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1955 commits

Author SHA1 Message Date
Harry Moffat
039696dcc6 More changes for solaris compile 2010-02-09 20:39:03 +00:00
Harry Moffat
a5ea91b56a Changes due to compilation problems on solaris 2010-02-09 20:24:11 +00:00
Harry Moffat
e2fb5d3483 Fixed compilation errors on solaris. 2010-02-09 19:57:02 +00:00
Harry Moffat
66ea343cea Doxygen update 
- no code changed
  - All the easy warning messages are eliminated now from the trunk.
 2010-01-17 18:17:55 +00:00
Harry Moffat
36e4040750 Doxygen update 
- beat down the warning messages from this directory.
   - no code changed other than reformatting.
 2010-01-17 17:55:28 +00:00
Harry Moffat
180fbef55d Doxygen update 
- no code has been changed other than a change of symbols.
 2010-01-17 17:05:46 +00:00
Harry Moffat
8af585eeab Doxygen update - no code changed. 
Working on beating down the warnings
 2010-01-16 18:57:05 +00:00
Harry Moffat
3587de40b7 Doxygen update on SingleSpeciesTP 
double to doublereal conversions

made sure const parameters match on setTemperature()
 2010-01-15 20:22:09 +00:00
Harry Moffat
8ea0c8197e Made sure all double values were doublereal 2010-01-13 22:12:27 +00:00
Harry Moffat
bedb314545 Eliminated a doxygen error. 2010-01-12 21:34:40 +00:00
Harry Moffat
ab38d29228 Fixed a doxygen compatibility problem. 2010-01-12 21:27:32 +00:00
Harry Moffat
3d392242d9 Added documentation for an external int 2010-01-12 21:23:08 +00:00
Harry Moffat
41e207d762 Added comments. 2010-01-12 17:16:57 +00:00
Harry Moffat
e381001c95 Merged changes from the 1.8.0 branch ontl the main trunk. 2010-01-04 00:46:26 +00:00
Harry Moffat
a0cdf79771 Reduced the accuracy on the comparisons 2010-01-03 23:56:43 +00:00
Harry Moffat
fd287e1d89 reduced the precision on the comparisons 2010-01-03 23:54:24 +00:00
Harry Moffat
23c50efe35 rebaselined the solution 2010-01-03 23:44:55 +00:00
Harry Moffat
2cb7eb7580 Added two new files that will be used in the windows debug compile. 2009-12-30 23:08:17 +00:00
Harry Moffat
c03e7c2ab5 Merged the changes made in the 1.8.0 branch into the main trunk. 2009-12-29 02:47:28 +00:00
Harry Moffat
0ddc9d4186 Finished adding to the ignore lists... 2009-12-29 02:34:56 +00:00
Harry Moffat
01852ed442 Worked on the ignore file list 2009-12-29 02:09:01 +00:00
Harry Moffat
9cf35bff4f Removed errors in the makefiles. 2009-12-29 01:41:41 +00:00
Harry Moffat
7113dd53da Reblessed this solution -> may be changing arbitrarily and problematically 2009-12-29 01:41:01 +00:00
Harry Moffat
3a7cca584c Rebaselined a few tests. 
Worked on changing the solution for 2 problematic tests: 
            catcomb_stagflow
            surf_rxn

  The catcomb problem actually needed the surface mechanism to be 
changed for it to become a reliable solve.
 2009-12-29 01:28:09 +00:00
Harry Moffat
5b725eec64 Fixed the problem so that convergence would occur. 
The time step in the inner loop was decreased by a factor of 100.
   Previously, there were convergence problems with this example problem.
 2009-12-28 23:04:55 +00:00
Harry Moffat
2ee8ae220d Fixed an error with the assignment and copy constructor. 
The VPSSMgr object needed to be resynched with the VPStandardStateTP
object after it was set up. This was not done.
 2009-12-22 22:35:30 +00:00
Harry Moffat
d96464f0c2 Fixed an error in the assignment and copy constructor. 
The VPSSMgr object needed to be resynced at the end of the
assignment. This wasn't being done.
 2009-12-22 22:27:01 +00:00
Harry Moffat
acf0c3f7c3 Fixed a typo that was causing sundials version 2.3 builds to fail. 
The define variable was spelled incorrectly.
 2009-12-21 21:02:28 +00:00
Harry Moffat
4420038d29 Fixed an error that caused sundials version 2.3 not to work as intended. 
There was an error in the ifdef variable's spelling.
 2009-12-21 20:27:18 +00:00
Harry Moffat
321d387930 MetalSHEelectrons 
Added a built-in type to handle electrons in metals that
    follow the SHE convention.

