def main(argv=sys.argv):
argv = sys.argv
args = read_inputs(argv[1:])
in_files_path = args.infiles
#Import silver data
wave_s, diel_rs, diel_is = numpy.loadtxt(
'../data/wave_silver_diel_3700-4000.txt', skiprows=1, unpack=True)
#Import water data
wave_w, diel_rw, diel_iw = numpy.loadtxt(
'../data/wave_water_diel_3700-4000.txt', skiprows=1, unpack=True)
#Creating dielectric list first dielectric outside, then inside
diel_list = [
list(eps)
for eps in zip(diel_rw + 1j * diel_iw, diel_rs + 1j * diel_is)
]
#Set enviornment variable for PyGBe
folder_path = in_files_path + 'BSA_sensorR8_d=infty'
full_path = os.path.abspath(folder_path) + '/'
os.environ['PYGBE_PROBLEM_FOLDER'] = full_path
#Creating dictionary field. We will modify the 'E' key in the for loop.
field_dict_Ag = read_fields(full_path + 'sph_sensor.config')
#Calculate Cext(lambda) for silver
tic_ss = time.time()
e_field = -0.0037
wave, Cext_silver = Cext_wave_scan(e_field, wave_s, diel_list,
field_dict_Ag, full_path)
toc_ss = time.time()
#Calculate Cext_analytical(lambda) for silver, radius of sphere=8 nm
tic_sa = time.time()
r = 8.
#Silver
Cext_an_silver = Cext_analytical(r, wave_s / 10, diel_rw + 1j * diel_iw,
diel_rs + 1j * diel_is)
toc_sa = time.time()
#Save wavelength, Cext, Cext_analytical, error
#Silver
numpy.savetxt('../results/lambda_Cext_Cext_an_silver.txt',
list(zip(wave / 10, Cext_silver, Cext_an_silver)),
fmt='%.5f %.5f %.5f ',
header='lambda [ang], Cext, Cext_analytical')
time_simulation = (toc_ss - tic_ss)
time_analytical = (toc_sa - tic_sa)
time_silver = (toc_ss - tic_ss) + (toc_sa - tic_sa)
with open('../results/time_verification.txt', 'w') as f:
print('time_total: {} s (simulation: {} + analytical: {}) '.format(
time_silver, time_simulation, time_analytical),
file=f)
def initialize_field(filename, param, field=None):
"""
Initialize all the regions in the surface to be solved.
Arguments
---------
filename : name of the file that contains the surface information.
param : class, parameters related to the surface.
field : dictionary with preloaded field values for programmatic
interaction with PyGBe
Returns
-------
field_array: array, contains the Field classes of each region on the surface.
"""
if not field:
field = read_fields(filename)
for key in ['E', 'kappa']:
for i, e in enumerate(field[key]):
if not numpy.iscomplexobj(e) and not isinstance(e, str):
field[key][i] = param.REAL(field[key][i])
Nfield = len(field['LorY'])
field_array = []
Nchild_aux = 0
for i in range(Nfield):
field_aux = Field(field['LorY'][i], field['kappa'][i], field['E'][i],
field['coulomb'][i], field['pot'][i])
if int(field['charges'][i]) == 1: # if there are charges
field_aux.load_charges(field['qfile'][i], param.REAL)
if int(field['Nparent'][i]) == 1: # if it is an enclosed region
field_aux.parent.append(int(field['parent'][i]))
# pointer to parent surface (enclosing surface)
if int(field['Nchild'][i]) > 0: # if there are enclosed regions inside
for j in range(int(field['Nchild'][i])):
field_aux.child.append(int(
field['child'][Nchild_aux +
j])) # Loop over children to get pointers
Nchild_aux += int(
field['Nchild'][i]) # Point to child for next surface
if field['pot'][i] == 1:
param.E_field.append(i) # Field where surface energy is calculated
field_array.append(field_aux)
return field_array
def initialize_field(filename, param, field=None):
"""
Initialize all the regions in the surface to be solved.
Arguments
---------
filename : name of the file that contains the surface information.
param : class, parameters related to the surface.
field : dictionary with preloaded field values for programmatic
interaction with PyGBe
Returns
-------
field_array: array, contains the Field classes of each region on the surface.
