[yt-svn] commit/yt: 3 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Tue Jul 22 13:28:53 PDT 2014
3 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/ebb8fd34c4ae/
Changeset: ebb8fd34c4ae
Branch: yt-3.0
User: karraki
Date: 2014-07-22 19:03:41
Summary: Cleaning up NMSU-ART unit conversions.
Affected #: 1 file
diff -r e816afd0f0637f5a4eb1136a01309ad4875a97ce -r ebb8fd34c4ae907640b88be3a8d0acf590da60ad yt/frontends/art/data_structures.py
--- a/yt/frontends/art/data_structures.py
+++ b/yt/frontends/art/data_structures.py
@@ -245,55 +245,20 @@
aexpn = self.parameters["aexpn"]
hubble = self.parameters['hubble']
- cf = defaultdict(lambda: 1.0)
r0 = boxh/ng
- P0 = 4.697e-16 * Om0**2.0 * r0**2.0 * hubble**2.0
- T_0 = 3.03e5 * r0**2.0 * wmu * Om0 # [K]
- S_0 = 52.077 * wmu**(5.0/3.0)
- S_0 *= hubble**(-4.0/3.0)*Om0**(1.0/3.0)*r0**2.0
- # v0 = r0 * 50.0*1.0e5 * np.sqrt(self.omega_matter) #cm/s
v0 = 50.0*r0*np.sqrt(Om0)
- t0 = r0/v0
- rho1 = 1.8791e-29 * hubble**2.0 * self.omega_matter
rho0 = 2.776e11 * hubble**2.0 * Om0
- tr = 2./3. * (3.03e5*r0**2.0*wmu*self.omega_matter)*(1.0/(aexpn**2))
aM0 = rho0 * (boxh/hubble)**3.0 / ng**3.0
- cf['r0'] = r0
- cf['P0'] = P0
- cf['T_0'] = T_0
- cf['S_0'] = S_0
- cf['v0'] = v0
- cf['t0'] = t0
- cf['rho0'] = rho0
- cf['rho1'] = rho1
- cf['tr'] = tr
- cf['aM0'] = aM0
+ velocity = v0/aexpn*1.0e5 # proper cm/s
+ mass = aM0 * 1.98892e33
- # factors to multiply the native code units to CGS
- cf['Pressure'] = P0 # already cgs
- cf['Velocity'] = v0/aexpn*1.0e5 # proper cm/s
- cf["Mass"] = aM0 * 1.98892e33
- cf["Density"] = rho1*(aexpn**-3.0)
- cf["GasEnergy"] = rho0*v0**2*(aexpn**-5.0)
- cf["Potential"] = 1.0
- cf["Entropy"] = S_0
- cf["Temperature"] = tr
- cf["Time"] = 1.0
- cf["particle_mass"] = cf['Mass']
- cf["particle_mass_initial"] = cf['Mass']
self.cosmological_simulation = True
+ self.mass_unit = self.quan(mass, "g*%s" % ng**3)
+ self.particlemass_unit = self.quan(mass, "g")
+ self.length_unit = self.quan(box_proper, "Mpc")
+ self.velocity_unit = self.quan(velocity, "cm/s")
+ self.time_unit = self.length_unit / self.velocity_unit
- # I have left much of the old code above.for historical reference, but
- # it is largely or completely vestigial. The subsequent unit setting
- # is from ARTIO, which I have been assured has identical units to
- # NMSU-ART for hydrodynamic quantities..
- #
- # That being said, these are a bit uncertain to me.
-
- self.mass_unit = self.quan(cf["Mass"], "g*%s" % ng**3)
- self.length_unit = self.quan(box_proper, "Mpc")
- self.velocity_unit = self.quan(cf["Velocity"], "cm/s")
- self.time_unit = self.length_unit / self.velocity_unit
def _parse_parameter_file(self):
"""
https://bitbucket.org/yt_analysis/yt/commits/d0c5b6c47043/
Changeset: d0c5b6c47043
Branch: yt-3.0
User: karraki
Date: 2014-07-22 19:29:20
Summary: Added changes to NMSU-ART file that I had made in March.
