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Added OpenCL CIC code

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This commit is contained in:
Guilhem Lavaux 2014-09-23 11:54:44 +02:00
parent 1e733f2318
commit f6ad248f75
8 changed files with 297 additions and 78 deletions
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10
python/_cosmotool.pyx
View File

@ -463,6 +463,8 @@ cdef class CosmologyPower:
return self._compute(k)
@cython.boundscheck(False)
@cython.cdivision(True)
@cython.wraparound(False)
def leanCic(float[:,:] particles, float L, int Resolution):
cdef CICParticles p
cdef CICFilter *cic
@ -470,6 +472,8 @@ def leanCic(float[:,:] particles, float L, int Resolution):
cdef CICType *field
cdef np.uint32_t dummyRes
cdef np.ndarray[np.float64_t, ndim=3] out_field
cdef np.ndarray[np.float64_t, ndim=1] out_field0
cdef np.float64_t[:] out_field_buf
cdef np.uint64_t j
cic = new CICFilter(Resolution, L)
@ -490,8 +494,10 @@ def leanCic(float[:,:] particles, float L, int Resolution):
cic.getDensityField(field, dummyRes)
out_field = np.empty((dummyRes, dummyRes, dummyRes), dtype=np.float64)
for j in xrange(out_field.size):
out_field[j] = field[j]
out_field0 = out_field.reshape(out_field.size)
out_field_buf = out_field
for j in xrange(out_field_buf.size):
out_field_buf[j] = field[j]
del cic
return out_field

