[yt-svn] commit/yt: 6 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Thu Aug 6 09:08:56 PDT 2015
6 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/906c4120dbac/
Changeset: 906c4120dbac
Branch: yt
User: karraki
Date: 2015-08-05 15:25:34+00:00
Summary: Replacing dummy time variables with meaningful names
Affected #: 2 files
diff -r fffa77d2fdc205b54fb87befaa50ade850f826d6 -r 906c4120dbacb3a85b3fac321836d90d7fe0be7c yt/frontends/art/definitions.py
--- a/yt/frontends/art/definitions.py
+++ b/yt/frontends/art/definitions.py
@@ -110,7 +110,7 @@
]
star_struct = [
- ('>d', ('tdum', 'adum')),
+ ('>d', ('t_stars', 'a_stars')),
('>i', 'nstars'),
('>d', ('ws_old', 'ws_oldi')),
('>f', 'particle_mass'),
diff -r fffa77d2fdc205b54fb87befaa50ade850f826d6 -r 906c4120dbacb3a85b3fac321836d90d7fe0be7c yt/frontends/art/io.py
--- a/yt/frontends/art/io.py
+++ b/yt/frontends/art/io.py
@@ -300,11 +300,11 @@
def interpolate_ages(data, file_stars, interp_tb=None, interp_ages=None,
current_time=None):
if interp_tb is None:
- tdum, adum = read_star_field(file_stars,
- field="tdum")
+ t_stars, a_stars = read_star_field(file_stars,
+ field="t_stars")
# timestamp of file should match amr timestamp
if current_time:
- tdiff = b2t(tdum)-current_time/(sec_per_year*1e9)
+ tdiff = b2t(t_stars)-current_time/(sec_per_year*1e9)
if np.abs(tdiff) < 1e-4:
mylog.info("Timestamp mismatch in star " +
"particle header")
https://bitbucket.org/yt_analysis/yt/commits/66e66bbf3619/
Changeset: 66e66bbf3619
Branch: yt
User: karraki
Date: 2015-08-05 16:13:32+00:00
Summary: Convert units correctly in data_structures
Affected #: 1 file
diff -r 906c4120dbacb3a85b3fac321836d90d7fe0be7c -r 66e66bbf36197c65d4936d31335189fe4b78c006 yt/frontends/art/data_structures.py
--- a/yt/frontends/art/data_structures.py
+++ b/yt/frontends/art/data_structures.py
@@ -28,10 +28,7 @@
OctreeSubset
from yt.geometry.oct_container import \
ARTOctreeContainer
-from .fields import \
- ARTFieldInfo
-from yt.utilities.definitions import \
- mpc_conversion
+from .fields import ARTFieldInfo
from yt.utilities.io_handler import \
io_registry
from yt.utilities.lib.misc_utilities import \
@@ -41,6 +38,7 @@
from yt.geometry.particle_geometry_handler import \
ParticleIndex
from yt.utilities.lib.geometry_utils import compute_morton
+from yt.units.yt_array import YTQuantity
from yt.frontends.art.definitions import *
import yt.utilities.fortran_utils as fpu
@@ -50,14 +48,10 @@
from .io import b2t
from .io import a2b
-from yt.utilities.definitions import \
- mpc_conversion, sec_conversion
from yt.utilities.io_handler import \
io_registry
from yt.fields.field_info_container import \
FieldInfoContainer, NullFunc
-from yt.utilities.physical_constants import \
- mass_hydrogen_cgs, sec_per_Gyr
class ARTIndex(OctreeIndex):
@@ -358,7 +352,8 @@
if self.force_max_level is not None:
self.max_level = self.force_max_level
self.hubble_time = 1.0/(self.hubble_constant*100/3.08568025e19)
- self.current_time = b2t(self.parameters['t']) * sec_per_Gyr
+ self.current_time = YTQuantity(b2t(self.parameters['t']),'Gyr').\
+ in_units('s')
self.gamma = self.parameters["gamma"]
mylog.info("Max level is %02i", self.max_level)
@@ -600,7 +595,8 @@
# self.max_level = self.force_max_level
self.hubble_time = 1.0/(self.hubble_constant*100/3.08568025e19)
self.parameters['t'] = a2b(self.parameters['aexpn'])
- self.current_time = b2t(self.parameters['t']) * sec_per_Gyr
+ self.current_time = YTQuantity(b2t(self.parameters['t']),'Gyr').\
+ in_unit('s')
self.gamma = self.parameters["gamma"]
mylog.info("Max level is %02i", self.max_level)
https://bitbucket.org/yt_analysis/yt/commits/bc44673c5171/
