ToDo
MD: periodic writing of restarts containing velocities, to allow real restart
MD: reading velocities
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
Web
- License
- Description of modules, their keywords and output files
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
Extensions
Drivers
- L-BFGS ???
- Langevin dynamics
- Internal coordinates
- implement constraints
- preselection of primitive coordinates (like demon?)
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
Tools
- geometry_scan
- cartesian_translate
- cartesian rotate
- geometry
- standard orientation
- set orientation (origin, vector, plane) - to be used further in scans
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
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.
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