def build_namelist_pc(rho_core,Mcore): import f90nml #fortran namelist tools from f90nml.namelist import Namelist as NmlDict #namelist class #build namelist nml=NmlDict() sj=NmlDict() #star_job cn=NmlDict() #controls pg=NmlDict() #pgplot pg['read_extra_pgstar_inlist1']=True pg['extra_pgstar_inlist1_name']='inlist_pgstar' sj['read_extra_star_job_inlist1']=True sj['extra_star_job_inlist1_name']='inlist_cache' sj['show_log_description_at_start'] = False sj['load_saved_model'] = True sj['saved_model_name'] = 'model_in.mod' sj['save_model_when_terminate'] = True sj['save_model_filename'] = 'model_out.mod' sj['set_initial_age'] = True sj['initial_age'] = 0 sj['pgstar_flag'] = False sj['change_v_flag'] = True sj['new_v_flag'] = False sj['eos_file_prefix'] = 'mesa' sj['kappa_file_prefix'] = 'gs98' sj['kappa_lowT_prefix'] = 'lowT_Freedman11' sj['change_lnPgas_flag'] = True sj['new_lnPgas_flag'] = True sj['set_initial_model_number'] = True sj['initial_model_number'] = 0 sj['relax_core'] = True sj['new_core_mass'] = Mcore sj['core_avg_rho'] = rho_core sj['dlg_core_mass_per_step'] = 0.05 sj['relax_core_years_for_dt'] = 0.1 sj['core_avg_eps'] = 0 cn['T_mix_limit'] = -1 cn['logQ_limit'] = 10 cn['mixing_length_alpha'] = 1.89 cn['MLT_option'] = 'Henyey' cn['write_header_frequency'] = 1 cn['terminal_cnt'] = 10 cn['profile_interval'] = 10000 cn['varcontrol_target'] = 0.01 cn['mesh_delta_coeff'] = 1 cn['max_age'] = 1e3 cn['max_model_number']=2000 nml['star_job']=sj nml['controls']=cn nml['pgstar']=pg return nml;
def build_namelist_get_profile(log_directory="."):
import f90nml #fortran namelist tools
from f90nml.namelist import Namelist as NmlDict #namelist class
#build namelist
nml = NmlDict()
sj = NmlDict() #star_job
cn = NmlDict() #controls
pg = NmlDict() #pgplot
#declare some xctrl arrays
x_ctrl = [0.0] * 30
x_integer_ctrl = [0] * 5
x_logical_ctrl = [False] * 10
x_ctrl[8] = 1 #safety factor
x_ctrl[9] = 1 #safety factor
x_ctrl[11] = 100 # sep AU
x_ctrl[12] = 1 # stellar mass Msun
pg['read_extra_pgstar_inlist1'] = False
sj['read_extra_star_job_inlist1'] = False
cn['photostep'] = 1000
# Store photos and logs in user-specified directory
cn['log_directory'] = log_directory
cn['photo_directory'] = log_directory
sj['show_log_description_at_start'] = False
sj['load_saved_model'] = True
sj['saved_model_name'] = 'model_in.mod'
sj['save_model_when_terminate'] = False
sj['profile_starting_model'] = True
sj['set_initial_age'] = False
cn['max_age'] = 0.0
nml['star_job'] = sj
nml['controls'] = cn
nml['pgstar'] = pg
return nml
def test_f90repr(self):
nml = NmlDict()
self.assertEqual(nml.f90repr(1), "1")
self.assertEqual(nml.f90repr(1.0), "1.0")
self.assertEqual(nml.f90repr(1 + 2j), "(1.0, 2.0)")
self.assertEqual(nml.f90repr(True), ".true.")
self.assertEqual(nml.f90repr(False), ".false.")
self.assertEqual(nml.f90repr("abc"), "'abc'")
for ptype in ({}, [], set()):
self.assertRaises(ValueError, nml.f90repr, ptype)
def read(self, nml_fname, nml_patch_in=None, patch_fname=None):
"""Parse a Fortran 90 namelist file and store the contents.