Affected #: 2 files
diff -r ebb8fd34c4ae907640b88be3a8d0acf590da60ad -r d0c5b6c470431679aaf39aa619f8017b8a7a0315 yt/frontends/art/data_structures.py
--- a/yt/frontends/art/data_structures.py
+++ b/yt/frontends/art/data_structures.py
@@ -74,7 +74,7 @@
"""
# Overloaded
ds = self.dataset
- return (1.0/pf.domain_dimensions.astype('f8') /
+ return (1.0/ds.domain_dimensions.astype('f8') /
(2**self.max_level)).min()
def _initialize_oct_handler(self):
@@ -102,7 +102,7 @@
def _detect_output_fields(self):
self.particle_field_list = [f for f in particle_fields]
- self.field_list = [("gas", f) for f in fluid_fields]
+ self.field_list = [("art", f) for f in fluid_fields]
# now generate all of the possible particle fields
if "wspecies" in self.dataset.parameters.keys():
wspecies = self.dataset.parameters['wspecies']
@@ -175,6 +175,7 @@
limit_level=None, spread_age=True,
force_max_level=None, file_particle_header=None,
file_particle_data=None, file_particle_stars=None):
+ self.fluid_types += ("art", )
if fields is None:
fields = fluid_fields
filename = os.path.abspath(filename)
@@ -240,7 +241,6 @@
wmu = self.parameters["wmu"]
Om0 = self.parameters['Om0']
ng = self.parameters['ng']
- wmu = self.parameters["wmu"]
boxh = self.parameters['boxh']
aexpn = self.parameters["aexpn"]
hubble = self.parameters['hubble']
@@ -254,7 +254,6 @@
self.cosmological_simulation = True
self.mass_unit = self.quan(mass, "g*%s" % ng**3)
- self.particlemass_unit = self.quan(mass, "g")
self.length_unit = self.quan(box_proper, "Mpc")
self.velocity_unit = self.quan(velocity, "cm/s")
self.time_unit = self.length_unit / self.velocity_unit
@@ -305,7 +304,6 @@
self.iOctFree, self.nOct = fpu.read_vector(f, 'i', '>')
self.child_grid_offset = f.tell()
self.parameters.update(amr_header_vals)
- self.parameters['ncell0'] = self.parameters['ng']**3
# estimate the root level
float_center, fl, iocts, nocts, root_level = _read_art_level_info(
f,
@@ -326,9 +324,10 @@
self.parameters['wspecies'] = wspecies[:n]
self.parameters['lspecies'] = lspecies[:n]
ls_nonzero = np.diff(lspecies)[:n-1]
+ ls_nonzero = np.append(lspecies[0], ls_nonzero)
self.star_type = len(ls_nonzero)
mylog.info("Discovered %i species of particles", len(ls_nonzero))
- mylog.info("Particle populations: "+'%1.1e '*len(ls_nonzero),
+ mylog.info("Particle populations: "+'%9i '*len(ls_nonzero),
*ls_nonzero)
for k, v in particle_header_vals.items():
if k in self.parameters.keys():
@@ -339,6 +338,10 @@
else:
self.parameters[k] = v
self.parameters_particles = particle_header_vals
+ self.parameters.update(particle_header_vals)
+ self.parameters['ng'] = self.parameters['Ngridc']
+ self.parameters['ncell0'] = self.parameters['ng']**3
+
# setup standard simulation params yt expects to see
self.current_redshift = self.parameters["aexpn"]**-1.0 - 1.0
diff -r ebb8fd34c4ae907640b88be3a8d0acf590da60ad -r d0c5b6c470431679aaf39aa619f8017b8a7a0315 yt/frontends/art/definitions.py
--- a/yt/frontends/art/definitions.py
+++ b/yt/frontends/art/definitions.py
@@ -119,8 +119,7 @@
"gamma": 5./3.,
"T_CMB0": 2.726,
"T_min": 300.,
- "ng": 128,
- "wmu": 4.0/(8.0-5.0*0.245)
+ "wmu": 4.0/(8.0-5.0*0.245),
}
seek_extras = 137
https://bitbucket.org/yt_analysis/yt/commits/3c4dc9e27719/
Changeset: 3c4dc9e27719
Branch: yt-3.0
User: MatthewTurk
Date: 2014-07-22 22:28:27
Summary: Merged in karraki/yt/yt-3.0 (pull request #1051)
NMSU-ART frontend unit cleanup
Affected #: 2 files
diff -r f7f16f1a8e05b03faa91c8ba436b6d378af5bd60 -r 3c4dc9e27719f260e29bcbc6ad18c4a3601ed1f9 yt/frontends/art/data_structures.py
--- a/yt/frontends/art/data_structures.py
+++ b/yt/frontends/art/data_structures.py
@@ -74,7 +74,7 @@
"""
# Overloaded
ds = self.dataset
- return (1.0/pf.domain_dimensions.astype('f8') /
+ return (1.0/ds.domain_dimensions.astype('f8') /
(2**self.max_level)).min()
def _initialize_oct_handler(self):
@@ -102,7 +102,7 @@
def _detect_output_fields(self):
self.particle_field_list = [f for f in particle_fields]
- self.field_list = [("gas", f) for f in fluid_fields]
+ self.field_list = [("art", f) for f in fluid_fields]
# now generate all of the possible particle fields
if "wspecies" in self.dataset.parameters.keys():
