Issue281 new default configs - AUG by Didou09 · Pull Request #333 · ToFuProject/tofu

Didou09 · 2020-01-23T15:47:58Z

Main changes:

A bug was fixed in _GG.Poly_isClockwise() via PR [bf #331] raising exceptions when poly ill defined #332 (fork of this branch)
A new pre-defined tokamak geometry is available in an axisymmetric version: ASDEX Upgrade (AUG)

And AUG now appears in the available configs message created by PR #327

In [1]: import tofu as tf 

In [2]: tf.geom.utils.get_available_config()
A config is the geometry of a tokamak
You can define your own, see online tutorial at:
	https://tofuproject.github.io/tofu/auto_examples/tutorials/tuto_plot_create_geometry.html
tofu also also provides some pre-defined config ready to load
They are available via their name or via shortcuts

	unique names	shortcuts
	------------ 	-------------------------
	- AUG-V1      	['AUG-V1', 'AUG']
	- ITER-V1     	['ITER-V1', 'A2']
	- ITER-V2     	['ITER-V2', 'B4', 'ITER']
	- JET-V0      	['JET-V0', 'JET']
	- NSTX-V0     	['NSTX-V0', 'NSTX']
	- WEST-Sep    	['WEST-Sep', 'A3']
	- WEST-V1     	['WEST-V1', 'A1']
	- WEST-V2     	['WEST-V2', 'B1']
	- WEST-V3     	['WEST-V3', 'B2']
	- WEST-V4     	['WEST-V4', 'B3', 'WEST']

  => to get a pre-defined config, call for example:
	config = tf.geom.utils.create_config('ITER')

In [3]: conf = tf.geom.utils.create_config('AUG')

In [4]: conf.plot()

Perspectives:

A more detailed version (with non-axisymmetric details for PFC) should be made available in a future version

Issues:

Progress on issue Add new default configs #281

Acknowledgements:

A contribution obtained with the help of @jdhare

…ve double points, to be corrected

… in Struct._checkformat_dgeom() and cleaner error handling in tf.geom._comp._Struct_set_Poly()

…uts for archive

…ct not valid due to bug in _GG.Poly_isClockwise() inducing error on Vol in _GG.Poly_Order(), probably solved by lasofivec on another branch

…t 3 txt files still not loaded due to bug in _GG. tf.geom.utils.create_Config() more robust vs Struct that can't be loaded (warnings not fatal)

…nto Issue281_fork

[bf #331] raising exceptions when poly ill defined

pep8speaks · 2020-01-23T15:48:05Z

Hello @Didou09! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2020-01-23 15:51:03 UTC

codecov-io · 2020-01-23T16:03:56Z

Codecov Report

Merging #333 into devel will increase coverage by 0.05%.
The diff coverage is 48%.

@@            Coverage Diff             @@
##            devel     #333      +/-   ##
==========================================
+ Coverage   40.02%   40.08%   +0.05%     
==========================================
  Files          79       79              
  Lines       24128    24172      +44     
==========================================
+ Hits         9658     9689      +31     
- Misses      14470    14483      +13

Impacted Files	Coverage Δ
tofu/version.py	`100% <100%> (ø)`	⬆️
tofu/geom/_comp.py	`59.91% <40%> (-0.26%)`	⬇️
tofu/geom/_core.py	`63.08% <47.36%> (-0.08%)`	⬇️
tofu/geom/utils.py	`44.61% <0%> (+2.84%)`	⬆️

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lasofivec · 2020-01-23T16:47:37Z


        # Elimininate any double identical point
-        ind = np.sum(np.diff(Poly, axis=1) ** 2, axis=0) < 1.0e-12
+        ind = np.sum(np.diff(np.concatenate((Poly, Poly[:, 0:1]), axis=1),


why do you close the poly ?

We want a bool array ind the same shape as Poly, to tell us which successive points are redundant.
So:

We use np.diff() => ind will be of shape (npts-), if poly has shape (2, npts). Concatenating the first poitn at the end (i.e. closing the polygon) will yield the good shape for ind

If we don't close the poly here, and if the first point and the last point are identical (poly already closed), np.diff() will not detect it. So closing the poly in np.diff() is actually a good way of making sure we remove (at line 443) the last point if the poly was already closed

lasofivec · 2020-01-23T16:51:12Z

-            lS.append(obj)
+            elif len(ff) > 1:
+                # More demanding criterion
+                ssbis, Expbis = '_'+ss+'.txt', '_Exp'+Exp+'_'


what are ss files ?