112
python/_project.pyx
View File

@ -21,6 +21,7 @@ cdef extern from "project_tool.hpp" namespace "":
@cython.boundscheck(False)
@cython.cdivision(True)
@cython.wraparound(False)
cdef int interp3d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y,
DTYPE_t z,
DTYPE_t[:,:,:] d, DTYPE_t Lbox, DTYPE_t *retval) nogil:
@ -45,6 +46,10 @@ cdef int interp3d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y,
ry -= iy
rz -= iz
ix = ix % Ngrid
iy = iy % Ngrid
iz = iz % Ngrid
jx = (ix+1)%Ngrid
jy = (iy+1)%Ngrid
jz = (iz+1)%Ngrid
@ -53,13 +58,6 @@ cdef int interp3d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y,
iy = iy%Ngrid
iz = iz%Ngrid
if (ix < 0) or (jx >= Ngrid):
return -1
if (iy < 0) or (jy >= Ngrid):
return -2
if (iz < 0) or (jz >= Ngrid):
return -3
f[0][0][0] = (1-rx)*(1-ry)*(1-rz)
f[1][0][0] = ( rx)*(1-ry)*(1-rz)
f[0][1][0] = (1-rx)*( ry)*(1-rz)
@ -80,10 +78,9 @@ cdef int interp3d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y,
d[ix ,jy ,jz ] * f[0][1][1] + \
d[jx ,jy ,jz ] * f[1][1][1]
return 0
@cython.boundscheck(False)
@cython.cdivision(True)
@cython.wraparound(False)
cdef int ngp3d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y,
DTYPE_t z,
DTYPE_t[:,:,:] d, DTYPE_t Lbox, DTYPE_t *retval) nogil:
@ -110,14 +107,13 @@ cdef int ngp3d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y,
retval[0] = d[ix ,iy ,iz ]
return 0
@cython.boundscheck(False)
@cython.cdivision(True)
@cython.wraparound(False)
cdef int ngp3d_INTERNAL(DTYPE_t x, DTYPE_t y,
DTYPE_t z,
DTYPE_t[:,:,:] d, DTYPE_t Lbox, DTYPE_t *retval) nogil:
DTYPE_t[:,:,:] d, DTYPE_t Lbox, DTYPE_t *retval, DTYPE_t inval) nogil:
cdef int Ngrid = d.shape[0]
cdef DTYPE_t inv_delta = Ngrid/Lbox
@ -134,23 +130,18 @@ cdef int ngp3d_INTERNAL(DTYPE_t x, DTYPE_t y,
iy = int(round(ry))
iz = int(round(rz))
if (ix < 0 or ix >= Ngrid):
return -1
if (iy < 0 or iy >= Ngrid):
return -2
if (iz < 0 or iz >= Ngrid):
return -3
if ((ix < 0) or (ix+1) >= Ngrid or (iy < 0) or (iy+1) >= Ngrid or (iz < 0) or (iz+1) >= Ngrid):
retval[0] = inval
retval[0] = d[ix ,iy ,iz ]
return 0
@cython.boundscheck(False)
@cython.cdivision(True)
@cython.wraparound(False)
cdef int interp3d_INTERNAL(DTYPE_t x, DTYPE_t y,
DTYPE_t z,
DTYPE_t[:,:,:] d, DTYPE_t Lbox, DTYPE_t *retval) nogil:
DTYPE_t[:,:,:] d, DTYPE_t Lbox, DTYPE_t *retval, DTYPE_t inval) nogil:
cdef int Ngrid = d.shape[0]
cdef DTYPE_t inv_delta = Ngrid/Lbox
@ -170,14 +161,8 @@ cdef int interp3d_INTERNAL(DTYPE_t x, DTYPE_t y,
ry -= iy
rz -= iz
if ((ix < 0) or (ix+1) >= Ngrid):
return -1
if ((iy < 0) or (iy+1) >= Ngrid):
return -2
if ((iz < 0) or (iz+1) >= Ngrid):
return -3
if ((ix < 0) or (ix+1) >= Ngrid or (iy < 0) or (iy+1) >= Ngrid or (iz < 0) or (iz+1) >= Ngrid):
retval[0] = inval
# assert ((ix >= 0) and ((ix+1) < Ngrid))
# assert ((iy >= 0) and ((iy+1) < Ngrid))
# assert ((iz >= 0) and ((iz+1) < Ngrid))
@ -202,13 +187,11 @@ cdef int interp3d_INTERNAL(DTYPE_t x, DTYPE_t y,
d[ix ,iy+1,iz+1] * f[0][1][1] + \
d[ix+1,iy+1,iz+1] * f[1][1][1]
return 0
@cython.boundscheck(False)
def interp3d(x not None, y not None,
z not None,
npx.ndarray[DTYPE_t, ndim=3] d not None, DTYPE_t Lbox,
bool periodic=False, bool centered=True, bool ngp=False):
bool periodic=False, bool centered=True, bool ngp=False, DTYPE_t inval = 0):
