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Author SHA1 Message Date
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
ade2f69c1f committed configure 2010-01-04 00:58:30 +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
4658281213 Fixed a few errors. There was a name error. 2010-01-03 23:13:17 +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
c24a59deff Added a few files for the windows debug compile, which now uses _d libraries. 2009-12-30 23:07:15 +00:00
Harry Moffat
35f32314b9 Modifications to beat down the compiler warnings. Merged from the 
liquidTransportDevelop
 2009-12-29 03:01:18 +00:00
Harry Moffat
5eb5371cbc Added files. 2009-12-29 02:48:22 +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
06876f5ad5 Copied changes from 1.8.0 branch to trunk. 
Changes in the mechanism to make the solution more numerically stable.
 2009-12-29 02:37:30 +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
dfd9bc2c94 Added a reaction to the mechanism to promote numerical stability. 
Added a unimolecular dissociation rxn to avoid singular jacobians.
 2009-12-29 00:00:37 +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
c436da103e Changes for cygwin that have been implemented on the other branches. 2009-12-24 23:14:53 +00:00
Harry Moffat
a5cee7e389 Some needed changes added for the new cygwin environment. 2009-12-24 22:46:10 +00:00
Harry Moffat
dbf8f0cfa5 The new cygwin version 1.7.1 caused install commands to fail. Apparently, there is a problem 
with the native install command. I changed it to config/install-sh.
 2009-12-24 18:39:01 +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
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