* Clarifies the meaning of ID
* Creates a PEP8 compliant attribute that does not conflict with
a built-in function name that is also consistent with the YAML entry.
* Change associated member function names in C++ SolutionBase
* Deprecate `ID` in Python (to be removed after Cantera 2.5)
* Add Base.h/Base.cpp with definition of SolutionBase
* Link C++ object into Cython interface
* Add unique_name and type attributes to Cython _SolutionBase
In order to generate links to pages in the development docs, the
cantera-website build process needs a local copy of the current dev docs,
which this provides in a format which can be easily downloaded.
The water-IAPWS95 instantiates either WaterSSTP or PDSS_water objects,
both of which are intended for liquid phases only. Clarify the phase
name to liquid-water-IAPWS95 to allow a future phase that could
represent the full liquid<->vapor phase space.
This commit implements new methods for SolutionArray:
* `restore_data` can restore data previously exported by `collect_data`
* `read_csv` restores data previously saved by `write_csv`
* unit tests are added for SolutionArray's based on ThermoPhase and PureFluid
* setter for `PureFluid.TPX` property is added to allow for automatic
restoration of consistent thermodynamic data
* alternative to 'TP', 'TX' or 'PX' which may not uniquely describe
a valid thermodynamic state
* add unit test
Avoid NaN results in entropy_mole calculations when there are small negative
mass fractions. Consistent with the approach used elsewhere,
e.g. IdealGasPhase::getPartialMolarEntropies.
Further:
* revert unit tests to previous species definitions (some case mis-matches)
* remove non-essential comments
* opt to maintain case-sensitive species maps with lowercase as fallback
* store species information with case sensitive names
* retain lookup for non-case sensitive species names, e.g. Phase::speciesIndex
* implement flag that enforces case sensitive species names as a member
variable of Phase
* add exception handling for species that are not uniquely defined unless case
sensitive (e.g. Cs and CS in nasa.cti if cs is specified and case sensitivity
is not enforced)
* deprecate Phase::species(std::string&)
Solving with auto=True and then solving with auto=False would leave the domain
width check in place, but without the logic for automatically increasing the
domain width, resulting in unexpected solver failures.
* The commit implements saving of data extracted from SolutionArrays
to HDF containers using pandas infrastructure.
* Two methods are introduced: `write_hdf` and `to_pandas`.
* Both methods only work if the pandas module can be imported; an
exception is raised only if the method is called without a working
pandas installation.
The "catching polymorphic type" warnings appear during compilation with GCC 8:
src/base/global.cpp: In function ‘void Cantera::setLogger(Cantera::Logger*)’:
src/base/global.cpp:28:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
} catch (std::bad_alloc) {
^~~~~~~~~
src/equil/vcs_MultiPhaseEquil.cpp: In member function ‘int Cantera::vcs_MultiPhaseEquil::equilibrate_HP(doublereal, int, double, double, int, int, doublereal, int, int)’:
src/equil/vcs_MultiPhaseEquil.cpp:228:31: warning: catching polymorphic type ‘class Cantera::CanteraError’ by value [-Wcatch-value=]
} catch (CanteraError err) {
^~~
src/equil/vcs_MultiPhaseEquil.cpp: In member function ‘int Cantera::vcs_MultiPhaseEquil::equilibrate_SP(doublereal, double, double, int, int, doublereal, int, int)’:
src/equil/vcs_MultiPhaseEquil.cpp:354:31: warning: catching polymorphic type ‘class Cantera::CanteraError’ by value [-Wcatch-value=]
} catch (CanteraError err) {
^~~
This commit fix this warnings via caught by reference.
The changelog of Sundials 4.0.0 states:
"With the introduction of SUNNonlinSol modules, the input parameter iter
to CVodeCreate has been removed along with the function CVodeSetIterType
and the constants CV_NEWTON and CV_FUNCTIONAL.
Similarly, the ITMETH parameter has been removed from the Fortran interface
function FCVMALLOC. Instead of specifying the nonlinear iteration type
when creating the CVODE(S) memory structure, CVODE(S) uses
the SUNNONLINSOL_NEWTON module implementation of a Newton iteration by default."
so the appropreate conditional changes are added to control
the code execution via CT_SUNDIALS_VERSION preprocessor variable
to omit the parameters of Sundials solver that are no longer required.
In the atomic weights struct in Elements.cpp, ensure that there is no
space before the closing brace of an element and that there is one
space between the longest element name and a 3-digit weight.
Use data from the periodic table at
http://www.ciaaw.org/atomic-weights.htm and
https://iupac.org/wp-content/uploads/2018/12/IUPAC_Periodic_Table-01Dec18.pdf
Elements without any atomic weight in either table do not have a stable
isotope. These are deleted from elements.xml and have their atomic
weight set to -1.0 in Elements.cpp. Add elements after plutonium that
were not previously listed. None of these elements have stable
isotopes.
These elements are retained/added so their symbols, names, and atomic
numbers can still be retrieved and the mapping of atomic number to
index - 1 in the struct is maintained.
Modify the element weight lookup functions to throw errors when an
element with no weight is requested (i.e., the weight is -1.0 in the
struct).
* differentiated Valve::setValveCoeff from PressureController::setPressureCoeff
and introduced MassFlowController::setMassFlowCoeff for consistency.
* introduced FlowDevice::setTimeFunction and FlowDevice::setPressureFunction to
differentiate time-dependent and pressure-dependent functions.
* introduced arbitrary pressure dependence for PressureController
* deprecated FlowDevice::setFunction which is replaced by time and pressure
specific functions.
* introduced properties Valve.valve_coeff / PressureController.pressure_coeff /
MassFlowController.mass_flow_coeff in Cython interface and deprecated
Valve.set_pressure_coeff / PressureController.set_pressure_coeff
* deprecated corresponding function calls in clib interface
* deprecate FlowDevice.setParameters (which was only used by MATLAB interface)
Replace data/inputs/diamond.cti with test_problems version that has
more information. This results in a change in the default pressure and
mole fractions of the gas phase, which in turn changes the result of
one of the regression tests. This is fixed by setting the composition
and pressure of the gas phase in the test to their original values. The
default state from the CTI file matches from the paper.
In addition, there was a difference in the reversibility of reaction u
between the files. Since the thermo for C(d) specifies that the
reaction is irreversible, this is the sense of the reaction that is
chosen.
Include plotting in the diamond_cvd.py and use open properly.
