def findCenter(group2='All', method = 'pot' ):
"""Finds the center of a given group based on method as 'com' or 'pot'"""
if (method=='pot'):
if (group2=='All'):
charm.createGroup_AttributeRange('highres', 'All', 'mass', -1, 7e-12)
cntHr = charm.getCenterOfMass('highres')
charm.createGroupAttributeSphere('centerhr', 'All', 'position', cntHr[0], cntHr[1], cntHr[2], 1000./136986.30137)
cnt = charm.findAttributeMin('centerhr', 'potential')
else:
cnt = charm.findAttributeMin(group2, 'potential')
elif (method=='com'):
cnt = charm.getCenterOfMass(group2)
return cnt
def setsphere(group, *args) :
"""Select particles within radius from coordinate."""
import charm
try :
# parse args
if len(args) < 3 : raise TypeError('Too few arguments')
if type(args[0]) == str :
if args[0] == 'pot' or args[0] == 'potential ':
center = charm.findAttributeMin(args[1], 'potential')
radius = args[2]
if(len(args) == 4) : parent = args[3]
else : parent = 'All'
elif args[0] == 'com' :
if type(args[1]) != str : raise StandardError('third argument should be a group')
if args[2] == 'all' or args[2] == 'All' :
center = charm.getCenterOfMass(args[1])
radius = args[3]
if(len(args) == 5) : parent = args[4]
else : parent = 'All'
elif args[2] == 'gas' :
charm.createGroup_Family("__tmpgroup", args[1], 'gas')
center = charm.getCenterOfMass(args[1])
radius = args[3]
if(len(args) == 5) : parent = args[4]
else : parent = 'All'
elif args[2] == 'dark' :
charm.createGroup_Family("__tmpgroup", args[1], 'dark')
center = charm.getCenterOfMass(args[1])
radius = args[3]
if(len(args) == 5) : parent = args[4]
else : parent = 'All'
elif args[2] == 'star' :
charm.createGroup_Family("__tmpgroup", args[1], 'star')
center = charm.getCenterOfMass(args[1])
radius = args[3]
if(len(args) == 5) : parent = args[4]
else : parent = 'All'
else : raise StandardError('unknown particle type: ' + args[2])
else : raise StandardError('unknown center type: ' + args[0])
else :
center = (args[0], args[1], args[2])
radius = args[3]
if(len(args) == 5) : parent = args[4]
else : parent = 'All'
# check if simulation loaded
if charm.getGroups() == None :
raise StandardError('Simulation not loaded')
charm.createGroupAttributeSphere(group, parent, 'position', center[0], center[1],
center[2], radius)
except :
print traceback.format_exc()
def profile(group='All', center='pot', family='all', projection='sph', bin_type='log', nbins=30, filename='profile.DAT', min_radius=0., fit_radius=0.) :
"""Perform the Tipsy profile() function.
profile is a command that produces a file of name, file-
name, that contains various physical profiles as a func-
tion of radius for particles of type particle in group.
The center of the radial distribution is taken to be the
center of mass of the particles of the type particle in
group center. If the string "pot" is given instead of
a group name for the argument center, the particle in
group with the lowest potential energy is used as the
center of the radial bins.
The projection argument refers to the shape of the bins
and the bin_type argument refers to how the particles are
binned, either linearly or log in radius. There are nbins
bins distributed equally in either radius or log radius
between min_radius and the size of group.
The output file has the following columns: radius, number
in bin, density, cumulative mass (M(<r)), circular veloc-
ity (sqrt(M(<r)/r)), radial velocity, radial velocity dis-
persion, tangential velocity, tangential velocity disper-
sion, specific angular momentum (j),j_theta, j_phi. The
j_theta and j_phi angles specify the direction of the spe-
cific angular momentum vector (in degrees). If family is
is either gas, baryon, or all, four additional columns
containing the mean mass weighted gas density, mass weigh-
ted gas temperature, mass weighted gas pressure, and mass
weighted gas entropy are added. If particle is either
star, baryon, or all an additional column containing the
stellar luminosity in the Johnson V band is added. This
is calculated using the ages of the star particles
as in Katz (Ap.J. 391: 502, 1992).
