def _load_par(self):
self.par = pa.get_params(self.files['par'])
self.dz = self.par['x3max'] / self.par['Nx3'] * 2
self.Lx = self.par['x1max'] - self.par['x1min']
self.Ly = self.par['x2max'] - self.par['x2min']
self.Lz = self.par['x3max'] - self.par['x3min']
self.area = self.Lx * self.Ly
def doall(base,problem_id,problem_dir=None,do_pickling=True,use_yt=True,
force_recal=False, force_redraw=False,vtkdir=None):
"""
This function will do following tasks:
(1) reoranizing files
* .hst, .sn --> hst/
* .zprof --> zprof/
* .starpar.vtk --> starpar/
* .rst --> rst/
(2) creating a parameter file from a restart header
(3) creating merged (along the time axis) zprof files for each thermal phase (using xarray)
(4) creating history data using zprof dumps, including new fields
(5) [if do_pickling] creating pickle files for slice and projection (will use yt [if use_yt])
"""
if problem_dir is None: problem_dir = problem_id
print('preparing metadata for {}...'.format(problem_id))
done=cleanup_directory(base,problem_id,problem_dir=problem_dir)
for k in done:
if done[k]: print('{}.{} is moved'.format(problem_id,k))
parfile='{}{}/{}.par'.format(base,problem_dir,problem_id)
params=pa.get_params(parfile)
zpfile='{}{}/zprof_merged/{}.phase5.zprof.nc'.format(base,problem_dir,problem_id)
from pyathena.utils import compare_files
zpfiles=glob.glob('{}{}/zprof/{}.*.whole.zprof'.format(base,problem_dir,problem_id))
zpfiles.sort()
if len(zpfiles) > 0:
if not compare_files(zpfiles[-1],zpfile): zprof_to_xarray(base,problem_dir,problem_id)
#zpfile='{}{}/zprof_merged/{}.zprof.nc'.format(base,problem_id,problem_id)
#if not os.path.isfile(zpfile): merge_xarray(base,problem_id)
hstzpfile='{}{}/hst/{}.hst_zp.p'.format(base,problem_dir,problem_id)
if os.path.isfile(zpfile): recal_history(base,problem_dir,problem_id)
if do_pickling:
kwargs={'base_directory':base,
'directory':'{}/'.format(problem_dir),
'id':problem_id,
'parallel':False,
'phase':False,
'rotation':params['Omega']*1.e3,
'range':''
}
if use_yt:
print('slicing and projecting with yt ...')
from pyathena.yt_analysis import yt_analysis
yt_analysis.main(force_recal=force_recal,force_redraw=force_redraw,verbose=50,**kwargs)
else:
if not (vtkdir is None): kwargs['vtk_directory']=vtkdir
print('slicing and projecting with pyathena ...')
from pyathena.create_pickle import create_all_pickles
create_all_pickles(force_recal=force_recal,force_redraw=force_redraw,verbose=True,**kwargs)
def doall(base, problem_id, problem_dir=None, do_pickling=True, use_yt=True):
"""
do all preprocessing for a model
"""
if problem_dir is None: problem_dir = problem_id
print('preparing metadata for {}...'.format(problem_id))
done = cleanup_directory(base, problem_id, problem_dir=problem_dir)
for k in done:
if done[k]: print('{}.{} is moved'.format(problem_id, k))
parfile = '{}{}/{}.par'.format(base, problem_dir, problem_id)
params = pa.get_params(parfile)
zpfile = '{}{}/zprof_merged/{}.whole.zprof.nc'.format(
base, problem_dir, problem_id)
from pyathena.utils import compare_files
zpfiles = glob.glob('{}{}/zprof/{}.*.whole.zprof'.format(
base, problem_dir, problem_id))
zpfiles.sort()
if not compare_files(zpfiles[-1], zpfile):
zprof_to_xarray(base, problem_dir, problem_id)
#zpfile='{}{}/zprof_merged/{}.zprof.nc'.format(base,problem_id,problem_id)
#if not os.path.isfile(zpfile): merge_xarray(base,problem_id)
hstzpfile = '{}{}/hst/{}.hst_zp.p'.format(base, problem_dir, problem_id)
if os.path.isfile(zpfile): recal_history(base, problem_dir, problem_id)
if do_pickling:
kwargs = {
'base_directory': base,
'directory': '{}/'.format(problem_dir),
'id': problem_id,
'parallel': False,
'phase': False,
'rotation': params['Omega'] * 1.e3,
'range': ''
}
if use_yt:
print('slicing and projecting with yt ...')
from pyathena.yt_analysis import yt_analysis
yt_analysis.main(force_recal=False,
force_redraw=False,
verbose=50,
**kwargs)
else:
print('slicing and projecting with pyathena ...')