Changeset: bc44673c5171
Branch: yt
User: karraki
Date: 2015-08-05 16:17:37+00:00
Summary: Correct stellar ages in interpolate_ages
Affected #: 1 file
diff -r 66e66bbf36197c65d4936d31335189fe4b78c006 -r bc44673c5171edc931026ddff59473e161c827d0 yt/frontends/art/io.py
--- a/yt/frontends/art/io.py
+++ b/yt/frontends/art/io.py
@@ -31,6 +31,7 @@
from yt.utilities.physical_constants import sec_per_year
from yt.utilities.lib.geometry_utils import compute_morton
from yt.geometry.oct_container import _ORDER_MAX
+from yt.units.yt_array import YTQuantity
class IOHandlerART(BaseIOHandler):
@@ -304,10 +305,10 @@
field="t_stars")
# timestamp of file should match amr timestamp
if current_time:
- tdiff = b2t(t_stars)-current_time/(sec_per_year*1e9)
- if np.abs(tdiff) < 1e-4:
+ tdiff = YTQuantity(b2t(t_stars),'Gyr') - current_time.in_units('Gyr')
+ if np.abs(tdiff) > 1e-4:
mylog.info("Timestamp mismatch in star " +
- "particle header")
+ "particle header: %s", tdiff)
mylog.info("Interpolating ages")
interp_tb, interp_ages = b2t(data)
temp = np.interp(data, interp_tb, interp_ages)
https://bitbucket.org/yt_analysis/yt/commits/7cefb7212efb/
Changeset: 7cefb7212efb
Branch: yt
User: karraki
Date: 2015-08-05 18:24:28+00:00
Summary: Correcting particle creation time values
Affected #: 3 files
diff -r bc44673c5171edc931026ddff59473e161c827d0 -r 7cefb7212efbc63b2f0439bfc9f99333345567ec yt/frontends/art/data_structures.py
--- a/yt/frontends/art/data_structures.py
+++ b/yt/frontends/art/data_structures.py
@@ -38,7 +38,6 @@
from yt.geometry.particle_geometry_handler import \
ParticleIndex
from yt.utilities.lib.geometry_utils import compute_morton
-from yt.units.yt_array import YTQuantity
from yt.frontends.art.definitions import *
import yt.utilities.fortran_utils as fpu
@@ -352,8 +351,7 @@
if self.force_max_level is not None:
self.max_level = self.force_max_level
self.hubble_time = 1.0/(self.hubble_constant*100/3.08568025e19)
- self.current_time = YTQuantity(b2t(self.parameters['t']),'Gyr').\
- in_units('s')
+ self.current_time = self.quan(b2t(self.parameters['t']), 'Gyr')
self.gamma = self.parameters["gamma"]
mylog.info("Max level is %02i", self.max_level)
@@ -595,8 +593,7 @@
# self.max_level = self.force_max_level
self.hubble_time = 1.0/(self.hubble_constant*100/3.08568025e19)
self.parameters['t'] = a2b(self.parameters['aexpn'])
- self.current_time = YTQuantity(b2t(self.parameters['t']),'Gyr').\
- in_unit('s')
+ self.current_time = self.quan(b2t(self.parameters['t']), 'Gyr')
self.gamma = self.parameters["gamma"]
mylog.info("Max level is %02i", self.max_level)
diff -r bc44673c5171edc931026ddff59473e161c827d0 -r 7cefb7212efbc63b2f0439bfc9f99333345567ec yt/frontends/art/fields.py
--- a/yt/frontends/art/fields.py
+++ b/yt/frontends/art/fields.py
@@ -55,7 +55,7 @@
("particle_mass", ("code_mass", [], None)),
("particle_index", ("", [], None)),
("particle_species", ("", ["particle_type"], None)),
- ("particle_creation_time", ("code_time", [], None)),
+ ("particle_creation_time", ("Gyr", [], None)),
("particle_mass_initial", ("code_mass", [], None)),
("particle_metallicity1", ("", [], None)),
("particle_metallicity2", ("", [], None)),
diff -r bc44673c5171edc931026ddff59473e161c827d0 -r 7cefb7212efbc63b2f0439bfc9f99333345567ec yt/frontends/art/io.py
--- a/yt/frontends/art/io.py
+++ b/yt/frontends/art/io.py
@@ -305,14 +305,15 @@
field="t_stars")
# timestamp of file should match amr timestamp
if current_time:
- tdiff = YTQuantity(b2t(t_stars),'Gyr') - current_time.in_units('Gyr')
+ tdiff = YTQuantity(b2t(t_stars), 'Gyr') - current_time.in_units('Gyr')
if np.abs(tdiff) > 1e-4:
