#!/usr/bin/env python """ Tests of Larch Scripts """ import os import time import shutil import pytest import numpy as np from numpy.testing import assert_allclose from xraydb import (chemparse, validate_formula, material_mu, material_mu_components, find_material, get_materials, get_material, add_material) from xraydb.materials import get_user_materialsfile def test_chemparse(): examples = {'H2O': {'H':2, 'O':1}, 'Mn(SO4)2(H2O)7': {'H': 14.0, 'S': 2.0, 'Mn': 1, 'O': 15.0}, 'Mg(SO4)2': {'Mg': 1, 'S': 2, 'O':8}, 'Mg0.5Fe0.5' : {'Mg': 0.5, 'Fe': 0.5}, 'Mg.3Fe.7' : {'Mg': 0.3, 'Fe': 0.7}, 'CO': {'C': 1, 'O': 1} } for formula, cert in examples.items(): ret = chemparse(formula) for elem, quant in cert.items(): v = ret.pop(elem) assert_allclose(v, quant, rtol=1.e3) assert len(ret)==0 def test_validate_formula(): examples = {'H2O': True, 'Mn(SO4)2(H2O)7': True, 'Mn(SO42(H2O)7': False, 'Z': False} for formula, cert in examples.items(): ret = validate_formula(formula) assert (ret == cert) def test_get_materials(): examples = {'water': True, 'lead': True, 'acetone': True, 'kapton': True, 'sapphire': True, 'cheese': False, 'spice': False, 'bicycle': False} known_materials = get_materials() for name, found in examples.items(): if found: assert (name in known_materials) else: assert (name not in known_materials) def test_material_mu1(): en = np.linspace(8500, 9500, 21) known_mu = np.array([236.2, 232.4, 228.7, 225.1, 221.5, 218.1, 214.7, 211.4, 208.1, 204.9, 1403.6, 1385.6, 1367.9, 1350.6, 1333.5, 1316.7, 1300.3, 1284.0, 1268.1, 1252.4, 1237.0]) mu = material_mu('CuO', en, density=6.3) assert_allclose(mu, known_mu, rtol=0.005) def test_material_mu2(): en = np.linspace(5000, 10000, 21) known_mu = np.array([0.04934, 0.04267, 0.03715, 0.03254, 0.02866, 0.02538, 0.02257, 0.02016, 0.01809, 0.01629, 0.01472, 0.01334, 0.01214, 0.01108, 0.01014, 0.00930, 0.00856, 0.00789, 0.00729, 0.00675, 0.00626]) mu = material_mu('air', en) assert_allclose(mu, known_mu, rtol=0.05) air_formula, air_density = get_material('air') air_comps = chemparse(air_formula) assert air_comps['Ar'] < 0.013 assert air_comps['Ar'] > 0.007 mu = material_mu('air', en, density=2.0*air_density) assert_allclose(mu, 2.0*known_mu, rtol=0.05) def test_material_mu3(): en = np.linspace(5000, 10000, 21) known_mu = np.array([42.592, 36.801, 32.006, 28.005, 24.641, 21.794, 19.367, 17.288, 15.496, 13.943, 12.592, 11.411, 10.373, 9.458, 8.649, 7.931, 7.291, 6.719, 6.206, 5.745, 5.330]) mu = material_mu('H2O', en) assert_allclose(mu, known_mu, rtol=0.05) def test_material_mu4(): en = np.linspace(5000, 10000, 21) known_mu = np.array([42.592, 36.801, 32.006, 28.005, 24.641, 21.794, 19.367, 17.288, 15.496, 13.943, 12.592, 11.411, 10.373, 9.458, 8.649, 7.931, 7.291, 6.719, 6.206, 5.745, 5.330]) with pytest.raises(Warning): out = material_mu('H2SO4', en) def test_material_mu_components1(): mu = material_mu('quartz', 10000) assert_allclose(mu, 50.368, rtol=0.001) comps = material_mu_components('quartz', 10000) known_comps = {'mass': 60.08, 