MESMER Code

* Modified Mesmer.dvi, Mesmer.tex.
* Corrected OH_acetylene_association.xml. Updated OH_acetylene_association baseline.
* Added several control sequence printing values. See MesmerEnv.h for additional control flags.
Printing:
grain density of states
cell density of states
collision operator column sums
cell k(e)'s
number of eigenvalues being printed
Also, values are enclosed by braces, easier for copying and comparing.
* Moved some longer definitions of accessors in Molecule.h to Molecule.cpp
* Note: There should have a complaint over missing parameter on epsilon and sigma from HSO2, but the program will run with
default values. (Need to give correct values.)
* Updated pentyl and HSO2 baselines. HSO2 baseline does not change but pentyl baseline change because of the rounding
difference between two versions. There are three differences on ClassicalRotor.cpp. also for the electron excitation
energy. Another difference is on the starting count of electron excitation energy.
* Other minor modifications.

* Added two static variables sigmaDefault, and epsilonDefault.
* Some comments on dMatrix.cpp
* Modified some information reports.
* reorganised some orders of molecular initialization.
* Added setPersistentPointer() for Molecule
* Added some codes in MoleculeManager.cpp & Reaction.cpp about adding SuperMolecule (some errors still exist)
* Problem for SuperMolecule: 1. After adding a SuperMolecule into m_molmap, still cannot use GetNextMolecule() to
retrieve it!?
2. Matrix diagonalization does not converge.

* modified some tags in bin/pentyl_isomerizationJul.xml
bin/OH_acetylene_association.xml
Windows VC8/Mesmer/pentyl_isomerization.xml
Windows VC8/Mesmer/pentyl_isomerizationJul.xml

* modified function names: cellEnergies() -> getCellEnergies
cellDensityOfStates -> getCellDensityOfStates
for the fact that these two functions only performs get functionality. Note: Result credibility should check before
execution.
* Added files ClassicalRotor.cpp/h, DensityOfStates.cpp/h
* Moved counterDimerDOS() to a plugin class DensityOfStatesCalculator (DensityOfStates.h)
* modified the original ModelledMolecule::calcDensityOfStates() so that it governs the calculation of DOS in both
ModelledMolecule and SuperMolecule
* m_VibFreq temporarily become a public variable (if necessary will add accessors and privatize it later)
* Added DensityOfStatesCalculator *m_pDensityOfStatesCalculator ; in ModelledMolecule.
* Added functions to get individual member of participant Molecules in SuperMolecule
* Important: Now all isomers have to be specified `colliding' instead of being only `modelled' in xml.
Both second reactant/product are ModelledMolecule. Please read MoleculeManager.cpp
line 33 to line 44.
* Important: Added a tag me:DOSCMethod in each molecular element of XML input.
This makes it possible to use different methods to calculate the DOS in different species.
* Added a new function addSuperMol() in MoleculeManager
* rearranged the variable definition and function declaration order in Reaction.h
* Add bool return to BuildSystemCollisionOperator()
* Add another test file Windows VC8\Mesmer\OH_acetylene_association.xml

To do Next: 1. Debug
2. Add an element in xml file for SuperMolecule.
3. Test systems.

* Added a new class SuperMolecule (originally pairedMoleucles)
Note: This new class is derived from CollidingMolecule; in addition, it includes two pointers to CollidingMolecule and
ModelledMolecule respectively. This class takes the position of the source terms, any of which composed of two
reactant molecules in an association reaction. All SuperMolecule(s) go into sources.
* Added a new member SuperMolecule* m_srct in Reaction to represent the reactants.
* Added int return values for get_unimolecularspecies and get_bi_molecularspecies (to differntiate reactions on the fly)
* Errors, warnings and progress information all report to oberror.
* rearranged the order of variables/functions in Molecule.h
* Other minor modifications
* Note: Need to solve initialization of some pointers here. Later develop plugin to calculate density of states etc of
whatever.

* modified the starting position of iteration in AddAssocReactionTerms() (consider revising)
* Added a new class pairedMoleucles
* privatise protected member variables in Molecule.h & setup accessors/mutators for these variables
* rearranged the order initializing a molecule in classes
* Changed temp into beta
* include dMartix and Matrix into namespace mesmer
* removed some typecast warnings in VC compiler
* removed m_alloc
* Add lines in bool MoleculeManager::addmols() preventing user from inputting duplicated molecules
* Modified oberror report level from obWarning to obInfo.
* moved m_SpinMultiplicity to ModelledMolecule
* some other minor modifications

* modified the way of classifying rotors
* modified calcDensityOfStates() & testDensityOfStates() for additional rotors
* still cannot calculate microcanonical rate constants correctly, keep on checking.
* A sample file OH_acetylene_association.xml is provided to check association.

* modified MesmerILT.cpp --- now it is a working (testing not complete) version of ILT, but need to modify
ModelledMolecule::calcDensityOfStates() to account for 2-D linear rotors & non-rotors.
* Added some error reporting for InitializeMolecule()
* Added get_VibFreq() in Molecule.h
* other minor modifications

* Updated "Mesmer FAQ.doc"
* Updated source.ps
* modified main.cpp so that the output filename is date stamped.
* added TimeCounter.cpp
* Modified TimeCounter.h
Time stamp can now be applied to occasions where proper. Please check TimeCounter.h for usage.

* Add a ToDo file
* Add qd source into trunk directory
* Precision definitions in MesmerConfig.h
* More edits to MesmerILT.cpp
* Modified namings of variables: kfmc -> cellKfmc
m_kfgrn -> m_GrainKfmc
m_kfmc -> m_CellKfmc
dosGrn -> grainDOS
eGrn -> grainEne
m_gdos -> m_grainDOS
m_egrn -> m_grainEne
rctDos -> rctDOS
pdtDos -> pdtDOS

* change CellEne and CellDOS to vectors
* some other minor modifications

* cygwin rules
* formatfloat.h includes
* additional Makefile commands
* Now compile with cywgin
* Updated source.ps
* Other minor code format adjustments (Molecule.h/cpp, MoleculeManager.cpp, etc.)
* Resolved some g++ compiler complaints.