    Took out electrodeElectron, since it was hidden and not used.

    MetalSHEelectrons have a standard concentration of 1, instead
    of the previous treatment where SHE electrons had a standard
    concentration equal to the concentration of an ideal gas.
 2009-12-11 01:32:26 +00:00
Harry Moffat
204f6bff33 Made the destructor virtual 2009-12-11 01:19:09 +00:00
Harry Moffat
9b90beb0e0 Merged changes from LiquidTransportDevelopment 
There were two changes:

Additions to support some reversible reactions which have fractional
stoichiometries. These were not allowed previously. However, if
the species with fractional stoichiometries are in single-species
phases, this is ok, and actually necessary for some solid-phase
reactions.

Removed comments from DEBUG_MODE about about too high or low an activation
for electrode reactions.
 2009-12-10 23:20:44 +00:00
Harry Moffat
9c6080e3c9 Turned on keyword substitution in the cpp files. 2009-12-09 17:50:27 +00:00
Harry Moffat
6d02467b7e Added the change for the bugfix to HMWSoln to the static branch 
The function getActivityConcentration in the HMWSoln object had
a bug in it that caused it to be incompatible with standardConcentration()
and getActivities(). This meant that the ROP in kinetics managers
for this object was being calculated incorrectly.

This is now fixed.
 2009-12-09 17:34:13 +00:00
Harry Moffat
20c74f21af Added the change for the bugfix to HMWSoln to the main branch. 
The function getActivityConcentration in the HMWSoln object had
a bug in it that caused it to be incompatible with standardConcentration
and getActivities(). This meant that the ROP in kinetics managers
for this object was being calculated incorrectly.
 2009-12-09 17:29:23 +00:00
Harry Moffat
392683283a An initial implemention of a string representation of the 
phase eos type.  We've not had this until now. 

The idea here is to have a 1 to 1 mapping between an
eosType int and a string, which can be used for writing output.
 2009-12-08 17:36:40 +00:00
Harry Moffat
e09bf8c244 Added a note about deprecation. 2009-12-05 23:18:36 +00:00
Harry Moffat
1922aa9fe0 Took executable prop off these files. 2009-12-05 22:42:07 +00:00
Harry Moffat
fc14dfe7f7 Added comments. 2009-12-05 22:40:10 +00:00
Harry Moffat
7b3b9b186a Transfering bugfixes from liquidTransport to the main branch. 
This mainly involved fixing the copy and assignment operators
for the IonsFromNeutralVPSSTP operator.

Added docs for PDSS_SSVol

Turned on keyword substitution
 2009-12-05 19:08:43 +00:00
Harry Moffat
b6c6d090f6 Expanded the capability of getFloatArray to read the current XML node 
or a child node with a specified name. Before it would just read
an XML node named floatArray.
 2009-12-05 15:40:33 +00:00
Harry Moffat
2b56d54a09 Added some sample scripts for compiling under cygwin. 
The most important is the numpy script, as numpy now comes bundled with cygwin.
 2009-10-22 21:48:32 +00:00
Harry Moffat
686fb46591 Added back in a clear 2009-10-13 01:57:50 +00:00
Harry Moffat
0cafca6aaf First problem with SimpleTransport is done. Nominally, this object 
is in working order.
 2009-10-13 01:42:59 +00:00
Harry Moffat
9593d2996e Another update aimed at getting a SimpleTransport model up and running. 
SimpleTransport now can read its XML file.
 2009-10-13 00:27:48 +00:00
Harry Moffat
3b4401a77d Added into Transport Factory an option to read the phase XML file 
and implement the transport manager listed there.
 2009-10-12 14:13:10 +00:00
Harry Moffat
a258cdf083 Added an xml storage section to importPhase(). Note this represents a 
long standing bug in some ThermoPhase implementations, where the
xml tree was not being storred for the phase node in some cases.
 2009-10-11 21:38:42 +00:00
Harry Moffat
d503c55864 Added a clear() function to the xml object. This will wipe 
out the current level and everything below it.
 2009-10-11 21:34:06 +00:00
Harry Moffat
5fd13d3591 Took out default parameters for some of the transport initialization 
routines. It makes no sense to call these things if you don't have
a ThermoPhase already created.
 2009-10-11 20:46:57 +00:00
Harry Moffat
4ee4b4891f Added a missing function to AqueousTransport 2009-10-11 19:20:11 +00:00