     *
+     * For HDF and YAML, the entire content of the object is saved; for CSV, only the
+     * main 1D domain is saved.
+     *
      * @param fname  Name of output container file
      * @param id  Identifier of solution within the container file
      * @param desc  Description of the solution
      * @param overwrite  Force overwrite if name exists; optional (default=false)
      * @param compression  Compression level (optional; HDF only)
+     * @param basis  Output mass ("Y"/"mass") or mole ("X"/"mole") fractions (CSV only);
+     *      if omitted (default=""), the native storage mode is used
      */
     void save(const std::string& fname, const std::string& id,
-              const std::string& desc, bool overwrite=false, int compression=0);
+              const std::string& desc, bool overwrite=false, int compression=0,
+              const string& basis="");
 
     /**
      * Save the residual of the current solution to a container file.

interfaces/cython/cantera/_onedim.pxd

@@ -114,7 +114,7 @@ cdef extern from "cantera/oneD/Sim1D.h":
         void refine(int) except +translate_exception
         void setRefineCriteria(size_t, double, double, double, double) except +translate_exception
         vector[double] getRefineCriteria(int) except +translate_exception
-        void save(string&, string&, string&, cbool, int) except +translate_exception
+        void save(string&, string&, string&, cbool, int, string&) except +translate_exception
         CxxAnyMap restore(string&, string&) except +translate_exception
         void writeStats(int) except +translate_exception
         void clearStats()

interfaces/cython/cantera/_onedim.pyx

@@ -1537,20 +1537,26 @@ cdef class Sim1D:
             return self.sim.fixedTemperatureLocation()
 
     def save(self, filename='soln.yaml', name='solution', description=None,
-             loglevel=None, overwrite=False, compression=0):
+             loglevel=None, *, overwrite=False, compression=0, basis=None):
         """
-        Save the solution in YAML or HDF format.
+        Save the solution to a container or CSV format.
+
+        For HDF and YAML files, the entire content of the `Sim1D` object is saved; for
+        CSV, only the main 1D domain is saved.
 
         :param filename:
             solution file
         :param name:
-            solution name within the file
+            solution name within the file (HDF/YAML only)
         :param description:
-            custom description text
+            custom description text (HDF/YAML only)
         :param overwrite:
             Force overwrite if name exists; optional (default=`False`)
         :param compression:
             compression level 0..9; optional (HDF only)
+        :param basis:
+            Output mass (``Y``/``mass``) or mole (``X``/``mole``) fractions (CSV only);
+            if not specified (`None`), the native storage mode is used
 
         >>> s.save(filename='save.yaml', name='energy_off',
         ...        description='solution with energy eqn. disabled')
@@ -1562,7 +1568,7 @@ cdef class Sim1D:
             warnings.warn("Argument 'loglevel' is deprecated and will be ignored.",
                 DeprecationWarning)
         self.sim.save(stringify(str(filename)), stringify(name),
-                      stringify(description), overwrite, compression)
+                      stringify(description), overwrite, compression, stringify(basis))
 
     def restore(self, filename='soln.yaml', name='solution', loglevel=None):
         """Set the solution vector to a previously-saved solution.

interfaces/cython/cantera/onedim.py

@@ -406,7 +406,13 @@ def write_csv(self, filename, species='X', quiet=True, normalize=True):
         :param normalize:
             Boolean flag to indicate whether the mole/mass fractions should
             be normalized.
+
+        .. deprecated:: 3.0
+
+            Method to be removed after Cantera 3.0; superseded by `save`.
         """
+        warnings.warn("'write_csv' is superseded by 'save' and will be removed "
+                      "after Cantera 3.0.", DeprecationWarning)
 
         # save data
         cols = ('extra', 'T', 'D', species)
@@ -773,7 +779,7 @@ def getter(self):
               'entropy_mass', 'g', 'gibbs_mole', 'gibbs_mass', 'cv',
               'cv_mole', 'cv_mass', 'cp', 'cp_mole', 'cp_mass',
               'isothermal_compressibility', 'thermal_expansion_coeff',
-              'sound_speed', 'viscosity', 'thermal_conductivity', 
+              'sound_speed', 'viscosity', 'thermal_conductivity',
               'heat_release_rate', 'mean_molecular_weight']:
     setattr(FlameBase, _attr, _array_property(_attr))
 FlameBase.volume = _array_property('v') # avoid confusion with velocity gradient 'V'

src/oneD/Sim1D.cpp

@@ -126,10 +126,25 @@ void Sim1D::save(const std::string& fname, const std::string& id,
 }
 
 void Sim1D::save(const std::string& fname, const std::string& id,
-                 const std::string& desc, bool overwrite, int compression)
+                 const std::string& desc, bool overwrite, int compression,
+                 const string& basis)
 {
     size_t dot = fname.find_last_of(".");
     string extension = (dot != npos) ? toLowerCopy(fname.substr(dot+1)) : "";
+    if (extension == "csv") {
+        for (auto dom : m_dom) {
+            auto arr = dom->asArray(m_state->data() + dom->loc());
+            if (dom->size() > 1) {
+                arr->writeEntry(fname, overwrite, basis);
+                break;
+            }
+        }
+        return;
+    }
+    if (basis != "") {
+        warn_user("Sim1D::save",
+            "Species basis '{}' not implemented for HDF5 or YAML output.", basis);
+    }
     if (extension == "h5" || extension == "hdf"  || extension == "hdf5") {
         SolutionArray::writeHeader(fname, id, desc, overwrite);
         for (auto dom : m_dom) {