""" interp3d(x,y,z,d,Lbox,periodic=False,centered=True,ngp=False) -> interpolated values
Compute the tri-linear interpolation of the given field (d) at the given position (x,y,z). It assumes that they are box-centered coordinates. So (x,y,z) == (0,0,0) is equivalent to the pixel at (Nx/2,Ny/2,Nz/2) with Nx,Ny,Nz = d.shape. If periodic is set, it assumes the box is periodic
@ -253,41 +236,29 @@ def interp3d(x not None, y not None,
if not myngp:
if myperiodic:
for i in prange(Nelt):
if interp3d_INTERNAL_periodic(shifter+ax[i], shifter+ay[i], shifter+az[i], in_slice, Lbox, &out_slice[i]) < 0:
with gil:
raise ierror
interp3d_INTERNAL_periodic(shifter+ax[i], shifter+ay[i], shifter+az[i], in_slice, Lbox, &out_slice[i])
else:
for i in prange(Nelt):
if interp3d_INTERNAL(shifter+ax[i], shifter+ay[i], shifter+az[i], in_slice, Lbox, &out_slice[i]) < 0:
with gil:
raise ierror
interp3d_INTERNAL(shifter+ax[i], shifter+ay[i], shifter+az[i], in_slice, Lbox, &out_slice[i], inval)
else:
if myperiodic:
for i in prange(Nelt):
if ngp3d_INTERNAL_periodic(shifter+ax[i], shifter+ay[i], shifter+az[i], in_slice, Lbox, &out_slice[i]) < 0:
with gil:
raise ierror
ngp3d_INTERNAL_periodic(shifter+ax[i], shifter+ay[i], shifter+az[i], in_slice, Lbox, &out_slice[i])
else:
for i in prange(Nelt):
if ngp3d_INTERNAL(shifter+ax[i], shifter+ay[i], shifter+az[i], in_slice, Lbox, &out_slice[i]) < 0:
with gil:
raise ierror
ngp3d_INTERNAL(shifter+ax[i], shifter+ay[i], shifter+az[i], in_slice, Lbox, &out_slice[i], inval)
return out
else:
if not myngp:
if periodic:
if interp3d_INTERNAL_periodic(shifter+x, shifter+y, shifter+z, d, Lbox, &retval) < 0:
raise ierror
interp3d_INTERNAL_periodic(shifter+x, shifter+y, shifter+z, d, Lbox, &retval)
else:
if interp3d_INTERNAL(shifter+x, shifter+y, shifter+z, d, Lbox, &retval) < 0:
raise ierror
interp3d_INTERNAL(shifter+x, shifter+y, shifter+z, d, Lbox, &retval, inval)
else:
if periodic:
if ngp3d_INTERNAL_periodic(shifter+x, shifter+y, shifter+z, d, Lbox, &retval) < 0:
raise ierror
ngp3d_INTERNAL_periodic(shifter+x, shifter+y, shifter+z, d, Lbox, &retval)
else:
if ngp3d_INTERNAL(shifter+x, shifter+y, shifter+z, d, Lbox, &retval) < 0:
raise ierror
ngp3d_INTERNAL(shifter+x, shifter+y, shifter+z, d, Lbox, &retval, inval)
return retval
@cython.boundscheck(False)
@ -410,8 +381,7 @@ def interp2d(x not None, y not None,
@cython.boundscheck(False)
@cython.cdivision(True)
cdef void INTERNAL_project_cic_no_mass(npx.ndarray[DTYPE_t, ndim=3] g,
npx.ndarray[DTYPE_t, ndim=2] x, int Ngrid, float Lbox):
cdef double half_Box = 0.5*Lbox
npx.ndarray[DTYPE_t, ndim=2] x, int Ngrid, double Lbox, double shifter):
cdef double delta_Box = Ngrid/Lbox
cdef int i
cdef double a[3], c[3]
@ -422,7 +392,7 @@ cdef void INTERNAL_project_cic_no_mass(npx.ndarray[DTYPE_t, ndim=3] g,
do_not_put = 0
for j in range(3):
a[j] = (x[i,j]+half_Box)*delta_Box
a[j] = (x[i,j]+shifter)*delta_Box
b[j] = int(floor(a[j]))
a[j] -= b[j]
c[j] = 1-a[j]
@ -446,8 +416,7 @@ cdef void INTERNAL_project_cic_no_mass(npx.ndarray[DTYPE_t, ndim=3] g,
@cython.boundscheck(False)
@cython.cdivision(True)
cdef void INTERNAL_project_cic_no_mass_periodic(npx.ndarray[DTYPE_t, ndim=3] g,
npx.ndarray[DTYPE_t, ndim=2] x, int Ngrid, double Lbox):
cdef double half_Box = 0.5*Lbox