"""
if not field:
field = read_fields(filename)
for key in ['E', 'kappa']:
for i, e in enumerate(field[key]):
if not numpy.iscomplexobj(e) and not isinstance(e, str):
field[key][i] = param.REAL(field[key][i])
Nfield = len(field['LorY'])
field_array = []
Nchild_aux = 0
for i in range(Nfield):
field_aux = Field(field['LorY'][i], field['kappa'][i], field['E'][i],
field['coulomb'][i], field['pot'][i])
if int(field['charges'][i]) == 1: # if there are charges
field_aux.load_charges(field['qfile'][i], param.REAL)
if int(field['Nparent'][i]) == 1: # if it is an enclosed region
field_aux.parent.append(int(field['parent'][i]))
# pointer to parent surface (enclosing surface)
if int(field['Nchild'][i]) > 0: # if there are enclosed regions inside
for j in range(int(field['Nchild'][i])):
field_aux.child.append(int(field['child'][Nchild_aux + j])
) # Loop over children to get pointers
Nchild_aux += int(field['Nchild'][i]) # Point to child for next surface
if field['pot'][i] == 1:
param.E_field.append(i) # Field where surface energy is calculated
field_array.append(field_aux)
return field_array
def main(argv=sys.argv):
argv = sys.argv
args = read_inputs(argv[1:])
in_files_path = args.infiles
#Import surface data
wave_s, diel_rs, diel_is = numpy.loadtxt(
'../dielectric_data/4H-SIC_permittivity_10-12_microns.csv',
skiprows=1,
unpack=True)
air_diel = [1. + 1j * 0.] * len(wave_s)
#Creating dielectric list first dielectric outside, then inside
diel_list = [list(eps) for eps in zip(air_diel, diel_rs + 1j * diel_is)]
#Set enviornment variable for PyGBe
folder_path = in_files_path + 'prism_reg_SE'
full_path = os.path.abspath(folder_path) + '/'
os.environ['PYGBE_PROBLEM_FOLDER'] = full_path
#Creating dictionary field. We will modify the 'E' key in the for loop.
field_dict_pillars = read_fields(full_path + 'prism_reg_38K.config')
#Calculate Cext(lambda) for pillars' surface
tic_ss = time.time()
e_field = -1.
wave, Cext_pillars = Cext_wave_scan(e_field, wave_s, diel_list,
field_dict_pillars, full_path)
toc_ss = time.time()
numpy.savetxt('../results_data/prism_regular_SE_LE_res/' +
'prism_reg_38K_short_edge' + '10-20microns.txt',
list(zip(wave, Cext_pillars)),
fmt='%.9f %.9f',
header='lambda [Ang], Cext [nm^2]')
time_simulation = (toc_ss - tic_ss)
with open(
'../results_data/prism_regular_SE_LE_res/Time_' +
'prism_reg_38K_short_edge' + '.txt', 'w') as f:
print('time_total: {} s'.format(time_simulation), file=f)
try:
all(l_w == l_s) & all(l_s == l_p)
wavelength = l_w
except:
raise ValueError(
'The wavelength ranges are not equal, check data generation')
#Complex dielectric assembly
e_w = er_w + 1j * ei_w #water
e_s = er_s + 1j * ei_s #silver
e_p = er_p + 1j * ei_p #protein
#Building E field for single sphere dictionary
E_field_single = [list(eps) for eps in zip(e_w, e_s)]
field_dict_single = read_fields(
'../../../pygbe/examples/BSA_sensor_d=infty/sph_sensor.config')
tic_single = time.time()
elec_field = -1
wave_single, Cext_single = Cext_wave_scan(
elec_field, wavelength, E_field_single, field_dict_single,
'../../../pygbe/examples/BSA_sensor_d=infty')
toc_single = time.time()
numpy.savetxt('../../data/wave_cext_d_prot_sensor/wave_cext_d_infty.txt',
list(zip(wave_single, Cext_single)),
fmt='%.1f %.8f',
header='lambda [Ang], Cext, d=infty')
#Building E field for dictionary (protein)
E_field = [list(eps) for eps in zip(e_w, e_s, e_p)]
def main(argv=sys.argv):
'''Creates lspr response data for the following cases:
BSA_sensorR8_2pz_d=0.5_00, BSA_sensorR8_2pz_d=1_00, BSA_sensorR8_2pz_d=2_00
and for the case of no protein BSA_sensorR8_d=infty.
