def s_order(job):
dim = 1
box_range = [0.167, 1.167]
pore_center = (box_range[1]-box_range[0])/2 + box_range[0]
fig, ax = plt.subplots()
s_list = list()
for trj in md.iterload(os.path.join(job.ws, 'nvt.dcd'), top=os.path.join(job.ws, 'init.mol2'), chunk=9000, skip=2001):
water_bonds = get_bond_array(trj)
bins, s_values = compute_s(trj,
dim,
pore_center=pore_center,
bond_array=water_bonds)
s_list.append(s_values)
s_mean = np.mean(s_list, axis=0)
s_std = np.std(s_list, axis=0)
plt.plot(bins, s_mean)
plt.fill_between(bins, s_mean + s_std, s_mean - s_std, alpha=0.2)
plt.xlabel('z-position (nm)')
plt.ylabel('S')
with job:
plt.savefig('s_order.pdf')
np.savetxt('s_order.txt', np.transpose(np.vstack([bins, s_mean, s_std])),
header='Bins\tS_mean\tS_std')
np.savetxt(f'data/{job.sp.nwater}_mol_s_order.txt', np.transpose(np.vstack([bins, s_mean, s_std])),
header='Bins\tS_mean\tS_std')
def s_order(job, symmetrize=False):
dim = 1
box_range = [0.167, 1.167]
pore_center = (box_range[1] - box_range[0]) / 2 + box_range[0]
fig, ax = plt.subplots()
s_list = list()
if job.sp.nwater == 1:
skip = 1
else:
skip = 5001
for trj in md.iterload(
os.path.join(job.ws, "nvt.trr"),
top=os.path.join(job.ws, "init.mol2"),
chunk=5000,
skip=skip,
):
water_bonds = get_bond_array(trj)
bins, s_values = compute_s(
trj,
dim,
pore_center=pore_center,
bond_array=water_bonds,
symmetrize=symmetrize,
)
s_list.append(s_values)
s_mean = np.mean(s_list, axis=0)
s_std = np.std(s_list, axis=0)
plt.plot(bins, s_mean)
plt.fill_between(bins, s_mean + s_std, s_mean - s_std, alpha=0.2)
plt.xlabel("z-position (nm)")
plt.ylabel("S")
if symmetrize == True:
extension = "_symmetrize"
else:
extension = ""
with job:
plt.savefig(f"s_order{extension}.pdf")
np.savetxt(
f"s_order{extension}.txt",
np.transpose(np.vstack([bins, s_mean, s_std])),
header="Bins\tS_mean\tS_std",
)
np.savetxt(
f"data/{job.sp.nwater}_mol_s_order{extension}.txt",
np.transpose(np.vstack([bins, s_mean, s_std])),
header="Bins\tS_mean\tS_std",
)
def s_order(job):
dim = 1
box_range = [0.837, 2.837]
pore_center = (box_range[1] - box_range[0]) / 2 + box_range[0]
fig, ax = plt.subplots()
s_list = list()
for trj in md.iterload(
os.path.join(job.ws, "nvt.trr"),
top=os.path.join(job.ws, "init.mol2"),
chunk=5000,
skip=5001,
):
water_bonds = get_bond_array(trj)
bins, s_values = compute_s(trj,
dim,
pore_center=pore_center,
bond_array=water_bonds)
s_list.append(s_values)
s_mean = np.mean(s_list, axis=0)
s_std = np.std(s_list, axis=0)
plt.plot(bins, s_mean)
plt.fill_between(bins, s_mean + s_std, s_mean - s_std, alpha=0.2)
plt.xlabel("z-position (nm)")
plt.ylabel("S")
plt.ylim((-0.45, 0.45))
with job:
plt.savefig("s_order.pdf")
np.savetxt(
"s_order.txt",
np.transpose(np.vstack([bins, s_mean, s_std])),
header="Bins\tS_mean\tS_std",
)
np.savetxt(
f"data/{job.sp.nwater}_mol_s_order.txt",
np.transpose(np.vstack([bins, s_mean, s_std])),
header="Bins\tS_mean\tS_std",
)
def angle_dist(job):
dim = 1
#box_range = [0.167, 1.167]
box_range = [0.5, 0.8]
pore_center = (box_range[1] - box_range[0]) / 2 + box_range[0]
