[yt-svn] commit/yt: 3 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Tue Apr 8 10:23:27 PDT 2014
3 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/7ea355912acb/
Changeset: 7ea355912acb
Branch: yt-3.0
User: MatthewTurk
Date: 2014-03-23 18:28:19
Summary: A few updates to the rockstar_groupies file
Affected #: 1 file
diff -r 8837ee7c34661a606808d55b17878207f9e8da36 -r 7ea355912acb4334a8e25ce85533bf4922db6e08 yt/analysis_modules/halo_finding/rockstar/rockstar_groupies.pyx
--- a/yt/analysis_modules/halo_finding/rockstar/rockstar_groupies.pyx
+++ b/yt/analysis_modules/halo_finding/rockstar/rockstar_groupies.pyx
@@ -11,234 +11,232 @@
# Importing relevant rockstar data types particle, fof halo, halo
cdef import from "particle.h":
- struct particle:
- np.int64_t id
- float pos[6]
+ struct particle:
+ np.int64_t id
+ float pos[6]
cdef import from "fof.h":
- struct fof:
- np.int64_t num_p
- particle *particles
+ struct fof:
+ np.int64_t num_p
+ particle *particles
cdef import from "halo.h":
- struct halo:
- np.int64_t id
- float pos[6], corevel[3], bulkvel[3]
- float m, r, child_r, vmax_r, mgrav, vmax, rvmax, rs, klypin_rs, vrms
- float J[3], energy, spin, alt_m[4], Xoff, Voff, b_to_a, c_to_a, A[3]
- float bullock_spin, kin_to_pot
- np.int64_t num_p, num_child_particles, p_start, desc, flags, n_core
- float min_pos_err, min_vel_err, min_bulkvel_err
+ struct halo:
+ np.int64_t id
+ float pos[6], corevel[3], bulkvel[3]
+ float m, r, child_r, vmax_r, mgrav, vmax, rvmax, rs, klypin_rs, vrms
+ float J[3], energy, spin, alt_m[4], Xoff, Voff, b_to_a, c_to_a, A[3]
+ float bullock_spin, kin_to_pot
+ np.int64_t num_p, num_child_particles, p_start, desc, flags, n_core
+ float min_pos_err, min_vel_err, min_bulkvel_err
# For finding sub halos import finder function and global variable
# rockstar uses to store the results
cdef import from "groupies.h":
- void find_subs(fof *f)
- halo *halos
- np.int64_t num_halos
- void calc_mass_definition()
+ void find_subs(fof *f) nogil
+ halo *halos
+ np.int64_t num_halos
+ void calc_mass_definition() nogil
# For outputing halos, rockstar style
cdef import from "meta_io.h":
- void output_halos(np.int64_t id_offset, np.int64_t snap, np.int64_t chunk, float *bounds)
+ void output_halos(np.int64_t id_offset, np.int64_t snap, np.int64_t chunk, float *bounds) nogil
# For setting up the configuration of rockstar
cdef import from "config.h":
- void setup_config()
+ void setup_config() nogil
cdef import from "config_vars.h":
- # Rockstar cleverly puts all of the config variables inside a templated
- # definition of their vaiables.
- char *FILE_FORMAT
- np.float64_t PARTICLE_MASS
+ # Rockstar cleverly puts all of the config variables inside a templated
+ # definition of their vaiables.
