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()