>>> from f90nml.parser import Parser
>>> parser = Parser()
>>> data_nml = parser.read('data.nml')"""
nml_file = open(nml_fname, 'r')
if nml_patch_in:
nml_patch = copy.deepcopy(nml_patch_in)
if not patch_fname:
patch_fname = nml_fname + '~'
elif nml_fname == patch_fname:
nml_file.close()
raise ValueError('f90nml: error: Patch filepath cannot be the '
'same as the original filepath.')
self.pfile = open(patch_fname, 'w')
else:
nml_patch = {}
f90lex = shlex.shlex(nml_file)
f90lex.whitespace = ''
f90lex.wordchars += '.-+' # Include floating point tokens
if nml_patch:
f90lex.commenters = ''
else:
f90lex.commenters = '!'
self.tokens = iter(f90lex)
nmls = NmlDict()
# TODO: Replace "while True" with an update_token() iterator
self.update_tokens(write_token=False)
while True:
try:
# Check for classic group terminator
if self.token == 'end':
self.update_tokens()
# Ignore tokens outside of namelist groups
while self.token not in ('&', '$'):
self.update_tokens()
except StopIteration:
break
# Create the next namelist
self.update_tokens()
g_name = self.token
g_vars = NmlDict()
v_name = None
grp_patch = nml_patch.get(g_name, {})
# Populate the namelist group
while g_name:
if self.token not in ('=', '%', '('):
self.update_tokens()
# Set the next active variable
if self.token in ('=', '(', '%'):
try:
v_name, v_values = self.parse_variable(
g_vars, patch_nml=grp_patch)
except ValueError:
nml_file.close()
if self.pfile:
self.pfile.close()
raise
if v_name in g_vars:
v_prior_values = g_vars[v_name]
v_values = merge_values(v_prior_values, v_values)
if v_name in g_vars and type(g_vars[v_name]) is NmlDict:
g_vars[v_name].update(v_values)
else:
g_vars[v_name] = v_values
# Deselect variable
v_name = None
v_values = []
# Finalise namelist group
if self.token in ('/', '&', '$'):
# Append any remaining patched variables
for v_name, v_val in grp_patch.items():
g_vars[v_name] = v_val
v_strs = var_strings(v_name, v_val)
for v_str in v_strs:
self.pfile.write(' {0}\n'.format(v_str))
# Append the grouplist to the namelist
if g_name in nmls:
g_update = nmls[g_name]
# Update to list of groups
if not type(g_update) is list:
g_update = [g_update]
g_update.append(g_vars)
else:
g_update = g_vars
nmls[g_name] = g_update
# Reset state
g_name, g_vars = None, None
try:
self.update_tokens()
except StopIteration:
break
nml_file.close()
if self.pfile:
self.pfile.close()
return nmls
def parse_variable(self, parent, patch_nml=None):
"""Parse a variable and return its name and values."""
if not patch_nml:
patch_nml = {}
v_name = self.prior_token
v_values = []
# Patch state
patch_values = None
write_token = v_name not in patch_nml
if self.token == '(':
v_indices = self.parse_index()
# TODO: Multidimensional support
i_s = 1 if not v_indices[0][0] else v_indices[0][0]
i_e = v_indices[0][1]
i_r = 1 if not v_indices[0][2] else v_indices[0][2]
if i_e:
v_idx = iter(range(i_s, i_e, i_r))
else:
v_idx = (i_s + i_r * k for k in itertools.count())
else:
v_idx = None
if self.token == '%':
# Resolve the derived type
if parent and v_name in parent:
v_parent = parent[v_name]
else:
v_parent = []
self.update_tokens()
self.update_tokens()
v_att, v_att_vals = self.parse_variable(v_parent)
next_value = NmlDict()
next_value[v_att] = v_att_vals
append_value(v_values, next_value, v_idx)
else:
# Construct the variable array
assert self.token == '='
