adding option to get and set rotation period from SeBa

[silviatoonen]

No description provided.

[rieder]

The test (pytest src/amuse/test/suite/codes_test/test_seba.py results in a few fails where it was all successful before, probably because of internal changes in the SeBa models - see below.
Could you update the test where needed? It can be merged afterwards.

============================= test session starts ==============================
platform darwin -- Python 3.10.1, pytest-6.2.5, py-1.11.0, pluggy-1.0.0
rootdir: /Users/srieder/Code/amuse-clean
collected 22 items

test_seba.py ...........F.....FFFFF                                      [100%]

=================================== FAILURES ===================================
__________________ TestSeBa.test_add_stars_at_different_times __________________

self = <amuse.test.suite.codes_tests.test_seba.TestSeBa testMethod=test_add_stars_at_different_times>

    def test_add_stars_at_different_times(self):
        instance = self.new_instance_of_an_optional_code(SeBa)
        stars = Particles(2)
        stars[0].mass = 10.0 | units.MSun
        stars[1].mass = 9 | units.MSun
    
        instance.particles.add_particles(stars)
        instance.evolve_model(30|units.Myr)
    
        self.assertAlmostRelativeEquals(instance.particles.age, [30,30] |units.Myr)
        self.assertAlmostRelativeEquals(instance.model_time, 30 | units.Myr)
>       self.assertAlmostRelativeEquals(instance.particles[0].mass, 1.2476 | units.MSun, 4)

test_seba.py:531: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../../amusetest.py:140: in failUnlessAlmostRelativeEqual
    self._raise_exceptions_if_any(failures, first, second, "{0!r} != {1!r} within {2!r} places", msg, places)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <amuse.test.suite.codes_tests.test_seba.TestSeBa testMethod=test_add_stars_at_different_times>
failures = array([ True], dtype=bool), first = quantity<1.25072398252 MSun>
second = quantity<1.2476 MSun>
err_fmt_string = '{0!r} != {1!r} within {2!r} places', msg = None, args = (4,)

    def _raise_exceptions_if_any(self, failures, first, second, err_fmt_string, msg, *args):
        if len(failures) == 1:
            if failures[0]:
>               raise self.failureException(msg or err_fmt_string.format(first, second, *args))
E               AssertionError: quantity<1.25072398252 MSun> != quantity<1.2476 MSun> within 4 places

../../amusetest.py:73: AssertionError
__________________ TestSeBa.test_supernova_stopping_condition __________________

self = <amuse.test.suite.codes_tests.test_seba.TestSeBa testMethod=test_supernova_stopping_condition>

    def test_supernova_stopping_condition(self):
        """ Test supernova stopping condition """
        instance = self.new_instance_of_an_optional_code(SeBa)
        instance.stopping_conditions.supernova_detection.enable()
    
        p = Particle()
        p.mass = 10 | units.MSun
        p.metallicity = 0.02
    
        p = instance.particles.add_particle(p)
        instance.set_supernova_kick_velocity(0.0|units.kms)
        instance.evolve_model(30 | units.Myr)
        self.assertEqual(instance.stopping_conditions.supernova_detection.is_set(), True)
        self.assertEqual(instance.stopping_conditions.supernova_detection.particles(0)[0].key, p.key)
    
>       self.assertAlmostRelativeEqual(p.age, 27.35866 | units.Myr, 4)

test_seba.py:561: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../../amusetest.py:140: in failUnlessAlmostRelativeEqual
    self._raise_exceptions_if_any(failures, first, second, "{0!r} != {1!r} within {2!r} places", msg, places)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <amuse.test.suite.codes_tests.test_seba.TestSeBa testMethod=test_supernova_stopping_condition>
failures = array([ True], dtype=bool), first = quantity<27.2715197541 Myr>
second = quantity<27.35866 Myr>
err_fmt_string = '{0!r} != {1!r} within {2!r} places', msg = None, args = (4,)

    def _raise_exceptions_if_any(self, failures, first, second, err_fmt_string, msg, *args):
        if len(failures) == 1:
            if failures[0]:
>               raise self.failureException(msg or err_fmt_string.format(first, second, *args))
E               AssertionError: quantity<27.2715197541 Myr> != quantity<27.35866 Myr> within 4 places

