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various update

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This commit is contained in:
Noe Brucy
2024-03-22 15:06:07 +01:00
parent 006cbca80f
commit ca984eac44
5 changed files with 154 additions and 61 deletions
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plotter.py
+11 -9
View File
@@ -99,7 +99,7 @@ def quiver(ax, map_h, map_v, extent, key_v=None, lognorm=False, label="", **kwar
hh, vv = gethv(map_h, map_v, extent)
# get norm information
norm_v = np.sqrt(map_h ** 2 + map_v ** 2)
norm_v = np.sqrt(map_h**2 + map_v**2)
max_v = np.max(norm_v)
min_v = np.min(norm_v)
@@ -456,7 +456,7 @@ class Plotter(Aggregator, BaseProcessor):
run=run,
**kwargs,
)
if movie:
filenames[run].append(plot_filename)
@@ -968,8 +968,10 @@ class Plotter(Aggregator, BaseProcessor):
if sinks:
try:
self.current_processor.sinks()
data = pd.DataFrame(self.current_processor.get_value("/datasets/sinks"))
self.current_processor.load_sinks_rule()
data = pd.DataFrame(
self.current_processor.get_value("/datasets/load_sinks_rule")
)
part_pos = data[["x", "y", "z"]].values
unit_length /= self.current_processor.lbox
except KeyError:
@@ -1435,7 +1437,7 @@ class Plotter(Aggregator, BaseProcessor):
self.logger.warning(
"Errorbar may be meaningless when ytransform is used"
)
# Offset to start x when y in over a given value
if wait_until_over is not None:
offset = np.argmax(y > wait_until_over)
@@ -1480,7 +1482,7 @@ class Plotter(Aggregator, BaseProcessor):
(a, b, rho, _map_rule, stderr) = linregress(np.log10(x), np.log10(y))
self.logger.info(
"Power law fit y = x^({}) * {} with R^2 = {} and error is {}".format(
a, 10 ** b, rho, stderr
a, 10**b, rho, stderr
)
)
else:
@@ -1504,12 +1506,12 @@ class Plotter(Aggregator, BaseProcessor):
residual = errfunc(c, np.log10(x), np.log10(y), yerr / y)
self.logger.info(
"Power law fit y = x^({}) * {} with residual {}".format(
a, 10 ** b, residual
a, 10**b, residual
)
)
if label is None:
label = r"Power-law fit with index {:.1f}".format(a)
plt.plot(x, (10 ** b) * x ** a, label=label, **kwargs)
plt.plot(x, (10**b) * x**a, label=label, **kwargs)
def _gen_from_log(self, logrule, name_y, name_x="time", description="Generated"):
if name_x == "time":
@@ -1723,7 +1725,7 @@ class Plotter(Aggregator, BaseProcessor):
"/series/sinks_from_log/time",
"/series/sinks_from_log/ssm",
xunit=U.Myr,
yunit=U.Msun / U.pc ** 2,
yunit=U.Msun / U.pc**2,
),
"Mass of the sinks as a function of time divided by surface",
kind="run",
snapshotprocessor.py
+45 -35
View File
@@ -293,6 +293,37 @@ class SnapshotProcessor(HDF5Container):
"id": U.none,
"level": U.none,
}
# Units sinks
unit_sinks = {
"id": U.none,
"msink": U.Msun,
"dmfsink": U.Msun,
"x": "unit_density",
"y": "unit_density",
"z": "unit_density",
"vx": "unit_velocity",
"vy": "unit_velocity",
"vz": "unit_velocity",
"rot_period": "unit_time",
"lx": {"unit_mass": 1, "unit_length": 2, "unit_time": -1},
"ly": {"unit_mass": 1, "unit_length": 2, "unit_time": -1},
"lz": {"unit_mass": 1, "unit_length": 2, "unit_time": -1},
"acc_rate": {"unit_mass": 1, "unit_time": -1},
"acc_lum": U.none,
"age": U.year,
"int_lum": U.none,
"Teff": U.K,
"level": U.none,
"mbh": "unit_mass",
"tform": "unit_time",
"del_mass": U.Msun,
"rho_gas": "unit_density",
"cs**2": {"unit_velocity": 2},
"etherm": {"unit_mass": 1, "unit_velocity": 2},
"vx_gas": "unit_velocity",
"vy_gas": "unit_velocity",
"vz_gas": "unit_velocity",
}
G = 1.0 # Gravitational constant
@@ -675,9 +706,10 @@ class SnapshotProcessor(HDF5Container):
self.save_data(data, filename, group)
return data
def save_data(self, data, filename, group, overwrite=False):
def save_data(self, data, filename, group, overwrite=False, units=None):
self.logger.debug(f"Writing {filename}")
hdf5 = tables.open_file(filename, mode="a")
units = units or self.unit_key