Arguments passed (read docs of read_inputs)
----------------
infiles: str, absolute path where the input files are located.
For example: if input_problem_folders was downloaded in the directory
home/Downloads, then the path will be:
home/Downloads/input_problem_folders/
'''
argv = sys.argv
args = read_inputs(argv[1:])
in_files_path = args.infiles
#Importing dielectrics data
l_w, er_w, ei_w = numpy.loadtxt(
'../dielectrics_data/wave_ang_water_diel_3820-3870.txt', unpack=True)
l_s, er_s, ei_s = numpy.loadtxt(
'../dielectrics_data/wave_ang_silver_diel_3820-3870.txt', unpack=True)
l_p, er_p, ei_p = numpy.loadtxt(
'../dielectrics_data/wave_ang_prot_diel_3820-3870.txt', unpack=True)
#Check the wavelength ranges are all equal
try:
all(l_w == l_s) & all(l_s == l_p)
wavelength = l_w
except:
raise ValueError(
'The wavelength ranges are not equal, check data generation')
#Complex dielectric assembly
e_w = er_w + 1j * ei_w #water
e_s = er_s + 1j * ei_s #silver
e_p = er_p + 1j * ei_p #protein
#Building E field for single sphere dictionary
E_field_single = [list(eps) for eps in zip(e_w, e_s)]
field_dict_single = read_fields(in_files_path +
'BSA_sensorR8_d=infty/sph_sensor.config')
tic_single = time.time()
elec_field = -0.0037
wave_single, Cext_single = Cext_wave_scan(
elec_field, wavelength, E_field_single, field_dict_single,
in_files_path + 'BSA_sensorR8_d=infty/')
toc_single = time.time()
numpy.savetxt(
'../Cext_variation_with_distance_two_bsa_z_results/BSA_sensorR8_d=infty_3820-3870ang.txt',
list(zip(wave_single, Cext_single)),
fmt='%.1f %.8f',
header='lambda [Ang],Cext_' + 'BSA_sensorR8_d=infty')
#Building E field for dictionary (one protein) uncomment the following line
#E_field = [list(eps) for eps in zip(e_w, e_s, e_p)
#If only one protein comment the following 4 lines of code
#Building E field for dictionary for case of 2 proteins
e_list = [list(eps) for eps in zip(e_w, e_s, e_p)]
E_field = []
for lst in e_list:
E_field.append(lst +
[lst[-1]] * 1) #works for 2 proteins, if n proteins
# needed replace lst+[lst[-1]]*1 by
#lst+[lst[-1]]*(n-1)
distance_path_folders = [
'BSA_sensorR8_2pz_d=0.5_00', 'BSA_sensorR8_2pz_d=1_00',
'BSA_sensorR8_2pz_d=2_00'
]
tic_d = time.time()
elec_field = -0.0037
for path in distance_path_folders:
folder_path = in_files_path + path
full_path = os.path.abspath(folder_path) + '/'
os.environ['PYGBE_PROBLEM_FOLDER'] = full_path
field_dict = read_fields(folder_path + '/sphere_bsa.config')
wave, Cext = Cext_wave_scan(elec_field, wavelength, E_field,
field_dict, in_files_path + path)
numpy.savetxt('../Cext_variation_with_distance_two_bsa_z_results/' +
path + '_3820-3870ang.txt',
list(zip(wave, Cext)),
fmt='%.1f %.8f',
header='lambda [Ang], Cext_' + path)
toc_d = time.time()
with open(
'../Cext_variation_with_distance_two_bsa_z_results/Time_Cext_variation_with_distance_two_bsa_z.txt',
'w') as f:
print('single sphere run time: {}'.format((toc_single - tic_single)),
file=f)
print('sphere-bsa run time: {}'.format((toc_d - tic_d)), file=f)
print('total run time: {}'.format((toc_single - tic_single) +
(toc_d - tic_d)),
file=f)
lambda_75, ns_75, ks_75, nw_75, kw_75 = numpy.loadtxt('../../data/lambda_n_k_silver-7.5.txt',
unpack = True)
#Import gold case
lambda_76, ng_76, kg_76, nw_76, kw_76 = numpy.loadtxt('../../data/lambda_n_k_gold-7.6.txt',
unpack = True)
#Creating dielectric list for silver
diel_wat_75, diel_sil_75, diel_list_75 = create_diel_list(nw_75, kw_75, ns_75, ks_75)
#Creating dielectric list for gold
diel_wat_76, diel_gold_76, diel_list_76 = create_diel_list(nw_76, kw_76, ng_76, kg_76)
#Creating dictionary field. We will modify the 'E' key in the for loop.
