b_head = []
b_tail = []
for i in range(len(cont)):
if cont[i][:3] == 'd13':
head = {"C": 10, "D": 13, "H": 5, "O": 8, "N": 1, "P": 1}
tail = {"C": t_length * 2, "H": t_length * 4 + 2}
elif cont[i][:3] == 'd70':
head = {"C": 10, "D": 5, "H": 13, "O": 8, "N": 1, "P": 1}
tail = {"C": t_length * 2, "D": t_length * 4 + 2}
elif cont[i][:3] == 'd83':
head = {"C": 10, "D": 18, "O": 8, "N": 1, "P": 1}
tail = {"C": t_length * 2, "D": t_length * 4 + 2}
elif cont[i][:1] == 'h':
head = {"C": 10, "H": 18, "O": 8, "N": 1, "P": 1}
tail = {"C": t_length * 2, "H": t_length * 4 + 2}
b_head.append(rh.get_scattering_length(head, 1))
b_tail.append(rh.get_scattering_length(tail, 1))
d_h = 8.5
V_h = 339.5
V_t = 1100.0
min_d_t = 9
lipids = []
for i in range(len(cont)):
lipids.append(
mv.VolMono([V_h, V_t], [b_head[i], b_tail[i]],
d_h,
t_length,
name=label))
data_dir = "../data/reflectometry1/{}".format(label)
fig_dir = "../reports/figures/reflectometry1/"
anal_dir = "../output/reflectometry1/{}".format(label)
datasets = []
for i in range(sp.size):
datasets.append(
ReflectDataset("{}/{}_sp_{}.dat".format(data_dir, label, sp[i])))
datasets[i].mask = datasets[i].x <= 0.6
if lipid == "dmpg":
head = {"C": 8, "H": 12, "O": 10, "Na": 1, "P": 1}
else:
head = {"C": 10, "H": 18, "O": 8, "N": 1, "P": 1}
tail = {"C": t_length * 2, "H": t_length * 4 + 2}
b_head = rh.get_scattering_length(head, neutron)
b_tail = rh.get_scattering_length(tail, neutron)
d_h = 12.0
V_h = 330.0
if lipid[:2] == "dl":
V_t = 667.0
min_d_t = 5
elif lipid[:2] == "dm":
V_t = 779.0
min_d_t = 7
elif lipid[:2] == "dp":
V_t = 891.0
min_d_t = 9
t = sp.size
b_head = []
b_tail = []
for i in range(len(cont)):
if cont[i][:3] == 'd13':
head = {"C": 10, "D": 13, "H": 5, "O": 8, "N": 1, "P": 1}
tail = {"C": t_length * 2, "H": t_length * 4 + 2}
elif cont[i][:3] == 'd70':
head = {"C": 10, "D": 5, "H": 13, "O": 8, "N": 1, "P": 1}
tail = {"C": t_length * 2, "D": t_length * 4 + 2}
elif cont[i][:3] == 'd83':
head = {"C": 10, "D": 18, "O": 8, "N": 1, "P": 1}
tail = {"C": t_length * 2, "D": t_length * 4 + 2}
elif cont[i][:1] == 'h':
head = {"C": 10, "H": 18, "O": 8, "N": 1, "P": 1}
tail = {"C": t_length * 2, "H": t_length * 4 + 2}
b_head.append(rh.get_scattering_length(head, 1))
b_tail.append(rh.get_scattering_length(tail, 1))
else:
if lipid == "dmpg":
head = {"C": 8, "H": 12, "O": 10, "Na": 1, "P": 1}
else:
head = {"C": 10, "H": 18, "O": 8, "N": 1, "P": 1}
if neutron:
tail = {"C": t_length * 2, "D": t_length * 4 + 2}
else:
tail = {"C": t_length * 2, "H": t_length * 4 + 2}
b_head = rh.get_scattering_length(head, neutron)
b_tail = rh.get_scattering_length(tail, neutron)
