- relax_liquid_redo calculation added that simplifies liquid relaxations by removing the mean squared displacement and evaluating the radial distribution function from generated dump files.
- diffusion_liquid calculation added that estimates the diffusion of a liquid using both mean squared displacement and the velocity auto correlation function.
- viscosity_driving calculation added that estimates the viscosity of a liquid directly by applying a driving force. For most purposes, it is recommended to use the Green-Kubo variation instead as this method is strongly sensitive to the size of the driving force used.
- viscosity_green_kubo calculation added that estimates the viscosity of a liquid using the Green-Kubo method.
- melting_temperature calculation added that estimates the melting temperature using a two-phase equilibrium configuration. Polyhedral template matching is used to estimate the ratio of solid/liquid to verify both phases exist in equilibrium.
- dislocation_dipole calculation added that generates and relaxes small cell dislocation dipole configurations. This is useful for computationally expensive potentials and compact (non-splitting) dislocation cores.
- grain_boundary_grip calculation added that uses the GRIP (grand canonical
- interface predictor) algorithm for exploring grain boundary configurations.
- diatom_scan calculation bug fix for when symbols are not str.
- crystal_space_group calculation updated for compatibility with newer versions of spglib.
- dislocation_monopole calculation updated to remove unnecessary dump files generated during the relaxation from being created. Also, methods were added allowing for the dump files and png plots hosted on potentials.nist.gov for finished calculations to be downloaded. Bug fix for when the calculation function is called and annealsteps is not given a value.
- dislocation_periodic_array calculation updated to remove unnecessary dump files generated during the relaxation from being created. Bug fix for when the calculation function is called and annealsteps is not given a value.
- energy_check calculation is updated to include the system pressure in the results and to optionally save a dump file with atomic forces.
- relax_static calculation's master_prepare settings changed to reduce the total number of minimization cycles and to not throw an error if the max number of cycles is reached without the tolerance being achieved.
- phonon calculation has been updated so that it saves the band structure, density of states and thermo data are now saved in separate files rather than being included in the calculation's record. This eliminates the memory issues that were associated with loading multiple phonon results.
- stacking_fault_map_2D calculation's minimum energy path is now better integrated in the calculation's class and as a method in the analysis submodule.
- grain_boundary_static method added that replaces the older grain_boundary_search. The method has been reworked for consistency with the new grain_boundary_grip calculation.
- MeltCommander script added to bin that manages melting_temperature calculation runs by rerunning them with different input temperatures until a set number of successful/unsuccessful runs finish.
- StackingFaultCommander script added to bin that oversees running the MEP calculations on the stacking_fault_map_2D results.
- XSL and XSD files added to many of the iprPy calculations. This supports uploading the results to potentials.nist.gov and rendering the results as HTML.
- AtommanSystemLoad calculation subset was updated to include extra terms family_url and parent_key. The URL term allows for the public version of calculation records on potentials.nist.gov to point to the associated family structure pages. The parent_key term standardizes how calculations know which previous record they are based on.
- LammpsPotential calculation subset was updated to include the extra terms potential_url and potential_LAMMPS_url. These terms allow for the public version of calculation records on potential.nist.gov to point to the associated potential pages.
- The base Calculation class now makes the "script" value optional. This value will be removed in future updates after it has been purged from all calculation records.
- prepare now returns a list of the prepared calculation names. This can be used with a runner to target only the newest prepared calculations in the run_directory. The list is also passed to fix_lammps_versions so that the fixes are only applied to the newest calculations.
- prepare also can now take a tar_dict parameter allowing for pre-loaded tar contents to be passed in, and for tar contents to be retained in memory rather than accessing them from the database every time they are needed.
- Bug fix in the buildcombos functions associated with preparing KIM potentials.
- runner no longer generates log files by default. A "free" parameter has been added that when set to True runs through the prepared calculations without any database interactions. Finished calculations can later be uploaded with finish_calculations. Bug fix to ensure calculations are built correctly.
- CijValue, InputValue and ResultValue subclasses of yabadaba.Value have been added. CijValue allows for the standard handling of elastic constants objects in records. The other two Value objects are added to support future reworking of the Calculation classes. If done correctly, these could be used to greatly reduce the amount of code in the Calculation class definitions improving maintenance of existing calculations and speeding up implementing new calculations.
- Fixes to QuickCheck for support of troublesome potentials. A quick_check option was also added to the iprPy command line.
- EmperorPrepare and various other scripts added/updated in the bin folder. multi_runner_slurm.py for submitting multiple SLURM jobs simultaneously. clean_bad_guys.py for removing prepared calculations and assigning them error messages. reposition_orphans.py to separate prepared calculations in one run_directory into other run_directories based on their calculation styles. add_urls_and_backup.py fills in the URL fields of calculation records with the correct potentials.nist.gov sites, and copies the records to multiple locations as needed. sleep_until_done.py tells a job to sleep until a run_directory is empty. targeted_runner.py includes an example script where runners can be started that target calculations for a given potential rather than the default random selection.