try:
nb_written = 0
for key in data:
@@ -688,7 +720,7 @@ class SnapshotProcessor(HDF5Container):
hdf5.create_array(
f"/{group}", key, data[key], "", createparents=True
)
unit = self._get_units(self.unit_key[key])
unit = self._get_units(units[key])
hdf5.get_node(f"/{group}/{key}").unit = unit
nb_written += 1
else:
@@ -775,10 +807,13 @@ class SnapshotProcessor(HDF5Container):
def convert_hdf5(self, filename=None):
self.load_destructured(save=False)
self.load_sinks()
sinks = {key: self.sinks[key].values for key in self.sinks}
if filename is None:
filename = self.snap_filename
self.save_data(self.cells, filename, "cells")
self.save_data(self.parts, filename, "parts")
self.save_data(sinks, filename, "sinks", units=self.unit_sinks)
self.unload_destructured()
def get_nml(self, nml_key):
@@ -1600,12 +1635,15 @@ class SnapshotProcessor(HDF5Container):
alpha_g = (2.0 / 3) * alpha_g
return alpha_g
def _sinks(self):
def load_sinks(self):
csv_name = f"{self.path}/output_{self.num:05}/sink_{self.num:05}.csv"
if not os.path.exists(csv_name): # If ratarmount was used
csv_name = f"{self.path}/output_{self.num:05}/output_{self.num:05}/sink_{self.num:05}.csv"
if not os.path.exists(csv_name):
self.sinks = {}
return {}
f = open(csv_name)
first_line = f.readline()
second_line = f.readline()
@@ -1642,6 +1680,7 @@ class SnapshotProcessor(HDF5Container):
"Teff",
]
df = pd.read_csv(csv_name, header=None, names=header)
self.sinks = df
return {key: df[key].values for key in df}
@@ -1935,39 +1974,10 @@ class SnapshotProcessor(HDF5Container):
"/maps",
dependencies=["coldens", "T_mwavg", "omega_mwavg"],
),
"sinks": Rule(
self._sinks,
"load_sinks_rule": Rule(
self.load_sinks,
group="/datasets",
unit={
"id": U.none,
"msink": U.Msun,
"dmfsink": U.Msun,
"x": "unit_density",
"y": "unit_density",
"z": "unit_density",
"vx": "unit_velocity",
"vy": "unit_velocity",
"vz": "unit_velocity",
"rot_period": "unit_time",
"lx": {"unit_mass": 1, "unit_length": 2, "unit_time": -1},
"ly": {"unit_mass": 1, "unit_length": 2, "unit_time": -1},
"lz": {"unit_mass": 1, "unit_length": 2, "unit_time": -1},
"acc_rate": {"unit_mass": 1, "unit_time": -1},
"acc_lum": U.none,
"age": U.year,
"int_lum": U.none,
"Teff": U.K,
"level": U.none,
"mbh": "unit_mass",
"tform": "unit_time",
"del_mass": U.Msun,
"rho_gas": "unit_density",
"cs**2": {"unit_velocity": 2},
"etherm": {"unit_mass": 1, "unit_velocity": 2},
"vx_gas": "unit_velocity",
"vy_gas": "unit_velocity",
"vz_gas": "unit_velocity",
},
unit=self.unit_sinks,
),
"pspec": Rule(self.pspec, "Power spectrum", "/hdf5"),
"write_particles": Rule(self._write_particles, "Particles file", "/hdf5"),
turbox/__init__.py
+1
View File
@@ -2,6 +2,7 @@ from .turbox import (
get_pspec,
get_pspec_slope,
build_turbox_data,
rho_pdf,
apply_rule_pdf,
span_resolution,
)
turbox/turbox_params.yml
+85
View File
@@ -0,0 +1,85 @@
plot : # Plot parameters
put_title : False # Add a title to plot
# Maps
ntick : 6 # Number of ticks for maps
# Overlays
vel_red : 40 # Take point each vel_red for velocities
tight_layout : False # Wheter to apply tight_layout
time_fmt : "{:.3g} {}" # Time format string, 1st field is time and 2nd is unit
rcParams: # Anything there will be passed to matplotlib's rcParams
{} # remove and replace by rcParams keys
pymses: # Parameters for Pymses reader
# Source settings
variables : ["rho","vel"] # Read these grid variables
part_variables : []
check_variables : False
order : '<' # Bit order
# Processing options
levelmax : 20 # Maximal AMR level visited when looking levels
fft : False # Quick and dirty rendering using FFT
verbose : False # Let pymses write on standart output
multiprocessing : True # Whether to use multiprocessing
# Camera settings
center : [0.5, 0.5, 0.5] # Center of the image
zoom : 1. # Zoom of the image
map_size : 256 # Size of the computed maps in pixel