def get_value(file):
def get_lgts(head, tail, sol, forcefield):
if forcefield == 'martini':
nc3 = {'N': 1, 'C': 5, head: 13}
po4 = {'P': 1, 'O': 4}
gl1 = {'C': 2, 'O': 2, tail: 2}
gl2 = {'C': 3, 'O': 2, tail: 3}
c1a = {'C': 5, tail: 10}
c2a = {'C': 4, tail: 8}
c3a = {'C': 4, tail: 8}
c4a = {'C': 4, tail: 9}
c1b = {'C': 5, tail: 10}
c2b = {'C': 4, tail: 8}
c3b = {'C': 4, tail: 8}
c4b = {'C': 4, tail: 9}
w = {'O': 2, sol: 4}
wp = {'O': 1, sol: 2}
wm = {'O': 1, sol: 2}
scat_lens = []
types = [nc3, po4, gl1, gl2, c1a, c2a, c3a, c4a, c1b, c2b, c3b, c4b]
types_strings = ['NC3', 'PO4', 'GL1', 'GL2', 'C1A', 'C2A', 'C3A', 'C4A', 'C1B', 'C2B', 'C3B', 'C4B', 'W', 'WP', 'WM']
for atom in types:
comp = (mv.get_scattering_length(atom, neutron=True))
scat_lens.append([comp.real, comp.imag])
if sol == 'acmw':
scat_lens.append([0, 0])
scat_lens.append([0, 0])
scat_lens.append([0, 0])
else:
types = [w, wp, wm]
for atom in types:
comp = (mv.get_scattering_length(atom, neutron=True))
scat_lens.append([comp.real, comp.imag])
elif forcefield == 'berger':
c1 = {'C': 1, head: 3}
c2 = {'C': 1, head: 3}
c3 = {'C': 1, head: 3}
n4 = {'N': 1}
c5 = {'C': 1, head: 2}
c6 = {'C': 1, head: 2}
o7 = {'O': 1}
p8 = {'P': 1}
o9 = {'O': 1}
o10 = {'O': 1}
o11 = {'O': 1}
c12 = {'C': 1, tail: 2}
c13 = {'C': 1, tail: 1}
o14 = {'O': 1}
c15 = {'C': 1}
o16 = {'O': 1}
c17 = {'C': 1, tail: 2}
c18 = {'C': 1, tail: 2}
c19 = {'C': 1, tail: 2}
c20 = {'C': 1, tail: 2}
c21 = {'C': 1, tail: 2}
c22 = {'C': 1, tail: 2}
c23 = {'C': 1, tail: 2}
c24 = {'C': 1, tail: 2}
c25 = {'C': 1, tail: 2}
c26 = {'C': 1, tail: 2}
c27 = {'C': 1, tail: 2}
c28 = {'C': 1, tail: 2}
c29 = {'C': 1, tail: 2}
c30 = {'C': 1, tail: 2}
c31 = {'C': 1, tail: 2}
c32 = {'C': 1, tail: 2}
c33 = {'C': 1, tail: 3}
c34 = {'C': 1, tail: 2}
o35 = {'O': 1}
c36 = {'C': 1}
o37 = {'O': 1}
c38 = {'C': 1, tail: 2}
c39 = {'C': 1, tail: 2}
c40 = {'C': 1, tail: 2}
c41 = {'C': 1, tail: 2}
c42 = {'C': 1, tail: 2}
c43 = {'C': 1, tail: 2}
c44 = {'C': 1, tail: 2}
c45 = {'C': 1, tail: 2}
c46 = {'C': 1, tail: 2}
c47 = {'C': 1, tail: 2}
c48 = {'C': 1, tail: 2}
c49 = {'C': 1, tail: 2}
c50 = {'C': 1, tail: 2}
c51 = {'C': 1, tail: 2}
c52 = {'C': 1, tail: 2}
c53 = {'C': 1, tail: 2}
c54 = {'C': 1, tail: 3}
ow = {'O': 1}
hw1 = {sol: 1}
hw2 = {sol: 1}
scat_lens = []
types = [c1, c2, c3, n4, c5, c6, o7, p8, o9, o10, o11, c12, c13, o14, c15, o16, c17, c18, c19,
c20, c21, c22, c23, c24, c25, c26, c27, c28, c29, c30, c31, c32, c33, c34, o35, c36,
o37, c38, c39, c40, c41, c42, c43, c44, c45, c46, c47, c48, c49, c50, c51, c52, c53, c54]
types_strings = ['C1', 'C2', 'C3', 'N4', 'C5', 'C6', 'O7', 'P8', 'O9', 'O10', 'O11', 'C12', 'C13',
