ToDo
Difference between revisions from 2010/01/14 14:14 and 2010/01/14 13:51.MD: periodic writing of restarts containing velocities, to allow real restart
MD: reading velocities
DFTB: kontrola neznamych atomu
!General
* Online GIT repository
* New domain for website
* Build versioning on web, git branches
* Integrate the standalone installer to installcuby
* Put tests online
* Go through all interfaces, check possible combinations of supported/unsuppported functionality
* Build a mechanism to not to include 'work in progress' in the public build
* Unified results printing - now Result in calulation.rb and JobResult in job_result.rb
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!Web
* License
* Description of modules, their keywords and output files
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!Interfaces
*deMon
**NBO charges (not in maual)
*Gaussian
**Point charges
**Atomic charges
**Frequencies
*MOLCAS
*Molpro
** Add to cuby (patch on lithium)
** MP2.5
*Extrapolate
*AmberTools/NAB
** Check difference from AMBER results
** Energy decomposition
** Frequencies
** User specified MD setup
*WaterBall
** Add electrostatic term
** Add the angular correction
*QMMM
**Microiterations as a part of the energy/gradient calculation
**Advanced charge handling - removal near link atoms
**Advanced charge handling - select only some by distance
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!Extensions
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!Drivers
*L-BFGS ???
*Langevin dynamics
* Internal coordinates
** implement constraints
** preselection of primitive coordinates (like demon?)
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!Modules and protocols
*cuby_freq
** Heat capacities
** Fix projector for linear molecules
** temperature, pressure and symmetry number in the input
** thermodynamic analysis as a standalone tool? Write frequencies in reusable yaml format along with geometry?
** Rewrite Thermodynamics as a class (initialize with geometry and parameters, then use)
*cuby_optimize
**Save restart info from time to time (geometry and hessian)
**Partial optimizer (for big systems)
*cuby_neb
** Convert to Protocol?
** ? Internal coordinates
** Freezing
* Atomization
** Works only for main group elements, for others, table of atomic multiplicities would be needed
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!Tools
*geometry_scan
** cartesian_translate
** cartesian rotate
*geometry
** standard orientation
** set orientation (origin, vector, plane) - to be used further in scans
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!Tests
* Tests for all interfaces
* Tests for all executables
* Tests for all tools
* Automated gradient test - numerical vs analytical
* Automated hessian test - numerical vs analytical
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!Code
* Rework LOG output - no puts in code
* Remote submit
* Reusable YAML output (like freq)
* Runtime update
** flag stored in keywords.yaml
** Method settings.update(cycle) called by driver
* New class Energy, to contain energy and its components, derived from Float. This will be used in Results and JobResults.
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!Calculation
* Dipole moment
* prepare_info:
** Other interfaces (now amber, turbomole, dftb)
** ? delete calc. dir and prepare it again if info does not match (according to config)
* Interface has information on separate run of E, grad, freq etc
* Both gradients and hessian can be requested to be numerical
!Local pages:
* Cuby on clusters: [Clusters]