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ChangeLog
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2014-February-16 Struan Robertson
* MESMER manual.docx: Added content on examples, distribution plots and
convergent eigenvalues.
2014-February-14 Struan Robertson
* CollisionOperator.cpp: Minor change to make eigenvalue convergence
warning more visible.
2014-February-09 Struan Robertson
* MESMER manual.docx: Added documentation corrections from CM and RS.
2014-February-09 Struan Robertson
* HinderRotorQM1D.cpp: Added methods to locate the minimum in a hindered
rotor potential and shift the potential so that the minimum is at zero.
* DensityOfStates.h, HinderRotorQM1D.cpp, Morse.cpp, BeyerSwineehart.cpp:
Introduce methods for calculating the zero point energy.
2014-January-27 Struan Robertson
* MESMER manual.docx: Added content on analytical representation and command
line options.
2014-January-26 Struan Robertson
* AnalyticalRepresentation.cpp, System.cpp, unitsConvertsion.cpp/.h: Added
precision to analytical representation method.
2014-January-26 Struan Robertson
* MesmerQA: Update of smoke tests and baseline files to use supported energy
transfer model syntax.
2014-January-26 Struan Robertson
* examples: Update of tests and baseline files to use supported energy
transfer model syntax.
2014-January-21 Struan Robertson
* src/plugins/AnalyticalRepresentation.cpp: Fix for inverse temperature
bug.
2014-January-15 Chris Morley
* src/plugins/AnalyticalRepresentation.cpp: rateUnits attribute on
<format> to choose units of output bimolecular rate constants.
Correct previous incorrect calculation of bimolecular rates.
* examples/Methoxymethyl/ChebyshevCK.xml: now outputs in moles units
* schemas/mesmerPlugins.xsd; update schema
2014-January-14 Struan Robertson
* MESMER manual.docx: Added documentation for analytical representation.
2014-January-10 Chris Morley
* src/error.h: StopCTestOutput works only when ErrorLevel is > obDebug,
i.e. ctest output is enabled with -w5 option in command or
ChangeErrorLevel e(obDebug); in C++ code if fitting function.
* src/plugins/fitting.cpp,src/plugins/Marquardt.cpp,
src/plugins/SensitivityAnalysis.cpp: ctest output supressed by default.
2013-December-29 Struan Robertson
* MESMER manual.docx: Added content regarding XML Schema.
2013-December-20 Struan Robertson
* MolecularComponents.h/.cpp: Minor changes related to the rationalization
of the reservoir state code.
2013-December-19 Chris Morley
* src/plugins/AnalyticalRepresentation.cpp: expand reaction strings
to include all the species for easier pasting to Cantera.
* src/BimolecularSinkReaction.cpp,src/BimolecularSinkReaction.h,
src/IrreversibleUnimolecularReaction.cpp,src/IrreversibleUnimolecularReaction.h,
src/CollisonOperator.cpp: increase possible number of sink products to three.
* src/Reaction.cpp,src/Reaction.h,src/ReactionManager.cpp,
src/ReactionManager.h,src/CollisionOperator.cpp: add some reasonably
gereneral functions for reaction strings.
2013-December-14 Struan Robertson
* AnalyticalRepresentation.cpp: Initial revision of Chemkin format writer.
2013-December-13 Chris Morley
Fix crash with Methyl_H_to_Methane_FTST.xml
* src/MolecularComponents.cpp,src/Rdouble.cpp,src/unitsConversion.cpp:
Make "units" attribute on me:ZPE optional. On any range variable it
is ignored when there is a "derivedFrom" attribute. Provide more
meaningful cinfo message.
Extra functions which may be needed for AnalyticalRepresentation.
* src/Reaction.cpp,src/Reaction.h,src/AssociationReaction.h,
src/BimolecularSinkReaction.h,src/IrreversibleExchangeReaction.h,
src/IrreversibleUnimolecularReaction.h,src/IsomerizationReaction.h:
Provide a virtual functions to get reactants and to output a reaction
string.
* src/System.h: add getReactionManager()
MesmerQA/UnitTests/UnitTests.xml: make more schema friendly
2013-December-07 Struan Robertson
* HinderedRotorQM1D.cpp, UnitTests.cpp, UnitTests.xml: MEIC test
for hindered rotors added.
2013-November-19 Chris Morley
* examplesSchema/Methoxymethyl: Chebyshev.xml modified to be
schema-friendly and added to examplesSchema.