'O14', 'C15', 'O16', 'C17', 'C18', 'C19', 'C20', 'C21', 'C22', 'C23', 'C24',
'C25', 'C26', 'C27', 'C28', 'C29', 'C30', 'C31', 'C32', 'C33', 'C34', 'O35',
'C36', 'O37', 'C38', 'C39', 'C40', 'C41', 'C42', 'C43', 'C44', 'C45', 'C46',
'C47', 'C48', 'C49', 'C50', 'C51', 'C52', 'C53', 'C54', 'OW', 'HW1', 'HW2']
for atom in types:
comp = (mv.get_scattering_length(atom, neutron=True))
scat_lens.append([comp.real, comp.imag])
if sol == 'acmw':
scat_lens.append([0, 0])
scat_lens.append([0, 0])
scat_lens.append([0, 0])
else:
types = [ow, hw1, hw2]
for atom in types:
comp = (mv.get_scattering_length(atom, neutron=True))
scat_lens.append([comp.real, comp.imag])
elif forcefield == 'slipids':
n = {'N': 1}
c13 = {'C': 1}
h13a = {head: 1}
h13b = {head: 1}
h13c = {head: 1}
c14 = {'C': 1}
h14a = {head: 1}
h14b = {head: 1}
h14c = {head: 1}
c15 = {'C': 1}
h15a = {head: 1}
h15b = {head: 1}
h15c = {head: 1}
c12 = {'C': 1}
h12a = {head: 1}
h12b = {head: 1}
c11 = {'C': 1}
h11a = {head: 1}
h11b = {head: 1}
p = {'P': 1}
o13 = {'O': 1}
o14 = {'O': 1}
o11 = {'O': 1}
o12 = {'O': 1}
c1 = {'C': 1}
ha = {tail: 1}
hb = {tail: 1}
c2 = {'C': 1}
hs = {tail: 1}
o21 = {'O': 1}
c21 = {'C': 1}
o22 = {'O': 1}
c22 = {'C': 1}
h2r = {tail: 1}
h2s = {tail: 1}
c3 = {'C': 1}
hx = {tail: 1}
hy = {tail: 1}
o31 = {'O': 1}
c31 = {'C': 1}
o32 = {'O': 1}
c32 = {'C': 1}
h2x = {tail: 1}
h2y = {tail: 1}
c23 = {'C': 1}
h3r = {tail: 1}
h3s = {tail: 1}
c24 = {'C': 1}
h4r = {tail: 1}
h4s = {tail: 1}
c25 = {'C': 1}
h5r = {tail: 1}
h5s = {tail: 1}
c26 = {'C': 1}
h6r = {tail: 1}
h6s = {tail: 1}
c27 = {'C': 1}
h7r = {tail: 1}
h7s = {tail: 1}
c28 = {'C': 1}
h8r = {tail: 1}
h8s = {tail: 1}
c29 = {'C': 1}
h9r = {tail: 1}
h9s = {tail: 1}
c210 = {'C': 1}
h10r = {tail: 1}
h10s = {tail: 1}
c211 = {'C': 1}
h11r = {tail: 1}
h11s = {tail: 1}
c212 = {'C': 1}
h12r = {tail: 1}
h12s = {tail: 1}
c213 = {'C': 1}
h13r = {tail: 1}
h13s = {tail: 1}
c214 = {'C': 1}
h14r = {tail: 1}
h14s = {tail: 1}
c215 = {'C': 1}
h15r = {tail: 1}
h15s = {tail: 1}
c216 = {'C': 1}
h16r = {tail: 1}
h16s = {tail: 1}
c217 = {'C': 1}
h17r = {tail: 1}
h17s = {tail: 1}
c218 = {'C': 1}
h18r = {tail: 1}
h18s = {tail: 1}
h18t = {tail: 1}
c33 = {'C': 1}
h3x = {tail: 1}
h3y = {tail: 1}
c34 = {'C': 1}
h4x = {tail: 1}
h4y = {tail: 1}
c35 = {'C': 1}
h5x = {tail: 1}
h5y = {tail: 1}
c36 = {'C': 1}
h6x = {tail: 1}
h6y = {tail: 1}
c37 = {'C': 1}
h7x = {tail: 1}
h7y = {tail: 1}
c38 = {'C': 1}
h8x = {tail: 1}
h8y = {tail: 1}
c39 = {'C': 1}
h9x = {tail: 1}
h9y = {tail: 1}
c310 = {'C': 1}
h10x = {tail: 1}
h10y = {tail: 1}
c311 = {'C': 1}
h11x = {tail: 1}
h11y = {tail: 1}
c312 = {'C': 1}
h12x = {tail: 1}
h12y = {tail: 1}