npx.ndarray[DTYPE_t, ndim=2] x, int Ngrid, double Lbox, double shifter):
cdef double delta_Box = Ngrid/Lbox
cdef int i
cdef double a[3], c[3]
@ -463,7 +432,7 @@ cdef void INTERNAL_project_cic_no_mass_periodic(npx.ndarray[DTYPE_t, ndim=3] g,
do_not_put = 0
for j in range(3):
a[j] = (ax[i,j]+half_Box)*delta_Box
a[j] = (ax[i,j]+shifter)*delta_Box
b[j] = int(floor(a[j]))
b1[j] = (b[j]+1) % Ngrid
@ -488,8 +457,7 @@ cdef void INTERNAL_project_cic_no_mass_periodic(npx.ndarray[DTYPE_t, ndim=3] g,
cdef void INTERNAL_project_cic_with_mass(npx.ndarray[DTYPE_t, ndim=3] g,
npx.ndarray[DTYPE_t, ndim=2] x,
npx.ndarray[DTYPE_t, ndim=1] mass,
int Ngrid, double Lbox):
cdef double half_Box = 0.5*Lbox
int Ngrid, double Lbox, double shifter):
cdef double delta_Box = Ngrid/Lbox
cdef int i
cdef double a[3], c[3]
@ -500,7 +468,7 @@ cdef void INTERNAL_project_cic_with_mass(npx.ndarray[DTYPE_t, ndim=3] g,
do_not_put = False
for j in range(3):
a[j] = (x[i,j]+half_Box)*delta_Box
a[j] = (x[i,j]+shifter)*delta_Box
b[j] = int(a[j])
a[j] -= b[j]
c[j] = 1-a[j]
@ -525,7 +493,7 @@ cdef void INTERNAL_project_cic_with_mass(npx.ndarray[DTYPE_t, ndim=3] g,
cdef void INTERNAL_project_cic_with_mass_periodic(npx.ndarray[DTYPE_t, ndim=3] g,
npx.ndarray[DTYPE_t, ndim=2] x,
npx.ndarray[DTYPE_t, ndim=1] mass,
int Ngrid, double Lbox):
int Ngrid, double Lbox, double shifter):
cdef double half_Box = 0.5*Lbox, m0
cdef double delta_Box = Ngrid/Lbox
cdef int i
@ -535,7 +503,7 @@ cdef void INTERNAL_project_cic_with_mass_periodic(npx.ndarray[DTYPE_t, ndim=3] g
for i in range(x.shape[0]):
for j in range(3):
a[j] = (x[i,j]+half_Box)*delta_Box
a[j] = (x[i,j]+shifter)*delta_Box
b[j] = int(floor(a[j]))
b1[j] = b[j]+1
while b1[j] < 0:
@ -559,14 +527,20 @@ cdef void INTERNAL_project_cic_with_mass_periodic(npx.ndarray[DTYPE_t, ndim=3] g
def project_cic(npx.ndarray[DTYPE_t, ndim=2] x not None, npx.ndarray[DTYPE_t, ndim=1] mass, int Ngrid,
double Lbox, bool periodic = False):
double Lbox, bool periodic = False, centered=True):
"""
project_cic(x array (N,3), mass (may be None), Ngrid, Lbox, periodict)
project_cic(x array (N,3), mass (may be None), Ngrid, Lbox, periodict, centered=True)
This function does a Cloud-In-Cell projection of a 3d unstructured dataset. First argument is a Nx3 array of coordinates.
Second argument is an optinal mass. Ngrid is the size output grid and Lbox is the physical size of the grid.
"""
cdef npx.ndarray[DTYPE_t, ndim=3] g
cdef double shifter
if centered:
shifter = 0.5*Lbox
else:
shifter = 0
if x.shape[1] != 3:
raise ValueError("Invalid shape for x array")
@ -578,14 +552,14 @@ def project_cic(npx.ndarray[DTYPE_t, ndim=2] x not None, npx.ndarray[DTYPE_t, nd
if not periodic:
if mass == None:
INTERNAL_project_cic_no_mass(g, x, Ngrid, Lbox)
INTERNAL_project_cic_no_mass(g, x, Ngrid, Lbox, shifter)
else:
INTERNAL_project_cic_with_mass(g, x, mass, Ngrid, Lbox)
INTERNAL_project_cic_with_mass(g, x, mass, Ngrid, Lbox, shifter)
else:
if mass == None:
INTERNAL_project_cic_no_mass_periodic(g, x, Ngrid, Lbox)
INTERNAL_project_cic_no_mass_periodic(g, x, Ngrid, Lbox, shifter)
else:
INTERNAL_project_cic_with_mass_periodic(g, x, mass, Ngrid, Lbox)
INTERNAL_project_cic_with_mass_periodic(g, x, mass, Ngrid, Lbox, shifter)
return g