../../amusetest.py:73: AssertionError
____________ TestSeBa.test_supernova_stopping_condition_in_a_binary ____________

self = <amuse.test.suite.codes_tests.test_seba.TestSeBa testMethod=test_supernova_stopping_condition_in_a_binary>

    def test_supernova_stopping_condition_in_a_binary(self):
        """ Test supernova stopping condition in a binary """
        instance = self.new_instance_of_an_optional_code(SeBa)
        instance.stopping_conditions.supernova_detection.enable()
    
        stars =  Particles(2)
        stars[0].mass = 10.0 | units.MSun
        stars[1].mass = 5.0 | units.MSun
        instance.particles.add_particles(stars)
    
        binaries =  Particles(1)
        binary = binaries[0]
        binary.semi_major_axis = 1.e6|units.RSun
        binary.eccentricity = 0.1
        binary.child1 = stars[0]
        binary.child2 = stars[1]
        instance.binaries.add_particles(binaries)
    
        instance.evolve_model(30 | units.Myr)
        self.assertEqual(instance.stopping_conditions.supernova_detection.is_set(), True)
        self.assertEqual(instance.stopping_conditions.supernova_detection.particles(0)[0].key, instance.binaries[0].child1.key)
        self.assertEqual(instance.stopping_conditions.supernova_detection.particles(0)[0].key, instance.particles[0].key)
    
        print(instance.parameters)
>       self.assertAlmostRelativeEqual(instance.particles[0].age, 27.35866 | units.Myr, 4)

test_seba.py:591: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../../amusetest.py:140: in failUnlessAlmostRelativeEqual
    self._raise_exceptions_if_any(failures, first, second, "{0!r} != {1!r} within {2!r} places", msg, places)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <amuse.test.suite.codes_tests.test_seba.TestSeBa testMethod=test_supernova_stopping_condition_in_a_binary>
failures = array([ True], dtype=bool), first = quantity<27.2715197541 Myr>
second = quantity<27.35866 Myr>
err_fmt_string = '{0!r} != {1!r} within {2!r} places', msg = None, args = (4,)

    def _raise_exceptions_if_any(self, failures, first, second, err_fmt_string, msg, *args):
        if len(failures) == 1:
            if failures[0]:
>               raise self.failureException(msg or err_fmt_string.format(first, second, *args))
E               AssertionError: quantity<27.2715197541 Myr> != quantity<27.35866 Myr> within 4 places

../../amusetest.py:73: AssertionError
----------------------------- Captured stdout call -----------------------------
is_logging_of_evolve_enabled: False
metallicity: 0.02
stopping_condition_maximum_density: 1.79769313486e+308 mass / (length**3)
stopping_condition_maximum_internal_energy: 1.79769313486e+308 length**2 / (time**2)
stopping_condition_minimum_density: -1.0 mass / (length**3)
stopping_condition_minimum_internal_energy: -1.0 length**2 / (time**2)
stopping_conditions_number_of_steps: 1
stopping_conditions_out_of_box_size: 0.0 length
stopping_conditions_out_of_box_use_center_of_mass: True
stopping_conditions_timeout: 4.0 s
supernova_kick_velocity: 600.0 kms

________ TestSeBa.test_supernova_stopping_condition_with_multiple_stars ________

self = <amuse.test.suite.codes_tests.test_seba.TestSeBa testMethod=test_supernova_stopping_condition_with_multiple_stars>

    def test_supernova_stopping_condition_with_multiple_stars(self):
        """ Test supernova stopping condition with multiple stars """
        instance = self.new_instance_of_an_optional_code(SeBa)
        instance.stopping_conditions.supernova_detection.enable()
    
        stars =  Particles(3)
        stars[0].mass = 10.0 | units.MSun
        stars[1].mass = 5.0 | units.MSun
        stars[2].mass = 0.5 | units.MSun
        instance.particles.add_particles(stars)
    
    
        instance.evolve_model(30 | units.Myr)
        self.assertEqual(instance.stopping_conditions.supernova_detection.is_set(), True)
        self.assertEqual(instance.stopping_conditions.supernova_detection.particles(0)[0].key, instance.particles[0].key)
    