* src/plugins/AnalyticalRepresentation.cpp, defaults.xml:
Update parsing and get concentration units from an attribute on either
concentration value or from defaults.xml.
* src/MesmerEnv.cpp, src/plugins/SensitivityAnalysis.cpp: remove
some minor compiler warnings.
2013-November-18 Chris Morley
* mesmer1.xsl,src/System.cpp: make Firefox output report bath gas
* schemas/mesmer.xsd,schemas/mesmerPlugins.xsd,schemas/CMLforMesmer.xsd:
add derivedFrom, etc.
* src/MolecularComponents.cpp,src/plugins/ExponentialDown.cpp: label name
or general bath gas is always like HONO:deltaEDown without : or :He
* src/Rdouble.cpp: use derivedFrom as well as me:derivedFrom.
2013-November-12 Chris Morley
* src/main.cpp,src/MesmerConfig.h: Change QACompare() to use .test files
with same name as .xml file if the -N option used.
-N option now does not need to be before xmlfile name.
* src/MesmerConfig.h: change baseline folder name for Windows.
(Why is there no Linux entry?)
* MesmerQAschema/QA.bat: subsidiary projects like ipropyl_reservoir.xml
now checked. NOTE: not altered in MesmerQA folder which I shall soon
replace with the MesmerQAschema folder.
2013-November-10 Struan Robertson
* AnalyticalRepresentation.cpp, System.cpp, CollisionOperator.cpp:
Altered analytical representation to fit all reaction data, add reaction
expression to Cantera output and write Cantera input to .log file.
* HinderedRotorQM1D.cpp: Altered output stream of potential data to
.test file.
2013-November-3 Chris Morley
* schemas/mesmerPlugins.xsd: add gaussian EnergyTransferModel
* src/EnergyTransferModel.h, src/plugins/ExponentialDown.cpp: remove
ReadParameters(). (Replaced by ParseData()).
* src/plugins/GaussianModel.cpp: Rewrite parsing to work with old and
new formats.
* examplesSchema/diamond/diamond-expDown.xml,
examplesSchema/diamond/diamond-gaussianModel.xml: made schema friendly.
2013-October 31 Robin Shannon
*src/System.cpp, System.h, CollisionOperator.cpp, CollisionOpperator.h:
Changes to the calculate function for the analytical representation. Also added code to get
Kp matrix from bartis widom analysis.
*src/Plugins/AnalyticalRepresentation.cpp:
Changes to recognise Bimolecular and Ireversible reactions correctly.
2013-October 31 Robin Shannon
*src/Plugins/DefinedTunnelingCoefficients.cpp: Refactoring and correcting.
* src/XMLPersist.cpp: Improve default handling for attributes. The
element name is now also matched. Allows the default units to be
depent on the context.
* defaults.xml: correct PTpair mis-spelling.
2013-October-26 Struan Robertson
* AnalyticalRepresentation.cpp: Altered analytical representation to
allow for different pressure units.
2013-October-26 Struan Robertson
* CollisionOperator.cpp, and all derived reaction classes: removed the
(temporary) method that got the reduced collision operator size.
* MicroRate.h and dreived classes: renamed microcanoical flux method to
make it clearer what it does.
2013-October-25 Struan Robertson
* CollisionOperator.cpp, and all derived sink reaction classes: Fix for
irreversible exchange reaction broken during refactoring.
2013-October-15 Struan Robertson
* CollisionOperator.cpp, MolecularComponent.h/.cpp and all derived reaction
classes: Final refactoring changes to make the code more transparent to
reservoir states.
2013-October-13 Struan Robertson
* AnalyticalRepresentation.cpp: Analytical representation output altered
to be consistent with Cantera format. Baselines added.
2013-October-12 Struan Robertson
* CollisionOperator.cpp, MolecularComponent.h/.cpp and all derived reaction
classes: More refactoring changes to make the code more transparent to
reservoir states.
2013-September-30 Robin Shannon
*SensitivityAnalysis.cpp, Rdouble.h: Changed SensitvityAnalysis to read
errors from Rdouble ranges. Rdouble.h changed to allow SensitivityAnalysis
read upper and lower values.
2013-September-28 Struan Robertson
* CollisionOperator.cpp, MolecularComponent.h/.cpp: Refactoring changes
to make the code more transparent to reservoir states. These changes
are likely to be the first in a series of changes.
