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Allow fetching of equi data if one dosn't converge

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rasmusthog 2022-10-13 20:52:37 +02:00
parent 536160666e
commit c6842f6196
1 changed files with 11 additions and 5 deletions
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16
nafuma/dft/structure.py
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@ -894,9 +894,10 @@ def get_equilibrium_data(path, atoms_per_formula_unit, eos=None):
atoms, atom_num, atoms_dict = get_atoms(os.path.join(dir, 'POSCAR')) atoms, atom_num, atoms_dict = get_atoms(os.path.join(dir, 'POSCAR'))
scaling_factor = sum(atom_num) / atoms_per_formula_unit scaling_factor = sum(atom_num) / atoms_per_formula_unit
label = dir.split('/')[-1] label = os.path.basename(dir)
dft_df = pd.read_csv(os.path.join(dir, 'energ.dat'), header=None, delim_whitespace=True) dft_df = pd.read_csv(os.path.join(dir, 'energ.dat'), header=None, delim_whitespace=True, index_col=0)
dft_df.reset_index(drop=True, inplace=True)
dft_df.columns = ['Volume', 'Energy'] dft_df.columns = ['Volume', 'Energy']
volume = dft_df["Volume"].to_numpy() / scaling_factor volume = dft_df["Volume"].to_numpy() / scaling_factor
@ -904,10 +905,15 @@ def get_equilibrium_data(path, atoms_per_formula_unit, eos=None):
p0 = get_initial_guesses(volume, energy) p0 = get_initial_guesses(volume, energy)
equilibrium_constants = fit_eos_curve(volume, energy, p0, eos) try:
e0, v0, b0, bp = equilibrium_constants[0], equilibrium_constants[1], equilibrium_constants[2], equilibrium_constants[3] equilibrium_constants = fit_eos_curve(volume, energy, p0, eos)
data.append([label, e0, v0, b0/kJ*1e24, bp]) e0, v0, b0, bp = equilibrium_constants[0], equilibrium_constants[1], equilibrium_constants[2], equilibrium_constants[3]
data.append([label, e0, v0, b0/kJ*1e24, bp])
except:
data.append([label, None, None, None, None])
df = pd.DataFrame(data) df = pd.DataFrame(data)