Mlxtk

Description:
------------
This update simplifies the code to calculate expectation values. The computation of static expectation values is now handled in an extra task type.
Furthermore the number state analysis (static version only yet) has been added as well as script to plot the depletion in parameter scans.

Included Commits:
-----------------
- 1ec38e5: Add fixed number state analysis (static version).
- 84df607: Revert accidental change to `pyproject.toml`.
- 66a5d92: Fix naming issue in expval tasks.
- d72c9b5: Remove obsolete file.
- 41d0470: Simplify code to compute ExpectationValues; make static expectation values a separate task type.
- 44822fd: Add `scan_plot_depletion` script.
- 57f309a: Merge pull request 39 from f-koehler/dependabot/pip/numba-gte-0.43.1-and-lt-0.45.0
- e5c4a37: Update numba requirement from ^0.43.1 to >=0.43.1,<0.45.0

Description:
------------
This update extends the functionality of `mlxtkrc` files which also have been rename from `.mlxtkrc` to `mlxtkrc`. Now one can easily set environment variables in these files and also extend `$PATH` like variables. Furhtermore, settings files from different levels are automatically merged while loading while the one on the highest level gets the highest priority in case of conflicts (allowing to override settings locally).

The `MBOperatorSpecification` class got a function format instances for easier debugging.

Included Commits:
-----------------
- 11c3826: Add function to create truncated center of mass operators.
- 9d88cec: Add `__str__` method to `MBOperatorSpecification`.
- 4602395: Combine settings file from parent directories.
- e3dbb87: Add easy way to set environment variables to mlxtkrc files.
- 683950b: Format code.
- 41d23b1: Settings file should be named `mlxtkrc` instead `.mlxtkrc` from now on.

Description:
------------
This update adds the harmonic interaction model (HIM) as a new system.
Furthermore, the performance of the `foreach` and `plot_foreach` methods of `ParameterSelection` has been improved by parallelization. This requires the `ProcessPool` from the [pathos](https://pathos.readthedocs.io/en/latest/pathos.html) library as python's `multiprocessing.Pool` cannot be used with local functions (due to the pickling).

Additionally some bugs, mainly related to pathlib, have been resolved.

Included Commits:
-----------------
- 31403fc: Merge pull request 38 from f-koehler/dependabot/pip/numpy-1.16.4
- de5f894: Update numpy requirement from 1.16.3 to 1.16.4
- 7655c10: Parallelize `foreach`/`plot_foreach` methods of parmeter selections.
- 59e847a: Add `scan_plot_expval` script.
- 14b5a3f: Fix `pathlib`-related issue in `clean` operation.
- c03dc9a: Add HIM model.
- 96bc397: Remove `setup.py`.
- 1744dcc: Specify yapf & isort version; reformat code with current versions.
- 8ad953d: Recreate documentation facilities.
- 04c02da: Add function to create `ParameterSelections` for each value of a parameter.
- 83ee06d: Add functionality to create truncated unit operators; reformat `plot_expval.py`.
- 47bc5b1: Tell pyling that we use PySide2.
- a3693ac: Fix an issue with `plot_expval`/`units` related to the recent change to pathlib.
- a21cdaf: Remove unused imports/variables.

Description:
------------
This update adds a script to perform a fixed number state analysis on demand and to analyse the result. Furthermore scripts are added that allow the time-dependent analysis of the one-body density and the reduced two-body density matrix by offering a slider for the time. Many small features have been added as well. Under the hood path handling has been changed to `pathlib` almost everywhere. Additionally many small issues have been fixed.