2013-September-25 Struan Robertson
* sobol.h/.cpp: Move sobol array initialization to .cpp file in order to
improve compilation time.
2013-September 13 Chris Morley
* src/Reaction.h, src/Molecule.h,.src/plugin.h: remove obsolete Base.h
* src/MicroRate.h, src/plugins/MesmerILT.cpp: use as plugin example files
by adding add verbose comment.
* src/plugins/LandauZenerCrossingCoeff.cpp,src/plugins/WKBCrossingCoeff.cpp,
src/plugins/WKBTunnellingCoefficients.cpp, src/plugins/DefinedTunnelingCoefficients.cpp
src/Reaction.cpp, src/MolecularComponents.cpp, src/ParseForPlugin.h:
remove two call method of finding data in Reaction or in TS (possible
because plugins now have a pointer to a parent object).
2013-September 06 Chris Morley
Progress towards unifying the parsing of plugin data via ParseForPlugin()
which scans the XML for a plugin type, makes a new instance, reads its
data via the plugin's virtual ParseData() function, and inserts defaults.
Most plugins now work this way but DOS calculators are a little more
complicated and remain to be done.
src/ParseForPlugin.h: All plugins given a pointer to a parent which is
an instance of Molecule, Reaction or System, depending on the plugin type.
src/plugins/ExponentialDown.cpp: Read deltaEDown data in child elements
of <me:energyTransferModel> (as well as the old way in CML properties).
The complexity of this class makes it unsuitable as an annotated plugin
example file which needs to be transferred to another class.
Many XML files updated to a schema-friendly format which allows plugin
data to be validated by the schema. Old format files should still work,
but use the forms in MesmerQAschema and examplesSchema as models. We'll
get rid of the original files eventually.
CMLforMesmer.xsd,mesmer.xsd,mesmerPlugins.xsd: extended and modified but
still need work to make them more consistent.
2013-August-26 Robin Shannon
* System.cpp, System.h, AnalyticalRepresentation.cpp: Intial working check-in
of method to calculate coefficients for a chebyshev polynomial represenation
2013-August-25 Struan Robertson
* CollisionOperator.cpp, System.cpp, MesmerFlags.h/.cpp: Addition
of keyword me:ForceMacroDetailedBalance, which enforces macroscopic
detailed balance for non-conservative systems.
2013-August-21 Struan Robertson
* CollisionOperator.cpp: Fix for energy cut-off method based on
equilibrium population.
2013-August-18 Struan Robertson
* AnalyticalRepresentation.cpp, ipropyl_AR.xml: Update of parameter
reading method and example for Chebyshev representation.
2013-August-18 Struan Robertson
* AssociationReaction.cpp/.h, CollisionOperator.cpp/.h, System.cpp:
Re-working of method to use the equilibrium population to determine
energy cut-off.
* examples/benzene_oxidation_test.xml: Input file altered to test
above method.
2013-August-15 Chris Morley
* src/plugins/DefinedTunnelingCoefficients.cpp: modified for new plugin
parsing format
* examplesSchema/DefinedTunellingCoefficients,
examplesSchema/DefinedTunellingCoefficients/OH+methanol.xml: updated
* schemas/mesmer.xsd, schemas/mesmerPlugins.xsd: Add SensitivityAnalysis
DefinedTunnelingCoefficients, + minor tweaks.
* src/plugins/ExponentialDown.cpp: reversed a change by Struan which
prevented default being used. But what was the problem it was solving?
* src/Reaction.cpp: minor comment and text changes
* src/CollisionOperator.cpp(SetMaximumCellEnergy): replace some doubles by
unsigned ints to avoid compiler warnings.
2013-August-11 Struan Robertson
* System.cpp/*.h, SensitivityAnalysis.cpp: Sensitivity analysis plugin
updated to generated data using Sobol random vectors to perturb fitted
parameters.
2013-August-10 Struan Robertson
* Sobol.cpp/*.h, UnitTests.cpp: Addition of Sobol random number sequence.
2013-July-28 Struan Robertson
* CollisionOperator.cpp, System.cpp, AnalyticalRepresentation.cpp:
Addition of method to calculate rate coefficients in bulk as required
for analytical representation.
2013-July-27 Struan Robertson
* CollisionOperator.cpp, System.cpp: Bug fix for grain size/grain number
change with temperature (modified from Robin's original).
2013-July-24 Chris Morley
Support for new format of plugin data. Not all plugins done yet.
