Cylinder transformation and observables #4114

christophlohrmann · 2021-02-12T15:26:48Z

Description of changes:

Adds automatic orientation to core HollowConicalFrustum
Reworks the cylindrical observables tests
Fixes the LB fluxdensity observable by implementing a LB density interpolation
introduces a new object CylTrafoParams to make sure axis and orientation are always orthogonal
all cylindrical observables use CylTrafoParams

…ables

testsuite/python/tests_common.py

KaiSzuttor · 2021-02-19T08:36:41Z

src/python/espressomd/observables.py

-                    kwargs["orientation"] = vec / np.linalg.norm(vec)
+                orthogonal_component = vec - np.dot(vec, axis) * axis
+                norm = np.linalg.norm(orthogonal_component)
+                if norm > 0.01:


what is this magic 0.01 here? do want to check for sys.float_info.epsilon, maybe?

why do we replicate the logic from the core here?

1.) if the orthogonal component is 2 epsilon long and we scale it to 1, it will probably not be very orthogonal due to precision error. I chose a very generous value of 0.1 because we always have the second vector to try which will be more orthogonal. I guess using 1/sqrt(2) as a threshold will choose the vector that is the most orthogonal already and remove some arbitraryness
2.) The core logic for default orientation is for hollowconicalfrustum, the python one for observables

okay

i think the logic is in the wrong place then?

Where would you suggest is the right place to unite it?

algorithmically I think we could do something like: https://math.stackexchange.com/a/1681815

but that is what I am doing here :)
The Gram-Schmidt-type orthogonalisation works in whatever dimension
You just have to start with a trial vector that is not parallel

src/shapes/include/shapes/HollowConicalFrustum.hpp

src/utils/include/utils/math/orthonormal_vec.hpp

christophlohrmann · 2021-03-04T16:48:04Z

I know I still have to adapt the tutorial and do the documentation, I will do that as soon as I get green light on the stuff that is here

KaiSzuttor · 2021-03-05T10:24:10Z

could you please fix the sanitizer warnings

src/python/espressomd/observables.py

KaiSzuttor · 2021-03-08T16:25:34Z

@christophlohrmann could you please take the final steps here? We can then merge this soon I think...

jngrad

a few formatting issues

doc/sphinx/analysis.rst

src/python/espressomd/observables.py

testsuite/python/observable_cylindrical.py

testsuite/python/observable_cylindricalLB.py

testsuite/python/observable_cylindrical.py

testsuite/python/tests_common.py

Co-authored-by: Jean-Noël Grad <[email protected]>

src/core/observables/CylindricalDensityProfile.hpp

…bles (#4152) Fixes #4023, fixes #4067, closes #4114 Description of changes: - add `orientation` to `HollowConicalFrustum` - add an optional argument to control the orientation of cylindrical observables - fix the LB fluxdensity observable by implementing a LB density interpolation

jngrad and others added 12 commits December 14, 2020 21:33

utils: Calculate the angle between vectors

c77a985

tests: Add floating point tolerance

27fbcde

utils: Refactor coordinate transformation code

5af53cf

merge python

f3d4731

fix merge aftermath

2ce79ff

add orientation to hollowconicalfrustum

5be670e

remove default orientation if axis is provided

e67e09f

observables: introduce orientation argument to all cylindrical observ…

432a29e

…ables

fix leftover transformation with axis

2686215

rework cylindrical tests

d33df38

fix fluxdensity observable

cca7158

no density inerpolation for GPU LB

f32182d

jngrad reviewed Feb 12, 2021

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KaiSzuttor reviewed Feb 19, 2021

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KaiSzuttor reviewed Feb 19, 2021

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KaiSzuttor reviewed Feb 19, 2021

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This was referenced Feb 24, 2021

Cylindrical transformations with well-defined phi angle #4019

Closed

Cylindrical transformations with well-defined phi angle #4042

Closed

KaiSzuttor reviewed Mar 5, 2021

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jngrad mentioned this pull request Mar 6, 2021

Script interface maintenance #4138

Merged

jngrad reviewed Mar 8, 2021

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christophlohrmann added 5 commits March 9, 2021 14:59

fix tests, tests common

70ee1fd

fix undefined behaviour in density interpolation, remove debug clutter

a0bb5c4

better handling for default orientations

74505cd

separate and test orthonormal vector generation

9a00b4d

add cyltrafoparams class

d4c5b9b

christophlohrmann and others added 14 commits March 9, 2021 14:59

cyltrafoparams as a standalone class

0fd837f

use cyltrafoparams in observables

63371ec

observables own only pointers to cyk_tafo_params

af1c9d9

remove python-level default orientation

2667d9c

adapt tests tp ctp

bd0d752

inject default behaviour if no ctp is given

249fd24

Beautification.

a54af97

Remove default from scriptinterface.

d1ef4e1

move ctp default to python

263d77a

using std::move to pass shared ptrs

a9e1fe6

rename cyltraforparams

17b81c4

docs

9be3f01

tutorial, samples

b23aa44

Apply suggestions from code review

0e67661

Co-authored-by: Jean-Noël Grad <[email protected]>

christophlohrmann force-pushed the pr_4042 branch from 24930cd to 0e67661 Compare March 9, 2021 14:00

KaiSzuttor reviewed Mar 9, 2021

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src/core/observables/CylindricalDensityProfile.hpp Outdated Show resolved Hide resolved

core: trafo_params -> transform_params

ad00106

jngrad mentioned this pull request Mar 10, 2021

Refactor cylindrical coordinates transformation and dependent observables #4152

Merged

kodiakhq bot closed this in #4152 Mar 10, 2021

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Cylinder transformation and observables #4114

Cylinder transformation and observables #4114

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Cylinder transformation and observables #4114

Cylinder transformation and observables #4114

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