Base #276
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Base #276
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Remove unused imports/variables/functions, fix mistakes, simplify expressions, replace some magic numbers by expressions, replace sys.stdout() by print(), remove commented code.
More cleanup and apply code review feedback: remove max_num_cells, revert espressomd.System and box_l changes, use str.format().
Replace all occurrences of custom force_cap-based warmup code by the steepest descent algorithm. Initialize the thermostat after steepest descent. Don't print LJ interaction parameters again after minimization.
Remove code writing out (sometimes incomplete) Tcl files. Write out observables in tab-separated values files suitable for np.loadtxt() and xmgrace plotting. Remove clutter from print() statements.
End links with a double underscore to make anonymous references and avoid overshadowing explicit references (here the title reference).
core/testsuite: engine_lb test fix from christophlohrmann
3277: Removed ENGINE shear torque calculation r=RudolfWeeber a=fweik @RudolfWeeber @christophlohrmann is this what you had in mind? If so the simplification is quite significant because all of the custom communication code for ENGINE can be removed. Also the LB coupling should now work in parallel. Description of changes: - Removed ENGINE shear torque calculation - Moved swimmer parameters into ParticleProperties - Removed custom communiication code for ENGINE - Adaped docs Co-authored-by: Florian Weik <[email protected]>
3282: utils: Re-add uniform test + docstring r=jngrad a=fweik Description of changes: - The Utils::uniform test was moved to the correct place and readded to the build system. - Docstring Co-authored-by: Florian Weik <[email protected]>
Reference solutions for forces on shear planes and for stokes drag need dynamic viscosity, but LB uses kinetmatic viscosity. This switches the tests to dynamic viscosity and removes a 1/rho from the unit conversion in the script interface. Also, a force balance test is added, which does not depend on the density.
3267: Upgrade samples r=RudolfWeeber a=jngrad Fixes #2089 Description of changes: - remove unused variables/imports/functions and some of the commented out code - remove Tcl-specific code, replace manual warmup by steepest descent - use `argparse` to process user input and document the parameters, stop printing features - improve docstrings and use them to generate an always up-to-date sample list in the docs Co-authored-by: Jean-Noël Grad <[email protected]> Co-authored-by: RudolfWeeber <[email protected]>
3287: LB Boundary force: fix unit conversion and tests r=fweik a=RudolfWeeber Reference solutions for forces on shear planes and for stokes drag need dynamic viscosity, but LB uses kinetmatic viscosity. This switches the tests to dynamic viscosity and removes a 1/rho from the unit conversion in the script interface. Also, a force balance test is added, which does not depend on the density. Fixes # Description of changes: - PR Checklist ------------ - [ ] Tests? - [ ] Interface - [ ] Core - [ ] Docs? Co-authored-by: Rudolf Weeber <[email protected]>
switch conditionals as suggested by JNGrad Co-Authored-By: Jean-Noël Grad <[email protected]>
3288: core: Simplify particle removal r=RudolfWeeber a=fweik Fixes #3286. Description of changes: - Simplify particle removal by doing one linear pass over all particles instead using index 3290: fix writevtk() bug where types=all was ignored r=jngrad a=christophlohrmann Description of changes: - fixed bug where the argument ``types='all'`` was ignored by ``system.part.writevtk()`` PR Checklist ------------ - [ ] Tests? - [ ] Interface - [ ] Core - [ ] Docs? Co-authored-by: Florian Weik <[email protected]> Co-authored-by: Christoph Lohrmann <[email protected]> Co-authored-by: christophlohrmann <[email protected]>
2748: Additional LB test cases r=fweik a=RudolfWeeber * Buyancy force on a sphere in a box of fluid under gravity * Momentum conservation in a fluid with an external volume force applied and a particle with an oposite force applied @KaiSzuttor @mkuron Could you please take a look at the lb_buoyancy_force test? It only passes, when the fluid density is set to 1. On the other hand, the lb_shear and lb_stokes_sphere tests check boundary forces which do not (and should not) depend on the density. They pass when run with different densities. Also, the application of an external volume force is tested in lb.py in test_a_ext_force... Furthermore, to the lb_momentum_conservation.py test checks the balance between forces applied to the lb and those applied to a particle. Co-authored-by: Rudolf Weeber <[email protected]> Co-authored-by: Florian Weik <[email protected]>
… removed special overload for boost::optional
POSIX does not specify test for > 4 arguments: https://pubs.opengroup.org/onlinepubs/9699919799/utilities/test.html
3291: Factor out and test memcpy serialization r=RudolfWeeber a=fweik Description of changes: - This splits off the memcpy serialization used in the ghost communication and adds unit test for it. - Added customization point to opt-in to memcpy serialization for types that are not [TriviallyCopyable](https://en.cppreference.com/w/cpp/named_req/TriviallyCopyable), but serializes to a bounded size, like `boost::optional`. This is so we can use `optional` and `variant` in `ParticleProperties`, which is planned. 3292: Pypresso: Remove "test -a" and quote $@ r=jngrad a=hirschsn Description of changes: - Remove `test -a` since calls to test with more than 4 arguments are unspecified: https://pubs.opengroup.org/onlinepubs/9699919799/utilities/test.html - Quote `$@` to avoid splitting $@. Currently `./pypresso --gdb "test me.py"` will fail because tries to find the file `test`. Quoting avoids this. PR Checklist ------------ - [ ] Tests? - [ ] Interface - [ ] Core - [ ] Docs? Co-authored-by: Florian Weik <[email protected]> Co-authored-by: Steffen Hirschmann <[email protected]>
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Fixes #
Description of changes:
PR Checklist