from pyathena.create_pickle import create_all_pickles
create_all_pickles(force_recal=False,
force_redraw=False,
verbose=True,
**kwargs)
def recal_history(base, problem_dir, problem_id):
parfile = '{}{}/{}.par'.format(base, problem_dir, problem_id)
params = pa.get_params(parfile)
hstfile = '{}{}/hst/{}.hst'.format(base, problem_dir, problem_id)
hst = pa.hst_reader(hstfile)
hstrecalfile = '{}_cal.p'.format(hstfile)
h = processing_history_dump(hst, params, hstrecalfile)
snfile = '{}{}/hst/{}.sn'.format(base, problem_dir, problem_id)
sn = pa.hst_reader(snfile)
rates = recal_rates(h, sn, base, problem_dir, problem_id)
hstzpfile = '{}_zp.p'.format(hstfile)
zprof_ds = merge_xarray(base, problem_dir, problem_id)
#print("zprof dataset is loaded")
h_zp = processing_zprof_dump(h, rates, params, zprof_ds, hstzpfile)
def print_info(parfile, h, h_zp, pid=None, outdir='./'):
if pid is None: problem_id = os.path.basename(parfile).replace('.par', '')
else: problem_id = pid
params = pa.get_params(parfile)
with open('{}/mds/{}.md'.format(outdir, problem_id), 'w') as fp:
fp.write('## {}\n'.format(problem_id))
# gas info
fp.write('### INITIAL CONDITIONS\n')
fp.write(
'* Surface Density of Gas (M_sun/pc^2): {surf}\n'.format(**params))
fp.write('* Surface Density of Stars (M_sun/pc^2): {SurfS}\n'.format(
**params))
fp.write('* Scale Heights of Stars (pc): {zstar}\n'.format(**params))
fp.write('* Midplane density of DM (M_sun/pc^3): {rhodm}\n'.format(
**params))
fp.write('* Galactocentric Distance (pc): {R0}\n'.format(**params))
fp.write('* Galactic Rotation (km/s/pc): {Omega}\n'.format(**params))
fp.write('* Nscalars (Metal tracers): {nscalars}\n'.format(**params))
# domain info
fp.write('\n### DOMAIN\n')
for i in range(3):
params['Lx{:d}'.format(i + 1)] = params['x{:d}max'.format(
i + 1)] - params['x{:d}min'.format(i + 1)]
params['dx{:d}'.format(i + 1)] = params['Lx{:d}'.format(
i + 1)] / params['Nx{:d}'.format(i + 1)]
params['Lx{:d}'.format(i + 1)] = int(params['Lx{:d}'.format(i +
1)])
params['dx{:d}'.format(i + 1)] = int(params['dx{:d}'.format(i +
1)])
params['Nx{:d}'.format(i + 1)] = int(params['Nx{:d}'.format(i +
1)])
fp.write('* Lx: {Lx1} x {Lx2} x {Lx3}\n'.format(**params))
fp.write('* Nx: {Nx1} x {Nx2} x {Nx3}\n'.format(**params))
fp.write('* dx: {dx1} x {dx2} x {dx3}\n'.format(**params))
# perturbation info
fp.write('\n### SNe\n')
params['runaways'] = False
if 'fbin' in params:
if params['fbin'] > 0: params['runaways'] = True
params['random_SN_driving'] = False
if 'snrate_random' in params:
if (params['iprob'] == 5) & (params['snrate_random'] > 0):
params['random_SN_driving'] = True
#params['turb_driving']=False
#if params.has_key('dedt'):
# if (params['dedt'] >0) & ((params['iprob'] ==4) | (params['iprob'] == 5)): params['turb_driving']=True
# tdrive = params['driving_time']
params['Ia_SN'] = False
if 'Ia_amp' in params:
if (params['Ia_amp'] == 1): params['Ia_SN'] = True
for k in ['runaways', 'Ia_SN', 'random_SN_driving']:
fp.write('* {}: {}\n'.format(k, params[k]))
fp.write('\n### Movies\n')
fp.write(
'* [Slice](../movies/{}_slice_proj.mp4)\n\n'.format(problem_id))
fp.write('* [Surface Density](../movies/{}_surf.mp4)\n\n'.format(
problem_id))
fp.write('\n### History\n')
fp.write('* `{}`\n\n'.format(h))
fp.write('* `{}`\n\n'.format(h_zp))
fp.write('\n'.format(
problem_id, problem_id))
print('output: {}/mds/{}.md'.format(outdir, problem_id))
if os.path.isdir(dd):
if os.path.isdir(dd + '/slice/'):
ids.append(os.path.basename(dd))
if narg > 3:
overwrite = eval(sys.argv[3])
else:
overwrite = False
for pid in ids:
print(pid)
if os.path.isdir('{}{}/slab/'.format(base, pid)):
pdir = '{}/slab/'.format(pid)
else:
pdir = pid + '/'
par = get_params('{}{}{}.par'.format(base, pdir, pid))
if 'pattern' in par:
vy0 = par['Omega'] * (1.0 - par['pattern']) * par['R0']
print('v_y,circ = {}'.format(vy0))
else:
vy0 = 0.0
slc_files = glob.glob('{}{}/slice/{}.????.slice.p'.format(base, pdir, pid))
slc_files.sort()
nf = len(slc_files)
aux = set_aux.set_aux(pid)
aux_surf = aux['surface_density']
if system == 'tigress_rps':
field_list = [
'star_particles', 'surface_density', 'specific_scalar3_proj', 'nH',
'specific_scalar3', 'temperature', 'pok', 'ram_pok_z'
]