>       self.assertAlmostRelativeEqual(instance.particles[0].age, 27.35866 | units.Myr, 4)

test_seba.py:619: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../../amusetest.py:140: in failUnlessAlmostRelativeEqual
    self._raise_exceptions_if_any(failures, first, second, "{0!r} != {1!r} within {2!r} places", msg, places)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <amuse.test.suite.codes_tests.test_seba.TestSeBa testMethod=test_supernova_stopping_condition_with_multiple_stars>
failures = array([ True], dtype=bool), first = quantity<27.2715197541 Myr>
second = quantity<27.35866 Myr>
err_fmt_string = '{0!r} != {1!r} within {2!r} places', msg = None, args = (4,)

    def _raise_exceptions_if_any(self, failures, first, second, err_fmt_string, msg, *args):
        if len(failures) == 1:
            if failures[0]:
>               raise self.failureException(msg or err_fmt_string.format(first, second, *args))
E               AssertionError: quantity<27.2715197541 Myr> != quantity<27.35866 Myr> within 4 places

../../amusetest.py:73: AssertionError
_ TestSeBa.test_supernova_stopping_condition_with_multiple_stars_multiple_supernovae _

self = <amuse.test.suite.codes_tests.test_seba.TestSeBa testMethod=test_supernova_stopping_condition_with_multiple_stars_multiple_supernovae>

    def test_supernova_stopping_condition_with_multiple_stars_multiple_supernovae(self):
        """ Test supernova stopping condition with multiple stars """
        instance = self.new_instance_of_an_optional_code(SeBa)
        instance.stopping_conditions.supernova_detection.enable()
    
        stars =  Particles(3)
        stars[0].mass = 10.0 | units.MSun
        stars[1].mass = 11.0 | units.MSun
        stars[2].mass = 0.5 | units.MSun
        instance.particles.add_particles(stars)
    
    
        instance.evolve_model(30 | units.Myr)
        self.assertEqual(instance.stopping_conditions.supernova_detection.is_set(), True)
        self.assertEqual(instance.stopping_conditions.supernova_detection.particles(0)[0].key, instance.particles[1].key)
    
>       self.assertAlmostRelativeEqual(instance.particles[0].age, 23.08688 | units.Myr, 4)

test_seba.py:643: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../../amusetest.py:140: in failUnlessAlmostRelativeEqual
    self._raise_exceptions_if_any(failures, first, second, "{0!r} != {1!r} within {2!r} places", msg, places)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <amuse.test.suite.codes_tests.test_seba.TestSeBa testMethod=test_supernova_stopping_condition_with_multiple_stars_multiple_supernovae>
failures = array([ True], dtype=bool), first = quantity<23.0210208627 Myr>
second = quantity<23.08688 Myr>
err_fmt_string = '{0!r} != {1!r} within {2!r} places', msg = None, args = (4,)

    def _raise_exceptions_if_any(self, failures, first, second, err_fmt_string, msg, *args):
        if len(failures) == 1:
            if failures[0]:
>               raise self.failureException(msg or err_fmt_string.format(first, second, *args))
E               AssertionError: quantity<23.0210208627 Myr> != quantity<23.08688 Myr> within 4 places

../../amusetest.py:73: AssertionError
_ TestSeBa.test_supernova_stopping_condition_with_multiple_stars_of_equal_mass _

self = <amuse.test.suite.codes_tests.test_seba.TestSeBa testMethod=test_supernova_stopping_condition_with_multiple_stars_of_equal_mass>

    def test_supernova_stopping_condition_with_multiple_stars_of_equal_mass(self):
        """ Test supernova stopping condition with multiple stars of equal mass """
        instance = self.new_instance_of_an_optional_code(SeBa)
        instance.stopping_conditions.supernova_detection.enable()
    
        stars =  Particles(3)
        stars[0].mass = 10.0 | units.MSun
        stars[1].mass = 10.0 | units.MSun
        stars[2].mass = 0.5 | units.MSun
        instance.particles.add_particles(stars)
    
    
        instance.evolve_model(30 | units.Myr)
        self.assertEqual(instance.stopping_conditions.supernova_detection.is_set(), True)
        self.assertEqual(len(instance.stopping_conditions.supernova_detection.particles(0)), 2)
        self.assertEqual(instance.stopping_conditions.supernova_detection.particles(0)[0].key, instance.particles[0].key)
        self.assertEqual(instance.stopping_conditions.supernova_detection.particles(0)[1].key, instance.particles[1].key)
    
