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[WIP] Revision to Thermo target#61

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Commits on Apr 1, 2014

• Begin new data table parsing

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• Merge branch 'master' of github.com:leeping/forcebalance into thermo2

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Commits on Apr 4, 2014

• Implemented tri-format parser (broke Thermo)

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Commits on Apr 6, 2014

• Merge branch 'master' of github.com:leeping/forcebalance into thermo2

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• Fix up exception handling

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Commits on Apr 7, 2014

• Added file referencing in parser and build DataFrame

  

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• Added unit test for data file parsing (lipid)

  

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• Clean up

  

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• Create list of Ensembles and table of Observable objects

  

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• Map observable names to required simulations

  

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Commits on Apr 8, 2014

• Start modifying framework to require user input simulations.

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• Observable and simulation setup should be working correctly now

  

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• Clean up

  

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Commits on Apr 16, 2014

• Target now knows which simulations to launch. Next task: Pass in auxiliary files (.top, .mdp) and run the simulation.

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• Merge branch 'thermo2' of github.com:leeping/forcebalance into thermo2

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Commits on Apr 20, 2014

• A few changes for energy/force matching and Q-Chem output parsing (cherry pick over to main).

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Commits on Apr 21, 2014

• Improvements for energy/force and frequency matching

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• Merge branch 'master' of github.com:leeping/forcebalance into thermo2

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Commits on Apr 22, 2014

• Work in progress

  

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• Merge branch 'thermo2' of github.com:leeping/forcebalance into thermo2

  

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• Reduce the amount of printout

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• Work in progress

  

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Commits on Apr 23, 2014

• Added simulation.py which contains simulation class (container for simulation settings)

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• md_one.py creates Engine object.

  

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• md_one.py runs molecular dynamics!

  

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• Work on extracting timeseries

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• Clean up

  

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• Clean up

  

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Commits on Apr 24, 2014

• Density observable can calculate the density and gradient

  

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Commits on Apr 29, 2014

• Fix occasional failure in topology building

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Commits on May 8, 2014

• Merge branch 'thermo2' of github.com:leeping/forcebalance into thermo2

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