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2860 commits

Author SHA1 Message Date
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
Harry Moffat
26fb3aec3b Updating this directory 2009-09-25 18:41:20 +00:00
Harry Moffat
f4ed70d2ba Updating this directory 2009-09-25 18:41:20 +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
Harry Moffat
1d1fdcd8f3 A little bit of housecleaning.
Took out the file Makefile, which shouldn't be in the svn system,
and added some ignore files.
2009-09-24 23:01:26 +00:00
John Hewson
cc680c2b3c Cleanup and debugging of getLiquidTransportData. 2009-09-24 20:58:28 +00:00
John Hewson
1dad7e320a LiquidTransport.h LiquidTransport.cpp
Removed a number of variables relevant only to the gas-phase transport
coefficient models.  These include the following:
-    vector_fp  m_cond;
-    vector_fp                    m_polytempvec;
-    vector<vector_fp>            m_condcoeffs;
-    std::vector<vector_fp> viscCoeffsVector_;
-    vector_fp m_sqvisc;
-    vector_fp viscSpecies_;
-    DenseMatrix m_wratkj1;
-    DenseMatrix m_phi;
-    DenseMatrix m_wratjk;

Removed much code related to these variables.

Added a number of variables relevant to the liquid-phase transport
models including: 
+    vector_fp  m_condSpecies;
+    vector_fp m_viscSpecies;
+    vector_fp  m_visc_A;
+    vector_fp  m_visc_n;
+    vector_fp  m_visc_Tact;
+    vector_fp  m_thermCond_A;
+    vector_fp  m_thermCond_n;
+    vector_fp  m_thermCond_Tact;

Changed some of the relevant comments to
pertain to the liquid-phase models.
2009-09-24 20:46:26 +00:00