n_vals = None
prior_ws_sep = ws_sep = False
self.update_tokens()
if v_name in patch_nml:
patch_values = f90repr(patch_nml.pop(v_name))
if not type(patch_values) is list:
patch_values = [patch_values]
for p_val in patch_values:
self.pfile.write(p_val)
# Add variables until next variable trigger
while (self.token not in ('=', '(', '%')
or (self.prior_token, self.token) == ('=', '(')):
# Check for repeated values
if self.token == '*':
n_vals = self.parse_value(write_token)
assert type(n_vals) is int
self.update_tokens(write_token)
elif not n_vals:
n_vals = 1
# First check for implicit null values
if self.prior_token in ('=', '%', ','):
if (self.token in (',', '/', '&', '$')
and not (self.prior_token == ','
and self.token in ('/', '&', '$'))):
append_value(v_values, None, v_idx, n_vals)
elif self.prior_token == '*':
if self.token not in ('/', '&', '$'):
self.update_tokens(write_token)
if (self.token == '=' or (self.token in ('/', '&', '$')
and self.prior_token == '*')):
next_value = None
else:
next_value = self.parse_value(write_token)
append_value(v_values, next_value, v_idx, n_vals)
else:
next_value = self.parse_value(write_token)
# Finished reading old value, we can again write tokens
write_token = True
# Check for escaped strings
if (v_values and (type(v_values[-1]) is str)
and type(next_value) is str and not prior_ws_sep):
quote_char = self.prior_token[0]
v_values[-1] = quote_char.join(
[v_values[-1], next_value])
else:
append_value(v_values, next_value, v_idx, n_vals)
# Exit for end of nml group (/, &, $) or null broadcast (=)
if self.token in ('/', '&', '$', '='):
break
else:
prior_ws_sep = ws_sep
ws_sep = self.update_tokens(write_token)
if patch_values:
v_values = patch_values
if not v_idx:
v_values = delist(v_values)
return v_name, v_values
def build_namelist_mp_hold(Thold, L_M_ratio, Flux, Sigma, log_directory="."):
import f90nml #fortran namelist tools
from f90nml.namelist import Namelist as NmlDict #namelist class
#build namelist
nml = NmlDict()
sj = NmlDict() #star_job
cn = NmlDict() #controls
pg = NmlDict() #pgplot
#declare some xctrl arrays
x_ctrl = [0.0] * 30
x_integer_ctrl = [0] * 5
x_logical_ctrl = [False] * 10
x_ctrl[8] = 1 #safety factor
x_ctrl[9] = 1 #safety factor
x_ctrl[11] = 100 # sep AU
x_ctrl[12] = 1 # stellar mass Msun
x_ctrl[21] = L_M_ratio # luminisoity to core mass ratio
x_logical_ctrl[0] = True # radio-active heating
x_logical_ctrl[5] = True # core/envelope heating
pg['read_extra_pgstar_inlist1'] = False
sj['read_extra_star_job_inlist1'] = False
cn['photostep'] = 1000
# Store photos and logs in user-specified directory
cn['log_directory'] = log_directory
cn['photo_directory'] = log_directory
sj['show_log_description_at_start'] = False
sj['load_saved_model'] = True
sj['saved_model_name'] = 'model_in.mod'
sj['save_model_when_terminate'] = True
sj['save_model_filename'] = 'model_out.mod'
sj['set_initial_age'] = True
sj['initial_age'] = 0
sj['pgstar_flag'] = False
sj['change_v_flag'] = True
sj['new_v_flag'] = False
sj['eos_file_prefix'] = 'mesa'
sj['kappa_file_prefix'] = 'gs98'
sj['kappa_lowT_prefix'] = 'lowT_Freedman11'
sj['change_lnPgas_flag'] = True
sj['new_lnPgas_flag'] = True
sj['set_initial_model_number'] = True
sj['initial_model_number'] = 0
sj['set_irradiation'] = True
sj['set_to_this_irrad_flux'] = Flux