+ char *FILE_FORMAT
+ np.float64_t PARTICLE_MASS
- char *MASS_DEFINITION
- np.int64_t MIN_HALO_OUTPUT_SIZE
- np.float64_t FORCE_RES
+ char *MASS_DEFINITION
+ np.int64_t MIN_HALO_OUTPUT_SIZE
+ np.float64_t FORCE_RES
- np.float64_t SCALE_NOW
- np.float64_t h0
- np.float64_t Ol
- np.float64_t Om
+ np.float64_t SCALE_NOW
+ np.float64_t h0
+ np.float64_t Ol
+ np.float64_t Om
- np.int64_t GADGET_ID_BYTES
- np.float64_t GADGET_MASS_CONVERSION
- np.float64_t GADGET_LENGTH_CONVERSION
- np.int64_t GADGET_SKIP_NON_HALO_PARTICLES
- np.int64_t RESCALE_PARTICLE_MASS
+ np.int64_t GADGET_ID_BYTES
+ np.float64_t GADGET_MASS_CONVERSION
+ np.float64_t GADGET_LENGTH_CONVERSION
+ np.int64_t GADGET_SKIP_NON_HALO_PARTICLES
+ np.int64_t RESCALE_PARTICLE_MASS
- np.int64_t PARALLEL_IO
- char *PARALLEL_IO_SERVER_ADDRESS
- char *PARALLEL_IO_SERVER_PORT
- np.int64_t PARALLEL_IO_WRITER_PORT
- char *PARALLEL_IO_SERVER_INTERFACE
- char *RUN_ON_SUCCESS
+ np.int64_t PARALLEL_IO
+ char *PARALLEL_IO_SERVER_ADDRESS
+ char *PARALLEL_IO_SERVER_PORT
+ np.int64_t PARALLEL_IO_WRITER_PORT
+ char *PARALLEL_IO_SERVER_INTERFACE
+ char *RUN_ON_SUCCESS
- char *INBASE
- char *FILENAME
- np.int64_t STARTING_SNAP
- np.int64_t NUM_SNAPS
- np.int64_t NUM_BLOCKS
- np.int64_t NUM_READERS
- np.int64_t PRELOAD_PARTICLES
- char *SNAPSHOT_NAMES
- char *LIGHTCONE_ALT_SNAPS
- char *BLOCK_NAMES
+ char *INBASE
+ char *FILENAME
+ np.int64_t STARTING_SNAP
+ np.int64_t NUM_SNAPS
+ np.int64_t NUM_BLOCKS
+ np.int64_t NUM_READERS
+ np.int64_t PRELOAD_PARTICLES
+ char *SNAPSHOT_NAMES
+ char *LIGHTCONE_ALT_SNAPS
+ char *BLOCK_NAMES
- char *OUTBASE
- np.float64_t OVERLAP_LENGTH
- np.int64_t NUM_WRITERS
- np.int64_t FORK_READERS_FROM_WRITERS
- np.int64_t FORK_PROCESSORS_PER_MACHINE
+ char *OUTBASE
+ np.float64_t OVERLAP_LENGTH
+ np.int64_t NUM_WRITERS
+ np.int64_t FORK_READERS_FROM_WRITERS
+ np.int64_t FORK_PROCESSORS_PER_MACHINE
- char *OUTPUT_FORMAT
- np.int64_t DELETE_BINARY_OUTPUT_AFTER_FINISHED
- np.int64_t FULL_PARTICLE_CHUNKS
- char *BGC2_SNAPNAMES
+ char *OUTPUT_FORMAT
+ np.int64_t DELETE_BINARY_OUTPUT_AFTER_FINISHED
+ np.int64_t FULL_PARTICLE_CHUNKS
+ char *BGC2_SNAPNAMES
- np.int64_t BOUND_PROPS
- np.int64_t BOUND_OUT_TO_HALO_EDGE
- np.int64_t DO_MERGER_TREE_ONLY
- np.int64_t IGNORE_PARTICLE_IDS
- np.float64_t TRIM_OVERLAP
- np.float64_t ROUND_AFTER_TRIM
- np.int64_t LIGHTCONE
- np.int64_t PERIODIC
+ np.int64_t BOUND_PROPS
+ np.int64_t BOUND_OUT_TO_HALO_EDGE
+ np.int64_t DO_MERGER_TREE_ONLY
+ np.int64_t IGNORE_PARTICLE_IDS
+ np.float64_t TRIM_OVERLAP
+ np.float64_t ROUND_AFTER_TRIM
+ np.int64_t LIGHTCONE
+ np.int64_t PERIODIC
- np.float64_t LIGHTCONE_ORIGIN[3]
- np.float64_t LIGHTCONE_ALT_ORIGIN[3]
+ np.float64_t LIGHTCONE_ORIGIN[3]
+ np.float64_t LIGHTCONE_ALT_ORIGIN[3]
- np.float64_t LIMIT_CENTER[3]
- np.float64_t LIMIT_RADIUS
+ np.float64_t LIMIT_CENTER[3]
+ np.float64_t LIMIT_RADIUS
- np.int64_t SWAP_ENDIANNESS
- np.int64_t GADGET_VARIANT
+ np.int64_t SWAP_ENDIANNESS
+ np.int64_t GADGET_VARIANT
- np.float64_t FOF_FRACTION
- np.float64_t FOF_LINKING_LENGTH
- np.float64_t INCLUDE_HOST_POTENTIAL_RATIO
- np.float64_t DOUBLE_COUNT_SUBHALO_MASS_RATIO