* schemas/mesmer.xsd,schemas/mesmerPlugins.xsd: updated.
* schemas/schemaNotes.txt: added.
* examplesSchema/*.xml: put into new format (where supported).
src/plugins/AnalyticalRepresentation.cpp,src/plugins/ExponentialDown.cpp,
src/plugins/fitting.cpp,src/plugins/LandauZenerCrossingCoeff.cpp,
src/plugins/Marquardt.cpp,src/plugins/WKBCrossingCoeff.cpp,
src/plugins/WKBTunnellingCoefficients.cpp: can parse new (and old) format.
* src/CollisionOperator.cpp,src/MolecularComponents.cpp,src/ParseForPlugin.h,
src/Reaction.cpp,src/System.cpp: Use new ParseForPlugin code for new format XML
MesmerQA/QA.bat: correct display of Mesmer version
2013-July-20 Struan Robertson
* AnalyticalRepresentation.cpp: Addition of basic class structure for the
analytical representation method.
* HinderedRotorQM1D.cpp, WKBTunnellingCoefficients.cpp: Bug fixes checked
in on behalf of Robin.
2013-July-20 Struan Robertson
* UnitTests.cpp/qd_test.h: QD unit tests added to MESMER unit
tests and unit test baseline updated.
2013-June-16 Struan Robertson
* PseudoIsomerizationReaction.h/.cpp: Prior fragmentation distribution
corrected for threshold energy and cell-off-set.
2013-June-11 Struan Robertson
* PseudoIsomerizationReaction.cpp: Prior distribution (dissociation
distribution) calculation method (changes checked in on behalf of Robin).
2013-May-27 Struan Robertson
* PseudoIsomerizationReaction.h/.cpp: Initial revision of pseudo-
Isomerization reaction class.
2013-May-11 Struan Robertson
* CollisionOperator.cpp, System.cpp, TMatrix.h: Matrix printing
generalized and applied to eigenvector matrix.
2013-May-11 Struan Robertson
* CollisionOperator.cpp: Fix for grain number problem (checked-in
on behalf of Robin).
* MesmerQA: Baseline update following the above fix.
* MesmerQA: .xml update following the application of schema.
2013-May-6 Struan Robertson
* UnitTests.cpp/.h: Linear algebra unit tests added.
2013-May-5 Struan Robertson
* MolecularComponents.cpp/.h: Hessian projection method
extended to project out transition state modes.
2013-May-4 Chris Morley
src/System.cpp: From a problem Mark was having: ensure XML
output is well-formed even when range variable names contain
unsuitable characters )( : or space, probably arising from a
molecule name (now deprecated of course).
2013-April-30 Chris Morley
Update to parse xsi:type me:MesmerILT and similar. Mods like
required units atribute for pre-exponential etc.
2013-April-30 Chris Morley
Add MesmerQAschema and examplsSchema directories for
new(schema-friendly) XML file format versions.
[Several source files] Make C++ parsing compatible with both old
and new XML file formats.
schemas/CMLforMesmer.xsd,mesmer.xsd,mesmerPlugins.xsd, defaults.xml:
Update
2013-April-27 Chris Morley
src/XMLPersist.cpp:fix for corrupted output XML file bug
introduced in bath gas mod.
2013-April-27 Struan Robertson
* SensitivityAnalysis.cpp: Altered to read covariance matrix.
2013-April-14 Struan Robertson
* System.cpp: Update of version to 3.0.
* MESMER manual.docx: Updated to include material relating to hessian.
2013-April-10 Struan Robertson
* MolecularComponents.cpp: Minor change to account for transition
state imaginary frequency.
2013-April-10 Struan Robertson
* MolecularComponents.cpp/.h: Re-orientation of Hessian an part of
vibrational mode analysis.
2013-April-08 Struan Robertson
* CollisionOperator.cpp: Fix for linux build break.
2013-April-08 Chris Morley
Use different bath gases in the same run
* src/plugins/ExponentialDown.cpp,
src/EnergyTransferModel.h,src/plugins/GaussianModel.cpp:
parse for deltaEDown for specified bath gases
* src/MolecularComponents.cpp,src/MolecularComponents.h,
src/MoleculeManager.h: keep a map of bathGasName/energyTransferModel
rather than just m_bathGas.
