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Author SHA1 Message Date
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
b8ee78fc24 Modified the example installs 
The minor version number is now included in the install directory.
 2009-12-21 20:53:24 +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
b0e4592e77 Added ignore files. 2009-12-05 23:22:43 +00:00
Harry Moffat
50ae4a28b9 Added ignore files. 2009-12-05 23:21:32 +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
b229d1d5f9 Added a couple of files. 2009-12-05 22:38:56 +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
cad06c4ace Modified the naming scheme. 2009-10-22 22:05:49 +00:00
Harry Moffat
42f709a37f Moved names around to create a common naming scheme. 2009-10-22 22:01:08 +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
121f359baa Merged the LiquidTransportDevelop branch into the trunk. 
SimpleTransport is now operational, so it seemed like a 
good time.
 2009-10-13 02:09:37 +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
2ee219c50b Merging the changes that had been occurring on the change branch 
liquidTransportDevelop into the main trunk. This seemed like a good time
to do it. And, there were some fundamental bugs that were fixed just on
the change branch.
 2009-10-12 19:26:15 +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
Harry Moffat
787fd3778e More work on the SimpleTransport object. Nominally, the object is 
finished. But, it needs testing.
 2009-10-10 21:54:55 +00:00
Harry Moffat
c1d59a912b Got most of the way towards creating a new transport Object SimpleTransport 
that obeys the simplest formulas possible.
 2009-10-10 04:23:04 +00:00
Harry Moffat
10ab1af013 Added memory release statements. 2009-10-06 14:37:45 +00:00
Harry Moffat
636c63482b Took executable bits off 2009-10-02 21:10:26 +00:00
Harry Moffat
825d909875 Took executable bit off of the file. 2009-10-02 21:09:12 +00:00
Harry Moffat
ff82509600 Test commit with small functionality. 2009-10-02 21:08:16 +00:00
Harry Moffat
431f167c0f Changed the method model() to be a const function. 
Moved Transport methods back into the file TransportBase.cpp
Defined err() functions for LiquidTransport object so that
the code will link again.
 2009-09-28 16:09:58 +00:00
Harry Moffat
3f630e56a6 Eliminated a possible error that could wipe out the directory when make clean is invoked, if the build directory doesn't exist. 2009-09-26 02:13:34 +00:00
Harry Moffat
fd245bb194 Merging changes from the trunk into the change branch. 2009-09-26 01:55:27 +00:00
Harry Moffat
95c685dbe7 Merged changes from Revision_1.8 into the main trunk 2009-09-26 01:53:39 +00:00
Harry Moffat
c0e84560a1 Added ignore entries for doxygen stuff. 2009-09-26 01:22:22 +00:00
Harry Moffat
844b3cdce8 Doxygen update 2009-09-26 01:15:38 +00:00
Harry Moffat
f1d0698194 Doxygen updates - beating down the warnings. 2009-09-26 01:13:01 +00:00
Harry Moffat
f61308fe1d Doxygen changes -> beating down the warning messages 2009-09-25 23:23:05 +00:00
Harry Moffat
aa12b47ccc Doxygen updates -> filling in missing parameters. 2009-09-25 21:07:41 +00:00
Harry Moffat
e6e872b1e3 Doxygen update 2009-09-25 20:39:19 +00:00
Harry Moffat
5f7e88a634 Added missing doxygen documentation 2009-09-25 20:15:28 +00:00