# Filter parameters
filter : False # Enable filtering
min_coords : [0.35, 0.35, 0.45]
max_coords : [0.65, 0.65, 0.55]
input: # Parameters on how to look for input files (= output from Ramses)
log_prefix : "run.log" # Prefix of the log file
label_filename : "label.txt" # Name of the label file
nml_filename : "run.nml" # name of the namelist file
ramses_ism : False # If ramses-ism is used
out: # Parameters for post processing
copy_info : True # Copy logs, nml and info files to the outdir
tag : "" # Tag for the image
interactive : True # Interactive mode (keep figures open)
save : True # Save the plots on the disk
ext : '.jpeg' # extension for plots
ext_subfolder : True # Separate production by extension in subfolders
fmt : "" # Format of the output filename for plots
# The following keys are accepted
# {out} : The output directory (where hdf5 files are also stored)
# {run} : Name of the relevant run
# {num} : Name of the input file (from Ramses)
# {ext} : Extension defined above (with the dot)
# {name} : Name of the rule
# {subfolder} : replaced by /{ext[1:]}/ if ext_subfolder is true
# {tag} : Tag defined above
# {nml[nml_key]} : The value of nml_key in the namelist (ex: {nml[amr_params/levelmin]})
process: # General setting of the post-processor module
verbose : True # Give more infos on what is going on
num_process : 10 # Number of forks
save_cells : True # Save cells structure on disk
save_parts : True # Save particles on disk
unload_cells : True # Save memory usage
rules: # Specific rules parameters
turb_energy_threshold : -1 # Remove invalid data (<0 = no threshold)
astrophysix: # Parameters for astrophysix and galactica
simu_fmt : "{tag}_{run}" # Format of the name of simulation
descr_fmt : "{tag}_{run}" # Format of the default description
# The following keys are accepted
# {run} : Name of the relevant run
# {tag} : Tag defined above
# {nml[nml_key]} : The value of nml_key in the namelist (ex: {nml[amr_params/levelmin]})
utils/runselector.py
+12 -17
View File
@@ -52,7 +52,6 @@ class RunSelector:
time=None,
unit_time=None,
allow_nodata=False,
fallback_namelist=True,
):
"""
Select runs and outputs with several filter options.
@@ -72,7 +71,7 @@ class RunSelector:
"last" select only the last output.
"all" preselect all outputs (default)
nml_filename : str name of the namelist (should be the same for all outputs)
nml_filename : str name of the default namelist (otherwise look into the output files)
filter_name : str, filter runs by name. Default "*"
filter_nml : tuple or list of tupple.
@@ -107,15 +106,10 @@ class RunSelector:
self.path_in = path_in
self.nml_filename = nml_filename
self.fallback_nml = fallback_namelist
self.allow_nodata = allow_nodata
self.namelist = {}
do_tests = (
(not self.fallback_nml)
or (len(filter_nml) > 0)
or (sort_run_by is not None)
)
do_tests = not self.allow_nodata
self.runs = self.get_runs(
in_runs, filter_name, filter_nml, sort_run_by, do_tests=do_tests
)
@@ -226,7 +220,16 @@ class RunSelector:
def load_namelist(self, run, path=None):
if path is None:
path = f"{self.path_in}/{run}/{self.nml_filename}"
names = glob.glob(
self.path_in + "/" + run + "/output_[0-9][0-9][0-9][0-9][0-9]"
)
i = 0
path = self.path_in + "/" + run + "/" + self.nml_filename
while not os.path.exists(path) and i < len(names):
path = f"{names[i]}/namelist.txt"
i += 1
return NamelistRecursive(f90nml.read(path))
def get_nml_value(self, nml_key, run):
@@ -448,14 +451,6 @@ class RunSelector:
else:
return []
# Be sure we have a namelist
if self.fallback_nml and run not in self.namelist:
self.logger.warning(
f"Used fallback namelist for run {run} from output {nums[0]}"
)
path = f"{self.path_in}/{run}/output_{nums[0]:05}/namelist.txt"
self.namelist[run] = self.load_namelist(run, path=path)
# -- Time getter according to unit_time
if unit_time is None: