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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]
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