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Author SHA1 Message Date
Ray Speth
9ed23a57ab Move non-trivial functions out of header files 2016-04-08 19:13:09 -04:00
Ray Speth
0540cf26d0 Clean up Doxygen docs and comments in Reactor classes 2015-11-12 11:41:34 -05:00
Ray Speth
70fe821c19 Deprecate FuncEval::getInitialConditions and related functions 2015-11-06 14:40:48 -05:00
Thomas Fiala
16ab7dff51 [Reactor] Implement functions getState for reactors and reactor networks 
These are simpler forms of getInitialConditions.
 2015-11-03 14:34:28 -05:00
Ray Speth
0647823ada Replace DATA_PTR macro with calls to data() 2015-10-17 18:58:50 -04:00
Ray Speth
a945ef2c23 Make use of initializer lists where appropriate 2015-10-17 18:58:50 -04:00
Ray Speth
f9375e1a09 Use locks/mutexes from the standard library instead of Boost.Thread 
This eliminates the need to link against any of the compiled Boost libraries,
and means that we can always build in thread-safe mode
 2015-10-17 18:58:50 -04:00
Ray Speth
a03f370cfd Make use of emplace and emplace_back methods 2015-10-14 18:45:23 -04:00
Ray Speth
3f6d8b0aca Use cppformat instead of int2str and fp2str 2015-10-14 18:45:23 -04:00
Ray Speth
2589a27b6c Use range-based for and auto to simplify some loops 2015-10-14 18:45:23 -04:00
Ray Speth
16143b47b6 Replace most uses of sprintf with cppformat 2015-10-14 18:45:22 -04:00
Ray Speth
41527b1ea7 Rename two-argument version of writelog 'debuglog' 
This is a prerequisite to allowing writelog to take an arbitrary number
of arguments.
 2015-10-14 18:45:22 -04:00
Ray Speth
3d27dfa1a1 [Reactor] Eliminate unused variable ReactorNet::m_iown 2015-10-05 18:48:14 -04:00
Ray Speth
6e138d0ae4 [Reactor] Always check that input/output are finite 
This causes problems to be caught early, where they can at least sometimes be
handled as recoverable intergrator errors, rather than letting NaN values
propagate through the solution.
 2015-08-24 12:27:07 -04:00
Ray Speth
acdf9cf0ed Clean up interstitial whitespace 
Remove extra space around operators, between words, etc.
 2015-08-02 23:06:16 -04:00
Ray Speth
6a04193646 Fix un-bracketed if, for, and else statements 2015-08-02 23:06:15 -04:00
Ray Speth
e4c45b6429 General whitespace cleanup 
Remove unnecessary blank lines and trailing whitespace. Replace tabs with
spaces.
 2015-08-02 23:06:15 -04:00
Ray Speth
d8772f261b [Reactor] Cannot add sensitivity reactions to initialized ReactorNet 
Before, the attempt to add the reaction was silently ignored. Now, this raises
an exception.
 2015-07-21 14:54:13 -04:00
Ray Speth
546289f737 Remove deprecated code with functional alternatives 2015-07-13 18:59:09 -04:00
Ray Speth
d373e0751e Remove unnecessary explicit specification of namespace Cantera 2015-06-24 14:45:55 -04:00
Ray Speth
0590b2cda8 [Reactor] Deprecate possibly-ambiguous names in componentIndex 
Resolves #274.
 2015-06-22 18:12:05 -04:00
Ray Speth
be24e9daf1 [Reactor] Move reactor contents check into ReactorBase::contents 
The check introduced in f6f868fe28 takes place too late, as the pointer to
ReactorBase.m_thermo has already been dereferenced at this point. Most compilers
let this pass, but it is techincally incorrect.
 2015-06-18 17:51:46 -04:00
Ray Speth
f6f868fe28 [Reactor] Check for Reactor contents before installing FlowDevice 
Fixes #279.
 2015-06-18 14:37:54 -04:00
Ray Speth
8d4e9bff6e [Reactor] Make argument to ReactorNet.step optional and deprecated 
The value of this argument has almost no effect on the integrator, and
frequently confuses users since the ReactorNet can end up at a time either
greater or less than the specified time. By removing this argument, the
distinction betwen step() and advance(t) becomes much more clear.
 2015-06-11 14:03:20 -04:00
Ray Speth
392b0f5692 [Reactor] Do not use argument to step/advance to set the max time step 
Allow CVODES to take arbitrarily large timesteps by default. If a maximum time
step is desired, it can be set explicitly.
