diff --git a/README.rst b/README.rst index b8e3f11..e68c77e 100644 --- a/README.rst +++ b/README.rst @@ -140,7 +140,7 @@ As ``Formula``, also ``StatefulSpecies`` have ``html`` and ``latex`` attributes. \mathrm{Ne}^{+} \; 1s^{2}2s^{2}2p^{5}; \; {}^{2}P_{1/2} >>> StatefulSpecies('(52Cr)(1H) 1sigma2.2sigma1.1delta2.1pi2; 6SIGMA+; v=0; J=2').html - '52Cr1H 1σ2.2σ1.1δ2.1π2; 6Σ+; v=0; J=2' + '52Cr1H 1σ2.2σ1.1δ2.1π2 6Σ+ v=0 J=2' Reaction @@ -155,13 +155,13 @@ separated by ``' -> '``, such as >>> from pyvalem.reaction import Reaction >>> reaction = Reaction('He+2 + H -> He+ 3p1 + H+ + hv') >>> reaction - He+2 + H → He+ 3p1 + H+ + hν + He+2 + H → He+ 3p + H+ + hν >>> reaction.html - 'He2+ + H → He+ 3p1 + H+ + hν' + 'He2+ + H → He+ 3p + H+ + hν' >>> print(reaction.latex) - \mathrm{He}^{2+} + \mathrm{H} \rightarrow \mathrm{He}^{+} \; 3p^{1} + \mathrm{H}^{+} + h\nu + \mathrm{He}^{2+} + \mathrm{H} \rightarrow \mathrm{He}^{+} \; 3p + \mathrm{H}^{+} + h\nu The ``Reaction`` class also watches out for charge balance and stoichiometry conservation during instantiation. @@ -216,4 +216,4 @@ Always make sure to format your code before submitting a pull request, by runnin .. _GitHub: https://github.com/xnx/pyvalem .. _PyPI: https://pypi.org/project/pyvalem/ -.. _numpydoc: https://numpydoc.readthedocs.io/en/latest/format.html \ No newline at end of file +.. _numpydoc: https://numpydoc.readthedocs.io/en/latest/format.html diff --git a/doc/introduction.rst b/doc/introduction.rst index 4ccbb44..0295ac9 100644 --- a/doc/introduction.rst +++ b/doc/introduction.rst @@ -126,14 +126,14 @@ As ``Formula``, also ``StatefulSpecies`` have ``html`` and ``latex`` attributes. \mathrm{Ne}^{+} \; 1s^{2}2s^{2}2p^{5}; \; {}^{2}P_{1/2} >>> StatefulSpecies('(52Cr)(1H) 1sigma2.2sigma1.1delta2.1pi2; 6SIGMA+; v=0; J=2').html - '52Cr1H 1σ2.2σ1.1δ2.1π2; 6Σ+; v=0; J=2' + '52Cr1H 1σ2.2σ1.1δ2.1π2 6Σ+ v=0 J=2' These two examples render as: .. raw:: html - Ne+ 1s22s22p5; 2P1/2
- 52Cr1H 1σ2.2σ1.1δ2.1π2; 6Σ+; v=0; J=2 + Ne+ 1s22s22p5 2P1/2
+ 52Cr1H 1σ2.2σ1.1δ2.1π2 6Σ+ v=0 J=2 Reaction @@ -148,13 +148,13 @@ separated by ``' -> '``, such as >>> from pyvalem.reaction import Reaction >>> reaction = Reaction('He+2 + H -> He+ 3p1 + H+ + hv') >>> reaction - He+2 + H → He+ 3p1 + H+ + hν + He+2 + H → He+ 3p + H+ + hν >>> reaction.html - 'He2+ + H → He+ 3p1 + H+ + hν' + 'He2+ + H → He+ 3p + H+ + hν' >>> print(reaction.latex) - \mathrm{He}^{2+} + \mathrm{H} \rightarrow \mathrm{He}^{+} \; 3p^{1} + \mathrm{H}^{+} + h\nu + \mathrm{He}^{2+} + \mathrm{H} \rightarrow \mathrm{He}^{+} \; 3p + \mathrm{H}^{+} + h\nu The ``Reaction`` class also watches out for charge balance and stoichiometry conservation during instantiation. diff --git a/doc/reaction.rst b/doc/reaction.rst index 9140dbb..ae3e6ac 100644 --- a/doc/reaction.rst +++ b/doc/reaction.rst @@ -23,7 +23,7 @@ Examples An HTML representation of the reaction is stored as the ``html`` attribute:: >>> print(r2.html) - CO v=1 + O2 J=2; X3Σ-g → CO2 + O + CO v=1 + O2 J=2 X3Σ-g → CO2 + O >>> print(r4.html) C6H5OH + 7O2 → 6CO2 + 3H2O diff --git a/doc/stateful_species.rst b/doc/stateful_species.rst index 4088f05..646c594 