Commit graph

1421 commits

Author SHA1 Message Date
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
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
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
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
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
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
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
John Hewson
b933e64c79 LiquidTransportParams.h
Added some comments plus members
+       DenseMatrix  visc_Eij;
+       DenseMatrix  visc_Sij;
These members are not populated in any way at this point.  A message
to this effect is written in
TransportFactory::getLiquidTransportData. 


LiquidTransport.h LiquidTransport.cpp

Changed the types of viscosity models from 
   const int LVISC_CONSTANT     = 0;
-  const int LVISC_WILKES       = 1;
-  const int LVISC_MIXTUREAVG   = 2;
to
   const int LVISC_CONSTANT     = 0;
+  const int LVISC_INTERACTION  = 1;
+  const int LVISC_AVG_ENERGIES = 2;
These are not yet implemented.

Added members 
+    DenseMatrix m_visc_Eij;
+    DenseMatrix m_visc_Sij;
+    vector_fp  m_hydrodynamic_radius;
+    vector_fp  m_visc_logA; //logarithm of coefficient

Removed unneeded members:
-    vector_fp   m_eps;
-    doublereal m_sqrt_t;
-    doublereal m_t14;
-    doublereal m_t32;
-    doublereal m_sqrt_kbt;

Changed the name of m_cond to m_condSpecies in agreement with the
m_viscSpecies pattern.

Implemented some code in LiquidTransport::viscosity() to compute the
molecular interactions relevant to mixture viscosity, BUT none of the
required parameters or flags are implemented at this point.
2009-09-25 18:40:29 +00:00
Harry Moffat
8daac72a4e Fixed an error in a dimensioning statement that
was causing array overwites.
2009-09-25 18:37:48 +00:00
John Hewson
cc680c2b3c Cleanup and debugging of getLiquidTransportData. 2009-09-24 20:58:28 +00:00