* src/System.cpp: do parsing of <me:bathGas> before reactions and
molecules
* src/MesmerEnv.h,src/unitsConversion.h: extra variable to transmit
current bath gas.
* src/Persistence.h,src/XMLPersist.cpp,src/XMLPersist.h: added a
parameter to XmlMoveToProperty() to make it easier to move to the
next sibling CML property
* src/CollisionOperator.cpp: error message
*src/Constants.h,src/MolecularComponents.cpp: units conversion for
hessians from Robin
2013-April-07 Struan Robertson
* CollisionOperator.cpp/.h, TMatrix.h: Replaced d2D types with generic
STL types or TMatrix types.
2013-March-31 Struan Robertson
* MolecularComponents.cpp/.h: Re-orientation of molecular system and
orthogonalization of projected modes.
2013-March-28 Struan Robertson
* MolecularComponents.cpp/.h, Molecule.cpp: Units added for Hessian
and frequencies updated following diagonlization of Hessian.
* examples/Butyl_H_to_Butane/Butyl_H_to_Butane.xml: Added units for
Hessian.
2013-March-27 Chris Morley
* src/MolecularComponents.cpp: transparently read hessian matrices
with upper or lower triangle or complete. (CML files from Gaussian
use upper triangle.)
* examples/Butyl_H_to_Butane/Butyl_H_to_Butane.xml,
src/MolecularComponents.cpp: in dictRref use me:hessian rather
than me:Hessian.
2013-March-26 Struan Robertson
* MolecularComponents.cpp/.h, HinderedRotorQM1D.cpp: Implementation
of Sharma, Raman and Green algorithm for the elimination of internal
rotational mode frequencies.
2013-March-19 Struan Robertson
* MolecularComponents.cpp/.h: Hessian rotational projection added.
2013-March-11 Struan Robertson
* MolecularComponents.cpp/.h: Utility methods added to gStructure class.
2013-March-07 Struan Robertson
* MolecularComponents.cpp/.h, HinderedRotorQM1D.cpp : Infrastructure to
project internal rotor modes from Hessian.
2013-March-03 Struan Robertson
* MolecularComponents.cpp/.h : Initial revision of method to analyse
a Hessain to obtain vibration frequencies.
2013-March-03 Struan Robertson
* Rdouble.h/.cpp, fitting.cpp, gridsearch.cpp, Marquardt.cpp : Added methods
to convert fitted parameters back to original units (based on code changes
suggested by Robin).
2013-February-27 Struan Robertson
* PriorDistribution.cpp, CollisionOperator.cpp: Minor bug fixes checked-in
on behalf of Robin.
2013-February-25 Struan Robertson
* TMatrix.h: Moved Matrix CML I/O methods from temporary class onto TMatrix.
2013-February-22 Chris Morley
* src/RWmatrix.cpp, src/RWMatrix.h: functions to read and write Hessian
matrices to CML. These files and the RWMatrix class are temporary until
a suitable home is found for the functions.
* examples/Butyl_H_to_Butane/Butyl_H_to_Butane.xml: make experimental
matrix entry more CML compliant.
* src/MolecularComponents.cpp: commented out code at line 218 to test
RWMatrix functions.
* src/plugins/fitting.cpp: output hessian to XML (not fully tested)
* src/System.cpp, src/System.h: make PersistPtr to current analysis element
available.
* src/main.cpp: use throwing std::logic_error to terminate after writing
XML output (for debugging).
* src/Persistence.h, src/XMLPersist.cpp, src/XMLPersist.h: correct
parameters of XmlWrite().
2013-February-18 Struan Robertson
* MolecularComponents.cpp: Minor refactoring.
* Butyl_H_to_Butane.xml: Initial revision - example to be used for eigenmode
projection project.
2013-February-10 Struan Robertson
* Acetyl_O2_association.xml: Baseline updated related to VS9/VS10 differences.
2013-February-10 Struan Robertson
* CollisionOperator.cpp: Further fix for mean energy output for the case
where population is zero.
2013-February-08 Struan Robertson
* CollisionOperator.cpp: Fix for mean energy output added.
2013-February-07 Struan Robertson
Changes entered on behalf of Robin Shannon.
* CollisionOperator.cpp: Fix to use specified initial distribution.
* MolecularComponents.cpp: Check added for zero torsional moment of inertia.
* unitsConversion.cpp: Atomic mass table updated.
