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Automatic lattice vectors #213

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wants to merge 7 commits into from
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Automatic lattice vectors #213

wants to merge 7 commits into from

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mondracek
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Closes #52 and makes PR #197 obsolete. Formatting changes were done in the first commit. Then, a copy of the branch proposed under PR #197 was rebased on the reformatted branch. As a result, the substantial changes are in other commits than the formatting.

	modified:   ppafm/HighLevel.py
	modified:   ppafm/cli/fitting/plotLine.py
	modified:   ppafm/cli/fitting/plotZ.py
	modified:   ppafm/cli/gui/ppafm_gui.py
	modified:   ppafm/common.py
	modified:   ppafm/core.py
	modified:   ppafm/io.py
	modified:   ppafm/ocl/AFMulator.py
	modified:   ppafm/ocl/relax.py
	modified:   tests/test_common.py
	modified:   tests/test_io.py
	modified:   tests/test_vdw.py
…ini nor the input file specify them

Moreover
- remove premature call to autoGridN in loadParams
- enable reading ASE-style lattice vector from XYZ in ppafm_gui.py
- handle fzs/Fout deletion in plot_results.py correctly depending on tip tilt
- correct typo Lenard-Jones -> Lennard-Jones
- add 'self' argument to prepareFEConv() in relax.py to console precommit checks
- resolve conflicts in formatting resulting from limits on line length
- accept the solution from branch load-geometry-fix by Niko Oinonen
- read 'nDim' from 'gridN' for POSCAR and geometry.in inputs
@mondracek
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Hint for reviewers: You can use the tab "Files changed" to view the changes. Then, on the left-hand side of the bar just below these tabs, you see the option "Changes from all commits". Click on it and select only the commits you want to see. I recommend the range that covers all the commits but the first one, that is, 6 commits from 50c9fc7 to f33562c.

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Handling missing lattice vectors
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