#!/usr/bin/env python import sys, os, tempfile import unittest import gi gi.require_version('v_sim', '3.8') from gi.repository import GLib, v_sim import signals class TestLoader(unittest.TestCase): def setUp(self): super(TestLoader, self).setUp() self.addTypeEqualityFunc(float, self.fuzzyFloat) def fuzzyFloat(self, a, b, msg = None): if abs(b-a) > 1e-8: raise self.failureException(msg if msg is not None else "%g != %g (d = %g)" % (a, b, abs(a-b))) def _loader(self, l, path, expectation = {}): data = v_sim.DataAtomic.new(path, l) try: ok = data.load(0, None) except: ok = False self.assertEqual(ok, expectation["success"]) if ok: for (k, v) in expectation.items(): if k.startswith("data."): #print eval(k), v self.assertEqual(eval(k), v) def _tempFile(self, string): f = tempfile.NamedTemporaryFile() f.write(string) f.flush() return f def test_ascii_file(self): self._loader(v_sim.DataLoader.ascii_getStatic(), os.path.join(os.path.dirname(sys.argv[0]), "../../examples/demo.ascii"), {"success": True, "data.getNNodes()": 172, "data.getNElements(True)": 2, "data.containsElement(v_sim.Element.retrieveFromName(\"H\")[0])": False, "data.containsElement(v_sim.Element.lookup(\"Ni\"))": True, "data.containsElement(v_sim.Element.lookup(\"Au\"))": True, "data.getBox().getUnit()": v_sim.Units.ANGSTROEM, "data.getBox().getBoundary()": v_sim.BoxBoundaries.PERIODIC, "data.getBox().getPeriodicity()": [True, True, True], }) def test_ascii_wrong_file(self): self._loader(v_sim.DataLoader.ascii_getStatic(), os.path.join(os.path.dirname(sys.argv[0]), "../../examples/demo.xyz"), {"success": False}) def test_ascii_unit_bohr(self): with self._tempFile("""test 10 0 10 0 0 10 #keyword: bohr 0 0 0 Si """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.getBox().getUnit()": v_sim.Units.BOHR}) def test_ascii_unit_angstroem(self): with self._tempFile("""test 10 0 10 0 0 10 #keyword: Angstroem 0 0 0 Si """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.getBox().getUnit()": v_sim.Units.ANGSTROEM}) def test_ascii_unit_undefined(self): with self._tempFile("""test 10 0 10 0 0 10 0 0 0 Si """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.getBox().getUnit()": v_sim.Units.UNDEFINED}) def test_ascii_box_periodic(self): with self._tempFile("""test 10 0 10 0 0 10 #keyword: periodic 0 0 0 Si """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.getBox().getBoundary()": v_sim.BoxBoundaries.PERIODIC}) with self._tempFile("""test 10 0 10 0 0 10 0 0 0 Si """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.getBox().getBoundary()": v_sim.BoxBoundaries.PERIODIC}) def test_ascii_box_free(self): with self._tempFile("""test 10 0 10 0 0 10 #keyword: freeBC 0 0 0 Si """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.getBox().getBoundary()": v_sim.BoxBoundaries.FREE}) def test_ascii_box_surface(self): with self._tempFile("""test 10 0 10 0 0 10 #keyword: surface 0 0 0 Si """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.getBox().getBoundary()": v_sim.BoxBoundaries.SURFACE_ZX}) def test_ascii_box(self): with self._tempFile("""test 1 2 3 4 5 6 0 0 0 Si """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.getBox().getGeometry(v_sim.BoxVector.DXX)": 1., "data.getBox().getGeometry(v_sim.BoxVector.DYX)": 2., "data.getBox().getGeometry(v_sim.BoxVector.DYY)": 3., "data.getBox().getGeometry(v_sim.BoxVector.DZX)": 4., "data.getBox().getGeometry(v_sim.BoxVector.DZY)": 5., "data.getBox().getGeometry(v_sim.BoxVector.DZZ)": 6.}) def test_ascii_box_angdeg(self): with self._tempFile("""test 1 2 3 90 90 90 #keyword: angdeg 0 0 0 Si """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.getBox().getGeometry(v_sim.BoxVector.DXX)": 1., "data.getBox().getGeometry(v_sim.BoxVector.DYX)": 0., "data.getBox().getGeometry(v_sim.BoxVector.DYY)": 2., "data.getBox().getGeometry(v_sim.BoxVector.DZX)": 0., "data.getBox().getGeometry(v_sim.BoxVector.DZY)": 0., "data.getBox().getGeometry(v_sim.BoxVector.DZZ)": 3.