- np.int64_t TEMPORAL_HALO_FINDING
- np.int64_t MIN_HALO_PARTICLES
- np.float64_t UNBOUND_THRESHOLD
- np.int64_t ALT_NFW_METRIC
+ np.float64_t FOF_FRACTION
+ np.float64_t FOF_LINKING_LENGTH
+ np.float64_t INCLUDE_HOST_POTENTIAL_RATIO
+ np.float64_t DOUBLE_COUNT_SUBHALO_MASS_RATIO
+ np.int64_t TEMPORAL_HALO_FINDING
+ np.int64_t MIN_HALO_PARTICLES
+ np.float64_t UNBOUND_THRESHOLD
+ np.int64_t ALT_NFW_METRIC
- np.int64_t TOTAL_PARTICLES
- np.float64_t BOX_SIZE
- np.int64_t OUTPUT_HMAD
- np.int64_t OUTPUT_PARTICLES
- np.int64_t OUTPUT_LEVELS
- np.float64_t DUMP_PARTICLES[3]
+ np.int64_t TOTAL_PARTICLES
+ np.float64_t BOX_SIZE
+ np.int64_t OUTPUT_HMAD
+ np.int64_t OUTPUT_PARTICLES
+ np.int64_t OUTPUT_LEVELS
+ np.float64_t DUMP_PARTICLES[3]
- np.float64_t AVG_PARTICLE_SPACING
- np.int64_t SINGLE_SNAP
+ np.float64_t AVG_PARTICLE_SPACING
+ np.int64_t SINGLE_SNAP
cdef class RockstarGroupiesInterface:
-
- cdef public object pf
- cdef public object fof
+
+ cdef public object pf
+ cdef public object fof
- # For future use/consistency
- def __cinit__(self,pf):
- self.pf = pf
+ # For future use/consistency
+ def __cinit__(self,pf):
+ self.pf = pf
- def setup_rockstar(self,
- particle_mass,
- int periodic = 1, force_res=None,
- int min_halo_size = 25, outbase = "None",
- callbacks = None):
- global FILENAME, FILE_FORMAT, NUM_SNAPS, STARTING_SNAP, h0, Ol, Om
- global BOX_SIZE, PERIODIC, PARTICLE_MASS, NUM_BLOCKS, NUM_READERS
- global FORK_READERS_FROM_WRITERS, PARALLEL_IO_WRITER_PORT, NUM_WRITERS
- global rh, SCALE_NOW, OUTBASE, MIN_HALO_OUTPUT_SIZE
- global OVERLAP_LENGTH, TOTAL_PARTICLES, FORCE_RES
-
+ def setup_rockstar(self,
+ particle_mass,
+ int periodic = 1, force_res=None,
+ int min_halo_size = 25, outbase = "None",
+ callbacks = None):
+ global FILENAME, FILE_FORMAT, NUM_SNAPS, STARTING_SNAP, h0, Ol, Om
+ global BOX_SIZE, PERIODIC, PARTICLE_MASS, NUM_BLOCKS, NUM_READERS
+ global FORK_READERS_FROM_WRITERS, PARALLEL_IO_WRITER_PORT, NUM_WRITERS
+ global rh, SCALE_NOW, OUTBASE, MIN_HALO_OUTPUT_SIZE
+ global OVERLAP_LENGTH, TOTAL_PARTICLES, FORCE_RES
+
- if force_res is not None:
- FORCE_RES=np.float64(force_res)
+ if force_res is not None:
+ FORCE_RES=np.float64(force_res)
- OVERLAP_LENGTH = 0.0
-
- FILENAME = "inline.<block>"
- FILE_FORMAT = "GENERIC"
- OUTPUT_FORMAT = "ASCII"
- MIN_HALO_OUTPUT_SIZE=min_halo_size
-
- pf = self.pf
+ OVERLAP_LENGTH = 0.0
+
+ FILENAME = "inline.<block>"
+ FILE_FORMAT = "GENERIC"
+ OUTPUT_FORMAT = "ASCII"
+ MIN_HALO_OUTPUT_SIZE=min_halo_size
+
+ pf = self.pf
- h0 = pf.hubble_constant
- Ol = pf.omega_lambda
- Om = pf.omega_matter
-
- SCALE_NOW = 1.0/(pf.current_redshift+1.0)
-
- if not outbase =='None'.decode('UTF-8'):
- #output directory. since we can't change the output filenames
- #workaround is to make a new directory
- OUTBASE = outbase
+ h0 = pf.hubble_constant
+ Ol = pf.omega_lambda
+ Om = pf.omega_matter
+
+ SCALE_NOW = 1.0/(pf.current_redshift+1.0)
+
+ if not outbase =='None'.decode('UTF-8'):
+ #output directory. since we can't change the output filenames
+ #workaround is to make a new directory
+ OUTBASE = outbase
- PARTICLE_MASS = particle_mass.in_units('Msun/h')
- PERIODIC = periodic