1
python/cosmotool/__init__.py
View File

@ -3,6 +3,7 @@ from _project import *
from .grafic import writeGrafic, writeWhitePhase, readGrafic, readWhitePhase
from .borg import read_borg_vol
from .cic import cicParticles
from .cl_cic import cl_CIC_Density
from .simu import loadRamsesAll, simpleWriteGadget, SimulationBare
from .timing import time_block, timeit, timeit_quiet

232
python/cosmotool/cl_cic.py Normal file
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@ -0,0 +1,232 @@
from .timing import time_block as time_block_orig
import numpy as np
import pyopencl as cl
import pyopencl.array as cl_array
from contextlib import contextmanager
TIMER_ACTIVE=False
@contextmanager
def time_block_dummy(*args):
yield
if TIMER_ACTIVE:
time_block=time_block_orig
else:
time_block=time_block_dummy
CIC_PREKERNEL='''
#define NDIM {ndim}
#define CENTERED {centered}
typedef {cicType} BASIC_TYPE;
'''
CIC_KERNEL='''///CL///
#pragma OPENCL EXTENSION cl_khr_global_int32_base_atomics : enable
__kernel void init_pcell(__global int *p_cell, const int value)
{
int i = get_global_id(0);
p_cell[i] = value;
}
__kernel void build_indices(__global const BASIC_TYPE *pos,
__global int *part_mesh, __global int *part_list, const int N, const BASIC_TYPE delta, const BASIC_TYPE shift_pos)
{
int i_part = get_global_id(0);
long shifter = 1;
long idx = 0;
int d;
for (d = 0; d < NDIM; d++) {
BASIC_TYPE x;
if (CENTERED)
x = pos[i_part*NDIM + d] - shift_pos;
else
x = pos[i_part*NDIM + d];
int m = (int)floor(x*delta) %% N;
idx += shifter * m;
shifter *= N;
}
// Head of the list
int initial_elt = atom_xchg(&part_mesh[idx], i_part);
if (initial_elt == -1) {
return;
}
// Point the next pointer of old_end to i_part
part_list[i_part] = initial_elt;
}
__kernel void reverse_list(__global int *part_mesh, __global int *part_list)
{
int mid = get_global_id(0);
int current_part = part_mesh[mid];
if (current_part >= 0) {
int next_part = part_list[current_part];
part_list[current_part] = -1;
while (next_part != -1) {
int p = part_list[next_part];
part_list[next_part] = current_part;
current_part = next_part;
next_part = p;
}
part_mesh[mid] = current_part;
}
}
__kernel void dance(__global const BASIC_TYPE *pos,
__global BASIC_TYPE *density,
__global int *part_mesh, __global int *part_list, const int N, const BASIC_TYPE delta, const BASIC_TYPE shift_pos)
{
int m[NDIM];
int shifter = 1;
int i;
int first, i_part;
int idx = 0;
for (i = 0; i < NDIM; i++) {
m[i] = get_global_id(i);
idx += shifter * m[i];
shifter *= N;
}
first = 1;
//BEGIN LOOPER
%(looperFor)s
//END LOOPER
int idx_dance = 0;
BASIC_TYPE w = 0;
//LOOPER INDEX
int r[NDIM] = { %(looperVariables)s };
//END LOOPER
i_part = part_mesh[idx];
while (i_part != -1) {
BASIC_TYPE w0 = 1;
for (int d = 0; d < NDIM; d++) {
BASIC_TYPE x;
BASIC_TYPE q;
BASIC_TYPE dx;
if (CENTERED)
x = pos[i_part*NDIM + d]*delta - shift_pos;
else
x = pos[i_part*NDIM + d]*delta;
q = floor(x);
dx = x - q;
w0 *= (r[d] == 1) ? dx : ((BASIC_TYPE)1-dx);
}
i_part = part_list[i_part];
w += w0;
}
shifter = 1;
for (i = 0; i < NDIM; i++) {