}) def test_ascii_reduced(self): with self._tempFile("""test 1 0 2 0 0 3 #keyword: reduced 0.5 0.75 0.333333333333 Si """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.getNodeCoordinates(data.getFromId(0), False)": (0.5, 1.5, 1.)}) def test_ascii_coord(self): with self._tempFile("""test 1 0 2 0 0 3 1 2 3 Si """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.getNodeCoordinates(data.getFromId(0), False)": (1., 2., 3.)}) def test_ascii_coord_user(self): with self._tempFile("""test 1 0 2 0 0 3 #keyword: freeBC 1 2 3 Si """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.getNodeCoordinates(data.getFromId(0), True)": (1., 2., 3.), "data.getNodeCoordinates(data.getFromId(0), False)": (0., 0., 0.)}) def test_ascii_props(self): with self._tempFile("""test 1 0 2 0 0 3 1 2 3 Si hello 0 0 0 C {"IGSpin": -1} """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.getNodeLabelAt(data.getFromId(0))": "hello", "data.getNodeProperties(\"IGSpin\").getAt(data.getFromId(1))[1]": -1}) def test_ascii_energy(self): with self._tempFile("""test 1 0 2 0 0 3 #metaData: totalEnergy = 10. 1 2 3 Si # """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.get_property(\"totalEnergy\")": 10.}) def test_ascii_energy_ht(self): with self._tempFile("""test 1 0 2 0 0 3 #metaData: totalEnergy = 1. Ht 1 2 3 Si # """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.get_property(\"totalEnergy\")": 27.21138386}) def test_ascii_forces(self): with self._tempFile("""test 1 0 2 0 0 3 1 2 3 Si 0 0 0 Si #metaData: forces = [\ # 1, 2, 3, \ # 4, 5, 6] # """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.getForces(False).getAt(data.getFromId(0))": [1, 2, 3], "data.getForces(False).getAt(data.getFromId(1))": [4, 5, 6]}) def test_ascii_forces_none(self): with self._tempFile("""test 1 0 2 0 0 3 1 2 3 Si 0 0 0 Si """) as f: self._loader(v_sim.DataLoader.ascii_getStatic(), f.name, {"success": True, "data.getForces(False)": None, "data.getForces(True).getAt(data.getFromId(0))": [0, 0, 0]}) def test_xyz_file(self): self._loader(v_sim.DataLoader.xyz_getStatic(), os.path.join(os.path.dirname(sys.argv[0]), "../../examples/demo.xyz"), {"success": True, "data.getNNodes()": 950, "data.getNElements(True)": 2, "data.containsElement(v_sim.Element.retrieveFromName(\"H\")[0])": False, "data.containsElement(v_sim.Element.lookup(\"Ni\"))": True, "data.containsElement(v_sim.Element.lookup(\"C\"))": True, "data.getBox().getUnit()": v_sim.Units.UNDEFINED, "data.getBox().getBoundary()": v_sim.BoxBoundaries.FREE, "data.getBox().getPeriodicity()": [False, False, False], }) def test_xyz_wrong_file(self): self._loader(v_sim.DataLoader.xyz_getStatic(), os.path.join(os.path.dirname(sys.argv[0]), "../../examples/demo.ascii"), {"success": False}) def test_xyz_unit_bohr(self): with self._tempFile("""1 bohr Si 0 0 0 """) as f: self._loader(v_sim.DataLoader.xyz_getStatic(), f.name, {"success": True, "data.getBox().getUnit()": v_sim.Units.BOHR}) def test_xyz_unit_angstroem(self): with self._tempFile("""1 angstroem Si 0 0 0 """) as f: self._loader(v_sim.DataLoader.xyz_getStatic(), f.name, {"success": True, "data.getBox().getUnit()": v_sim.Units.ANGSTROEM}) def test_xyz_unit_undefined(self): with self._tempFile("""1 Si 0 0 0 """) as f: self._loader(v_sim.DataLoader.xyz_getStatic(), f.name, {"success": True, "data.getBox().getUnit()": v_sim.Units.UNDEFINED}) def test_xyz_box_periodic(self): with self._tempFile("""1 periodic 10 10 10 # coming from a surface file Si 0 0 0 """) as f: self._loader(v_sim.DataLoader.xyz_getStatic(), f.name, {"success": True, "data.getBox().getBoundary()": v_sim.BoxBoundaries.PERIODIC}) def test_xyz_box_free(self): with self._tempFile("""1 Si 