>       self.assertAlmostRelativeEqual(instance.particles[0].age, 27.35866 | units.Myr, 4)

test_seba.py:681: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../../amusetest.py:140: in failUnlessAlmostRelativeEqual
    self._raise_exceptions_if_any(failures, first, second, "{0!r} != {1!r} within {2!r} places", msg, places)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <amuse.test.suite.codes_tests.test_seba.TestSeBa testMethod=test_supernova_stopping_condition_with_multiple_stars_of_equal_mass>
failures = array([ True], dtype=bool), first = quantity<27.2715197541 Myr>
second = quantity<27.35866 Myr>
err_fmt_string = '{0!r} != {1!r} within {2!r} places', msg = None, args = (4,)

    def _raise_exceptions_if_any(self, failures, first, second, err_fmt_string, msg, *args):
        if len(failures) == 1:
            if failures[0]:
>               raise self.failureException(msg or err_fmt_string.format(first, second, *args))
E               AssertionError: quantity<27.2715197541 Myr> != quantity<27.35866 Myr> within 4 places

../../amusetest.py:73: AssertionError
=============================== warnings summary ===============================
src/amuse/test/suite/codes_tests/test_seba.py: 14 warnings
  /Users/srieder/Code/amuse-clean/src/amuse/datamodel/memory_storage.py:532: DeprecationWarning: `np.object` is a deprecated alias for the builtin `object`. To silence this warning, use `object` by itself. Doing this will not modify any behavior and is safe. 
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    elif dtype == numpy.object:

src/amuse/test/suite/codes_tests/test_seba.py::TestSeBa::test_add_binary_particles
src/amuse/test/suite/codes_tests/test_seba.py::TestSeBa::test_add_binary_particles
src/amuse/test/suite/codes_tests/test_seba.py::TestSeBa::test_evolution_of_close_binary_system
src/amuse/test/suite/codes_tests/test_seba.py::TestSeBa::test_evolution_of_close_binary_system
src/amuse/test/suite/codes_tests/test_seba.py::TestSeBa::test_set_semi_major_axis_eccentricity
src/amuse/test/suite/codes_tests/test_seba.py::TestSeBa::test_set_semi_major_axis_eccentricity
src/amuse/test/suite/codes_tests/test_seba.py::TestSeBa::test_supernova_stopping_condition_in_a_binary
src/amuse/test/suite/codes_tests/test_seba.py::TestSeBa::test_supernova_stopping_condition_in_a_binary
  /Users/srieder/Code/amuse-clean/src/amuse/datamodel/memory_storage.py:683: DeprecationWarning: `np.object` is a deprecated alias for the builtin `object`. To silence this warning, use `object` by itself. Doing this will not modify any behavior and is safe. 
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    dtype = numpy.object

src/amuse/test/suite/codes_tests/test_seba.py: 136 warnings
  /Users/srieder/Code/amuse-clean/src/amuse/support/interface.py:120: DeprecationWarning: `np.object` is a deprecated alias for the builtin `object`. To silence this warning, use `object` by itself. Doing this will not modify any behavior and is safe. 
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    result = base.LinkedArray(numpy.empty(len(keys), dtype= numpy.object))

-- Docs: https://docs.pytest.org/en/stable/warnings.html
=========================== short test summary info ============================
FAILED test_seba.py::TestSeBa::test_add_stars_at_different_times - AssertionE...
FAILED test_seba.py::TestSeBa::test_supernova_stopping_condition - AssertionE...
FAILED test_seba.py::TestSeBa::test_supernova_stopping_condition_in_a_binary
FAILED test_seba.py::TestSeBa::test_supernova_stopping_condition_with_multiple_stars
FAILED test_seba.py::TestSeBa::test_supernova_stopping_condition_with_multiple_stars_multiple_supernovae
FAILED test_seba.py::TestSeBa::test_supernova_stopping_condition_with_multiple_stars_of_equal_mass
================== 6 failed, 16 passed, 158 warnings in 5.83s ==================

[rieder]

@silviatoonen It would be good to also add tests for the new methods of course...

[rieder]

Ok, the tests are all passing again, so this can be merged (I'll do this).
Still, we should add tests for the new methods too!