- BOX_SIZE = pf.domain_width.in_units('Mpccm/h')[0]
+ PARTICLE_MASS = particle_mass.in_units('Msun/h')
+ PERIODIC = periodic
+ BOX_SIZE = pf.domain_width.in_units('Mpccm/h')[0]
- # Set up the configuration options
- setup_config()
+ # Set up the configuration options
+ setup_config()
- # Needs to be called so rockstar can use the particle mass parameter
- # to calculate virial quantities properly
- calc_mass_definition()
+ # Needs to be called so rockstar can use the particle mass parameter
+ # to calculate virial quantities properly
+ calc_mass_definition()
+ def output_halos(self):
+ output_halos(0, 0, 0, NULL)
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ def make_rockstar_fof(self, np.ndarray[np.int64_t, ndim=1] pid,
+ np.ndarray[np.float64_t, ndim=2] pos,
+ np.ndarray[np.float64_t, ndim=2] vel,
+ np.ndarray[np.int64_t, ndim=1] fof_tags,
+ np.int64_t nfof,
+ np.int64_t npart_max):
- def make_rockstar_fof(self,fof_ids, pos, vel):
+ # Define fof object
- # Turn positions and velocities into units we want
- pos = pos.in_units('Mpccm/h')
- vel = vel.in_units('km/s')
+ # Find number of particles
+ cdef np.int64_t i, j
+ cdef np.int64_t num_particles = pid.shape[0]
- # Define fof object
- cdef fof fof_obj
+ # Allocate space for correct number of particles
+ cdef particle* particles = <particle*> malloc(npart_max * sizeof(particle))
+ cdef fof fof_obj
+ fof_obj.particles = particles
- # Find number of particles
- cdef np.int64_t num_particles = len(fof_ids)
+ cdef np.int64_t last_fof_tag = 1
+ cdef np.int64_t k = 0
+ for i in range(num_particles):
+ if fof_tags[i] == 0:
+ continue
+ if fof_tags[i] != last_fof_tag:
+ last_fof_tag = fof_tags[i]
+ if k > 16:
+ print "Finding subs", k, i
+ fof_obj.num_p = k
+ find_subs(&fof_obj)
+ k = 0
+ particles[k].id = pid[i]
- # Allocate space for correct number of particles
- cdef particle* particles = <particle*> malloc(num_particles * sizeof(particle))
+ # fill in locations & velocities
+ for j in range(3):
+ particles[k].pos[j] = pos[i,j]
+ particles[k].pos[j+3] = vel[i,j]
+ k += 1
+ free(particles)
- # Fill in array of particles with particle that fof identified
- # This is possibly the slowest way to code this, but for now
- # I just want it to work
- for i,id in enumerate(fof_ids):
- particles[i].id = id
- # fill in locations & velocities
- for j in range(3):
- particles[i].pos[j] = pos[id][j]
- particles[i].pos[j+3] = vel[id][j]
-
- # Assign pointer to particles into FOF object
- fof_obj.particles = particles
-
- # Assign number of particles into FOF object
- fof_obj.num_p = num_particles
-
- # Make pointer to fof object
- cdef fof* fof_pointer = & fof_obj
-
- # Find the sub halos using rockstar by passing a pointer to the fof object
- find_subs( fof_pointer)
-
- # Output the halos, rockstar style
- output_halos(0, 0, 0, NULL)
-
- free(particles)
-
-
-
https://bitbucket.org/yt_analysis/yt/commits/7acb9512c76e/
Changeset: 7acb9512c76e
Branch: yt-3.0
User: MatthewTurk
Date: 2014-03-23 18:30:19
Summary: Updating setup.py
Affected #: 1 file
diff -r 7ea355912acb4334a8e25ce85533bf4922db6e08 -r 7acb9512c76ec78ebadf37aea196687b6daaf905 yt/analysis_modules/halo_finding/rockstar/setup.py