'density': 2.65, 'elements': ['Si', 'O'], 'Si': (1, 28.1, 33.879), 'O': (2.0, 16.0, 5.953)} assert 'Si'in comps['elements'] assert 'O'in comps['elements'] for attr in ('mass', 'density'): assert_allclose(comps[attr], known_comps[attr], rtol=0.01) for attr in ('Si', 'O'): assert_allclose(comps[attr][0], known_comps[attr][0], rtol=0.01) assert_allclose(comps[attr][1], known_comps[attr][1], rtol=0.01) assert_allclose(comps[attr][2], known_comps[attr][2], rtol=0.01) def test_material_mu_components2(): mu = material_mu('TiO2', 10000, density=4.23) assert_allclose(mu, 290.7, rtol=0.001) mu = material_mu('TiO2', 10000) assert_allclose(mu, 290.7, rtol=0.001) mu = material_mu('TiO2', 10000, density=4.5) assert_allclose(mu, 309.26, rtol=0.001) comps = material_mu_components('TiO2', 10000, density=4.23) known_comps = {'mass': 79.88, 'density': 4.23, 'elements': ['Ti', 'O'], 'Ti': (1, 47.88, 110.676), 'O': (2.0, 15.9994, 5.953)} assert 'Ti'in comps['elements'] assert 'O'in comps['elements'] for attr in ('mass', 'density'): assert_allclose(comps[attr], known_comps[attr], rtol=0.01) for attr in ('Ti', 'O'): assert_allclose(comps[attr][0], known_comps[attr][0], rtol=0.01) assert_allclose(comps[attr][1], known_comps[attr][1], rtol=0.01) assert_allclose(comps[attr][2], known_comps[attr][2], rtol=0.01) with pytest.raises(Warning): c = material_mu_components('TiO2', 10000) def test_material_find(): mat_ = {'kapton': ('C22H10N2O5', 1.43, 'polymer'), 'lead': ('Pb', 11.34, 'metal'), 'aluminum': ('Al', 2.72, 'metal'), 'water': ('H2O', 1.0, 'solvent')} for mname, mdat in mat_.items(): mat = find_material(mname) f1 = chemparse(mat.formula) f2 = chemparse(mdat[0]) for k, v in f2.items(): assert v == f1[k] assert_allclose(mat.density, mdat[1], rtol=0.1) assert(mdat[2] in mat.categories) for formula in ('WSO3', 'CdAs140CO3', 'KAs'): out = find_material(formula) assert out == None def test_material_get(): mat_ = {'kapton': ('C22H10N2O5', 1.43), 'lead': ('Pb', 11.34), 'aluminum': ('Al', 2.72), 'water': ('H2O', 1.0)} for mname in mat_.keys(): formula, density = get_material(mname) f1 = chemparse(formula) f2 = chemparse(mat_[mname][0]) for k, v in f2.items(): assert v == f1[k] assert_allclose(density, mat_[mname][1], rtol=0.1) for formula, density in mat_.values(): _f, _d = get_material(formula) assert _f == formula assert_allclose(density, _d, rtol=0.1) for formula in ('WSO3', 'CdAs140CO3', 'KAs'): out = get_material(formula) assert out == None @pytest.mark.skip("Unsafe test directory location.") def test_material_add(): matfile = get_user_materialsfile() savefile = matfile + '_Save' if os.path.exists(matfile): had_matfile = True shutil.move(matfile, savefile) time.sleep(2.0) add_material('caffeine', 'C8H10N4O2', density=1.23) assert get_material('caffeine') is not None time.sleep(2.0) add_material('rutile', 'TiO2', density=4.23) with open(matfile, 'r') as fh: text = fh.read() assert 'caffeine' in text assert 'rutile' in text os.unlink(matfile) if os.path.exists(savefile): shutil.move(savefile, matfile)