Note: some rarer configuration options are not implemented
e.g. non-uniform UV for star luminosity calculation."""
try:
import charm
# check initialization state of meanmwt attribute
if family in ['all', 'gas', 'baryon'] and not 'meanmwt' in charm.getAttributes('gas') :
print 'Attribute meanmwt not initialized. Initializing...'
import load_meanmwt
load_meanmwt.do_meanmwt()
print '\n'
# these should be moved to tipsyf
# fn to take the dot product of two vectors in R3
def dotprod(a, b) :
return a[0]*b[0] + a[1]*b[1] + a[2]*b[2]
# fn to take the cross product of two vectors in R3
def crossprod(a, b) :
return [a[1]*b[2] - a[2]*b[1], a[2]*b[0] - a[0]*b[2], a[0]*b[1] - a[1]*b[0]]
# fn to multiply a vector v by a scalar c
def scalevec(c, v) :
return [c * v[0], c * v[1], c * v[2]]
# fn to add two vectors
def addvec(a, b) :
return [a[0] + b[0], a[1] + b[1], a[2] + b[2]]
# fn to subtract vector b from vector a
def subvec(a, b) :
return [a[0] - b[0], a[1] - b[1], a[2] - b[2]]
# fn to find the length of a vector
def vlength(a) :
import math
return math.sqrt(pow(a[0], 2) + pow(a[1], 2) + pow(a[2], 2))
# fn to combine two vectors, weighting by their corresponding mass scalars
def weightvecs(m1, x1, m2, x2) :
return [(x1[0]*m1 + x2[0]*m2)/(m1+m2), (x1[1]*m1 + x2[1]*m2)/(m1+m2), (x1[2]*m1 + x2[2]*m2)/(m1+m2)]
# scrub input
# check if simulation loaded, store group list
groups = charm.getGroups()
if groups == None :
raise StandardError('Simulation not loaded')
# case is inconsistent between groups and families, work for either
if group == 'all' :
group = 'All'
if family == 'All' :
family = 'all'
# deal with group or center group does not exist
if group not in groups :
raise StandardError('Group does not exist!')
if (center not in groups) and (center != 'pot') :
raise StandardError('Center group does not exist!')
# set up families iterator and throw family related exceptions
families = charm.getFamilies()
if families == None :
raise StandardError('Simulation loaded but no families present.')
isbaryon = 0
if family == 'baryon' :
isbaryon = 1
if 'dark' in families:
families.remove('dark')
if len(families) == 0 :
raise StandardError('No baryon particles present in simulation.')
if (family != 'all') and (family != 'baryon') :
if family not in families :
raise StandardError('Family not present in simulation.')
else :
families = [family]
if len(families) == 0 :
raise StandardError('List of families to process has zero length.')
# create groups containing one family each, store names in famgroups list
famgroups = []
for each in families :
famgroup = group + 'FAM' + each
charm.createGroup_Family(famgroup, group, each)
if charm.getNumParticles(famgroup, each) != 0 :
famgroups += [famgroup]
if len(famgroups) == 0 :
raise StandardError('No particles in group of selected type.')
# validate other inputs
if bin_type == 'linear' :
bin_type = 'lin'
elif bin_type == 'logarithmic' :
bin_type = 'log'
elif bin_type not in ['lin', 'log'] :
raise StandardError('Value of bin_type must be lin or log.')
if (int(nbins) != nbins) or (nbins < 1) :
raise StandardError('Value of nbins must be a positive integer.')
if not min_radius >= 0 :
raise StandardError('Value of min_radius cannot be negative.')
if min_radius == 0 and bin_type == 'log' :
min_radius = config.LOG_MIN
print 'Parameter min_radius set to ' + str(min_radius) + ' to accomodate logarithmic binning.'
if not fit_radius >= 0 :
raise StandardError('Value of fit_radius cannot be negative.')
# begin calculating parameters
# find center point
if center == 'pot' :
center = charm.findAttributeMin(group, 'potential')
else:
center = charm.getCenterOfMass(center)
# get center_vel and center_angular_mom
# families must be parsed individually then combined
vmdata = charm.reduceParticle(famgroups[0], vmmap, vmreduce, None)
if vmdata == None :
raise StandardError('MapReduce returned NoneType object.')
center_vel = vmdata[0][2]
center_angular_mom = vmdata[0][3]
# if there are additional families, parse each then combine results weighting by mass
if len(famgroups) > 1 :
old_mass = vmdata[0][1]
for i in range(len(famgroups)-1) :
vmdata = charm.reduceParticle(famgroups[i+1], vmmap, vmreduce, None)
new_mass = vmdata[0][1]
center_vel = weightvecs(old_mass, center_vel, new_mass, vmdata[0][2])
center_angular_mom = weightvecs(old_mass, center_angular_mom, new_mass, vmdata[0][3])
old_mass += new_mass
# for an elliptical projection, use Katz to get shape & then find vel, mom
# when restoring this, find out what happened to center_ell?
if projection == 'ell' :
if fit_radius == 0. :
print 'fit_radius = 0 in an elliptical projection.\nusing all particles in batch to find shape of ellipses.'