mylog.info("Timestamp mismatch in star " +
"particle header: %s", tdiff)
mylog.info("Interpolating ages")
interp_tb, interp_ages = b2t(data)
+ interp_tb = YTArray(interp_tb, 'Gyr')
+ interp_ages = YTArray(interp_ages, 'Gyr')
temp = np.interp(data, interp_tb, interp_ages)
- temp *= 1.0e9*sec_per_year
return interp_tb, interp_ages, temp
https://bitbucket.org/yt_analysis/yt/commits/64c4ac6e4ae9/
Changeset: 64c4ac6e4ae9
Branch: yt
User: karraki
Date: 2015-08-05 19:49:57+00:00
Summary: Removed amr_header_vals and used self.parameters instead
Affected #: 1 file
diff -r 7cefb7212efbc63b2f0439bfc9f99333345567ec -r 64c4ac6e4ae939c36c5aaaf5de91a1789c282ea4 yt/frontends/art/data_structures.py
--- a/yt/frontends/art/data_structures.py
+++ b/yt/frontends/art/data_structures.py
@@ -293,6 +293,7 @@
self.iOctFree, self.nOct = fpu.read_vector(f, 'i', '>')
self.child_grid_offset = f.tell()
self.parameters.update(amr_header_vals)
+ amr_header_vals = None
# estimate the root level
float_center, fl, iocts, nocts, root_level = _read_art_level_info(
f,
@@ -340,14 +341,14 @@
# setup standard simulation params yt expects to see
self.current_redshift = self.parameters["aexpn"]**-1.0 - 1.0
- self.omega_lambda = amr_header_vals['Oml0']
- self.omega_matter = amr_header_vals['Om0']
- self.hubble_constant = amr_header_vals['hubble']
- self.min_level = amr_header_vals['min_level']
- self.max_level = amr_header_vals['max_level']
+ self.omega_lambda = self.parameters['Oml0']
+ self.omega_matter = self.parameters['Om0']
+ self.hubble_constant = self.parameters['hubble']
+ self.min_level = self.parameters['min_level']
+ self.max_level = self.parameters['max_level']
if self.limit_level is not None:
self.max_level = min(
- self.limit_level, amr_header_vals['max_level'])
+ self.limit_level, self.parameters['max_level'])
if self.force_max_level is not None:
self.max_level = self.force_max_level
self.hubble_time = 1.0/(self.hubble_constant*100/3.08568025e19)
https://bitbucket.org/yt_analysis/yt/commits/84097e00d5ac/
Changeset: 84097e00d5ac
Branch: yt
User: bwkeller
Date: 2015-08-06 16:08:46+00:00
Summary: Merged in karraki/yt (pull request #1679)
[BUGFIX] ART star particle creation time field
Affected #: 4 files
diff -r 803700f0f40882d5e291ce779e283fcfee509f22 -r 84097e00d5acbd688b998c638519237b86cffc50 yt/frontends/art/data_structures.py
--- a/yt/frontends/art/data_structures.py
+++ b/yt/frontends/art/data_structures.py
@@ -28,10 +28,7 @@
OctreeSubset
from yt.geometry.oct_container import \
ARTOctreeContainer
-from .fields import \
- ARTFieldInfo
-from yt.utilities.definitions import \
- mpc_conversion
+from .fields import ARTFieldInfo
from yt.utilities.io_handler import \
io_registry
from yt.utilities.lib.misc_utilities import \
@@ -50,14 +47,10 @@
from .io import b2t
from .io import a2b
-from yt.utilities.definitions import \
- mpc_conversion, sec_conversion
from yt.utilities.io_handler import \
io_registry
from yt.fields.field_info_container import \
FieldInfoContainer, NullFunc
-from yt.utilities.physical_constants import \
- mass_hydrogen_cgs, sec_per_Gyr
class ARTIndex(OctreeIndex):
@@ -300,6 +293,7 @@
self.iOctFree, self.nOct = fpu.read_vector(f, 'i', '>')
self.child_grid_offset = f.tell()
self.parameters.update(amr_header_vals)
+ amr_header_vals = None
# estimate the root level
float_center, fl, iocts, nocts, root_level = _read_art_level_info(
f,
@@ -347,18 +341,18 @@
# setup standard simulation params yt expects to see
self.current_redshift = self.parameters["aexpn"]**-1.0 - 1.0
- self.omega_lambda = amr_header_vals['Oml0']
- self.omega_matter = amr_header_vals['Om0']