 2015-06-11 14:03:20 -04:00
Ray Speth
0562f18100 [Reactor] Wall coverages may be set using a compositionMap or string 2015-05-02 20:07:45 -04:00
Ray Speth
ab2beb4c64 [Reactor] Check that contents are assigned before starting integration 2015-02-28 00:24:38 +00:00
Ray Speth
2e53890adf Minor cleanup of constructors and destructors 2015-02-26 21:58:42 +00:00
Ray Speth
b8a99b4b83 Remove unnecessary explicit calls to default constructors 2015-01-22 00:04:12 +00:00
Ray Speth
a6a10b854c [Reactor] Add damping factor to setState Newton iteration 
This resolves convergence issues in somes cases where the iteration would
oscillate around the true solution.
 2014-11-07 02:14:55 +00:00
Ray Speth
002c158761 Cleanup include statements 
Move includes from header to implementation files where possible, and remove
unnecessary includes.
 2014-08-28 16:54:13 +00:00
Ray Speth
56ccc667df Fix some uninitialized member variables 2014-07-30 16:59:39 +00:00
Ray Speth
884dd36b9c [Reactor] Remove unused reactor connectivity calculation 2014-07-18 15:14:12 +00:00
Ray Speth
1b1703cc56 [Reactor] Remove unused variable ReactorBase::m_init 2014-07-18 15:14:07 +00:00
Ray Speth
6ffbaa5f77 [Reactor] Remove unneeded variables from ReactorBase 2014-06-10 16:23:43 +00:00
Ray Speth
8b5ca80303 [Reactor] Implement reactor network reinitialization 
Adds ReactorNet::reinitialize, which skips all one-time initialization and
re-uses the same CVODES integrator. The Reactor::syncState() method is
introduced for applying new initial conditions for individual Reactor objects.

This approach increases efficiency when solving many similar problems with short
integration times, for example when being used as the chemistry term integrator
in an operator-split CFD code.
 2014-06-10 16:23:03 +00:00
Ray Speth
1437aade8c [Reactor] Refactor updateState and getInitialConditions implementations 
Extract common parts related to surface species
 2014-06-10 16:22:46 +00:00
Ray Speth
67de2fa793 [Reactor] Refactor re-implementations of Reactor::initialize 
The base class methods does almost all the initialization needed for the derived
classes, so call that first and then do any additional steps needed.
 2014-06-10 16:22:37 +00:00
Ray Speth
0da063cdef [Reactor] Refactor wall / surface chemistry evaluation 
This creates a single implementation of the calculation of the contributions of
walls and surface chemistry to the governing equations for all reactor types.
 2014-06-10 16:21:56 +00:00
Ray Speth
a583949457 [Reactor] ReactorNet::addReactor takes a reference instead of a pointer 
This reflects how the function is usually used. The old signature is now
deprecated, as is the extra argument for transfering "ownership" to the
ReactorNet object.
 2014-06-06 00:17:41 +00:00
Ray Speth
b5396837b2 Make use of std::min, std::max, and clip 2014-06-03 16:52:43 +00:00
Ray Speth
a5d735f047 [Reactor] Disable verbose output by default, even in "debug mode" 2014-06-03 16:52:09 +00:00
Ray Speth
0e9ca0fc4b [Reactor] Eliminate tracking of Reservoirs by ReactorNet 
Since Reservoirs don't have any equations to solve, there is no reason to add
them to a ReactorNet.
 2014-06-03 16:52:00 +00:00
Ray Speth
2d1003271d [Reactor] Replace ReactorNet::m_size with m_start 
A small simplification since the offset into the global solution vector is
usually what we're interested in.
 2014-06-03 16:51:47 +00:00
Ray Speth
789574ac80 Remove commented-out code 2014-05-27 02:52:21 +00:00
Ray Speth
4587883d5e Remove try/catch from ReactorNet::evalJacobian 
This function isn't actually called by CVODE (which uses its own difference
quotient method for calculating the Jacobian), so the note here isn't correct.
 2014-03-28 23:12:17 +00:00
Ray Speth
95eb7ab3ba Remove newline after '::' in member function definitions 
This inconsistency makes it hard to directly search the code for a specific
member function definition.
 2014-03-24 04:03:09 +00:00
Ray Speth
c7ba8bfb84 Remove abandoned autotools build system 2014-03-04 17:38:53 +00:00
Ray Speth
d516d46f33 Remove unnecessary use of static_cast<int> 2014-01-31 23:15:09 +00:00
Bryan W. Weber
fc2d7e4ce0 [Reactor] Change 'species' to 'component' in context of sensitivities 
Change the variable named *species* to be named *component*. This
better matches the utility of this variable, since it can be used to
retrieve any of the state variables. Also, update the corresponding
documentation.
 2013-12-16 23:22:04 +00:00