ell_matrix = [[0., 0., 0.], [0., 0., 0.], [0., 0., 0.]]
center_ell = [0., 0., 0.]
ba = ca = phi = theta = psi = 0.
center = list(center)
shape_data = elliptical.find_shape(famgroups, center, fit_radius, ell_matrix, center_ell)
center = tuple(center)
if type(shape_data) == type(None) :
print 'find_shape() did not succeed'
return
# raise StandardError('Problem in elliptical.find_shape(): no fit found.')
else :
ba, ca, phi, theta, psi = shape_data
print 'b/a = %g, c/a = %g' % (ba, ca)
center = [0.]*config.MAXDIM
center_vel = [0.]*config.MAXDIM
center_angular_mom = [0.]*config.MAXDIM
vel_data = elliptical.find_vel(famgroups,center,center_vel,center_angular_mom, ell_matrix, center_ell, ba, ca, fit_radius)
else :
ba, ca, phi, theta, psi, center_ell, ell_matrix = (0., 0., 0., 0., 0., [0.]*config.MAXDIM, [[0.]*config.MAXDIM]*config.MAXDIM)
# find max_radius
# maxradmap iterates over all particles and compares each radius to the previous max found
p_param = (center)
max_radius = 0.
if family == 'all' :
max_radius = charm.reduceParticle(group, maxradmap, maxradreduce, p_param)[0][1]
else :
for i in range(len(famgroups)) :
fam_radius = charm.reduceParticle(famgroups[i], maxradmap, maxradreduce, p_param)[0][1]
max_radius = max(max_radius, fam_radius)
# TIPSY uses an approximation for max_radius which can't be adequately emulated here.
# for the run99 data file, the value of max_radius is 8.18829; set it manually.
# max_radius = 8.18829
# determine bin_size
# if min_radius > 0, then bin 0 should have the specified radius.
# other than this exception, all bins have constant size in either lin or log space as specified
if min_radius > max_radius and nbins > 1 :
raise StandardException('Value for min_radius encompasses all particles; cannot bin data.')
# min_radius > 0 case creates a scenario where nbins = 1 would create a /0 error, must handle here.
if nbins == 1 :
bin_size = max_radius
# bin_type and min_radius are superfluous to nbins = 1 case
bin_type = 'lin'
min_radius = 0.
# find size in lin space
elif bin_type == 'lin' :
if min_radius > 0. :
bin_size = (max_radius - min_radius) / float(nbins - 1)
else :
bin_size = (max_radius - min_radius) / float(nbins)
# find size in log space
else :
min_radius = math.log10(min_radius)
bin_size = (math.log10(max_radius) - min_radius) / float(nbins - 1)
# calculate bin boundary radii
bounds = [0.] * (nbins + 1)
# the first boundary radius is affected by min_radius, handle
if bin_type == 'lin' and min_radius == 0.:
bounds[1] = bin_size
else :
bounds[1] = min_radius
# each following bound should be bound[previous] + bin_size
for i in range(2, nbins + 1) :
bounds[i] = bounds[i - 1] + bin_size
# if logarithmic binning, convert values into linear space
if bin_type == 'log' :
for i in range(1, nbins + 1) :
bounds[i] = pow(10., bounds[i])
starlf = star_lum.star_lum()
sim_time = charm.getTime()
# do calculations which must see individual particles.
# the set of attributes on a particle varies by family, so each family must be processed seperately
params = [None, isbaryon, bounds, projection, nbins, bin_type, bin_size, min_radius, max_radius, center, center_vel, ell_matrix, center_ell, ba, ca, config.msolunit, config.gasconst, sim_time, config.time_unit, starlf.age, starlf.lum, starlf.lumv_fit, starlf.vv_dat, starlf.vv_fit, starlf.bv_dat, starlf.bv_fit, center_angular_mom]
fam_data = [None] * len(famgroups)
for i in range(len(famgroups)) :
params[0] = families[i]
fam_data[i] = charm.reduceParticle(famgroups[i], basemap, basereduce, tuple(params))
# shows per-family result of MapReduce, sometimes useful for debugging
# if debug_flag == 1 :
# print '\nThe current family is: ' + families[i]
# for line in fam_data[i] :
# print line
if len(fam_data) < 1 or fam_data == None :
raise StandardException('MapReduce for fam_data has length zero or is NoneType.')
