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Update sas_gen.py #2617

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merged 2 commits into from
Sep 20, 2023
Merged

Update sas_gen.py #2617

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db16caa
Update sas_gen.py
timsnow Sep 18, 2023
6029972
Correction for Na to NA
timsnow Sep 19, 2023
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23 changes: 15 additions & 8 deletions src/sas/sascalc/calculator/sas_gen.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1192,6 +1192,7 @@ def read(self, path):
x_lines = []
y_lines = []
z_lines = []
atom_value_dict = {}
try:
input_f = open(path, 'rb')
buff = decode(input_f.read())
Expand Down Expand Up @@ -1222,14 +1223,20 @@ def read(self, path):
pos_y.append(_pos_y)
pos_z.append(_pos_z)
try:
val = nsf.neutron_sld(atom_name)[0]
# sld in Ang^-2 unit
val *= 1.0e-6
sld_n.append(val)
atom = formula(atom_name)
# cm to A units
vol = 1.0e+24 * atom.mass / atom.density / NA
vol_pix.append(vol)
if atom_name in atom_value_dict:
sld_n.append(atom_value_dict[atom_name][0])
vol_pix.append(atom_value_dict[atom_name][1])
else:
val = nsf.neutron_sld(atom_name)[0]
# sld in Ang^-2 unit
val *= 1.0e-6
sld_n.append(val)
atom = formula(atom_name)
# # cm to A units
vol = 1.0e+24 * atom.mass / atom.density / NA
vol_pix.append(vol)
atom_value_dict[atom_name] = [val, vol]

except Exception:
logging.warning("Warning: set the sld of %s to zero"% atom_name)
sld_n.append(0.0)
Expand Down