sj['irrad_col_depth'] = Sigma
cn['T_mix_limit'] = -1
cn['logQ_limit'] = 10
cn['mixing_length_alpha'] = 1.89
cn['MLT_option'] = 'Henyey'
cn['write_header_frequency'] = 10
cn['terminal_cnt'] = 100
cn['profile_interval'] = 10000
cn['varcontrol_target'] = 0.01
cn['mesh_delta_coeff'] = 1
cn['max_age'] = Thold
cn['use_other_energy'] = True
cn['x_ctrl'] = x_ctrl
cn['x_logical_ctrl'] = x_logical_ctrl
cn['x_integer_ctrl'] = x_integer_ctrl
cn['max_model_number'] = 2000
nml['star_job'] = sj
nml['controls'] = cn
nml['pgstar'] = pg
return nml
def build_namelist_ev_Fsigma_we(Tmax,
Flux,
Sigma,
Temp,
sep,
stop_mass,
ES,
log_directory=".",
HIST_CADENCE=5.e7,
include_core=True):
import f90nml #fortran namelist tools
from f90nml.namelist import Namelist as NmlDict #namelist class
#build namelist
nml = NmlDict()
sj = NmlDict() #star_job
cn = NmlDict() #controls
pg = NmlDict() #pgplot
#declare some xctrl arrays
x_ctrl = [0.0] * 30
x_integer_ctrl = [0] * 5
x_logical_ctrl = [False] * 10
x_ctrl[8] = 1 #safety factor
x_ctrl[9] = 1 #safety factor
x_ctrl[11] = sep # sep AU
x_ctrl[12] = 1 # stellar mass Msun
x_ctrl[18] = Temp
x_ctrl[23] = 6.9183e7 #saturation for X-rays
x_ctrl[24] = 10**-3.6
x_ctrl[25] = 1.19
x_logical_ctrl[0] = include_core # radio-active heating
x_logical_ctrl[1] = include_core # core heat capacity
x_logical_ctrl[5] = False # core/envelope heating
x_logical_ctrl[6] = True #evaporation
x_logical_ctrl[7] = ES # include evolution of star or not
x_logical_ctrl[8] = True # uniform history data
x_ctrl[0] = HIST_CADENCE # history cadence
cn['max_years_for_timestep'] = HIST_CADENCE # history cadence
pg['read_extra_pgstar_inlist1'] = False
sj['read_extra_star_job_inlist1'] = False
cn['photostep'] = 1000
# Store photos and logs in user-specified directory
cn['log_directory'] = log_directory
cn['photo_directory'] = log_directory
sj['show_log_description_at_start'] = False
sj['load_saved_model'] = True
sj['saved_model_name'] = 'model_in.mod'
sj['save_model_when_terminate'] = True
sj['save_model_filename'] = 'model_out.mod'
sj['set_initial_age'] = True
sj['initial_age'] = 0
sj['set_initial_dt'] = True
sj['years_for_initial_dt'] = 1e5
sj['pgstar_flag'] = False
sj['change_v_flag'] = True
sj['new_v_flag'] = True
sj['eos_file_prefix'] = 'mesa'
sj['kappa_file_prefix'] = 'gs98'
sj['kappa_lowT_prefix'] = 'lowT_Freedman11'
sj['change_lnPgas_flag'] = True
sj['new_lnPgas_flag'] = True
sj['set_initial_model_number'] = True
sj['initial_model_number'] = 0
sj['set_irradiation'] = True
sj['set_to_this_irrad_flux'] = Flux
sj['irrad_col_depth'] = Sigma
cn['T_mix_limit'] = -1
cn['logQ_limit'] = 10
cn['mixing_length_alpha'] = 1.89
cn['MLT_option'] = 'Henyey'
cn['write_header_frequency'] = 10
cn['terminal_cnt'] = 100
cn['profile_interval'] = 10000
cn['varcontrol_target'] = 3e-4
cn['mesh_delta_coeff'] = 1
cn['max_age'] = Tmax
cn['max_years_for_timestep'] = 5e7
cn['use_other_energy'] = True
cn['use_other_wind'] = True
cn['star_mass_min_limit'] = stop_mass
cn['x_ctrl'] = x_ctrl
cn['x_logical_ctrl'] = x_logical_ctrl
cn['x_integer_ctrl'] = x_integer_ctrl
cn['min_q_for_k_below_const_q'] = 0.9
cn['min_q_for_k_const_mass'] = 0.5
nml['star_job'] = sj
nml['controls'] = cn
nml['pgstar'] = pg
return nml
def read(self, nml_fname, nml_patch_in=None, patch_fname=None):
"""Parse a Fortran 90 namelist file and store the contents.