- Alternate Emperor scripts added that combine prepare with runner job submission allowing for automated workflows of certain calculations.
- Automatic importing of calculations now safely checks if the calculation is incomplete.
- Calculation.run() now tries to save results.json up to 5 times.
- run_calculation() updated to infer a calculation's name from its parent directory if needed. This helps ensure that the command line "iprPy run" calls assign the correct name/key rather than some random value.
- Many improvements to the analysis submodule as new calculation results are being prepared for release on the NIST Repository website.
- The diatom and E_vs_r_scan website plots are now generated using ploty instead of Bokeh. The phonon plot generation is updated for the changes to the phonon calculation and to reduce the file size.
- Minor doc updates - still need a thorough revisit.
- elastic_constants_dynamic calculation completely reworked to use the deformation-fluctuation hybrid method which converges better than the old deformation-only way.
- point_defect_mobility calculation added that evaluates the point defect mobility energy barrier associated with point defects jumping from one stable position to a nearby position using nudged-elastic band (NEB) calculations.
- grain_boundary_static calculation added that explores and relaxes a grain boundary configuration. Calculation still in development and will likely result in the other grain boundary calculations being removed.
- relax_static now has a raise_at_maxcycles that can be set to False allowing calculations that reach maxcycles to finish successfully rather than raising an error.
- relax_dynamic removed computing the stress/atom as it was unused and doesn't work with some of the newer ML potentials. The master_prepare settings now have separate at_temp and at_temp_50K branches reflecting that the higher temperatures are incrementally prepared from the lower temperature results.
- The free_energy and free_energy_liquid calculations' master_prepare settings have been added.
- Base Calculation updated so all calculations now have a URL field, clean(), clean_files() methods, and a calc_output_files list of files generated by the calculation. The URL field provides a means of assigning a persistent identifier (PID) to a calculation's record once uploaded to a CDCS database. The clean_files() method deletes all files listed in calc_output_files allowing for the work space where a calculation was performed to be cleaned up. The clean() method resets the calculation's status to 'not calculated', clears any error message, and deletes the calc_files if requested.
- The clean_files operation as described above has also been added as a command line option.
- Fix across multiple calculations to dump at maxiter rather than maxeval so that dump files are created at the end of unconverged minimizations rather than throwing errors.
- QuickCheck class added that provides a simple means of running many of the cheaper iprPy calculation in succession and collects the results in a clear manner. This is primarily designed to support potential development by allowing a set of target properties to be specified and quickly evaluated as an initial screening step of potential fits.
- Base IprPyDatabase updated with a finish_bad_calculations() method that finishes calculations in a run directory by setting their status to "error", and uploading both the record and calculation tar to the database. This is largely used to clean up calculations that fail to finish in a reasonable amount of time.
- The prepare and master_prepare methods are updated for faster and more efficient operations by reducing the database access overhead.
- runner has been made slightly smarter when selecting a calculation to bid on.
- A BaseEmperorPrepare class has been added that adds an object-oriented means of defining different calculation pools for a given machine. This further abstracts from master_prepare and gets one step closer to true automated calculation preparation.
- Updates for newer versions of importlib.resources.
- Updates form newer versions of Bokeh for iprPy.analysis.PropertyProcessor.
- Bug fix related to interpreting lammps_command values with the LammpsCommands subset.
- relax_liquid now has the option to restart and continue incomplete simulations.
- All records now have a database parameter giving them a default database to pull more content from, if needed. This makes it possible to add methods that retrieve information if it is not directly stored in the records themselves.
- iprPy retrieve command line updated to make database specification optional and allow both the remote and local databases to be changed.
- More potentials now included in the old_pots list.
- phonon calculation: bug fixed, Notebook updated, and analysis methods added.
- relax_liquid master_prepare options added and updated to reflect how the IPR workflow is being performed.
- raise_error option added to calculation runs to raise any calculation error rather than save the error message to the results.json file.
- Records updated to reflect the changes to queries in yabadaba 0.2.0.
- free_energy calculation method added that evaluates the Gibbs free energy of a solid structure through thermodynamic integration from a Einstein solid.
- phonon calculation fixed and now properly performs QHA. Default parameter values updated to give better results.
- relax_dynamic default parameter values for at_temp master prepare changed.
- Analysis tools for building PropertyProcessor records added to iprPy from previously private code.
- The StackingFaultMap2D calculation/record class now reads in and interprets results from the JSON/XML files.
- XSL transformations added for some calculations.
- Bug fix for crystal_space_group calculation's pandasfilter method.
- Bug fix for E_vs_r_scan calculation's cdcsquery method.
- Fix in diatom_scan calculation for potentials that don't like multiple atypes.
- Bug fix with running surface_energy_static and point_defect_static calculations, where "E_coh" is now properly updated to "E_pot".