def test_p2():
LC = nCB("5cb_traj/run.tpr","5cb_traj/traj_comp.xtc",5,trjconv=False)
pv_ = ProbeVolume_Box("5cb_traj/run.tpr","5cb_traj/traj_comp.xtc",min_,max_)
LC_tilde= nCB_PV("5cb_traj/run.tpr","5cb_traj/traj_comp.xtc",5,pv_,trjconv=False)
p2_list = np.zeros((len(LC),))
p2tilde_list = np.zeros((len(LC),))
p2cos_list = np.zeros((len(LC),))
for i in range(len(LC)):
p2_list[i] = LC.p2(i)
p2tilde_list[i] = LC_tilde.p2tilde(i)
p2cos_list[i] = LC.p2_cos(i,n)
p2_ref = np.load("5cb_traj/p2_ref.npy")
p2tilde_ref = np.load("5cb_traj/p2tilde_ref.npy")
p2cos_ref = np.load("5cb_traj/p2cos_ref.npy")
err1 = np.max(np.abs(p2_ref - p2_list)/np.abs(p2_ref))
err2 = np.max(np.abs(p2tilde_ref - p2tilde_list)/np.abs(p2tilde_ref))
err3 = np.max(np.abs(p2cos_ref - p2cos_list)/np.abs(p2cos_list))
assert(err1 < 1e-10)
assert(err2 < 1e-10)
assert(err3 < 1e-10)
def make_reference_cylinder():
# for Cylinder
base = np.array([0, 0, 0])
h = 30
radius = 20
pv_cylinder = ProbeVolume_cylinder("5cb_traj/run.tpr",
"5cb_traj/traj_comp.xtc",
base,
h,
radius,
pbc=True,
dir_='z')
LC = nCB("5cb_traj/run.tpr", "5cb_traj/traj_comp.xtc", 5, trjconv=False)
natoms = LC.natoms
nresidues = LC.Nresidues_
Ntilde_ref = np.zeros((len(LC), 1))
indicator_ref = np.zeros((len(LC), natoms * nresidues, 1))
hx_ref = np.zeros((len(LC), natoms * nresidues, 3))
for i in range(len(LC)):
pos = LC.pos(i)
indicator, hx = pv_cylinder.calculate_Indicator(pos, i)
indicator_ref[i] = indicator
hx_ref[i] = hx
Ntilde_ref[i] = pv_cylinder.get_Ntilde()
np.save("INDUS_test/indicator_cyl_ref.npy", indicator_ref)
np.save("INDUS_test/hx_cyl_ref.npy", hx_ref)
np.save("INDUS_test/Ntilde_cyl_ref.npy", Ntilde_ref)
def make_ref():
LC = nCB("5cb_traj/run.tpr","5cb_traj/traj_comp.xtc",4, trjconv=False)
COM_mat = np.zeros((len(LC),LC.Nresidues_,3))
for t in range(len(LC)):
COM_mat[t] = LC.COM(t)
np.save("unittests_data/COM_ref.npy",COM_mat)
def test_COM():
LC = nCB("5cb_traj/run.tpr","5cb_traj/traj_comp.xtc",4, trjconv=False)
COM_mat = np.zeros((len(LC),LC.Nresidues_,3))
for t in range(len(LC)):
COM_mat[t] = LC.COM(t)
COM_ref = np.load("unittests_data/COM_ref.npy")
err = np.max(np.abs(COM_mat - COM_ref))
assert err < 1e-10
def make_reference():
LC = nCB("5cb_traj/run.tpr", "5cb_traj/traj_comp.xtc", 5, trjconv=False)
director_ref = np.zeros((len(LC), 3))
OP_ref = np.zeros((len(LC), ))
n = np.array([1, 0, 0])
dv0_ref = np.zeros((len(LC), LC.Nresidues_, 3))
for t in range(len(LC)):
director_ref[t] = LC.director(t, MOI=False)
OP_ref[t] = LC.v0(t, n)
dv0_ref[t] = LC.dv0_dr(t, n)
np.save("5cb_traj/director_ref.npy", director_ref)
np.save("5cb_traj/OP_ref.npy", OP_ref)
np.save("5cb_traj/dv0_ref.npy", dv0_ref)
def make_ref():
LC = nCB("5cb_traj/run.tpr","5cb_traj/traj_comp.xtc",5,trjconv=False)
pv_ = ProbeVolume_Box("5cb_traj/run.tpr","5cb_traj/traj_comp.xtc",min_,max_)
LC_tilde= nCB_PV("5cb_traj/run.tpr","5cb_traj/traj_comp.xtc",5,pv_,trjconv=False)
p2_list = np.zeros((len(LC),))
p2tilde_list = np.zeros((len(LC),))
p2cos_list = np.zeros((len(LC),))
for i in range(len(LC)):
p2_list[i] = LC.p2(i)
p2tilde_list[i] = LC_tilde.p2tilde(i)
p2cos_list[i] = LC.p2_cos(i,n)
print("p2 at {} is {:.5f}".format(i, p2_list[i]))
print("p2tilde at {} is {:.5f}".format(i, p2tilde_list[i]))
print("p2cos at {} is {:.5f}".format(i, p2cos_list[i]))
np.save("5cb_traj/p2_ref.npy",p2_list)
np.save("5cb_traj/p2tilde_ref.npy",p2tilde_list)
np.save("5cb_traj/p2cos_ref.npy",p2cos_list)
def test_director():
LC = nCB("5cb_traj/run.tpr", "5cb_traj/traj_comp.xtc", 5, trjconv=False)
director = np.zeros((len(LC), 3))
OP = np.zeros((len(LC), ))
n = np.array([1, 0, 0])
dv0 = np.zeros((len(LC), LC.Nresidues_, 3))
for t in range(len(LC)):
director[t] = LC.director(t, MOI=False)
OP[t] = LC.v0(t, n)
dv0[t] = LC.dv0_dr(t, n)
director_ref = np.load("5cb_traj/director_ref.npy")
OP_ref = np.load("5cb_traj/OP_ref.npy")
dv0_ref = np.load("5cb_traj/dv0_ref.npy")
err1 = np.max(np.abs(director_ref - director) / np.abs(director_ref))
err2 = np.max(np.abs(OP_ref - OP) / np.abs(OP_ref))
err3 = np.max(np.abs(dv0_ref - dv0) / np.abs(dv0_ref))
assert (err1 < 1e-10)
assert (err2 < 1e-10)
assert (err3 < 1e-10)