def yt_octree_generate(fname, field_add):
print('[grid_construction]: bbox_lim = ', cfg.par.bbox_lim)
bbox = [[-2. * cfg.par.bbox_lim, 2. * cfg.par.bbox_lim],
[-2. * cfg.par.bbox_lim, 2. * cfg.par.bbox_lim],
[-2. * cfg.par.bbox_lim, 2. * cfg.par.bbox_lim]]
# load the DS and add pd fields; no need to put in stellar ages yet
# as this will happen downstream in zoom
pf = field_add(fname, bounding_box=bbox)
# zoom if necessary
# if cfg.par.zoom == True:
pf = octree_zoom_bbox_filter(fname, pf, bbox, field_add)
pf.index
ad = pf.all_data()
# ---------------------------------------------------------------
# PLOTTING DIAGNOSTIC PROJECTION PLOTS
# ---------------------------------------------------------------
# proj_plots(pf)
from yt.data_objects.particle_unions import ParticleUnion
pu = ParticleUnion("all", list(pf.particle_types_raw))
saved = pf.index.oct_handler.save_octree()
always = AlwaysSelector(None)
ir1 = pf.index.oct_handler.ires(always) # refinement levels
fc1 = pf.index.oct_handler.fcoords(always) # coordinates in code_length
fw1 = pf.index.oct_handler.fwidth(always) # width of cell in code_length
# convert fc1 and fw1 to YTArrays
fc1 = pf.arr(fc1, 'code_length')
fw1 = pf.arr(fw1, 'code_length')
print('----------------------------')
print('yt Octree Construction Stats')
print('----------------------------')
print(' n_ref = ', pf.index.oct_handler.n_ref)
print(' max_level = ', pf.index.oct_handler.max_level)
print(' nocts = ', pf.index.oct_handler.nocts)
print('----------------------------')
gridstats(ir1, fc1, fw1)
# ==================================
refined = saved['octree'].astype('bool')
try:
refined.reshape(len(ir1))
except:
refinements = 2**(3 * cfg.par.oref)
refined2 = []
for r in refined:
if r == 1:
refined2.append(True)
if r == 0:
refined2.append(np.zeros(refinements).astype('bool'))
refined = np.hstack(refined2)
# smooth the data on to the octree
volume = np.zeros(len(refined))
if cfg.par.CONSTANT_DUST_GRID == False:
# crash the code if the parameter choice for dust grid type isn't in
# the hard coded valid list below
dust_grid_type_list = ['dtm', 'rr', 'manual']
try:
dust_choice = dust_grid_type_list.index(cfg.par.dust_grid_type)
except ValueError as e:
print(
'You chose a dust_choice that isnt a valid selection within the list: '
+ dust_grid_type_list + '....crashing now!')
sys.exit()
if cfg.par.dust_grid_type == 'dtm':
dust_smoothed_dtm = dtm_grid(pf, refined)
dust_smoothed = dust_smoothed_dtm
if cfg.par.dust_grid_type == 'rr':
dust_smoothed_remy_ruyer = remy_ruyer(pf, refined)
dust_smoothed = dust_smoothed_remy_ruyer
if cfg.par.dust_grid_type == 'manual':
dust_smoothed_manual = manual(pf, refined)
dust_smoothed = dust_smoothed_manual
else:
print('cfg.par.CONSTANT_DUST_GRID=True')
print('setting constant dust grid to 4.e-22')
dust_smoothed = np.zeros(len(refined)) + 4.e-23
# return refined,dust_smoothed,xmin,xmax,ymin,ymax,zmin,zmax,boost
return refined, dust_smoothed, fc1, fw1, pf, ad
def yt_octree_generate(fname, field_add):
print('[grid_construction]: bbox_lim = ', cfg.par.bbox_lim)
bbox = [[-2. * cfg.par.bbox_lim, 2. * cfg.par.bbox_lim],
[-2. * cfg.par.bbox_lim, 2. * cfg.par.bbox_lim],
[-2. * cfg.par.bbox_lim, 2. * cfg.par.bbox_lim]]
# load the DS and add pd fields. this is the first field addition
# of the simulation, so we don't yet need to add the smoothed
# quantities (which can take some time in yt4.x).
ds = field_add(fname, bounding_box=bbox, add_smoothed_quantities=False)
#now zoom in.
reg = octree_zoom_bbox_filter(fname, ds, bbox, field_add)
# ---------------------------------------------------------------
# PLOTTING DIAGNOSTIC PROJECTION PLOTS
# ---------------------------------------------------------------
# proj_plots(ds)
#from yt.data_objects.particle_unions import ParticleUnion
#pu = ParticleUnion("all", list(ds.particle_types_raw))
if yt.__version__ == '4.0.dev0':
refined = reg.parameters['octree'][('index', 'refined')].astype('bool')
#get central positions of cells as edges + width/2.