--- a/yt/analysis_modules/halo_finding/rockstar/setup.py
+++ b/yt/analysis_modules/halo_finding/rockstar/setup.py
@@ -24,5 +24,12 @@
include_dirs=[rd,
os.path.join(rd, "io"),
os.path.join(rd, "util")])
+ config.add_extension("rockstar_groupies",
+ "yt/analysis_modules/halo_finding/rockstar/rockstar_groupies.pyx",
+ library_dirs=[rd],
+ libraries=["rockstar"],
+ include_dirs=[rd,
+ os.path.join(rd, "io"),
+ os.path.join(rd, "util")])
return config
https://bitbucket.org/yt_analysis/yt/commits/bf628d9eec62/
Changeset: bf628d9eec62
Branch: yt-3.0
User: MatthewTurk
Date: 2014-04-08 19:23:21
Summary: Merged in MatthewTurk/yt/yt-3.0 (pull request #740)
A few updates to Rockstar's groupies interface
Affected #: 2 files
diff -r 689fca64a1840a993c017e2578eb3c5412cd4c38 -r bf628d9eec62eb47e086acc690d045f89b31ce4e yt/analysis_modules/halo_finding/rockstar/rockstar_groupies.pyx
--- a/yt/analysis_modules/halo_finding/rockstar/rockstar_groupies.pyx
+++ b/yt/analysis_modules/halo_finding/rockstar/rockstar_groupies.pyx
@@ -11,234 +11,232 @@
# Importing relevant rockstar data types particle, fof halo, halo
cdef import from "particle.h":
- struct particle:
- np.int64_t id
- float pos[6]
+ struct particle:
+ np.int64_t id
+ float pos[6]
cdef import from "fof.h":
- struct fof:
- np.int64_t num_p
- particle *particles
+ struct fof:
+ np.int64_t num_p
+ particle *particles
cdef import from "halo.h":
- struct halo:
- np.int64_t id
- float pos[6], corevel[3], bulkvel[3]
- float m, r, child_r, vmax_r, mgrav, vmax, rvmax, rs, klypin_rs, vrms
- float J[3], energy, spin, alt_m[4], Xoff, Voff, b_to_a, c_to_a, A[3]
- float bullock_spin, kin_to_pot
- np.int64_t num_p, num_child_particles, p_start, desc, flags, n_core
- float min_pos_err, min_vel_err, min_bulkvel_err
+ struct halo:
+ np.int64_t id
+ float pos[6], corevel[3], bulkvel[3]
+ float m, r, child_r, vmax_r, mgrav, vmax, rvmax, rs, klypin_rs, vrms
+ float J[3], energy, spin, alt_m[4], Xoff, Voff, b_to_a, c_to_a, A[3]
+ float bullock_spin, kin_to_pot
+ np.int64_t num_p, num_child_particles, p_start, desc, flags, n_core
+ float min_pos_err, min_vel_err, min_bulkvel_err
# For finding sub halos import finder function and global variable
# rockstar uses to store the results
cdef import from "groupies.h":
- void find_subs(fof *f)
- halo *halos
- np.int64_t num_halos
- void calc_mass_definition()
+ void find_subs(fof *f) nogil
+ halo *halos
+ np.int64_t num_halos
+ void calc_mass_definition() nogil
# For outputing halos, rockstar style
cdef import from "meta_io.h":
- void output_halos(np.int64_t id_offset, np.int64_t snap, np.int64_t chunk, float *bounds)
+ void output_halos(np.int64_t id_offset, np.int64_t snap, np.int64_t chunk, float *bounds) nogil
# For setting up the configuration of rockstar
cdef import from "config.h":
- void setup_config()
+ void setup_config() nogil
cdef import from "config_vars.h":
- # Rockstar cleverly puts all of the config variables inside a templated
- # definition of their vaiables.
- char *FILE_FORMAT
- np.float64_t PARTICLE_MASS
+ # Rockstar cleverly puts all of the config variables inside a templated
+ # definition of their vaiables.
+ char *FILE_FORMAT
+ np.float64_t PARTICLE_MASS
- char *MASS_DEFINITION
- np.int64_t MIN_HALO_OUTPUT_SIZE
- np.float64_t FORCE_RES
+ char *MASS_DEFINITION
+ np.int64_t MIN_HALO_OUTPUT_SIZE
+ np.float64_t FORCE_RES
- np.float64_t SCALE_NOW
- np.float64_t h0
- np.float64_t Ol
- np.float64_t Om
+ np.float64_t SCALE_NOW
+ np.float64_t h0
+ np.float64_t Ol
+ np.float64_t Om
- np.int64_t GADGET_ID_BYTES
- np.float64_t GADGET_MASS_CONVERSION
- np.float64_t GADGET_LENGTH_CONVERSION
- np.int64_t GADGET_SKIP_NON_HALO_PARTICLES
- np.int64_t RESCALE_PARTICLE_MASS
+ np.int64_t GADGET_ID_BYTES
+ np.float64_t GADGET_MASS_CONVERSION
+ np.float64_t GADGET_LENGTH_CONVERSION
+ np.int64_t GADGET_SKIP_NON_HALO_PARTICLES
+ np.int64_t RESCALE_PARTICLE_MASS
- np.int64_t PARALLEL_IO
- char *PARALLEL_IO_SERVER_ADDRESS
- char *PARALLEL_IO_SERVER_PORT
- np.int64_t PARALLEL_IO_WRITER_PORT
- char *PARALLEL_IO_SERVER_INTERFACE
- char *RUN_ON_SUCCESS
+ np.int64_t PARALLEL_IO
+ char *PARALLEL_IO_SERVER_ADDRESS
+ char *PARALLEL_IO_SERVER_PORT
+ np.int64_t PARALLEL_IO_WRITER_PORT
+ char *PARALLEL_IO_SERVER_INTERFACE
+ char *RUN_ON_SUCCESS
- char *INBASE
- char *FILENAME
- np.int64_t STARTING_SNAP
- np.int64_t NUM_SNAPS
- np.int64_t NUM_BLOCKS
- np.int64_t NUM_READERS
- np.int64_t PRELOAD_PARTICLES
- char *SNAPSHOT_NAMES
- char *LIGHTCONE_ALT_SNAPS
- char *BLOCK_NAMES
+ char *INBASE
+ char *FILENAME
+ np.int64_t STARTING_SNAP
+ np.int64_t NUM_SNAPS
+ np.int64_t NUM_BLOCKS
+ np.int64_t NUM_READERS
+ np.int64_t PRELOAD_PARTICLES
+ char *SNAPSHOT_NAMES
+ char *LIGHTCONE_ALT_SNAPS
+ char *BLOCK_NAMES
- char *OUTBASE
- np.float64_t OVERLAP_LENGTH
- np.int64_t NUM_WRITERS
- np.int64_t FORK_READERS_FROM_WRITERS
- np.int64_t FORK_PROCESSORS_PER_MACHINE
+ char *OUTBASE
+ np.float64_t OVERLAP_LENGTH
+ np.int64_t NUM_WRITERS
+ np.int64_t FORK_READERS_FROM_WRITERS
+ np.int64_t FORK_PROCESSORS_PER_MACHINE
- char *OUTPUT_FORMAT
- np.int64_t DELETE_BINARY_OUTPUT_AFTER_FINISHED
- np.int64_t FULL_PARTICLE_CHUNKS
- char *BGC2_SNAPNAMES
+ char *OUTPUT_FORMAT
+ np.int64_t DELETE_BINARY_OUTPUT_AFTER_FINISHED
+ np.int64_t FULL_PARTICLE_CHUNKS
+ char *BGC2_SNAPNAMES
- np.int64_t BOUND_PROPS
- np.int64_t BOUND_OUT_TO_HALO_EDGE
- np.int64_t DO_MERGER_TREE_ONLY
- np.int64_t IGNORE_PARTICLE_IDS
- np.float64_t TRIM_OVERLAP
- np.float64_t ROUND_AFTER_TRIM
- np.int64_t LIGHTCONE
- np.int64_t PERIODIC
+ np.int64_t BOUND_PROPS
+ np.int64_t BOUND_OUT_TO_HALO_EDGE
+ np.int64_t DO_MERGER_TREE_ONLY
+ np.int64_t IGNORE_PARTICLE_IDS
+ np.float64_t TRIM_OVERLAP
+ np.float64_t ROUND_AFTER_TRIM
+ np.int64_t LIGHTCONE
+ np.int64_t PERIODIC
- np.float64_t LIGHTCONE_ORIGIN[3]
- np.float64_t LIGHTCONE_ALT_ORIGIN[3]
+ np.float64_t LIGHTCONE_ORIGIN[3]
+ np.float64_t LIGHTCONE_ALT_ORIGIN[3]
- np.float64_t LIMIT_CENTER[3]
- np.float64_t LIMIT_RADIUS
+ np.float64_t LIMIT_CENTER[3]
+ np.float64_t LIMIT_RADIUS
- np.int64_t SWAP_ENDIANNESS
- np.int64_t GADGET_VARIANT
+ np.int64_t SWAP_ENDIANNESS
+ np.int64_t GADGET_VARIANT
- np.float64_t FOF_FRACTION
- np.float64_t FOF_LINKING_LENGTH
- np.float64_t INCLUDE_HOST_POTENTIAL_RATIO
- np.float64_t DOUBLE_COUNT_SUBHALO_MASS_RATIO
- np.int64_t TEMPORAL_HALO_FINDING
- np.int64_t MIN_HALO_PARTICLES
- np.float64_t UNBOUND_THRESHOLD
- np.int64_t ALT_NFW_METRIC
+ np.float64_t FOF_FRACTION