Included Commits:
-----------------
- fb8b3bf: Accept str as parameter for WorkingDir.
- ae2549d: Fix mistake in author field of pyproject.toml.
- b42bd16: Replace os.path with pathlib.Path in most parts of the code.
- b3de86a: Compute manitude instead of absolute value in `fixed_ns`.
- 4ba8386: Fix mistake in pyproject.toml.
- b5aa5ca: Add `load_path` function; replace os.path with pathlib at several places.
- 74bd20a: Add missing information to poetry config.
- a6cee06: Require python>=3.6.
- 301ab01: Format code.
- 3be7a37: Add poetry config.
- 470c567: Add `fixed_ns_table.py` script and store N and m in HDF5 file.
- e334293: Add script to perform fixed number state analysis.
- ba1a7ff: Add tool to plot SPFs from PSI file.
- 65327bd: Add tools/methods related to the eigenvalues/-vectors of the reduced one-body matrix (I/O routines, plotting scripts).
- 7bd9166: Add `get_path()` routine to parameter selection and format code.
- 168cd33: Add convenience functiosn for selecting multiple parameters and for loading the timing of a specific task action.
- c2efb95: Add routines to load DoIT information (especially timings) and to format an execution profile.
- f950932: Add missing dependencies.
- acf89e0: Add Hamiltonians with only the right well to `two_gaussian_traps` system.
- 0f95fa4: Add new task type to create a MCTDHB wave function from multiple one-body Hamiltonians.
- fe7d42b: Import dvr module into mlxtk.
- 19f1946: Fix an issue when calling DoitMain.
- 519fc45: Add `dmat2_slider` script.
- 93904c2: Add script to thin out psi files and add a routine to read dmat2 in grid representation.
- 29a9d3f: Add `gpop_slider` app.
- f8261a6: Add `scan_plot_scripts` for natpop and energy.
- c4958f5: Reformat code.
- 44a0cda: Add option to save in different formats to `scan_plot_gpop` script.
- 62940c4: Add option to specify DOF when plotting gpop for parameter scan.
- ab27b2f: Add script to plot gpop for parameter scans.
- 2bee9f6: Rename `get_settings()` -> `load_settings()`.
- 841930f: Add unit subsystem to perform calculations with units and automatically set axis labels.
- a5ab6ac: Functionality to load .mlxtkrc yaml configurations.
- ef6b507: Add general memoize class.
- 3b0aa17: Move methods for plot arguments.
- f242169: Make sure that gpop heatmaps are saved rasterized.
- c869cfe: Add option to optimize PDF file size using pdftocairo.
- f258176: Automatically import more things automatically in order to reduce overhead for the user.
- f6bebdd: Add `save_pdf` method that can crop PDF plots after saving.
- 6260a7a: Fix com2 operator.
- 61ba4c7: Add functions to look up bosonic number states in both directions.
- fdcc685: Allow `read_expval` to read data from static expectation values (these datasets have two instead of three columns).
- 995afea: Fix bug when computing an expectation value in the simulation root dir.
- 6338c21: Add functionality to compute static expectation values.
- 5e69e87: Expose Paramerters class in the master module and add return value to `plot_foreach` method of ParameterSelection.
- 2ab7b00: Fix multiple issues related to WaveFunctionDB (amongst others when calling it directly).
- bdf97e9: Add progress bar to foreach method of parameter selections.
- b088545: Add `plot_foreach` functionality to ParameterSelection to easily create plots for each included parameter tuple.
- 6291d76: Remove deprecated `keep_psi`-flag from examples; add dry-run functionality (useful to fill a wave function db with requests).
- 6ee4a36: Add colliding wells Hamiltonian for "two gaussian traps"-system.
- 0a8e2e8: Implent task to extend grid in MCTDHB; rename CreateMCTDHBWaveFunction -> MCTDHBCreateWaveFunction to fit naming scheme; implement `get_spfs` function.
- 10070bd: Add access to the left well Hamiltonian in a double gaussian well setup.
- 3246c1d: Fix two bugs in the flag handling for propagation tasks.
- a383386: Return a list when determining unique parameter values.
- 287430a: Add the clean operation to simulation sets.
- 287e67d: Add some docstrings.
- 93f495b: Improve code quality using suggestions by pylint and mypy.
- 5184451: Add new ParameterSelection class to work with parameter scans in an easy fashion.
- 7779411: Make sure that parameter scan symlinks get regenerated.

Description
-----------
This update is quite extensive feature wise, hence justifying the version jump. The most important new feature is the addition of cleanup tasks, which can used to remove operators from finished simulations at the moment. This helps to save a lot of disk space without losing track of the operator state, the operators are simply recreated on the next run.
Another big feature is the WaveFunctionDB facility which allows to create a central place where wave functions are computed on-demand. The user can build the wave function construction protocol like a normal simulation and request wave functions by parameter from any place.
An important change is the usage of SGE job arrays when submitting to a SGE cluster. This reduces the load of the scheduler and the time it takes to submit big chunks of jobs. Furthermore, job arrays have some benefits when it comes to management as all jobs share the same ID.
Additionally various small fixes (especially regarding some path problems) are included.