field_dict_Ag = read_fields('../../../pygbe_dev/pygbe/examples/lspr_silver/sphereAg_complex.config')
field_dict_Au = read_fields('../../../pygbe_dev/pygbe/examples/lspr_gold/sphereAu_complex.config')
#Calculate Cext(lambda) for silver
tic_s = time.time()
wave_s, Cext_silver = Cext_wave_scan(lambda_75, diel_list_75, field_dict_Ag,
'../../../pygbe_dev/pygbe/examples/lspr_silver')
toc_s = time.time()
#Calculate Cext(lambda) for gold
tic_g = time.time()
wave_g, Cext_gold = Cext_wave_scan(lambda_76, diel_list_76, field_dict_Au,
'../../../pygbe_dev/pygbe/examples/lspr_gold')
toc_g = time.time()
#Calculate Cext_analytical(lambda) for silver and gold, radius of sphere=10 nm
try:
all(l_w == l_s) & all(l_s == l_p)
wavelength = l_w
except:
raise ValueError(
'The wavelength ranges are not equal, check data generation')
#Complex dielectric assembly
e_w = er_w + 1j * ei_w #water
e_s = er_s + 1j * ei_s #silver
e_p = er_p + 1j * ei_p #protein
#Building E field for single sphere dictionary
E_field_single = [list(eps) for eps in zip(e_w, e_s)]
field_dict_single = read_fields(
'../../../pygbe_dev/pygbe/examples/lspr/sphere_complex.config')
tic_single = time.time()
wave_single, Cext_single = Cext_wave_scan(
wavelength, E_field_single, field_dict_single,
'../../../pygbe_dev/pygbe/examples/lspr')
toc_single = time.time()
numpy.savetxt('../../data/wave_cext_d/wave_cext_d_infty.txt',
list(zip(wave_single, Cext_single)),
fmt='%.3f %.8f',
header='lambda [nm], Cext, d=infty')
#Building E field for dictionary (protein)
e_list = [list(eps) for eps in zip(e_w, e_s, e_p)]
numpy.savetxt(
'../../data/lambda_refrac_water_silv_gold.txt',
list(zip(lambda_wsg, n_w, k_w, n_s, k_s, n_g, k_g)),
fmt='%.8f %.8e %.8e %.8e %.8e %.8e %.8e',
header=
'lambda [nm], refrac_real_water, refrac_imag_water, refrac_real_silver, refrac_imag_silver, refrac_real_gold, refrac_imag_gold'
)
#Creating dielectric list for silver
diel_wat_s, diel_sil, diel_list_silv = create_diel_list(n_w, k_w, n_s, k_s)
#Creating dielectric list for gold
diel_wat_g, diel_gold, diel_list_gold = create_diel_list(n_w, k_w, n_g, k_g)
#Creating dictionary field. We will modify the 'E' key in the for loop.
field_dict = read_fields(
'../../../pygbe_dev/pygbe/examples/lspr/sphere_complex.config')
#Calculate Cext(lambda) for silver
tic_s = time.time()
wave_s, Cext_silver = Cext_wave_scan(lambda_wsg, diel_list_silv, field_dict,
'../../../pygbe_dev/pygbe/examples/lspr')
toc_s = time.time()
#Calculate Cext(lambda) for gold
tic_g = time.time()
wave_g, Cext_gold = Cext_wave_scan(lambda_wsg, diel_list_gold, field_dict,
'../../../pygbe_dev/pygbe/examples/lspr')
toc_g = time.time()
#Calculate Cext_analytical(lambda) for silver and gold, radius of sphere=10 nm
r = 10.