2013-January-22 Chris Morley
* src/plugins/UnitTests.cpp: correct error which was prematurely
terminating anharmonic tests
* MesmerQA/UnitTests/baselines/Win32/mesmer.test: revert this baseline
which was subject to the above error. Still differences to be resolved.
src/DensityOfStates.h: some runtime documentation
2013-January-21 Struan Robertson
* MolecularComponents.cpp: Fix for DefinedStatesRotor, states now
read at creation.
2013-January-20 Chris Morley
* src/DensityOfStates.h, src/plugins/ClassicalRotor.cpp,
src/plugins/QMRotor.cpp, src/plugins/DefinedStatesRotor.cpp
Add includesRotations() virtual function to distinguish DOS methods
which include rotations.
Re-introduce ExtraDOSCMethod keyword and redo parsing. Simplifies setting
a default method and assurance of exactly one rotation method.
Add public RemoveDOSCalculator, AddDOSCalculator and GetDOSCalculator methods.
* src/MolecularComponents.h, src/MolecularComponents.cpp
* src/plugins/Morse.cpp: altered XML format for anharmonic vibrations.
Frequencies primarily in a property (as before) but used as key in
entries for anharmonic vibrations only under <me:MorseParameters> .
* src/plugins/UnitTests.cpp: use the existing Morse instance rather than
making a new one.
* MesmerQA/ThermodynamicTable/ThermodynamicTable.xml,
MesmerQA/UnitTests/UnitTests.xml, MesmerQA/i-propyl/ipropyl_test.xml:
ExtraDOSCMethod keyword reintroduced.
2013-January-13 Struan Robertson
* UnitTests.cpp: Fixed bug following the removal of ExtraDOSCMethod keyword.
2013-January-01 Struan Robertson
* MolecularComponents.cpp/.h: Fixed rotatonal states bug. The refactoring
of the density of states classes below removed the default behaviour of
adding a classical rotational states object to the density of states stack
if no such object is specified in the input.
2012-December-30 Struan Robertson
* PriorDistribution.cpp: Altered translation density of states to a
E^(1/2) dependence.
2012-December-30 Struan Robertson
* PriorDistribution.cpp: Alternative implementation of prior
distribution, based on FFT convolution, added.
2012-December-29 Struan Robertson
* PriorDistribution.cpp, Molecule.h/.cpp: Further refactoring of
prior distribution, cofragment now located and managed by the molecule
manager. This required backward navigation to the molecule manager
from a molecule to be added.
* Addition of pseudoisomerization class.
2012-December-29 Struan Robertson
* PriorDistribution.cpp: Refactoring.
2012-December-29 Struan Robertson
* PriorDistribution.cpp: Initial check-in of prior distribution, and
associated changes, on behalf of Robin Shannon.
* Updated ipropyl baseline.
2012-December-20 Chris Morley
* src/DensityOfStates.h,src/MolecularComponents.cpp,src/MolecularComponents.h,
src/plugin.h,src/plugins/BeyerSwinehart.cpp,src/plugins/ClassicalRotor.cpp,
src/plugins/DefinedStatesRotor.cpp,src/plugins/HinderedRotorCM1D.cpp,
src/plugins/HinderedRotorQM1D.cpp,src/plugins/Morse.cpp,src/plugins/QMRotor.cpp:
Complete unification of DOS calculators
* src/plugin.h: improve formatting of lists of plugins in error messages.
* src/System.cpp: reinstate reading of me:numberOfGrains, but optimization
of number of grains etc. remains to be done.
There are trivial rounding errors in the i-propyl QA test.
2012-December-16 Struan Robertson
* MolecularComponents.cpp/.h: Changes toward the removal of the division
of density of states calculators - all density of states calculator
instances now located in the same vector.
2012-December-2 Struan Robertson
* Miscellaneous changes following to fix Linux 64 bit compiler warnings
and to update Linux 64 baselines.
2012-December-7 Chris Morley
* src/CollisionOperator.cpp, src/CollisionOperator.h,src/System.cpp: XML
output for "the average of the grain energy in each isomer" already output to
ctest.
XML output is split a bit unhappily between CollisionOperator and
System and if we keep adding additional outputs there may need to be a
rationalisation.
Enabled by <me:printGrainedSpeciesProfile/>. These tags need to be reviewed
for consistency.
The ctest code is not right - I will pass on to Dave.
* popDiag.xsl: graph of above.