Included Commits:
-----------------
- 054b7b7: Reformat code and implement some of the pylint suggestions.
- 4d28cb0: Format code using yapf.
- bd68ef7: Fix some minor bugs.
- 4c18d85: Remove spectrum calculation from OperatorSpecification. It is not needed anymore since operators can be removed now after finishing the work.
- 59d3419: Add clean functionality tasks. Can be very helpful to remove operators after completion of simulation.
- 363d420: Get rid of the additional parentheses due to the new class-based approach to tasks.
- 36e16ea: Add some type hints to the task classes.
- 0801729: Move mctdhb wave function operations into classes.
- ef0b946: Move wave function request into a seperate class.
- 50170e4: Move computation of one-body spectrum into a class.
- 086bc06: Move propagate, (improved) relaxation and exact diagonalization in corresponding classes.
- aaf673a: Move mb operator creation to a class.
- b5eb99b: Move operator creation to a class.
- 144f55c: Move code to compute variance into a class.
- 7aeec91: Move expectation value computation to a class.
- 6abc873: Add option to calculate one-body spectra from OperatorSpecification directly; very helpful to save disk space when the operator file is not really needed.
- ccafdd4: Use SGE job arrays for simulation sets/parameter scans/etc. to reduce the load on the scheduler and the expenditure of time when submitting.
- d7c9d57: Fix another path issue.
- b966180: Implement the computation of a one-body spectrum as a task.
- f3f5816: Introduce well asymmetry to double gaussian well system.
- 264c2aa: Stop WaveFunctionDB from failing due to missing working directory.
- 7ea5f60: Fix storing missing/existing wave functions to prevent duplicates.
- 4a76bee: Continue implementation of WaveFunctionDB; fix a lot of cwd issues in the general code.
- 77e9c09: Implement the DB structure.
- a24a75a: Start working on the wave function DB feature.
- 4defff6: Also write parameters of scan as a pickle.
- f96fc38: Disable debug logging; add function to chain parameter generators/iterables.
- 87d7165: Fix qsub for SimulationSet (again). Hopefully, for good this time.
- 3b8fc2e: Fix qsub for parameter scan.
- 0134b4f: Fix a bug in harmonic trap scan example.
- d9492c5: Add preliminary README.md.

=============

Description:
------------
In this up-date I moved away from the practice of automatically converting all data to HDF5. For daily usage it is better to have the ASCII files. However, I think that HDF5 a good thing for the project (examples could be archiving, where also other formats like tar-balls might be helpful, and converting data on-demand whenever more performant I/O is required).
This update also adds some tools abd fixes some bugs.

Included commits:
-----------------
- 895edbc Add short versions of SGE flags.
- dd56f08 Add functionality to boost two spatial parts of a MCTDHB wave function in opposite directions; fix a bug in `GaussianTrap`.
- 15543b0 Add system with two gaussian wells.
- 2e162ce Add general com operator to single-species systems.
- cf11e99 Fix `create_operator functions`.
- 560d192 Add `create_gaussian_potential_operator()` function -> easier to create a second well.
- e7a2c84 Automatically generate labels when plotting more than one curve.
- 3d41ebb Fix bug in `read_expval`.
- 928373e Allow to plot multiple energy/entropy curves at once, probably needs some labelling.
- 9ace881 Fix bug in one-body potential operator for gaussian trap.
- 12ade7b Rename default files for energy, gpop and natpop plotting scripts.
- b4aec8b Fix two little bugs (parameters and `mb_operator`).
- c2c8e69 Fix submission of parameter sets.
- 53d2187 Rename `many_body` to `mb` for brevity.
- d0de6d0 Rename some task entries; fix `harmonic_trap_scan.py` example.
- 40dcc95 Disable data conversion for all tasks.
- c791c01 Fix qsub for `SimulationSet`.