Commit graph

2664 commits

Author SHA1 Message Date
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
c436da103e Changes for cygwin that have been implemented on the other branches. 2009-12-24 23:14:53 +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
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
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
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
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