wspecies = self.dataset.parameters['wspecies']
@@ -175,6 +175,7 @@
limit_level=None, spread_age=True,
force_max_level=None, file_particle_header=None,
file_particle_data=None, file_particle_stars=None):
+ self.fluid_types += ("art", )
if fields is None:
fields = fluid_fields
filename = os.path.abspath(filename)
@@ -240,60 +241,23 @@
wmu = self.parameters["wmu"]
Om0 = self.parameters['Om0']
ng = self.parameters['ng']
- wmu = self.parameters["wmu"]
boxh = self.parameters['boxh']
aexpn = self.parameters["aexpn"]
hubble = self.parameters['hubble']
- cf = defaultdict(lambda: 1.0)
r0 = boxh/ng
- P0 = 4.697e-16 * Om0**2.0 * r0**2.0 * hubble**2.0
- T_0 = 3.03e5 * r0**2.0 * wmu * Om0 # [K]
- S_0 = 52.077 * wmu**(5.0/3.0)
- S_0 *= hubble**(-4.0/3.0)*Om0**(1.0/3.0)*r0**2.0
- # v0 = r0 * 50.0*1.0e5 * np.sqrt(self.omega_matter) #cm/s
v0 = 50.0*r0*np.sqrt(Om0)
- t0 = r0/v0
- rho1 = 1.8791e-29 * hubble**2.0 * self.omega_matter
rho0 = 2.776e11 * hubble**2.0 * Om0
- tr = 2./3. * (3.03e5*r0**2.0*wmu*self.omega_matter)*(1.0/(aexpn**2))
aM0 = rho0 * (boxh/hubble)**3.0 / ng**3.0
- cf['r0'] = r0
- cf['P0'] = P0
- cf['T_0'] = T_0
- cf['S_0'] = S_0
- cf['v0'] = v0
- cf['t0'] = t0
- cf['rho0'] = rho0
- cf['rho1'] = rho1
- cf['tr'] = tr
- cf['aM0'] = aM0
+ velocity = v0/aexpn*1.0e5 # proper cm/s
+ mass = aM0 * 1.98892e33
- # factors to multiply the native code units to CGS
- cf['Pressure'] = P0 # already cgs
- cf['Velocity'] = v0/aexpn*1.0e5 # proper cm/s
- cf["Mass"] = aM0 * 1.98892e33
- cf["Density"] = rho1*(aexpn**-3.0)
- cf["GasEnergy"] = rho0*v0**2*(aexpn**-5.0)
- cf["Potential"] = 1.0
- cf["Entropy"] = S_0
- cf["Temperature"] = tr
- cf["Time"] = 1.0
- cf["particle_mass"] = cf['Mass']
- cf["particle_mass_initial"] = cf['Mass']
self.cosmological_simulation = True
+ self.mass_unit = self.quan(mass, "g*%s" % ng**3)
+ self.length_unit = self.quan(box_proper, "Mpc")
+ self.velocity_unit = self.quan(velocity, "cm/s")
+ self.time_unit = self.length_unit / self.velocity_unit
- # I have left much of the old code above.for historical reference, but
- # it is largely or completely vestigial. The subsequent unit setting
- # is from ARTIO, which I have been assured has identical units to
- # NMSU-ART for hydrodynamic quantities..
- #
- # That being said, these are a bit uncertain to me.
-
- self.mass_unit = self.quan(cf["Mass"], "g*%s" % ng**3)
- self.length_unit = self.quan(box_proper, "Mpc")
- self.velocity_unit = self.quan(cf["Velocity"], "cm/s")
- self.time_unit = self.length_unit / self.velocity_unit
def _parse_parameter_file(self):
"""
@@ -340,7 +304,6 @@
self.iOctFree, self.nOct = fpu.read_vector(f, 'i', '>')
self.child_grid_offset = f.tell()
self.parameters.update(amr_header_vals)
- self.parameters['ncell0'] = self.parameters['ng']**3
# estimate the root level
float_center, fl, iocts, nocts, root_level = _read_art_level_info(
f,
@@ -361,9 +324,10 @@
self.parameters['wspecies'] = wspecies[:n]
self.parameters['lspecies'] = lspecies[:n]
ls_nonzero = np.diff(lspecies)[:n-1]
+ ls_nonzero = np.append(lspecies[0], ls_nonzero)
self.star_type = len(ls_nonzero)
mylog.info("Discovered %i species of particles", len(ls_nonzero))
- mylog.info("Particle populations: "+'%1.1e '*len(ls_nonzero),
+ mylog.info("Particle populations: "+'%9i '*len(ls_nonzero),
*ls_nonzero)
for k, v in particle_header_vals.items():
if k in self.parameters.keys():
@@ -374,6 +338,10 @@
else:
self.parameters[k] = v
self.parameters_particles = particle_header_vals
+ self.parameters.update(particle_header_vals)
+ self.parameters['ng'] = self.parameters['Ngridc']
+ self.parameters['ncell0'] = self.parameters['ng']**3
+
# setup standard simulation params yt expects to see
self.current_redshift = self.parameters["aexpn"]**-1.0 - 1.0
diff -r f7f16f1a8e05b03faa91c8ba436b6d378af5bd60 -r 3c4dc9e27719f260e29bcbc6ad18c4a3601ed1f9 yt/frontends/art/definitions.py
--- a/yt/frontends/art/definitions.py
+++ b/yt/frontends/art/definitions.py
@@ -119,8 +119,7 @@
"gamma": 5./3.,
"T_CMB0": 2.726,
"T_min": 300.,
- "ng": 128,
- "wmu": 4.0/(8.0-5.0*0.245)
+ "wmu": 4.0/(8.0-5.0*0.245),
}
seek_extras = 137
Repository URL: https://bitbucket.org/yt_analysis/yt/
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