idx_dance += shifter * ((m[i]+r[i])%%N);
shifter *= N;
}
density[idx_dance] += w;
// One dance done. Wait for everybody for the next iteration
barrier(CLK_GLOBAL_MEM_FENCE);
%(looperForEnd)s
}
'''
class CIC_CL(object):
def __init__(self, context, ndim=2, ktype=np.float32, centered=False):
global CIC_PREKERNEL, CIC_KERNEL
translator = {}
if ktype == np.float32:
translator['cicType'] = 'float'
pragmas = ''
elif ktype == np.float64:
translator['cicType'] = 'double'
pragmas = '#pragma OPENCL EXTENSION cl_khr_fp64 : enable\n'
else:
raise ValueError("Invalid ktype")
# 2 dimensions
translator['ndim'] = ndim
translator['centered'] = '1' if centered else '0'
looperVariables = ','.join(['id%d' % d for d in xrange(ndim)])
looperFor = '\n'.join(['for (int id{dim}=0; id{dim} < 2; id{dim}++) {{'.format(dim=d) for d in xrange(ndim)])
looperForEnd = '}' * ndim
kern = pragmas + CIC_PREKERNEL.format(**translator) + (CIC_KERNEL % {'looperVariables': looperVariables, 'looperFor': looperFor, 'looperForEnd':looperForEnd})
self.kern_code = kern
self.ctx = context
self.queue = cl.CommandQueue(context)#, properties=cl.OUT_OF_ORDER_EXEC_MODE_ENABLE)
self.ktype = ktype
self.ndim = ndim
self.prog = cl.Program(self.ctx, kern).build()
self.centered = centered
def run(self, particles, Ng, L):
assert particles.strides[1] == self.ktype().itemsize # This is C-ordering
assert particles.shape[1] == self.ndim
print("Start again")
ndim = self.ndim
part_pos = cl_array.to_device(self.queue, particles)
part_mesh = cl_array.empty(self.queue, (Ng,)*ndim, np.int32, order='C')
density = cl_array.zeros(self.queue, (Ng,)*ndim, self.ktype, order='C')
part_list = cl_array.empty(self.queue, (particles.shape[0],), np.int32, order='C')
shift_pos = 0.5*L if self.centered else 0
if True:
delta = Ng/L
with time_block("Init pcell array"):
e = self.prog.init_pcell(self.queue, (Ng**ndim,), None, part_mesh.data, np.int32(-1))
e.wait()
with time_block("Init idx array"):
e=self.prog.init_pcell(self.queue, (particles.shape[0],), None, part_list.data, np.int32(-1))
e.wait()
with time_block("Build indices"):
self.prog.build_indices(self.queue, (particles.shape[0],), None,
part_pos.data, part_mesh.data, part_list.data, np.int32(Ng), self.ktype(delta), self.ktype(shift_pos))
if True:
with time_block("Reverse list"):
lastevt = self.prog.reverse_list(self.queue, (Ng**ndim,), None, part_mesh.data, part_list.data)
# We require pmax pass, particles are ordered according to part_idx
with time_block("dance"):
self.prog.dance(self.queue, (Ng,)*ndim, None, part_pos.data, density.data, part_mesh.data, part_list.data, np.int32(Ng), self.ktype(delta), self.ktype(shift_pos))
self.queue.finish()
del part_pos
del part_mesh
del part_list
with time_block("download"):
return density.get()
def cl_CIC_Density(particles, Ngrid, Lbox, context=None, periodic=True, centered=False):
"""
cl_CIC_Density(particles (Nx3), Ngrid, Lbox, context=None, periodic=True, centered=False)
"""
if context is None:
context = cl.create_some_context()
cic = CIC_CL(context, ndim=3, centered=centered)
return cic.run(particles, Ng, L)