In this loop, cc is the class str ('PFC', 'Ves'...) and ss is the name of the Struct considered.
The name of a .txt file containing the polygon of a Struct is formatted as

TFG_class_ExpTokamak_Name.txt

For example:

TFG_PFC_ExpAUG_TPLT1.txt

This file contains the polygon for a PFC of experiment ASDEX Upgrade (AUG) which is called TPLT1.

In this method we try to identify a unique txt fle corresponding to a given Struct (by class, Exp, name).
A first try is done with simple criteria which are sufficient 90% of the time.
But in some case multiple matches are found, because for example the names of several Struct share a common part, for example:

TFG_PFC_ExpAUG_D3BG1.txt
TFG_PFC_ExpAUG_D3BG10.txt

These are two different Struct. But the name of the first one is fully enclosed in the name of the second.
So if we look for all files containing the str 'D3BG1', we'll find these two solutions.
In that case, we search again with more strict criteria to identify the unique file.

Didou09 · 2020-01-24T14:54:44Z

Thanks for approving the merge :-)
I'm restoring the branch because this is branch that will live a long time since we will use it every time we'll add a new tokamak (I'm expecting GOLEM, TCV and JET in the coming weeks / months)

lasofivec · 2020-01-24T16:38:11Z

You can restore it when it is needed but you can also keep it on :)

VEZINET Didier and others added 16 commits January 17, 2020 09:22

[Issue281] Added diaggeom input file for AUG config in 2D

67d988b

[Issue281] First version of all AUG txt files from diaggeom, 13/33 ha…

8cf3812

…ve double points, to be corrected

[Issue281] More robust strategy for input polygons with double points…

0e006f9

… in Struct._checkformat_dgeom() and cleaner error handling in tf.geom._comp._Struct_set_Poly()

Merge branch 'devel' into Issue281_NewDefaultConfigs

ae6a650

[Issue281] Moving reference AUG diaggeom coords file to tofu/geom/inp…

6d60c25

…uts for archive

[Issue281] Corrected all double points in AUG txt files, still 3 Stru…

03dfe39

…ct not valid due to bug in _GG.Poly_isClockwise() inducing error on Vol in _GG.Poly_Order(), probably solved by lasofivec on another branch

[Issue281] Added 'AUG-V1' and shortcut 'AUG' to predefined config, bu…

4837932

…t 3 txt files still not loaded due to bug in _GG. tf.geom.utils.create_Config() more robust vs Struct that can't be loaded (warnings not fatal)

Merge branch 'devel' into Issue281_NewDefaultConfigs

cbcc34c

Merge branch 'devel' into Issue281_NewDefaultConfigs

8daec89

[bf #331] raising exceptions when poly ill defined

ebd494b

[bf #331] black changes

a0f432b

[Issue281_fork] Sligtly more explicit error message

9b83143

[bf #331] corrected last point index when lowest right is 0

967e02a

Merge branch 'Issue281_fork' of https://github.com/ToFuProject/tofu i…

ea9d745

…nto Issue281_fork

[bf #331] checking if poly is in wrong order in isclockwise

8d67f90

Merge pull request #332 from ToFuProject/Issue281_fork

f5b8d06

[bf #331] raising exceptions when poly ill defined

Didou09 added the geom - improve label Jan 23, 2020

Didou09 requested a review from lasofivec January 23, 2020 15:47

Didou09 self-assigned this Jan 23, 2020

[Issue281] PEP8 Compliance

c10784e

lasofivec reviewed Jan 23, 2020

View reviewed changes

lasofivec merged commit 3e5caf6 into devel Jan 24, 2020

lasofivec deleted the Issue281_NewDefaultConfigs branch January 24, 2020 14:36

Didou09 restored the Issue281_NewDefaultConfigs branch January 24, 2020 14:53

Didou09 mentioned this pull request Jan 24, 2020

[doc] updated gallery tuto: bf #329 #330

Merged

Didou09 mentioned this pull request Jan 24, 2020

Broken tutorial: default configuration #329

Closed

Didou09 mentioned this pull request Jan 30, 2020

tofu 1.4.2 preparation #339

Merged

Didou09 mentioned this pull request Mar 10, 2020

Preparing 1.4.3 #364

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Issue281 new default configs - AUG#333

Issue281 new default configs - AUG#333
lasofivec merged 17 commits intodevelfrom
Issue281_NewDefaultConfigs

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Didou09 commented Jan 23, 2020

Main changes:

Perspectives:

Issues:

Acknowledgements:

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Comment last updated at 2020-01-23 15:51:03 UTC

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