0 0 0 """) as f: self._loader(v_sim.DataLoader.xyz_getStatic(), f.name, {"success": True, "data.getBox().getBoundary()": v_sim.BoxBoundaries.FREE}) def test_xyz_box_surface(self): with self._tempFile("""1 surface 10 10 10 # coming from a periodic file Si 0 0 0 """) as f: self._loader(v_sim.DataLoader.xyz_getStatic(), f.name, {"success": True, "data.getBox().getBoundary()": v_sim.BoxBoundaries.SURFACE_ZX}) def test_xyz_box(self): with self._tempFile("""1 periodic 1 2 3 Si 0 0 0 """) as f: self._loader(v_sim.DataLoader.xyz_getStatic(), f.name, {"success": True, "data.getBox().getGeometry(v_sim.BoxVector.DXX)": 1., "data.getBox().getGeometry(v_sim.BoxVector.DYX)": 0., "data.getBox().getGeometry(v_sim.BoxVector.DYY)": 2., "data.getBox().getGeometry(v_sim.BoxVector.DZX)": 0., "data.getBox().getGeometry(v_sim.BoxVector.DZY)": 0., "data.getBox().getGeometry(v_sim.BoxVector.DZZ)": 3.}) def test_xyz_coord(self): with self._tempFile("""1 periodic 10 10 10 Si 1 2 3 """) as f: self._loader(v_sim.DataLoader.xyz_getStatic(), f.name, {"success": True, "data.getNodeCoordinates(data.getFromId(0), False)": (1., 2., 3.)}) def test_xyz_coord_user(self): with self._tempFile("""1 Si 1 2 3 """) as f: self._loader(v_sim.DataLoader.xyz_getStatic(), f.name, {"success": True, "data.getNodeCoordinates(data.getFromId(0), True)": (1., 2., 3.), "data.getNodeCoordinates(data.getFromId(0), False)": (0., 0., 0.)}) def test_xyz_props(self): with self._tempFile("""2 Si 1 2 3 hello C 0 0 0 {"IGSpin": -1} """) as f: self._loader(v_sim.DataLoader.xyz_getStatic(), f.name, {"success": True, "data.getNodeLabelAt(data.getFromId(0))": "hello", "data.getNodeProperties(\"IGSpin\").getAt(data.getFromId(1))[1]": -1}) def test_xyz_forces(self): with self._tempFile("""2 Si 1 2 3 Si 0 0 0 FoRceS Si 1 2 3 Si 4 5 6 """) as f: self._loader(v_sim.DataLoader.xyz_getStatic(), f.name, {"success": True, "data.getForces(False).getAt(data.getFromId(0))": [1, 2, 3], "data.getForces(False).getAt(data.getFromId(1))": [4, 5, 6]}) def test_xyz_forces_none(self): with self._tempFile("""2 Si 1 2 3 Si 0 0 0 """) as f: self._loader(v_sim.DataLoader.xyz_getStatic(), f.name, {"success": True, "data.getForces(False)": None, "data.getForces(True).getAt(data.getFromId(0))": [0, 0, 0]}) def test_yaml_file(self): self._loader(v_sim.DataLoader.yaml_getStatic(), os.path.join(os.path.dirname(sys.argv[0]), "../../examples/cinchonidine.yaml"), {"success": True, "data.getNNodes()": 44, "data.getNElements(True)": 4, "data.containsElement(v_sim.Element.retrieveFromName(\"Ni\")[0])": False, "data.containsElement(v_sim.Element.lookup(\"H\"))": True, "data.containsElement(v_sim.Element.lookup(\"C\"))": True, "data.containsElement(v_sim.Element.lookup(\"O\"))": True, "data.containsElement(v_sim.Element.lookup(\"N\"))": True, "data.getBox().getUnit()": v_sim.Units.BOHR, "data.getBox().getBoundary()": v_sim.BoxBoundaries.FREE, "data.getBox().getPeriodicity()": [False, False, False], }) def test_yaml_wrong_file(self): self._loader(v_sim.DataLoader.yaml_getStatic(), os.path.join(os.path.dirname(sys.argv[0]), "../../examples/demo.ascii"), {"success": False}) def test_yaml_unit_bohr(self): with self._tempFile("""positions: - H: [0., 0., 0.] """) as f: self._loader(v_sim.DataLoader.yaml_getStatic(), f.name, {"success": True, "data.getBox().getUnit()": v_sim.Units.BOHR}) with self._tempFile("""units: bohr positions: - H: [0., 0., 0.] """) as f: self._loader(v_sim.DataLoader.yaml_getStatic(), f.name, {"success": True, "data.getBox().getUnit()": v_sim.Units.BOHR}) def test_yaml_unit_angstroem(self): with self._tempFile("""units: angstroem positions: - H: [0., 0., 0.] """) as f: self._loader(v_sim.DataLoader.yaml_getStatic(), f.name, {"success": True, "data.getBox().getUnit()": v_sim.Units.ANGSTROEM}) def test_yaml_box_periodic(self): with