c313 = {'C': 1}
h13x = {tail: 1}
h13y = {tail: 1}
c314 = {'C': 1}
h14x = {tail: 1}
h14y = {tail: 1}
c315 = {'C': 1}
h15x = {tail: 1}
h15y = {tail: 1}
c316 = {'C': 1}
h16x = {tail: 1}
h16y = {tail: 1}
c317 = {'C': 1}
h17x = {tail: 1}
h17y = {tail: 1}
c318 = {'C': 1}
h18x = {tail: 1}
h18y = {tail: 1}
h18z = {tail: 1}
ow = {'O': 1}
hw1 = {sol: 1}
hw2 = {sol: 1}
scat_lens = []
types = [n, c13, h13a, h13b, h13c, c14, h14a, h14b, h14c, c15, h15a, h15b, h15c, c12, h12a, h12b,
c11, h11a, h11b, p, o13, o14, o11, o12, c1, ha, hb, c2, hs, o21, c21, o22, c22, h2r, h2s,
c3, hx, hy, o31, c31, o32, c32, h2x, h2y, c23, h3r, h3s, c24, h4r, h4s, c25, h5r, h5s, c26,
h6r, h6s, c27, h7r, h7s, c28, h8r, h8s, c29, h9r, h9s, c210, h10r, h10s, c211, h11r, h11s,
c212, h12r, h12s, c213, h13r, h13s, c214, h14r, h14s, c215, h15r, h15s, c216, h16r, h16s,
c217, h17r, h17s, c218, h18r, h18s, h18t, c33, h3x, h3y, c34, h4x, h4y, c35, h5x, h5y, c36,
h6x, h6y, c37, h7x, h7y, c38, h8x, h8y, c39, h9x, h9y, c310, h10x, h10y, c311, h11x, h11y,
c312, h12x, h12y, c313, h13x, h13y, c314, h14x, h14y, c315, h15x, h15y, c316, h16x, h16y,
c317, h17x, h17y, c318, h18x, h18y, h18z]
types_strings = ['N', 'C13', 'H13A', 'H13B', 'H13C', 'C14', 'H14A', 'H14B', 'H14C', 'C15', 'H15A',
'H15B', 'H15C', 'C12', 'H12A', 'H12B', 'C11', 'H11A', 'H11B', 'P', 'O13', 'O14',
'O11', 'O12', 'C1', 'HA', 'HB', 'C2', 'HS', 'O21', 'C21', 'O22', 'C22', 'H2R',
'H2S', 'C3', 'HX', 'HY', 'O31', 'C31', 'O32', 'C32', 'H2X', 'H2Y', 'C23', 'H3R',
'H3S', 'C24', 'H4R', 'H4S', 'C25', 'H5R', 'H5S', 'C26', 'H6R', 'H6S', 'C27', 'H7R',
'H7S', 'C28', 'H8R', 'H8S', 'C29', 'H9R', 'H9S', '0C21', 'H10R', 'H10S', '1C21',
'H11R', 'H11S', '2C21', 'H12R', 'H12S', '3C21', 'H13R', 'H13S', '4C21', 'H14R',
'H14S', '5C21', 'H15R', 'H15S', '6C21', 'H16R', 'H16S', '7C21', 'H17R', 'H17S',
'8C21', 'H18R', 'H18S', 'H18T', 'C33', 'H3X', 'H3Y', 'C34', 'H4X', 'H4Y', 'C35',
'H5X', 'H5Y', 'C36', 'H6X', 'H6Y', 'C37', 'H7X', 'H7Y', 'C38', 'H8X', 'H8Y',
'C39', 'H9X', 'H9Y', '0C31', 'H10X', 'H10Y', '1C31', 'H11X', 'H11Y', '2C31',
'H12X', 'H12Y', '3C31', 'H13X', 'H13Y', '4C31', 'H14X', 'H14Y', '5C31', 'H15X',
'H15Y', '6C31', 'H16X', 'H16Y', '7C31', 'H17X', 'H17Y', '8C31', 'H18X', 'H18Y', 'H18Z',
'OW', 'HW1', 'HW2']
for i, atom in enumerate(types):
comp = (mv.get_scattering_length(atom, neutron=True))
scat_lens.append([comp.real, comp.imag])
if sol == 'acmw':
scat_lens.append([0, 0])
scat_lens.append([0, 0])
scat_lens.append([0, 0])
else:
types = [ow, hw1, hw2]
for atom in types:
comp = (mv.get_scattering_length(atom, neutron=True))
scat_lens.append([comp.real, comp.imag])
return [types_strings, scat_lens]