+ np.float64_t FOF_LINKING_LENGTH
+ np.float64_t INCLUDE_HOST_POTENTIAL_RATIO
+ np.float64_t DOUBLE_COUNT_SUBHALO_MASS_RATIO
+ np.int64_t TEMPORAL_HALO_FINDING
+ np.int64_t MIN_HALO_PARTICLES
+ np.float64_t UNBOUND_THRESHOLD
+ np.int64_t ALT_NFW_METRIC
- np.int64_t TOTAL_PARTICLES
- np.float64_t BOX_SIZE
- np.int64_t OUTPUT_HMAD
- np.int64_t OUTPUT_PARTICLES
- np.int64_t OUTPUT_LEVELS
- np.float64_t DUMP_PARTICLES[3]
+ np.int64_t TOTAL_PARTICLES
+ np.float64_t BOX_SIZE
+ np.int64_t OUTPUT_HMAD
+ np.int64_t OUTPUT_PARTICLES
+ np.int64_t OUTPUT_LEVELS
+ np.float64_t DUMP_PARTICLES[3]
- np.float64_t AVG_PARTICLE_SPACING
- np.int64_t SINGLE_SNAP
+ np.float64_t AVG_PARTICLE_SPACING
+ np.int64_t SINGLE_SNAP
cdef class RockstarGroupiesInterface:
-
- cdef public object pf
- cdef public object fof
+
+ cdef public object pf
+ cdef public object fof
- # For future use/consistency
- def __cinit__(self,pf):
- self.pf = pf
+ # For future use/consistency
+ def __cinit__(self,pf):
+ self.pf = pf
- def setup_rockstar(self,
- particle_mass,
- int periodic = 1, force_res=None,
- int min_halo_size = 25, outbase = "None",
- callbacks = None):
- global FILENAME, FILE_FORMAT, NUM_SNAPS, STARTING_SNAP, h0, Ol, Om
- global BOX_SIZE, PERIODIC, PARTICLE_MASS, NUM_BLOCKS, NUM_READERS
- global FORK_READERS_FROM_WRITERS, PARALLEL_IO_WRITER_PORT, NUM_WRITERS
- global rh, SCALE_NOW, OUTBASE, MIN_HALO_OUTPUT_SIZE
- global OVERLAP_LENGTH, TOTAL_PARTICLES, FORCE_RES
-
+ def setup_rockstar(self,
+ particle_mass,
+ int periodic = 1, force_res=None,
+ int min_halo_size = 25, outbase = "None",
+ callbacks = None):
+ global FILENAME, FILE_FORMAT, NUM_SNAPS, STARTING_SNAP, h0, Ol, Om
+ global BOX_SIZE, PERIODIC, PARTICLE_MASS, NUM_BLOCKS, NUM_READERS
+ global FORK_READERS_FROM_WRITERS, PARALLEL_IO_WRITER_PORT, NUM_WRITERS
+ global rh, SCALE_NOW, OUTBASE, MIN_HALO_OUTPUT_SIZE
+ global OVERLAP_LENGTH, TOTAL_PARTICLES, FORCE_RES
+
- if force_res is not None:
- FORCE_RES=np.float64(force_res)
+ if force_res is not None:
+ FORCE_RES=np.float64(force_res)
- OVERLAP_LENGTH = 0.0
-
- FILENAME = "inline.<block>"
- FILE_FORMAT = "GENERIC"
- OUTPUT_FORMAT = "ASCII"
- MIN_HALO_OUTPUT_SIZE=min_halo_size
-
- pf = self.pf
+ OVERLAP_LENGTH = 0.0
+
+ FILENAME = "inline.<block>"
+ FILE_FORMAT = "GENERIC"
+ OUTPUT_FORMAT = "ASCII"
+ MIN_HALO_OUTPUT_SIZE=min_halo_size
+
+ pf = self.pf
- h0 = pf.hubble_constant
- Ol = pf.omega_lambda
- Om = pf.omega_matter
-
- SCALE_NOW = 1.0/(pf.current_redshift+1.0)
-
- if not outbase =='None'.decode('UTF-8'):
- #output directory. since we can't change the output filenames
- #workaround is to make a new directory
- OUTBASE = outbase
+ h0 = pf.hubble_constant
+ Ol = pf.omega_lambda
+ Om = pf.omega_matter
+
+ SCALE_NOW = 1.0/(pf.current_redshift+1.0)
+
+ if not outbase =='None'.decode('UTF-8'):
+ #output directory. since we can't change the output filenames
+ #workaround is to make a new directory
+ OUTBASE = outbase
- PARTICLE_MASS = particle_mass.in_units('Msun/h')
- PERIODIC = periodic
- BOX_SIZE = pf.domain_width.in_units('Mpccm/h')[0]
+ PARTICLE_MASS = particle_mass.in_units('Msun/h')
+ PERIODIC = periodic
+ BOX_SIZE = pf.domain_width.in_units('Mpccm/h')[0]
- # Set up the configuration options
- setup_config()
+ # Set up the configuration options