self._tempFile("""cell: [10., 10., 10.] positions: - H: [0., 0., 0.] """) as f: self._loader(v_sim.DataLoader.yaml_getStatic(), f.name, {"success": True, "data.getBox().getBoundary()": v_sim.BoxBoundaries.PERIODIC}) def test_yaml_box_free(self): with self._tempFile("""positions: - H: [0., 0., 0.] """) as f: self._loader(v_sim.DataLoader.yaml_getStatic(), f.name, {"success": True, "data.getBox().getBoundary()": v_sim.BoxBoundaries.FREE}) with self._tempFile("""cell: [.inf, .inf, .inf] positions: - H: [0., 0., 0.] """) as f: self._loader(v_sim.DataLoader.yaml_getStatic(), f.name, {"success": True, "data.getBox().getBoundary()": v_sim.BoxBoundaries.FREE}) def test_yaml_box_surface(self): with self._tempFile("""cell: [10., .inf, 10.] positions: - H: [0., 0., 0.] """) as f: self._loader(v_sim.DataLoader.yaml_getStatic(), f.name, {"success": True, "data.getBox().getBoundary()": v_sim.BoxBoundaries.SURFACE_ZX}) def test_yaml_box(self): with self._tempFile("""cell: [1., 2., 3.] positions: - H: [0., 0., 0.] """) as f: self._loader(v_sim.DataLoader.yaml_getStatic(), f.name, {"success": True, "data.getBox().getGeometry(v_sim.BoxVector.DXX)": 1., "data.getBox().getGeometry(v_sim.BoxVector.DYX)": 0., "data.getBox().getGeometry(v_sim.BoxVector.DYY)": 2., "data.getBox().getGeometry(v_sim.BoxVector.DZX)": 0., "data.getBox().getGeometry(v_sim.BoxVector.DZY)": 0., "data.getBox().getGeometry(v_sim.BoxVector.DZZ)": 3.}) def test_yaml_coord(self): with self._tempFile("""cell: [10., 10., 10.] positions: - Si: [1., 2., 3.] """) as f: self._loader(v_sim.DataLoader.yaml_getStatic(), f.name, {"success": True, "data.getNodeCoordinates(data.getFromId(0), False)": (1., 2., 3.)}) def test_yaml_coord_user(self): with self._tempFile("""positions: - Si: [1., 2., 3.] """) as f: self._loader(v_sim.DataLoader.yaml_getStatic(), f.name, {"success": True, "data.getNodeCoordinates(data.getFromId(0), True)": (1., 2., 3.), "data.getNodeCoordinates(data.getFromId(0), False)": (0., 0., 0.)}) def test_yaml_props(self): with self._tempFile("""positions: - {Si: [1., 2., 3.]} - {C: [0., 0., 0.], IGSpin: -1} """) as f: self._loader(v_sim.DataLoader.yaml_getStatic(), f.name, {"success": True, "data.getNodeLabelAt(data.getFromId(0))": None, "data.getNodeProperties(\"IGSpin\").getAt(data.getFromId(1))[1]": -1}) def test_yaml_forces(self): with self._tempFile("""positions: - Si: [1., 2., 3.] - C: [0., 0., 0.] forces: Values: - Si: [1., 2., 3.] - C: [4., 5., 6.] """) as f: self._loader(v_sim.DataLoader.yaml_getStatic(), f.name, {"success": True, "data.getForces(False).getAt(data.getFromId(0))": [1, 2, 3], "data.getForces(False).getAt(data.getFromId(1))": [4, 5, 6]}) def test_yaml_forces_none(self): with self._tempFile("""positions: - Si: [1., 2., 3.] - C: [0., 0., 0.] """) as f: self._loader(v_sim.DataLoader.yaml_getStatic(), f.name, {"success": True, "data.getForces(False)": None, "data.getForces(True).getAt(data.getFromId(0))": [0, 0, 0]}) def test_d3_file(self): self._loader(v_sim.DataLoader.d3_getStatic(), os.path.join(os.path.dirname(sys.argv[0]), "../../examples/aluminium.d3"), {"success": True, "data.getNNodes()": 134, "data.getNElements(True)": 1, "data.containsElement(v_sim.Element.retrieveFromName(\"Ni\")[0])": False, "data.containsElement(v_sim.Element.lookup(\"Al\"))": True, "data.getBox().getUnit()": v_sim.Units.UNDEFINED, "data.getBox().getBoundary()": v_sim.BoxBoundaries.PERIODIC, "data.getBox().getGeometry(v_sim.BoxVector.DXX)": 24.72848892, "data.getBox().getGeometry(v_sim.BoxVector.DYX)": -12.36424446, "data.getBox().getGeometry(v_sim.BoxVector.DYY)": 21.41550064, "data.getBox().getGeometry(v_sim.BoxVector.DZX)": 0., "data.getBox().getGeometry(v_sim.BoxVector.DZY)": 0., "data.getBox().getGeometry(v_sim.BoxVector.DZZ)": 24. }) if __name__ == '__main__': unittest.main()