Log file for hzdplugins

v0.0.41: 2021.03.19
- Add getGCN in info.py, getGCN can help us calculate the generalized coordination number of certain atom
- Modify the getStructureAnalysis and checkDistance, because in previous version, it cannot get all the possible atoms, but now it works fine!
v0.0.40: 2020.12.28
- Add setSpinStructure function in build.py
- Change the input parameter for getStructure and getStructureAnalysis to structure, not uuid.
- Add atomQuery function in build.py in order to query the atoms that I want to manipulate further.
v0.0.39: 2020.12.19
- remove all the results parameter in the submit.py, and add group parameter to make sure that we use the group functionality in Aiida, not something we create ourselves. Since the results parameter is no longer needed, we also need to remove the saveResults, readResults, showResults, getUnDoneTasks, getUnFinishedTasks, getUnConvergedTasks, assignValue, pkToUuidConverter from info.py to deprecated.py
- add inputgenerator.py in hzdplugins.aiidaplugins module in order to help me generate input data for the workchains.
  
  For the outputdict(), do we need to specify which parameter we need to exclude? (Use a dictionay to store the parameter list) –> For the future.
v0.0.38: 2020.12.12
- add projwfcOriginalSubmit, phOriginalSubmit in submit.py
- add getPdos in info.py to get the pdos for certain atom
- add getDos in info.py
- Since rotating the adsorbate by algorithm is very time-consuming and not efficient, so I just create the geometric structure of usual adsorbates in the hzdplugins.aiidaplugins.adsorbates folder. All formats are mol, which is very easy to be read by ase.
v0.0.34-37: 2020.12.12
- add some new functionalities in info.py which can show the charge & magnetic moments, and also the total forces for each atomic step. Write get_TotalForces and get_ChargeAndMagneticMoments
- add the info.py:getStructure function which can help visualize the struture.
- correct the info.py:checkDistance function
- modify the io.py to deal with uuid rather than pk.
- add math.py in hzdplugins/structure to store some mathematical functions
- correct functions in hzdplugins/aiidaplugins/submit.py
- add newStructure function in build.py to deal with the system which we need to specify different chemical states or spin states. Very useful for complex cases.
v0.0.33: 2020.12.05
- give some options for the plotting in build.py adsorptionSites function.
v0.0.32: 2020.12.05
- delete print in build.py, fixed.
v0.0.31: 2020.12.05
- Mising deepcopy in build.py, fixed.
v0.0.30: 2020.12.05
- Missing Dict in build.py, fixed.
v0.0.29: 2020.12.05
- Add a new module structure, which can help me create bulk structures and slab surfaces more easily.
- Make all the functions in structure module and submit.py in aiida’s standard, which means all the input variables are from aiida.orm types and all the functions are decorated by calcfunction in order to preserve the provenance.
- Add a powerful function in structure.py called adsorptionSites, in this function, if we set visualize=False, then it only gives us the position of the adsorption sites; but if visualize=True, then we will get a nice picture that shows all possible adsorption sites, and their ids, so we can visualize it and make plans for later calculations.
v0.0.26-28: 2020.12.04
- Assign uuid instead of pk for all the nodes, because uuid is unique, but pk is not, so this may cause some difficulties in the implementation. Also add a converter from pk based results dictionary to uuid based results dictionary.
- Correct a few mistakes
v0.0.25: 2020.12.04
- modified the constants file because I transfer the aiida from ubuntu to mac, so all the computer names have changed. e.g. from rwth-claix to rwth-claix-mac.
v0.0.24: 2020.12.01
- modified the assignValue method in info.py, now it can process both ‘pw.x’ and ‘projwfc’ calculations.
v0.0.23: 2020.11.30
- Correct constants.py
v0.0.22: 2020.11.30
- Remember that all the pk have to be change to str, otherwise it will look ugly (e.g. 211.0 not 211)
- change assignValue function in info.py: Now the killed process can also be identified.
v0.0.21: 2020.11.30
- Add son_calc to the constants in order to connect the “son” with the “father” CalcNode, because now not only we can search back, we can also search forward at the same time.
v0.0.20: 2020.11.30
- It turns out, the error is in constant.py, where max_wallclock_seconds is mistaken to max_walllock_seconds …
v0.0.19: 2020.11.30
- add assignment for restart_builder.metadata.options when cluster_options is empty.
v0.0.18: 2020.11.30
- change assignValue in info.py
v0.0.17: 2020.11.29
- add saveResults, readResults in info.py for save and read current results via json file.
v0.0.15: 2020.11.29
- change computer in qePwContinueSubmit in submit.py
v0.0.14: 2020.11.29
- change results_tmp[str(calc.pk)]['system'] = node.label in qePwContinueSubmit in submit.py
v0.0.13: 2020.11.29
- resolve a mistake that Code is not imported.
v0.0.12: 2020.11.29
- resubmit the package, because some mistakes in qePwOriginalSubmit haven’t been resolved, but now they are removed.
v0.0.11: 2020.11.29
- I’ve changed the keys in results, now it has the following keys: [‘system’, ‘uuid’, ‘comp_type’, ‘cluster’, ‘xc functional’, ‘exit_status’, ‘is_finished’, ‘is_finished_ok’, ‘E/eV’, ‘remove_remote_folder’, ‘previous_calc’]
- Add functions unDoneTasks, unFinishedTasks, unConvergedTasks, which can be used in selecting the tasks that still needs attention.
- put all the important information in constants.py
- change the qePwOriginalSubmit and qePwContinueSubmit with the usage of constants.py, now the input becomes simpler.
v0.0.5: 2020.11.28
- I’ve learn that if you want to make a python module, then you need to add __init__.py file in the folder.
v0.0.4: 2020.11.28
- change the structure of the folder
v0.0.3: 2020.11.28
- add qePwOriginalSubmit and qePwContinueSubmit methods.