Outputs - JDFTx IO Module

[benrich37]

Summary

Major changes:

-feature 0: hierarchy of class objects used to represent the data contained within a JDFTx out file. Hierarchy here is used to represent where each class object is stored - none of these classes inherit the class below it. Classes stored within a list in its parent are indicated by "[i]" (ie below where JDFTXOutfile.slices is a list of JDFTXOutfileSlice). Descriptions of each class are given below the tree.

                             JDFTXOutputs
                                   |
                             JDFTXOutputs.outfile
                                   |
                             JDFTXOutfile
                                   |
                         JDFTXOutfile.slices[i]
                                   |
                            JDFTXOutfileSlice
                          /                   \
  JDFTXOutfileSlice.jstrucs              JDFTXOutfileSlice.jsettings_(fluid, electronic, lattice, or ionic)
              |                                                          |
       JOutStructures                                               JMinSettings 
              |
       JOutStructures.slices[i]
              |
       JOutStructure(Structure)
              |
       JOutStructure.elecmindata
              |
          JElSteps
              |
          JElSteps.slices[i]
              |
          JElStep

• feature 1: outputs.py module containing JDFTXOutfile class to give robust pythonic representation of to a JDFTx "out" file. This class is initialized from the path to a JDFTx "out" file by the user. The initialization of a JDFTXOutfile will initialize the following JDFTx IO classes by
• feature 2: jdftxoutfileslice.py module containing JDFTXOutfileSlice class representing a "slice" of a JDFTx "out" file corresponding to a single call of the JDFTx executable (subsequent calls will append the same "out" file). This class is initialized for every call from an "out" file when JDFTXOutfile is initialized and stored in the list JDFTXOutfile.slices
• feature 3: joutstructures.py module containing JOutStructures class representing a series of structures from an "out" file "slice". This class is primarily helpful for representing a geometric optimization during a single call. This class is initialized once during the initialization of a JDFTXOutfileSlice and is stored in JDFTXOutfileSlice.jstrucs
• feature 4: joutstructure.py module containing JOutStructure class representing a single structure within an "out" file (specifically from a portion of the "out" file starting from the beginning of an SCF optimization down to the next log of Lowdin charges as the flag for the end of geometric optimization step). This class initialized once for every structure update when initializing JOutStructures, and is stored within the list JOutStructures.slices. An initial structure is given for initialization in the case that either lattice or ion positions are not being updated (and therefore not printed for parsing within the given slice of the "out" file "slice".
• feature 5: jelstep.py module containing JElStep and JElSteps class representing a single SCF step and a series of SCF steps, respectively. The JElSteps class is helpful for getting SCF convergence data. The JElSteps class is initialized once for every initialization of a JOutStructure, and is stored within JOutStructure.elecmindata. The JElStep class is helpful for analyzing the logged SCF optimization data (energy, chemical potential, line-minimization values, etc) for a single SCF step. The JElStep class initialized once for every SCF step when initializing a JElSteps, and is stored within JElSteps.slices.
• feature 6: jminsettings.py module containing JMinSettings abstract class for representing the input minimization settings of a JDFTx call. JMinSettings is inherited by the following classes within jminsettings.py - JMinSettingsElectronic to represent electronic minimization settings, JMinSettingsFluid for implicit fluid minimization, JMinSettingsLattice for lattice minimization, and JMinSettingsIonic for ionic minimization.

[computron]

@mkhorton , are you OK with merging this change?

@shyuep I am not sure why some of the optional checks are not running, I started the tests a couple of days ago.

Looks like all changes are restricted to the io/jdftx module, so not much likelihood of things breaking

[mkhorton]

I’ll try and review this later today, thanks @benrich37