# sum results into one list.
# Note that if a bin has no particles, it will be missing from the reduce result. data[] should have no missing rows.
# values are: bin, number, mass, vel_radial, vel_radial_sigma, vel_tang_sigma, angular_mom[x,y,z], lum, density, temp, pressure, entropy, gas_mass
data = [None] * nbins
for i in range(nbins) :
data[i] = [i, 0, 0., 0., 0., 0., [0., 0., 0.], 0., 0., 0., 0., 0., 0.]
for fam in fam_data :
for row in fam :
bin = row[0]
# merge fields 0 thru 5
for i in range(1, 6) :
data[bin][i] += row[i]
# merge field 6 (angular momentum vector)
for i in range(3) :
data[bin][6][i] += row[6][i]
# merge fields 7 thru 12
for i in range(7, 13) :
data[bin][i] += row[i]
if not len(data) == nbins :
raise StandardError('nbins != length of result after basemap')
# calculate remaining "base" values that did not need to be handled in the map
mass_r = 0.
for i in range(nbins) :
# get max radius, min radius, and mean radius
r_max = bounds[i + 1]
r_min = bounds[i]
r_mean = (r_max + r_min) / 2.
# number of particles in bin
number = data[i][1]
# if the bin is empty then some calculations e.g. 1/mass will explode; catch these.
if number != 0 :
# find volume by projection
pi = 3.141592653589793
if projection == 'ell' :
volume = 4. * ba * ca / 3. * pi * (pow((r_max),3) - pow((r_min),3))
elif projection == 'cyl' :
volume = pi * (pow((r_max),2) - pow((r_min),2))
else :
volume = (4. / 3.) * pi * (pow(r_max,3) - pow(r_min,3))
# unpack values. deal with non-sum calculations, largely n / mass
mass = data[i][2]
mass_r += mass
vel_radial = data[i][3] / mass
vel_radial_sigma = data[i][4] / mass
if vel_radial_sigma > vel_radial**2 :
vel_radial_sigma = math.sqrt(vel_radial_sigma - vel_radial**2)
else :
vel_radial_sigma = 0.
vel_tang_sigma = data[i][5] / mass
ang_mom = scalevec(1./mass, data[i][6])
ang = vlength(ang_mom)
if ang > 0.0 :
ang_theta = 180.0 * math.acos(ang_mom[2] / ang) / pi
else :
ang_theta = 0.0
ang_phi = 180.0 * math.atan2(ang_mom[1], ang_mom[0]) / pi
rho = mass / volume
vel_circ = ang / r_mean
c_vel = math.sqrt(mass_r / r_max)
if vel_tang_sigma > vel_circ**2 :
vel_tang_sigma = math.sqrt(vel_tang_sigma - vel_circ**2)
else :
vel_tang_sigma = 0.
# star stuff
lum_den = data[i][7] / volume
# gas stuff
if 'gas' in families and data[i][12] > 0 :
density = data[i][8] / data[i][12]
temp = data[i][9] / data[i][12]
pressure = data[i][10] / data[i][12]
entropy = data[i][11] / data[i][12]
else :
density = 0.
temp = 0.
pressure = 0.
entropy = -config.HUGE
data[i] = [r_max, number, rho, mass_r, c_vel, vel_radial, vel_radial_sigma, vel_circ, vel_tang_sigma, ang, ang_theta, ang_phi, density, temp, pressure, entropy, lum_den]
else :
c_vel = math.sqrt(mass_r / r_max)
data[i] = [r_max, 0, 0., mass_r, c_vel, 0., 0., 0., 0., 0., 0.,
0., 0., 0., 0., 0., 0.]
# build header row
# may need to update the exact text used for clarity or for consistency with TIPSY
headers = ('radius', 'number', 'rho', 'mass_r', 'c_vel', 'vel_radial', 'vel_radial_sigma', 'vel_circ', 'vel_tang_sigma', 'ang', 'ang_theta', 'ang_phi')
if family in ['gas', 'baryon', 'all'] :
headers += ('mmwg_density', 'mwg_temp', 'mwg_pres', 'mwg_entr')
if family in ['star', 'baryon', 'all'] :
headers += ('lum_V',)
# write output to file
f = open(filename, 'w')
# write headers according to families present
f.write('#')
for i in range(len(headers)) :
f.write(' ' + headers[i])
f.write('\n')
# write data according to families present
for i in range(nbins) :
f.write('%g %d %g %g %g %g %g %g %g %g %g %g' % tuple(data[i][0:12]))
if 'gas' in families :
f.write(' %g %g %g %g' % tuple(data[i][12:16]))
if 'star' in families :
f.write(' %g' % tuple(data[i][16:17]))
f.write('\n')
f.close()
# there is no current mechanism to delete groups.
# if one is added, delete temporary working groups here.
except :
print traceback.format_exc()