fig, ax = plt.subplots()
cos_angle_list = list()
all_cos_angle_list = list()
for trj in md.iterload(
os.path.join(job.ws, "nvt.trr"),
top=os.path.join(job.ws, "init.mol2"),
chunk=5000,
skip=1,
):
water_bonds = get_bond_array(trj)
bins, cos_angle_values, all_cos_angles = compute_angle(
trj, dim, pore_center=pore_center, bond_array=water_bonds)
cos_angle_list.append(cos_angle_values)
all_cos_angle_list.extend(all_cos_angles)
cos_angle_mean = np.mean(cos_angle_list, axis=0)
cos_angle_std = np.std(cos_angle_list, axis=0)
plt.plot(bins, cos_angle_mean)
plt.fill_between(bins,
cos_angle_mean + cos_angle_std,
cos_angle_mean - cos_angle_std,
alpha=0.2)
plt.xlabel("z-position (nm)")
plt.ylabel("cos(angle)")
with job:
plt.savefig(
project.root_directory() +
"/data/{}_mol_angle_profile.pdf".format(str(job.sp.nwater)))
np.savetxt(
project.root_directory() +
"/data/{}_mol_angle_profile.txt".format(str(job.sp.nwater)),
np.transpose(np.vstack([bins, cos_angle_mean, cos_angle_std])),
header="Bins\tcos_angle_mean\tcos_angle_std",
)
plt.figure()
all_cos_angle_list = np.asarray(all_cos_angle_list)
all_angle_list = (180 / np.pi) * np.arccos(all_cos_angle_list)
counts, cos_angle_bins, bars = plt.hist(all_cos_angle_list,
bins=60,
alpha=0.5,
density=True)
cos_angle_bins_center = (cos_angle_bins[:-1] + cos_angle_bins[1:]) / 2
plt.xlabel("cos(angle)")
plt.ylabel("Relative frequency")
with job:
plt.savefig(
project.root_directory() +
"/data/{}_mol_cos_angle_dist.pdf".format(str(job.sp.nwater)))
np.savetxt(
project.root_directory() +
"/data/{}_mol_cos_angle_dist.txt".format(str(job.sp.nwater)),
np.transpose(np.vstack([cos_angle_bins_center, counts])),
header="cos_Angle_bins\tRelativeFreq",
)
plt.figure()
bins = np.linspace(0, 180, num=61)
counts, angle_bins, bars = plt.hist(all_angle_list,
bins=bins,
alpha=0.5,
density=True)
plt.xlabel("Angle (degress)")
plt.ylabel("Relative frequency")
plt.title("Unnormalized distribution")
angle_bins_center = (angle_bins[:-1] + angle_bins[1:]) / 2
with job:
plt.savefig(project.root_directory() +
"/data/{}_mol_angle_dist_unnormalized.pdf".format(
str(job.sp.nwater)))
np.savetxt(
project.root_directory() +
"/data/{}_mol_angle_dist_unnormalized.txt".format(
str(job.sp.nwater)),
np.transpose(np.vstack([angle_bins_center, counts])),
header="Angle_bins\tRelativeFreq",
)
plt.figure()
normalized_counts = np.divide(
counts, abs(np.sin((np.pi / 180) * angle_bins_center)))
# Adjust so uniform corresponds to 1
normalized_counts /= np.sum(normalized_counts)
normalized_counts *= 60
arr = plt.hist(angle_bins_center,
weights=normalized_counts,
bins=np.linspace(0, 180, num=61),
density=False)
plt.xlabel("Angle (degress)")
plt.ylabel("Relative frequency")
plt.title("Normalized distribution")
with job:
plt.savefig(project.root_directory() +
"/data/{}_mol_angle_dist_normalized.pdf".format(
str(job.sp.nwater)))
np.savetxt(
project.root_directory() +
"/data/{}_mol_angle_dist_normalized.txt".format(str(
job.sp.nwater)),
np.transpose(np.vstack([angle_bins_center, normalized_counts])),
header="Angle_bins\tRelativeFreq",
)