The quaca from quacateam

Cross-check Simon's documentation

Fix input file constructor for Friction

The input file constructor for the Friction class is faulty.

Prepare QuaCa publication

Let us prepare for our upcoming publication of QuaCa in JOSS. They have a guide on how to publish and these are the requirements:

250 to 1000 words
A list of the authors of the software and their affiliations, using the correct format (see the example below).
A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience.
A Statement of Need section that clearly illustrates the research purpose of the software.
A list of key references, including to other software addressing related needs. Note that the references should include full names of venues, e.g., journals and conferences, not abbreviations only understood in the context of a specific discipline.
Mention (if applicable) a representative set of past or ongoing research projects using the software and recent scholarly publications enabled by it.
Acknowledgement of any financial support.

Remaining tasks

ToDos Paper:

look over references in paper/paper.bib (remove file links)
add "Statement of Need"

ToDos Repositories:

improve read me @chegerland
- expand test section (unit + integrated)
- explain apps Decay and Friction
- add badges
do tutorials again @chegerland @SiMaHer
(optional) add coverage job and badge

Tutorial 3 needs to be updated: Currently, no cpp file is created which prevents proper execution of the tutorial's result.

Originally posted by @ddanzer in #74 (review)

Should be done in branch UX_check before merge into main can be completed. Recommend reconfirming test of functionality of tutorial 3 before submitting.

Review Tutorials

Test and check tutorials with respect to consistency and functionality.

Transfer Ownership to the QuaCa Foundation

In github it is not possible to transfer the ownership to several persons. However, one can transfer the ownership to a organization. Thus, the repository should be transferred to the QuaCa Foundation.

ReflectionCoefficientLocBulk with PermittivityDrude blows up at omega = 0

The reflection coefficient returns nan's for a frequency of oemga = 0. This is due the fact, that the PermittivityDrude.calculate returns a value of (-inf, nan), leading to a return value of (-nan, -nan) in ReflectionCoefficientLocBulk.calculate

Unused function

The permittivity class has the member function

  virtual std::complex<double> calculate_times_omega(double omega) const = 0;

which never seems to be used. I also think that it is not very useful, e.g. in the lorentz permittivity, where it does not remove any singularities.

I think it is best to delete it.

Clean up QuaCa directory

Our git repository still contains directories/files that we would not want to track, such as: bin/, .idea/ and .DS_Store.

They should already be included in the .gitignore but have not been removed from tracking.

GreensTensorPlate is divergent at kappa_double == 0

The indices (0,2), (2,0) and (2,2) are divided by kappa_double, therefore returning a value of inf for kappa_double == 0. This could be resolved by correctly canceling all kappa's appearing in the Green's tensor.

Delete the Options class and move its functionality into the Friction executable

move Options class functionality to friction executable
delete Options class
fix progressbar in Friction executable

Alter .travis.yml to check every branch

Git version in output file

QuaCa installation

We should aim for a proper installation of QuaCa and its executables. This will also get rid of the bin/ and lib/ directory.

Check QuaCa for const correctness

Rewrite and reformulate Draft

Adjust draft with respect to the new core message, incorporate a Section of Need and avoid scientific jargon within the introductory section.

Cross-check Marty's documentation

Write Introduction

Please consider the JOSS guideline https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain

Edit draft

Please check the draft in the branch "paper_draft". Directly implement your modifications.

Correct Input-File Constructor of FrictionClass

The input-file constructor of the friction class is still incorrect. Several instances of greens tensor and polarizability are created.

Present QuaCa's capability and distinguish it from other codes

Replace indices by integer array

Several warnings are thrown in our test cases because we use vec::fixed<2> for our indices. Indices should be unsigned integers.

GreensTensorPlate sometimes computes wrong k

For some combinations of kappa_double and omega the reconstructed k in integrand_2d_k is incorreclty computed. It seems that this issue occurs as soon as v*|omega| > k.
An example being: k = 0.001, omega = 1., v = 0.01

Add description to project (add documentation)

Change the plot script to show the force with correct units

Currently the plot script shows the frictional force with natural units. This does not match the results shown in the paper, which is cited in the tutorial.

Prepare JOSS submission

Create example plots of friction and decay rate

Unify README und gettingstarted page

Employ MPI parallelization for the Friction executable

Add license to project

Introduce a characteristic decay rate

Besides an characteristic frequency of the memory kernel or Green's tensor, a characteristic decay rate should be calculated, too. This would give a more solid integration interval around omega_a as the current 0.99 to 1.01.
Either one calculates the decay rate for every point v (or za), or one does a reasonable estimate for each Green's tensor and memory kernel.

Make omega_ch a vector of arbitrary length

In order to provide an efficient integration scheme, we implemented a characteristic frequency $\omega_\mathrm{ch}$ in the Green's tensor class. Currently, this is only a double. However, it would be desirable to have probably more than characteristic frequency. This, effects the integration scheme over omega.

Restrict Travis CI to pull requests

To safe some time, it would probably sufficient to build and test solely the pull requests.

[JOSS Review] Performance

This issue shall resolve the comments from openjournals/joss-reviews#5160 (comment):

-Performance

It is mentioned that QuaCa is meant for efficient computation of
on any regular personal computer, but providing a few performance benchmarks and minimum prescribed hardware configuration would be ideal.

[...]

I would also suggest setting a default value for the no. of threads (OMP_NUM_THREADS) to 1 (when no environment variable is set) within the package to prevent high CPU usage or oversubscription of processors which could risk crashing the system.

Consistent scheme for shared_ptr getter functios

So far there is not a consistent scheme for shared_ptr getter functions (compare e.g. PowerSpectrum and Polarizability)

[JOSS Review] Unit tests are failing

Here is the output when running "test_quaca_unit"

test_quaca_unit is a Catch v2.13.9 host application.
Run with -? for options

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

-------------------------------------------------------------------------------
The operations calculate_tensor and the integrand_2d_k coincide
-------------------------------------------------------------------------------
/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:75
...............................................................................

/Users/livi/Arkajit/quaca/test/UnitTests/GreensTensor/test_GreensTensorPlate_unit.cpp:140: FAILED:
  REQUIRE( approx_equal(Green_fancy_I_ct, Green_fancy_I_ik2d, "reldiff", 10E-4) )
with expansion:
  false

===============================================================================
test cases:   44 |   43 passed |  1 failed
assertions: 2723 | 2697 passed | 26 failed

The following link in the readme is returning 404: https://github.com/QuaCaTeam/quaca/blob/master/dev/testing.md

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