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refactor trm parsing
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@wtbarnes
wtbarnes committed Nov 5, 2024
1 parent 8c95b41 commit ba82ec1
Showing 1 changed file with 70 additions and 60 deletions.
130 changes: 70 additions & 60 deletions pydrad/parse/parse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -367,67 +367,77 @@ def _read_trm(self):
-- Terms of electron energy equation (11 columns)
-- Terms of hydrogen energy equation (11 columns)
"""
mass_columns = ['mass_drhobydt','mass_advection']
momentum_columns = ['momentum_drho_vbydt','momentum_advection','momentum_pressure_gradient',
'momentum_gravity','momentum_viscous_stress','momentum_numerical_viscosity']
electron_columns = ['electron_dTEKEbydt','electron_enthalpy','electron_conduction',
'electron_gravity','electron_collisions','electron_heating','electron_radiative_loss',
'electron_electric_field','electron_viscous_stress','electron_numerical_viscosity',
'electron_ionization']
hydrogen_columns = ['hydrogen_dTEKEbydt','hydrogen_enthalpy','hydrogen_conduction',
'hydrogen_gravity','hydrogen_collisions','hydrogen_heating','hydrogen_radiative_loss',
'hydrogen_electric_field','hydrogen_viscous_stress','hydrogen_numerical_viscosity',
'hydrogen_ionization']

n_mass = len(mass_columns)
n_momentum = len(momentum_columns)
n_electron = len(electron_columns)
n_hydrogen = len(hydrogen_columns)

# Terms from the mass equation:
mass_terms = read_csv(self._trm_filename, sep='\t', header=None, names=mass_columns,
skiprows=lambda x: x % 5 != 1 )
# Terms from the momentum equation:
momentum_terms = read_csv(self._trm_filename, sep='\t', header=None, names=momentum_columns,
skiprows=lambda x: x % 5 != 2 )
# Terms from the electron energy equation:
electron_terms = read_csv(self._trm_filename, sep='\t', header=None, names=electron_columns,
skiprows=lambda x: x % 5 != 3 )

# Terms from the hydrogen energy equation:
hydrogen_terms = read_csv(self._trm_filename, sep='\t', header=None, names=hydrogen_columns,
skiprows=lambda x: x % 5 != 4 )

offsets = [n_mass,
n_mass+n_momentum,
n_mass+n_momentum+n_electron
]

n_elements = len(mass_terms)
self._trm_data = np.zeros([n_elements, offsets[2]+n_hydrogen])

units = {
'mass': 'g cm-3 s-1',
'momentum': 'dyne cm-3 s-1',
'electrons': 'erg cm-3 s-1',
'hydrogen': 'erg cm-3 s-1',
}
columns = {
'mass': [
'mass_drhobydt',
'mass_advection',
],
'momentum': [
'momentum_drho_vbydt',
'momentum_advection',
'momentum_pressure_gradient',
'momentum_gravity',
'momentum_viscous_stress',
'momentum_numerical_viscosity',
],
'electrons': [
'electron_dTEKEbydt',
'electron_enthalpy',
'electron_conduction',
'electron_gravity',
'electron_collisions',
'electron_heating',
'electron_radiative_loss',
'electron_electric_field',
'electron_viscous_stress',
'electron_numerical_viscosity',
'electron_ionization'
],
'hydrogen': [
'hydrogen_dTEKEbydt',
'hydrogen_enthalpy',
'hydrogen_conduction',
'hydrogen_gravity',
'hydrogen_collisions',
'hydrogen_heating',
'hydrogen_radiative_loss',
'hydrogen_electric_field',
'hydrogen_viscous_stress',
'hydrogen_numerical_viscosity',
'hydrogen_ionization',
]
}
offsets = {
'mass': 0,
'momentum': len(columns['mass']),
'electron': len(columns['mass'])+len(columns['momentum']),
'hydrogen': len(columns['mass'])+len(columns['momentum'])+len(columns['electron']),
}
# Read data from file into table per term category
terms = {}
for i,(k,v) in enumerate(columns.items()):
terms[k] = read_csv(self._trm_filename,

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sep='\t',
header=None,
names=v,
skiprows=lambda x: x % 5 != (i+1))
# Read into single matrix
n_elements = len(terms['mass'])
self._trm_data = np.zeros([n_elements, offsets['hydrogen']+len(columns['hydrogen'])])

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for i in range(n_elements):
for j in range(n_mass):
self._trm_data[i,j] = mass_terms[mass_columns[j]][i]
for j in range(n_momentum):
self._trm_data[i,j+offsets[0]] = momentum_terms[momentum_columns[j]][i]
for j in range(n_electron):
self._trm_data[i,j+offsets[1]] = electron_terms[electron_columns[j]][i]
for j in range(n_hydrogen):
self._trm_data[i,j+offsets[2]] = hydrogen_terms[hydrogen_columns[j]][i]

properties = []
for i in range(n_mass):
properties += [(mass_columns[i], '_trm_data', i, 'g cm-3 s-1')]
for i in range(n_momentum):
properties += [(momentum_columns[i], '_trm_data', i+offsets[0], 'dyne cm-3 s-1')]
for i in range(n_electron):
properties += [(electron_columns[i], '_trm_data', i+offsets[1], 'erg cm-3 s-1')]
for i in range(n_hydrogen):
properties += [(hydrogen_columns[i], '_trm_data', i+offsets[2], 'erg cm-3 s-1')]

for p in properties:
add_property(*p)
for k,v in columns.items():
for j in range(len(v)):
self._trm_data[i,j+offsets[k]] = terms[k][v[j]][i]

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# Add individual property for each term
for k,v in columns.items():
for i in range(len(v)):
add_property(v[i], '_trm_data', i+offsets[k], units[k])

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def _read_ine(self):
"""
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