* qd/include/qd/dd_real.h, qd/include/qd/qd_real.h: minor mods to reduce
compilation warnings
2012-December-2 Struan Robertson
* Main.cpp and Doc.: License updated to GPLv3.
* SensitivityAnalysis.cpp: Template added.
2012-November-28 Chris Morley
src/plugin.h: Add TopPlugin as parent of plugins. Provides:
- case and whitespace insensitivity of plugin names in the input file;
- listing of plugins from the command line: mesmer -t or mesmer -T ;
The latter displays Descriptions of the type or the plugin if present
(currently only in EnergyTransferModel and ExponentialDown).
- error message with a list of the possibilities if an unrecognized
plugin name supplied.
- registration of all plugins, rather than being done in type classes;
* Changes to housekeeping of all plugin classes
* src/plugins/simplecalc.cpp, src/System.cpp, src/System.h: take advantage of
new error messages (more to be done).
* MesmerQA/pentyl/pentyl_isomerization_test.xml: Use me:derivedFrom attribute
to provide a test of it.
* src/MolecularComponents.cpp, MesmerQA/UnitTests/UnitTests.xml: re-introduce
"thermodynamic" energy convention. When used with Hf298 input prevents an
unnecessary conversion to the "computational" convention and reduces error
messages in UnitTests.
2012-November-25 Struan Robertson
* Rdouble.cpp/.h: Added operator>> to allow direct reading into
Rdouble variable.
2012-November-24 Struan Robertson
* MolecularComponent.cpp/.h: Added energy transfer diagnostics.
* GaussianModel.cpp: Modified the energy transfer function in
order to improve normalization.
2012-November-18 Chris Morley
* mesmer1.xsl: Make "Comparison with Experimental Data" in
Firefox output collapsable.
2012-November-14 Struan Robertson
* MolecularComponent.cpp/.h, and related files: Removal of
cemetery state code.
2012-November-10 Struan Robertson
* MESMER manual.docx: Updated manual with more detail on ZPE
calculation.
2012-October-24 Struan Robertson
* UnitTest.cpp/.xml, Morse.cpp: Minor corrections to density of
state methods to use nint() (nearest integer) method.
2012-October-21 Struan Robertson
* UnitTest.cpp/.xml: Further addition of MEIC tests.
2012-October-21 Struan Robertson
* UnitTest.cpp/.xml: Addition of more MEIC tests.
2012-July-29 Struan Robertson
* ThermodynamicTable.cpp: Altered so that partition function data
can be printed.
* Morse.cpp: Implementation of density of states and canonical
partition function.
2012-July-24 Chris Morley
* popDiag.xsl TS energies in Grain Population diagrams now as
full length dotted lines.
2012-July-21 Struan Robertson
* MoleculeManager.cpp/.h: Minor change to add molecule method.
2012-July-21 Struan Robertson
* System.cpp/.h, UnitTests.cpp: Add new MEIC unit test for sum of states.
2012-July-21 Struan Robertson
* System.cpp/.h, ThermodynamicTable.cpp: Altered so that thermodynamic
table calculations do not need to specify a reaction sequence.
2012-July-16 Struan Robertson
* Morse.cpp: Initial template for Morse density of states class.
2012-July-13 Chris Morley
* src/error.cpp: flush log file on the way through so there is
something to look at after a crash
* src/CollisionOperator.cpp: Change "Cell number" to
"Number of Cells" and supressed multiple messages.
* src/MesmerMath.cpp: add "once" to supress multiple error messages.
Moved Error Context() (but may not be significant.
* src/MolecularComponents.cpp, src/MolecularComponents.h: remove log
messages about atoms not having vibrational frequencies and rot consts.
* src/System.cpp: Don't output elaspsed time unless > 0.
2012-June-17 Chris Morley
* src/oberror.cpp, src/oberror.h: An additional parameter on
ThrowError() causes error messages to be output only once.
Manipulator 'once' does this for output to cerr etc.
The files are renamed to error.h and error.cpp because they are
considerably different from the OpenBabel versions.
* src/plugins/ExponentialDown.cpp: Change the error "Delta E down is
smaller than grain size" to use this facility.
* src/MolecularComponents.cpp: minor tidying on an error message to
make it more consistent with current error handling.
2012-June-16 Chris Morley
* src/CollisionOperator.cpp: Add unnormalised log output for grain
populations.
* mesmer1.xsl: Add another text section in Firefox output for grain
populations, to make cutting and pasting for speadsheets possible.
