0.7.0

Version 0.7 makes significant changes to some of Dissolve’s workflows (in particular the interactions between the correlation modules which has been simplified), adds calculation of x-ray weighted structure factors and the capability to include those data within an EPSR refinement, improves the layout and usability of module controls and data within the GUI, and contains a myriad other bugfixes and improvements at the algorithm level.

Some information on converting files from 0.6.X to use in 0.7.0 can be found at https://forum.projectdissolve.com/t/moving-simulations-from-0-6-to-0-7-0/40.

Correlation Modules

Previously, simulations typically used an RDF module followed by many NeutronSQ modules of which the first in the layer took the RDF data and Fourier-transformed it into the S(Q)/F(Q) for use by all subsequent NeutronSQ modules in the layer. This approach, although efficient, had significant drawbacks, and was not transparent to the user. In addition, different configurations than those specified in the RDF module could be targeted in the NeutronSQ modules, leading to further confusion, and potential nonsense results.

As of version 0.7, an SQ module must be used to perform the Fourier transform of RDF data. The NeutronSQ (and now XRaySQ) modules then simply weight this data. Extraneous keyword options have been removed from NeutronSQ, and neither it nor XRaySQ target any configurations. Instead, they reference the SQ module containing the structure factors to apply weighting to. In a similar spirit, the SQ module refers only to the source RDF module. As such, existing input files will need to be modified in order to include the necessary SQ module in relevant workflows.

Restart File Compatibility

Restart files from previous version are highly likely to be incompatible with version 0.7, since changes to the naming and formatting of core class I/O has changed.

Summary of Major Changes

• Added XRaySQ module.
• Extend EPSRModule to handle x-ray datasets.
• Allow averaging of structure factors.
• Enforce more consistent relationships between correlation-type modules (i.e. RDF, SQ, NeutronSQ, and XRaySQ).
• Display module controls and output within the layer, rather than allowing it to be open in a separate tab.
• New forcefields: PCL2019 (ionic liquids), Kulmala2010 (aqueous H2SO4).
• Conversion of many base classes to use STL algorithms and template classes.

0.6.1

• New forcefields added (OPLS-AA alkanes, alkenes, alcohols, diols, and triols)
• Improved Add Forcefield Terms wizard, including assignment of terms to atom selections

Updating to 0.6.X

Input File Compatibility

Some small changes in the input file have been made and will cause errors on load. To fix these:

1. In the PairPotentials block, the Parameters keyword now takes the element associated to the atom type as the second argument, followed by the atomic charge and short range form/parameters. To maintain compatibility, these elements must be added in by hand.

Export Module(s)

The existing ExportModule has been split into separate ExportCoordinates, ExportPairPotentials, and ExportTrajectory modules for greater control. So, change any usages as follows:

ExportModule
  WriteCoordinates  xyz  saved/config.xyz
  EndWriteCoordinates
EndExportModule

... should now be ...

ExportCoordinatesModule
  Format  xyz  saved/config.xyz
  EndFormat
EndExportCoordinatesModule

0.6.0

• New forcefields added (OPLS-AA alkanes, alkenes, alcohols, diols, and triols)
• Improved Add Forcefield Terms wizard, including assignment of terms to atom selections

Updating to 0.6.X

Input File Compatibility

Some small changes in the input file have been made and will cause errors on load. To fix these:

1. In the PairPotentials block, the Parameters keyword now takes the element associated to the atom type as the second argument, followed by the atomic charge and short range form/parameters. To maintain compatibility, these elements must be added in by hand.

Export Module(s)

The existing ExportModule has been split into separate ExportCoordinates, ExportPairPotentials, and ExportTrajectory modules for greater control. So, change any usages as follows:

ExportModule
  WriteCoordinates  xyz  saved/config.xyz
  EndWriteCoordinates
EndExportModule

... should now be ...

ExportCoordinatesModule
  Format  xyz  saved/config.xyz
  EndFormat
EndExportCoordinatesModule