- self.hubble_constant = amr_header_vals['hubble']
- self.min_level = amr_header_vals['min_level']
- self.max_level = amr_header_vals['max_level']
+ self.omega_lambda = self.parameters['Oml0']
+ self.omega_matter = self.parameters['Om0']
+ self.hubble_constant = self.parameters['hubble']
+ self.min_level = self.parameters['min_level']
+ self.max_level = self.parameters['max_level']
if self.limit_level is not None:
self.max_level = min(
- self.limit_level, amr_header_vals['max_level'])
+ self.limit_level, self.parameters['max_level'])
if self.force_max_level is not None:
self.max_level = self.force_max_level
self.hubble_time = 1.0/(self.hubble_constant*100/3.08568025e19)
- self.current_time = b2t(self.parameters['t']) * sec_per_Gyr
+ self.current_time = self.quan(b2t(self.parameters['t']), 'Gyr')
self.gamma = self.parameters["gamma"]
mylog.info("Max level is %02i", self.max_level)
@@ -600,7 +594,7 @@
# self.max_level = self.force_max_level
self.hubble_time = 1.0/(self.hubble_constant*100/3.08568025e19)
self.parameters['t'] = a2b(self.parameters['aexpn'])
- self.current_time = b2t(self.parameters['t']) * sec_per_Gyr
+ self.current_time = self.quan(b2t(self.parameters['t']), 'Gyr')
self.gamma = self.parameters["gamma"]
mylog.info("Max level is %02i", self.max_level)
diff -r 803700f0f40882d5e291ce779e283fcfee509f22 -r 84097e00d5acbd688b998c638519237b86cffc50 yt/frontends/art/definitions.py
--- a/yt/frontends/art/definitions.py
+++ b/yt/frontends/art/definitions.py
@@ -110,7 +110,7 @@
]
star_struct = [
- ('>d', ('tdum', 'adum')),
+ ('>d', ('t_stars', 'a_stars')),
('>i', 'nstars'),
('>d', ('ws_old', 'ws_oldi')),
('>f', 'particle_mass'),
diff -r 803700f0f40882d5e291ce779e283fcfee509f22 -r 84097e00d5acbd688b998c638519237b86cffc50 yt/frontends/art/fields.py
--- a/yt/frontends/art/fields.py
+++ b/yt/frontends/art/fields.py
@@ -55,7 +55,7 @@
("particle_mass", ("code_mass", [], None)),
("particle_index", ("", [], None)),
("particle_species", ("", ["particle_type"], None)),
- ("particle_creation_time", ("code_time", [], None)),
+ ("particle_creation_time", ("Gyr", [], None)),
("particle_mass_initial", ("code_mass", [], None)),
("particle_metallicity1", ("", [], None)),
("particle_metallicity2", ("", [], None)),
diff -r 803700f0f40882d5e291ce779e283fcfee509f22 -r 84097e00d5acbd688b998c638519237b86cffc50 yt/frontends/art/io.py
--- a/yt/frontends/art/io.py
+++ b/yt/frontends/art/io.py
@@ -31,6 +31,7 @@
from yt.utilities.physical_constants import sec_per_year
from yt.utilities.lib.geometry_utils import compute_morton
from yt.geometry.oct_container import _ORDER_MAX
+from yt.units.yt_array import YTQuantity
class IOHandlerART(BaseIOHandler):
@@ -300,18 +301,19 @@
def interpolate_ages(data, file_stars, interp_tb=None, interp_ages=None,
current_time=None):
if interp_tb is None:
- tdum, adum = read_star_field(file_stars,
- field="tdum")
+ t_stars, a_stars = read_star_field(file_stars,
+ field="t_stars")
# timestamp of file should match amr timestamp
if current_time:
- tdiff = b2t(tdum)-current_time/(sec_per_year*1e9)
- if np.abs(tdiff) < 1e-4:
+ tdiff = YTQuantity(b2t(t_stars), 'Gyr') - current_time.in_units('Gyr')
+ if np.abs(tdiff) > 1e-4:
mylog.info("Timestamp mismatch in star " +
- "particle header")
+ "particle header: %s", tdiff)
mylog.info("Interpolating ages")
interp_tb, interp_ages = b2t(data)
+ interp_tb = YTArray(interp_tb, 'Gyr')
+ interp_ages = YTArray(interp_ages, 'Gyr')
temp = np.interp(data, interp_tb, interp_ages)
- temp *= 1.0e9*sec_per_year
return interp_tb, interp_ages, temp
Repository URL: https://bitbucket.org/yt_analysis/yt/
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