* popDiag.xsl: Add unnormalised log plots for grain populations. Include
energies of transition states on plot. Maybe duplicated code should be
tidied.
2012-June-10 Struan Robertson
* CollisionOperator.cpp/.h: Fixed bug relating to basis set method.
* ExponentialDown.cpp: Removed exit(1) statement as this prevented error
statements from being written.
2012-June-10 Chris Morley
* src/CollisionOperator.cpp, MesmerQA/pentyl/pentyl_isomerization_test.xml:
change XML syntax to request grain populations, which are now output
at the same times for each species. This should be good enough and avoids
complicating the XSLT display. Data structure in m_GrainProfileAtTimeData
is unchanged.
* popDiag.xsl: another try to get grain population diagram right.
* src/System.cpp: use sources other than %MESMER_AUTHOR% for author in
metadata.
2012-June-10 Struan Robertson
* SimpleILT.cpp: Fixed bug relating to reading of activation energy.
* Reaction.h: Minor refactoring.
* Revised header file include strategy.
2012-June-09 Struan Robertson
* DefinedSumOfStates.cpp: Splines added to calculate reaction flux.
2012-June-08 Chris Morley
* src/plugins/gridsearch.cpp: set all range variable values to their
lower bound at the start. Allows the value attribute to be freely set
and single or range runs to chosen by <me:calcMethod> alone.
* src/plugins/MesmerILT.cpp, src/plugins/SimpleILT.cpp: correct bug
which caused energy conversion during setup of a range variable to
be wrong when the value was 0.
* src/CollisionOperator.cpp, src/CollisionOperator.h, src/System.cpp:
modify writing of grain population XML output so that include T and
conc are included.
* src/System.cpp: modify range variable names in the XML output because
':' is incompatible with XML.
* mesmer1.xsl, popDiag.xsl: grain population diagram improved but
not yet ok when there are multiple conditions.
2012-June-05 Chris Morley
* src/CollisionOperator.cpp: make grain population output normalised
- for a given species at a a given time output sum to 1.0. Do not
output very small populations. Used fixed format (XSLT flakey with
scientific format.)
* src/Persistence.h,src/XMLPersist.h,src/XMLPersist.cpp: added
extra optional parameter to XmlWriteValueElement() to force
fixed rather than scientific format.
* MesmerQA/pentyl/pentyl_isomerization_test.xml: added request for
grain population output. (Doesn't affect QA.)
* popDiag.xsl: Firefox output now with grain population diagrams.
But not satisfactory as yet - different times are on separate graphs,
rather than multiple lines for the same species being on the same
graph. Multiple sets of conditions and range parameters untested.
The XSLT is proving difficult - still trying to improve this.
2012-June-03 Struan Robertson
* Acetyl O2 association\baselines\mesmer.test: Rolling back David's
change to the release VS 10 results as agreed for the release MESMER
1.0. Since version 706 there has been a marginal improvement in
agreement between VS 10 release and debug results as indicated by the
two largest eigenvalues:
Version 706: -1.563027e-003
-1.220829e-006
VS 10 debug (= VS 9 release or debug = Version 731): -1.569795e-003
-3.155523e-006
VS 10 release: -1.568043e-003
-2.798432e-007
Further investigation required.
2012-May-28 Struan Robertson
* MesmerMaths.cpp: Convolution method refactored and additional
checks added.
2012-May-20 Struan Robertson
* BeyerSwinehart.cpp, EckartCoefficients.cpp: Bug fixes to address
problems encountered for very shallow wells.
2012-May-19 Struan Robertson
* Spline.cpp/.h, UnitTest.cpp: Added test for spline class and fixed
bugs in spline class.
2012-May-14 Struan Robertson
* Spline.cpp/.h: Initial revision of Spline class added.
2012-May-04 Struan Robertson
* DefinedSumOfStates.cpp: Code added to parse data in XML structures.
* FittingUtils.cpp/.h: Redundant code removed.
2012-April-22 Struan Robertson
* Documentation changes following update for derived parameters.
2012-April-11 Struan Robertson
* ExponentialDown.cpp, MesmerILT.cpp: Fix for constrained value string
mapping bug.
* Add Linux64 baseline for UnitTest.xml smoke test.
2012-April-09 Struan Robertson
* UnitTests.cpp, MesmerMaths.h/.cpp: Added unit test for incomplete
gamma function (chi2 signifcance test) and corrected gamma function