>>> from f90nml.parser import Parser
>>> parser = Parser()
>>> data_nml = parser.read('data.nml')"""
nml_file = open(nml_fname, 'r')
if nml_patch_in:
if not isinstance(nml_patch_in, dict):
nml_file.close()
raise ValueError('Input patch must be a dict or an NmlDict.')
nml_patch = copy.deepcopy(NmlDict(nml_patch_in))
if not patch_fname:
patch_fname = nml_fname + '~'
elif nml_fname == patch_fname:
nml_file.close()
raise ValueError('f90nml: error: Patch filepath cannot be the '
'same as the original filepath.')
self.pfile = open(patch_fname, 'w')
else:
nml_patch = NmlDict()
f90lex = shlex.shlex(nml_file)
f90lex.whitespace = ''
f90lex.wordchars += '.-+' # Include floating point tokens
if nml_patch:
f90lex.commenters = ''
else:
f90lex.commenters = '!'
self.tokens = iter(f90lex)
nmls = NmlDict()
# TODO: Replace "while True" with an update_token() iterator
self.update_tokens(write_token=False)
while True:
try:
# Check for classic group terminator
if self.token == 'end':
self.update_tokens()
# Ignore tokens outside of namelist groups
while self.token not in ('&', '$'):
self.update_tokens()
except StopIteration:
break
# Create the next namelist
self.update_tokens()
g_name = self.token
g_vars = NmlDict()
v_name = None
grp_patch = nml_patch.get(g_name, {})
# Populate the namelist group
while g_name:
if self.token not in ('=', '%', '('):
self.update_tokens()
# Set the next active variable
if self.token in ('=', '(', '%'):
try:
v_name, v_values = self.parse_variable(
g_vars, patch_nml=grp_patch)
except ValueError:
nml_file.close()
if self.pfile:
self.pfile.close()
raise
if v_name in g_vars:
v_prior_values = g_vars[v_name]
v_values = merge_values(v_prior_values, v_values)
if v_name in g_vars and isinstance(g_vars[v_name], dict):
g_vars[v_name].update(v_values)
else:
g_vars[v_name] = v_values
# Deselect variable
v_name = None
v_values = []
# Finalise namelist group
if self.token in ('/', '&', '$'):
# Append any remaining patched variables
for v_name, v_val in grp_patch.items():
g_vars[v_name] = v_val
v_strs = nmls.var_strings(v_name, v_val)
for v_str in v_strs:
self.pfile.write(' {0}\n'.format(v_str))
# Append the grouplist to the namelist
if g_name in nmls:
g_update = nmls[g_name]
# Update to list of groups
if not isinstance(g_update, list):
g_update = [g_update]
g_update.append(g_vars)
else:
g_update = g_vars
nmls[g_name] = g_update
# Reset state
g_name, g_vars = None, None
try:
self.update_tokens()
except StopIteration:
break
nml_file.close()
if self.pfile:
self.pfile.close()
return nmls
def parse_variable(self, parent, patch_nml=None):
"""Parse a variable and return its name and values."""
if not patch_nml:
patch_nml = NmlDict()
v_name = self.prior_token
v_values = []
# Patch state
patch_values = None
write_token = v_name not in patch_nml
if self.token == '(':
v_indices = self.parse_index()
# TODO: Multidimensional support
i_s = 1 if not v_indices[0][0] else v_indices[0][0]
i_e = v_indices[0][1]
i_r = 1 if not v_indices[0][2] else v_indices[0][2]
if i_e:
v_idx = iter(range(i_s, i_e, i_r))
else:
v_idx = (i_s + i_r * k for k in itertools.count())
else:
v_idx = None
if self.token == '%':
# Resolve the derived type
if parent and v_name in parent:
v_parent = parent[v_name]
else:
v_parent = []
self.update_tokens()
self.update_tokens()
v_att, v_att_vals = self.parse_variable(v_parent)
next_value = NmlDict()
next_value[v_att] = v_att_vals
append_value(v_values, next_value, v_idx)
else:
# Construct the variable array
assert self.token == '='
n_vals = None
prior_ws_sep = ws_sep = False
self.update_tokens()
if v_name in patch_nml:
patch_values = patch_nml.f90repr(patch_nml.pop(v_name))
if not isinstance(patch_values, list):
patch_values = [patch_values]
for p_val in patch_values:
self.pfile.write(p_val)
# Add variables until next variable trigger
while (self.token not in ('=', '(', '%') or
(self.prior_token, self.token) == ('=', '(')):
# Check for repeated values
if self.token == '*':
n_vals = self.parse_value(write_token)
assert isinstance(n_vals, int)
self.update_tokens(write_token)
elif not n_vals:
n_vals = 1
# First check for implicit null values
if self.prior_token in ('=', '%', ','):
if (self.token in (',', '/', '&', '$') and
not (self.prior_token == ',' and
self.token in ('/', '&', '$'))):
append_value(v_values, None, v_idx, n_vals)
elif self.prior_token == '*':
if self.token not in ('/', '&', '$'):
self.update_tokens(write_token)
if (self.token == '=' or (self.token in ('/', '&', '$') and
self.prior_token == '*')):
next_value = None
else:
next_value = self.parse_value(write_token)
append_value(v_values, next_value, v_idx, n_vals)
else:
next_value = self.parse_value(write_token)
# Finished reading old value, we can again write tokens
write_token = True
# Check for escaped strings
if (v_values and isinstance(v_values[-1], str) and
isinstance(next_value, str) and not prior_ws_sep):
quote_char = self.prior_token[0]
v_values[-1] = quote_char.join([v_values[-1],
next_value])
else:
append_value(v_values, next_value, v_idx, n_vals)
# Exit for end of nml group (/, &, $) or null broadcast (=)
if self.token in ('/', '&', '$', '='):
break
else:
prior_ws_sep = ws_sep
ws_sep = self.update_tokens(write_token)
if patch_values:
v_values = patch_values
if not v_idx:
v_values = delist(v_values)
return v_name, v_values
def build_namelist_ev_nothing(Tmax): import f90nml #fortran namelist tools from f90nml.namelist import Namelist as NmlDict #namelist class #build namelist nml=NmlDict() sj=NmlDict() #star_job cn=NmlDict() #controls pg=NmlDict() #pgplot #declare some xctrl arrays x_ctrl=[0.0]*30 x_integer_ctrl=[0]*5 x_logical_ctrl=[False]*10 x_ctrl[8]=1 #safety factor x_ctrl[9]=1 #safety factor x_ctrl[11]=100 # sep AU x_ctrl[12]=1 # stellar mass Msun x_logical_ctrl[0]=False # radio-active heating x_logical_ctrl[5]=False # core/envelope heating x_logical_ctrl[7]=False # evolve star pg['read_extra_pgstar_inlist1']=True pg['extra_pgstar_inlist1_name']='inlist_pgstar' sj['read_extra_star_job_inlist1']=True sj['extra_star_job_inlist1_name']='inlist_cache' sj['show_log_description_at_start'] = False sj['load_saved_model'] = True sj['saved_model_name'] = 'model_in.mod' sj['save_model_when_terminate'] = True sj['save_model_filename'] = 'model_out.mod' sj['set_initial_age'] = True sj['initial_age'] = 0 sj['set_initial_dt']=True sj['years_for_initial_dt']=1e5 sj['pgstar_flag'] = False sj['change_v_flag'] = True sj['new_v_flag'] = True sj['eos_file_prefix'] = 'mesa' sj['kappa_file_prefix'] = 'gs98' sj['kappa_lowT_prefix'] = 'lowT_Freedman11' sj['change_lnPgas_flag'] = True sj['new_lnPgas_flag'] = True sj['set_initial_model_number'] = True sj['initial_model_number'] = 0 sj['set_irradiation'] = False cn['T_mix_limit'] = -1 cn['logQ_limit'] = 10 cn['mixing_length_alpha'] = 1.89 cn['MLT_option'] = 'Henyey' cn['write_header_frequency'] = 10 cn['terminal_cnt'] = 100 cn['profile_interval'] = 10000 cn['varcontrol_target'] = 1e-4 cn['mesh_delta_coeff'] = 1 cn['max_age'] = Tmax cn['max_years_for_timestep']=1e8 cn['use_other_energy']=True cn['x_ctrl']=x_ctrl cn['x_logical_ctrl']=x_logical_ctrl cn['x_integer_ctrl']=x_integer_ctrl cn['max_model_number']=2000 nml['star_job']=sj nml['controls']=cn nml['pgstar']=pg return nml;