4
python_sample/icgen/borgicgen.py
View File

@ -74,6 +74,7 @@ def run_generation(input_borg, a_borg, a_ic, cosmo, supersample=1, do_lpt2=True,
# Compute LPT scaling coefficient
D1 = cgrowth.D(a_ic)
D1_0 = D1/cgrowth.D(a_borg)
print "D1_0=%lg" % D1_0
velmul = cgrowth.compute_velmul(a_ic) if not psi_instead else 1
D2 = -3./7 * D1_0**2
@ -169,13 +170,12 @@ def whitify(density, L, cosmo, supergenerate=1, zero_fill=False, func='HU_WIGGLE
def write_icfiles(*generated_ic, **kwargs):
"""Write the initial conditions from the tuple returned by run_generation"""
supergenerate=1
supergenerate=kwargs.get('supergenerate', 1)
zero_fill=kwargs.get('zero_fill', False)
posx,vel,density,N,L,a_ic,cosmo = generated_ic
ct.simpleWriteGadget("Data/borg.gad", posx, velocities=vel, boxsize=L, Hubble=cosmo['h'], Omega_M=cosmo['omega_M_0'], time=a_ic)
for i,c in enumerate(["x","y","z"]):
for i,c in enumerate(["z","y","x"]):
ct.writeGrafic("Data/ic_velc%s" % c, vel[i].reshape((N,N,N)), L, a_ic, **cosmo)
ct.writeGrafic("Data/ic_deltab", density, L, a_ic, **cosmo)

13
python_sample/icgen/gen_ic_from_borg.py
View File

@ -1,6 +1,11 @@
import pyfftw
import numpy as np
import cosmotool as ct
import borgicgen as bic
import pickle
with file("wisdom") as f:
pyfftw.import_wisdom(pickle.load(f))
cosmo={'omega_M_0':0.3175, 'h':0.6711}
cosmo['omega_lambda_0']=1-cosmo['omega_M_0']
@ -9,11 +14,11 @@ cosmo['omega_B_0']=0.049
cosmo['SIGMA8']=0.8344
cosmo['ns']=0.9624
supergen=2
supergen=8
zstart=50
astart=1/69.#1/(1.+zstart)
astart=1/(1.+zstart)
halfPixelShift=False
zero_fill=True
zero_fill=False
if __name__=="__main__":
bic.write_icfiles(*bic.run_generation("initial_density_1380.dat", 0.001, astart, cosmo, supersample=1, shiftPixel=halfPixelShift, do_lpt2=False), supergenerate=supergen, zero_fill=zero_fill)
bic.write_icfiles(*bic.run_generation("initial_density_1872.dat", 0.001, astart, cosmo, supersample=1, shiftPixel=halfPixelShift, do_lpt2=False), supergenerate=supergen, zero_fill=zero_fill)

1
python_sample/ramsesToArray.py
View File

@ -8,6 +8,7 @@ s = ct.loadRamsesAll(sys.argv[1], int(sys.argv[2]), doublePrecision=True, loadVe
q = [p for p in s.getPositions()]
q += [p for p in s.getVelocities()]
q += [np.ones(q[0].size,dtype=q[0].dtype)]
q = np.array(q)
with h5.File("particles.h5", mode="w") as f:

2
sample/simple3DFilter.cpp
View File

@ -203,7 +203,7 @@ int main(int argc, char **argv)
bins, interpolated, getMass, rLimit2);
hdf5_write_array(out_f, "density", interpolated);
//out_f.flush();
for (int i = 0; i < 3; i++) {
for (int i = 0; i < 0; i++) {
computeInterpolatedField(&tree1, boxsize, Nres, cx, cy, cz,
bins, interpolated, boost::bind(getVelocity, _1, i), rLimit2);
hdf5_write_array(out_f, str(format("p%d") % i), interpolated);