100644 --- a/doc/stateful_species.rst +++ b/doc/stateful_species.rst @@ -26,13 +26,13 @@ An HTML representation is accessible through the ``html`` attribute: .. code-block:: pycon >>> print(ss4.html) - CrH 1σ2.2σ1.1π4.3σ1; 6Σ+ + CrH 1σ2.2σ1.1π4.3σ1 6Σ+ This example renders as: .. raw:: html - CrH 1σ2.2σ1.1π4.3σ1; 6Σ+ + CrH 1σ2.2σ1.1π4.3σ1 6Σ+ The ``Formula`` object and a list of the parse ``State`` objects are returned by the @@ -70,4 +70,4 @@ This is checked for: >>> StatefulSpecies('Li 1s2.2s1; 1s2.2p1') Traceback (most recent call last): ... - pyvalem.stateful_species.StatefulSpeciesError: Multiple states of type AtomicConfiguration specified for Li 1s2.2p1;1s2.2s1 + pyvalem.stateful_species.StatefulSpeciesError: Multiple states of type AtomicConfiguration specified for Li 1s2.2p;1s2.2s diff --git a/setup.py b/setup.py index 212d313..65bec1e 100644 --- a/setup.py +++ b/setup.py @@ -8,7 +8,7 @@ setup( name="pyvalem", - version="2.5.2", + version="2.5.3", description="A package for managing simple chemical species and states", long_description=long_description, long_description_content_type="text/x-rst", diff --git a/src/pyvalem/reaction.py b/src/pyvalem/reaction.py index 9c24f55..2df3f57 100644 --- a/src/pyvalem/reaction.py +++ b/src/pyvalem/reaction.py @@ -120,7 +120,7 @@ class Reaction: >>> # HTML attribute >>> r1.html - 'CO v=1 + O2 J=2; X3Σ-g → CO2 + O' + 'CO v=1 + O2 J=2 X3Σ-g → CO2 + O' >>> # Consistency checks >>> Reaction('BeH+ + I2 <-> BeI + HI') diff --git a/src/pyvalem/stateful_species.py b/src/pyvalem/stateful_species.py index f349b60..02610b2 100644 --- a/src/pyvalem/stateful_species.py +++ b/src/pyvalem/stateful_species.py @@ -139,7 +139,7 @@ def verify_multiple_key_value_pairs(self): def html(self): if not self.states: return self.formula.html - return "{} {}".format(self.formula.html, "; ".join(s.html for s in self.states)) + return "{} {}".format(self.formula.html, " ".join(s.html for s in self.states)) @property def latex(self): diff --git a/src/pyvalem/states/atomic_configuration.py b/src/pyvalem/states/atomic_configuration.py index 06a914f..b13bc65 100644 --- a/src/pyvalem/states/atomic_configuration.py +++ b/src/pyvalem/states/atomic_configuration.py @@ -63,7 +63,7 @@ class AtomicOrbital: l : int, optional The azimuthal quantum number (0, 1, 2, ..., n-1) At least one of {`l`, `lletter`} must be passed. - nocc : int, default: 0 + nocc : int, default: 1 Number of occupied electrons. lletter : str, optional The letter corresponding to l: 's', 'p', 'd', ... for l = 0, 1, 2, ... @@ -115,7 +115,9 @@ def __init__(self, n, l=None, nocc=0, lletter=None): self._validate_atomic_orbital() def __repr__(self): - return "{}{}{}".format(self.n, self.lletter, self.nocc) + if self.nocc != 1: + return "{}{}{}".format(self.n, self.lletter, self.nocc) + return "{}{}".format(self.n, self.lletter) @property def html(self): @@ -125,7 +127,9 @@ def html(self): ------- str """ - return "{}{}{}".format(self.n, self.lletter, self.nocc) + if self.nocc != 1: + return "{}{}{}".format(self.n, self.lletter, self.nocc) + return "{}{}".format(self.n, self.lletter) @property def latex(self): @@ -135,7 +139,9 @@ def latex(self): ------- str """ - return "{}{}^{{{}}}".format(self.n, self.lletter, self.nocc) + if self.nocc != 1: + return "{}{}^{{{}}}".format(self.n, self.lletter, self.nocc) + return "{}{}".format(self.n, self.lletter) def _validate_atomic_orbital(self): """Validator method for the atomic orbital class. @@ -209,11 +215,11 @@ class AtomicConfiguration(State): (3, 1, 1) >>> repr(ac1) - '1s2.2s2.2p6.3p1' + '1s2.2s2.2p6.3p' >>> ac2 = AtomicConfiguration("[Ne].3p") >>> repr(ac2) - '1s2.2s2.2p6.3p1' + '1s2.2s2.2p6.3p' """ def __init__(self, state_str): diff --git a/tests/test_atomic_configurations.py b/tests/test_atomic_configurations.py index e908927..f994b64 100644 --- a/tests/test_atomic_configurations.py +++ b/tests/test_atomic_configurations.py @@ -18,7 +18,7 @@ def test_atomic_configuration(self): c2 = AtomicConfiguration("1s2.2s2.2p6") c3 = AtomicConfiguration("1s2.2s2.2p6.3s2.3d10") c4 = AtomicConfiguration("[He].2s1") - c5 = AtomicConfiguration("2s2.2p1.3s1") + c5 = AtomicConfiguration("2s2.2p1.3s") self.assertRaises(AtomicConfigurationError, AtomicConfiguration, "s4.w2") self.assertRaises(AtomicConfigurationError, AtomicConfiguration, "1s 2.2s2") @@ -71,8 +71,8 @@ def test_excited_atomic_configuration(self): def test_atomic_configuration_repr(self): c1 = AtomicConfiguration("1s2.2s2.2p6.3s2.3p6.4s2.3d") c2 = AtomicConfiguration("[Ar].4s2.3d1") - self.assertEqual(repr(c1), "1s2.2s2.2p6.3s2.3p6.4s2.3d1") - self.assertEqual(repr(c2), "1s2.2s2.2p6.3s2.3p6.4s2.3d1") + self.assertEqual(repr(c1), "1s2.2s2.2p6.3s2.3p6.4s2.3d") + self.assertEqual(repr(c2), "1s2.2s2.2p6.3s2.3p6.4s2.3d") def test_atomic_configuration_default_nocc(self): c1 = AtomicConfiguration("1s") diff --git a/tests/test_reaction.py b/tests/test_reaction.py index dd3d274..c1c2dbc 100644 --- a/tests/test_reaction.py +++ b/tests/test_reaction.py @@ -68,7 +68,7 @@ def test_reaction_parsing(self): self.assertEqual(r2.reactants[1][1].states[1].__repr__(), "X(3Σ-g)") self.assertEqual( r2.html, - "CO v=1 + O2 J=2; " + "CO v=1 + O2 J=2 " "X3Σ-g → " "CO2 + O", ) diff --git a/tests/test_stateful_species.py b/tests/test_stateful_species.py index 23f4800..6b33137 100644 --- a/tests/test_stateful_species.py +++ b/tests/test_stateful_species.py @@ -68,7 +68,7 @@ def test_atomic_configuration_verification(self): self.assertTrue(ss1.verify_atomic_configuration()) ss2 = StatefulSpecies("Ar+ 1s2.2s2.2p6.3s2.3p6") ss3 = StatefulSpecies("Ar+ [Ne].3s2.3p6") - ss4 = StatefulSpecies("Ar+ [Ne].3s2.3p6.4s1") + ss4 = StatefulSpecies("Ar+ [Ne].3s2.3p6.4s") for ss in (ss2, ss3, ss4): self.assertRaises(StatefulSpeciesError, ss.verify_atomic_configuration) @@ -97,10 +97,10 @@ def test_stateful_species_repr(self): self.assertEqual(repr(ss2), "(235U) 3*;l=0;n=1") for ss_text in ["C+ 4P;2s2.2p1", "C+ 2s2.2p1;4P"]: - self.assertEqual(repr(StatefulSpecies(ss_text)), "C+ 2s2.2p1;4P") + self.assertEqual(repr(StatefulSpecies(ss_text)), "C+ 2s2.2p;4P") for ss_text in ["C+ 2P;2s2.2p1", "C+ 2s2.2p1;2P"]: - self.assertEqual(repr(StatefulSpecies(ss_text)), "C+ 2s2.2p1;2P") + self.assertEqual(repr(StatefulSpecies(ss_text)), "C+ 2s2.2p;2P") if __name__ == "__main__":