def test_plot_density(): dn_tmp, nve, f = get_nve_water32() try: fn_png = '%s/density1.png' % dn_tmp plot_density(f, fn_png) assert os.path.isfile(fn_png) finally: shutil.rmtree(dn_tmp) f.close()
def test_plot_epot_contribs_nve(): dn_tmp, nve, f = get_nve_water32() try: fn_png = '%s/epot_contribs.png' % dn_tmp plot_epot_contribs(f, fn_png) assert os.path.isfile(fn_png) finally: shutil.rmtree(dn_tmp) f.close()
def test_plot_temp_dist(): dn_tmp, nve, f = get_nve_water32() try: fn_png = '%s/temp_dist1.png' % dn_tmp plot_temp_dist(f, fn_png) assert os.path.isfile(fn_png) fn_png = '%s/temp_dist2.png' % dn_tmp plot_temp_dist(f, fn_png, select=[0,1,2,6,7,8]) assert os.path.isfile(fn_png) finally: shutil.rmtree(dn_tmp) f.close()
def test_rdf1_offline(): dn_tmp, nve, f = get_nve_water32() try: select = nve.ff.system.get_indexes('O') rdf = RDF(4.5*angstrom, 0.1*angstrom, f, select0=select) assert 'trajectory/pos_rdf' in f assert 'trajectory/pos_rdf/d' in f assert 'trajectory/pos_rdf/rdf' in f fn_png = '%s/rdf.png' % dn_tmp rdf.plot(fn_png) assert os.path.isfile(fn_png) finally: shutil.rmtree(dn_tmp) f.close()
def test_diff_offline(): dn_tmp, nve, f = get_nve_water32() try: select = nve.ff.system.get_indexes('O') diff = Diffusion(f, select=select) assert 'trajectory/pos_diff' in f assert 'trajectory/pos_diff/msds' in f assert 'trajectory/pos_diff/time' in f assert 'trajectory/pos_diff/msdcounters' in f assert 'trajectory/pos_diff/msdsums' in f assert 'trajectory/pos_diff/pars' in f fn_png = '%s/msds.png' % dn_tmp diff.plot(fn_png) assert os.path.isfile(fn_png) finally: shutil.rmtree(dn_tmp) f.close()
def test_spectrum_offline(): dn_tmp, nve, f = get_nve_water32() try: for bsize in 2, 4, 5: spectrum = Spectrum(f, bsize=bsize) assert 'trajectory/vel_spectrum' in f assert 'trajectory/vel_spectrum/amps' in f assert 'trajectory/vel_spectrum/freqs' in f assert 'trajectory/vel_spectrum/ac' in f assert 'trajectory/vel_spectrum/time' in f fn_png = '%s/spectrum%i.png' % (dn_tmp, bsize) spectrum.plot(fn_png) assert os.path.isfile(fn_png) fn_png = '%s/ac%i.png' % (dn_tmp, bsize) spectrum.plot_ac(fn_png) assert os.path.isfile(fn_png) assert f['trajectory/vel_spectrum'].attrs['nfft'] == 3*3*32*(6/bsize) del f['trajectory/vel_spectrum'] finally: shutil.rmtree(dn_tmp) f.close()
def test_spectrum_offline(): dn_tmp, nve, f = get_nve_water32() try: for bsize in 2, 4, 5: spectrum = Spectrum(f, bsize=bsize) assert 'trajectory/vel_spectrum' in f assert 'trajectory/vel_spectrum/amps' in f assert 'trajectory/vel_spectrum/freqs' in f assert 'trajectory/vel_spectrum/ac' in f assert 'trajectory/vel_spectrum/time' in f fn_png = '%s/spectrum%i.png' % (dn_tmp, bsize) spectrum.plot(fn_png) assert os.path.isfile(fn_png) fn_png = '%s/ac%i.png' % (dn_tmp, bsize) spectrum.plot_ac(fn_png) assert os.path.isfile(fn_png) assert f['trajectory/vel_spectrum'].attrs['nfft'] == 3 * 3 * 32 * ( 6 / bsize) del f['trajectory/vel_spectrum'] finally: shutil.rmtree(dn_tmp) f.close()
def test_rdf2_offline_pairs_sr_nimage(): dn_tmp, nve, f = get_nve_water32() try: select0 = nve.ff.system.get_indexes('O') select1 = nve.ff.system.get_indexes('H') pairs_sr = [] for i in xrange(32): pairs_sr.append((3*i+1,3*i)) pairs_sr.append((3*i+2,3*i)) pairs_sr = np.array(pairs_sr) rdf = RDF(9.0*angstrom, 0.1*angstrom, f, select0=select0, select1=select1, pairs_sr=pairs_sr, nimage=1) assert 'trajectory/pos_rdf' in f assert 'trajectory/pos_rdf/d' in f assert 'trajectory/pos_rdf/rdf' in f assert 'trajectory/pos_rdf/rdf_sr' in f assert (f['trajectory/pos_rdf/rdf'][:] != f['trajectory/pos_rdf/rdf_sr']).any() fn_png = '%s/rdf.png' % dn_tmp rdf.plot(fn_png) assert os.path.isfile(fn_png) finally: shutil.rmtree(dn_tmp) f.close()