Minor moving bug fixes

[RiesBen]

This branch contains my expirience with Euler and the submission system

This pull request grew a bit beyond! So it's time to merge !

Features:

• minor bug fixes for submission system
• visualization
• doc update
• more testing

• Ready To Go

[lgtm-com]

This pull request introduces 9 alerts and fixes 4 when merging fdc70c6 into 75a1664 - view on LGTM.com

new alerts:

• 6 for Wrong name for an argument in a call
• 1 for Except block handles 'BaseException'
• 1 for Syntax error
• 1 for Unreachable code

fixed alerts:

• 3 for Unused local variable
• 1 for Unused import

[lgtm-com]

This pull request introduces 10 alerts and fixes 4 when merging f0a92c6 into 75a1664 - view on LGTM.com

new alerts:

• 6 for Wrong name for an argument in a call
• 1 for Except block handles 'BaseException'
• 1 for Unused import
• 1 for Syntax error
• 1 for Unreachable code

fixed alerts:

• 3 for Unused local variable
• 1 for Unused import

[lgtm-com]

This pull request introduces 10 alerts and fixes 4 when merging a5f71ac into 75a1664 - view on LGTM.com

new alerts:

• 6 for Wrong name for an argument in a call
• 1 for Except block handles 'BaseException'
• 1 for Unused import
• 1 for Syntax error
• 1 for Unreachable code

fixed alerts:

• 3 for Unused local variable
• 1 for Unused import

[lgtm-com]

This pull request introduces 10 alerts when merging d19c481 into 75a1664 - view on LGTM.com

new alerts:

• 6 for Wrong name for an argument in a call
• 1 for Unused local variable
• 1 for Except block handles 'BaseException'
• 1 for Unused import
• 1 for Unreachable code

[RiesBen]

Hi hi,
@MTLehner I stumbled over a strange thing. My tre.get_totals are not working anymore (found it, when I added the function to the testing suite).

If I understand it correctly, the totals field has 38 fields and we expect 43 at the moment. I know, that the number of fields can very from gromos to gromos version. So is it a version problem or are some of the "wips" ready for vanishing?

tre - gromos_2020_tre_block_names_table:

    totals_subblock_names = ["totene","totkin","totpot","totcov","totbond","totangle","totimproper","totdihedral","totcrossdihedral","totnonbonded",
                             "totlj","totcrf","totls","totlspair","totlsreal","totlsk","totlsa","totlsself","totlssurf","totpolself","totspecial",
                             "totsasa","totsasavol","totconstraint","totdisres","totdisfieldres","totdihres","totposres","totjval","totxray","totle",
                             "totorder","totsymm","eds_vr,entropy","totqm","totbsleus","totrdc","wip1","wip2","wip3","wip4","wip5","wip6"]

Error message:

        except ValueError as e:
            blocks = [getattr(b, "values", b) for b in blocks]
            tot_items = sum(b.shape[0] for b in blocks)
>           raise construction_error(tot_items, blocks[0].shape[1:], axes, e)
E           ValueError: Shape of passed values is (105, 38), indices imply (105, 43)

[lgtm-com]

This pull request introduces 10 alerts when merging 27f26ee into 75a1664 - view on LGTM.com

new alerts:

• 6 for Wrong name for an argument in a call
• 1 for Unused local variable
• 1 for Except block handles 'BaseException'
• 1 for Unused import
• 1 for Unreachable code

[lgtm-com]

This pull request introduces 10 alerts when merging 9cd5acc into 75a1664 - view on LGTM.com

new alerts:

• 6 for Wrong name for an argument in a call
• 1 for Unused local variable
• 1 for Except block handles 'BaseException'
• 1 for Unused import
• 1 for Unreachable code

[lgtm-com]

This pull request introduces 10 alerts when merging c30cb23 into 75a1664 - view on LGTM.com

new alerts:

• 6 for Wrong name for an argument in a call
• 1 for Unused local variable
• 1 for Except block handles 'BaseException'
• 1 for Unused import
• 1 for Unreachable code

[lgtm-com]

This pull request introduces 10 alerts when merging ca3a4a0 into 75a1664 - view on LGTM.com

new alerts:

• 6 for Wrong name for an argument in a call
• 1 for Unused local variable
• 1 for Except block handles 'BaseException'
• 1 for Unused import
• 1 for Unreachable code

[lgtm-com]

This pull request introduces 4 alerts when merging 8e8b694 into 75a1664 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Except block handles 'BaseException'
• 1 for Unused import
• 1 for Unreachable code

[lgtm-com]

This pull request introduces 4 alerts when merging e68b332 into 75a1664 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Except block handles 'BaseException'
• 1 for Unused import
• 1 for Unreachable code

[RiesBen]

@MTLehner we only need to fix the get_totals now.

[lgtm-com]

This pull request introduces 4 alerts when merging adb9f39 into 75a1664 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Except block handles 'BaseException'
• 1 for Unused import
• 1 for Unreachable code

[RiesBen]

@MTLehner we only need to fix the get_totals now.

Ha! fixed :)

[lgtm-com]

This pull request introduces 4 alerts when merging d9eae65 into 75a1664 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Except block handles 'BaseException'
• 1 for Unused import
• 1 for Unreachable code