+ setup_config()
- # Needs to be called so rockstar can use the particle mass parameter
- # to calculate virial quantities properly
- calc_mass_definition()
+ # Needs to be called so rockstar can use the particle mass parameter
+ # to calculate virial quantities properly
+ calc_mass_definition()
+ def output_halos(self):
+ output_halos(0, 0, 0, NULL)
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ def make_rockstar_fof(self, np.ndarray[np.int64_t, ndim=1] pid,
+ np.ndarray[np.float64_t, ndim=2] pos,
+ np.ndarray[np.float64_t, ndim=2] vel,
+ np.ndarray[np.int64_t, ndim=1] fof_tags,
+ np.int64_t nfof,
+ np.int64_t npart_max):
- def make_rockstar_fof(self,fof_ids, pos, vel):
+ # Define fof object
- # Turn positions and velocities into units we want
- pos = pos.in_units('Mpccm/h')
- vel = vel.in_units('km/s')
+ # Find number of particles
+ cdef np.int64_t i, j
+ cdef np.int64_t num_particles = pid.shape[0]
- # Define fof object
- cdef fof fof_obj
+ # Allocate space for correct number of particles
+ cdef particle* particles = <particle*> malloc(npart_max * sizeof(particle))
+ cdef fof fof_obj
+ fof_obj.particles = particles
- # Find number of particles
- cdef np.int64_t num_particles = len(fof_ids)
+ cdef np.int64_t last_fof_tag = 1
+ cdef np.int64_t k = 0
+ for i in range(num_particles):
+ if fof_tags[i] == 0:
+ continue
+ if fof_tags[i] != last_fof_tag:
+ last_fof_tag = fof_tags[i]
+ if k > 16:
+ print "Finding subs", k, i
+ fof_obj.num_p = k
+ find_subs(&fof_obj)
+ k = 0
+ particles[k].id = pid[i]
- # Allocate space for correct number of particles
- cdef particle* particles = <particle*> malloc(num_particles * sizeof(particle))
+ # fill in locations & velocities
+ for j in range(3):
+ particles[k].pos[j] = pos[i,j]
+ particles[k].pos[j+3] = vel[i,j]
+ k += 1
+ free(particles)
- # Fill in array of particles with particle that fof identified
- # This is possibly the slowest way to code this, but for now
- # I just want it to work
- for i,id in enumerate(fof_ids):
- particles[i].id = id
- # fill in locations & velocities
- for j in range(3):
- particles[i].pos[j] = pos[id][j]
- particles[i].pos[j+3] = vel[id][j]
-
- # Assign pointer to particles into FOF object
- fof_obj.particles = particles
-
- # Assign number of particles into FOF object
- fof_obj.num_p = num_particles
-
- # Make pointer to fof object
- cdef fof* fof_pointer = & fof_obj
-
- # Find the sub halos using rockstar by passing a pointer to the fof object
- find_subs( fof_pointer)
-
- # Output the halos, rockstar style
- output_halos(0, 0, 0, NULL)
-
- free(particles)
-
-
-
diff -r 689fca64a1840a993c017e2578eb3c5412cd4c38 -r bf628d9eec62eb47e086acc690d045f89b31ce4e yt/analysis_modules/halo_finding/rockstar/setup.py
--- a/yt/analysis_modules/halo_finding/rockstar/setup.py
+++ b/yt/analysis_modules/halo_finding/rockstar/setup.py
@@ -24,5 +24,12 @@
include_dirs=[rd,
os.path.join(rd, "io"),
os.path.join(rd, "util")])
+ config.add_extension("rockstar_groupies",
+ "yt/analysis_modules/halo_finding/rockstar/rockstar_groupies.pyx",
+ library_dirs=[rd],
+ libraries=["rockstar"],
+ include_dirs=[rd,
+ os.path.join(rd, "io"),
+ os.path.join(rd, "util")])
return config
Repository URL: https://bitbucket.org/yt_analysis/yt/
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