# xpos = (ds.parameters['octree'][('index', 'x')]+(ds.parameters['octree'][('index','dx')]/2.))[~refined]
# ypos = (ds.parameters['octree'][('index', 'y')]+(ds.parameters['octree'][('index','dy')]/2.))[~refined]
# zpos = (ds.parameters['octree'][('index', 'z')]+(ds.parameters['octree'][('index','dz')]/2.))[~refined]
xpos = (reg.parameters['octree'][('index', 'x')])[~refined]
ypos = (reg.parameters['octree'][('index', 'y')])[~refined]
zpos = (reg.parameters['octree'][('index', 'z')])[~refined]
#comebine these into the fc1 array with dimensions (nparticles,3)
fc1 = np.array([xpos, ypos, zpos]).T
dx = reg.parameters['octree'][('index', 'dx')][~refined]
dy = reg.parameters['octree'][('index', 'dy')][~refined]
dz = reg.parameters['octree'][('index', 'dz')][~refined]
fw1 = np.array([dx, dy, dz]).T
n_ref = reg.parameters['octree'].n_ref
#max_level = find_max_level(refined)#'max_level not yet implemented in yt4.x'
#note, we could figure this out from the max number of trues in a row
nocts = len(refined) - np.sum(refined)
else:
#saved = ds.index.oct_handler.save_octree()
#always = AlwaysSelector(None)
#ir1 = ds.index.oct_handler.ires(always) # refinement levels
fc1 = reg.parameters["fc1"] #coordinates in code_length
fw1 = reg.parameters["fw1"] #width of cell in code_length
refined = reg.parameters["refined"]
n_ref = reg.parameters["n_ref"]
max_level = reg.parameters["max_level"]
nocts = reg.parameters["nocts"]
# convert fc1 and fw1 to YTArrays
fc1 = ds.arr(fc1, 'code_length')
fw1 = ds.arr(fw1, 'code_length')
print('----------------------------')
print('yt Octree Construction Stats')
print('----------------------------')
print(' n_ref = ', n_ref)
#print(' max_level = ', max_level)
print(' nocts = ', nocts)
print('----------------------------')
gridstats(fc1, fw1)
# ==================================
#try:
# refined.reshape(len(ir1))
#except:
refinements = 2**(3 * cfg.par.oref)
refined2 = []
for r in refined:
if r == 1:
refined2.append(True)
if r == 0:
refined2.append(np.zeros(refinements).astype('bool'))
refined = np.hstack(refined2)
if cfg.par.CONSTANT_DUST_GRID == False:
# crash the code if the parameter choice for dust grid type isn't in
# the hard coded valid list below
dust_grid_type_list = ['dtm', 'rr', 'manual', 'li_bestfit', 'li_ml']
try:
dust_choice = dust_grid_type_list.index(cfg.par.dust_grid_type)
except ValueError as e:
print(
'You chose a dust_choice that isnt a valid selection within the list: dust_grid_type_list....crashing now!'
)
sys.exit()
if cfg.par.dust_grid_type == 'dtm':
dust_smoothed_dtm = dtm_grid_oct(reg, refined)
dust_smoothed = dust_smoothed_dtm
if cfg.par.dust_grid_type == 'rr':
dust_smoothed_remy_ruyer = remy_ruyer_oct(reg, refined)
dust_smoothed = dust_smoothed_remy_ruyer
if cfg.par.dust_grid_type == 'manual':
dust_smoothed_manual = manual_oct(reg, refined)
dust_smoothed = dust_smoothed_manual
if cfg.par.dust_grid_type == 'li_bestfit':
dust_smoothed_li_bestfit = li_bestfit_oct(reg, refined)
dust_smoothed = dust_smoothed_li_bestfit
if cfg.par.dust_grid_type == 'li_ml':
dust_smoothed_li_ml = li_ml_oct(reg, refined)
dust_smoothed = dust_smoothed_li_ml
else:
print('cfg.par.CONSTANT_DUST_GRID=True')
print('setting constant dust grid to 4.e-22')
dust_smoothed = np.zeros(len(refined)) + 4.e-22
# return refined,dust_smoothed,xmin,xmax,ymin,ymax,zmin,zmax,boost
return refined, dust_smoothed, fc1, fw1, reg, ds