def write_snapshot(self,disk,disk_mesh,filename="disk.dat.hdf5",time=0):
Ngas = self.pos.shape[0]
f=ws.openfile(filename)
npart=np.array([Ngas,0,0,0,0,0], dtype="uint32")
massarr=np.array([0,0,0,0,0,0], dtype="float64")
header=ws.snapshot_header(npart=npart, nall=npart, massarr=massarr, time=time,
boxsize=disk_mesh.BoxSize, double = np.array([1], dtype="int32"))
ws.writeheader(f, header)
ws.write_block(f, "POS ", 0, self.pos)
ws.write_block(f, "VEL ", 0, self.vel)
ws.write_block(f, "MASS", 0, self.dens)
ws.write_block(f, "U ", 0, self.utherm)
ws.write_block(f, "ID ", 0, self.ids)
ws.closefile(f)
def write_snapshot(self,
disk,
disk_mesh,
filename="disk.dat.hdf5",
time=0):
Ngas = self.pos.shape[0]
f = ws.openfile(filename)
npart = np.array([Ngas, 0, 0, 0, 0, 0], dtype="uint32")
massarr = np.array([0, 0, 0, 0, 0, 0], dtype="float64")
header = ws.snapshot_header(npart=npart,
nall=npart,
massarr=massarr,
time=time,
boxsize=disk_mesh.BoxSize,
double=np.array([1], dtype="int32"))
ws.writeheader(f, header)
ws.write_block(f, "POS ", 0, self.pos)
ws.write_block(f, "VEL ", 0, self.vel)
ws.write_block(f, "MASS", 0, self.dens)
ws.write_block(f, "U ", 0, self.utherm)
ws.write_block(f, "ID ", 0, self.ids)
ws.closefile(f)
utherm = np.append(utherm,press_background/dens_background/(GAMMA-1))
UTHERM_BACKGROUND = (press_background/dens_background/(GAMMA-1)).min()
dens_gas[dens_gas < DENSITY_FLOOR] = DENSITY_FLOOR
N_total = N_gas + N_BACKGROUND
ids = np.append(ids,np.arange(N_gas+1,N_total+1))
print "done"
N_gas = N_total
##########################################################
print "Writing snapshot..."
f=ws.openfile(ic_filename+".hdf5")
ws.write_block(f, "POS ", 0, np.array([x_gas,y_gas,z_gas]).T)
ws.write_block(f, "VEL ", 0, np.array([vx_gas,vy_gas,vz_gas]).T)
ws.write_block(f, "U ", 0, utherm)
if (relax_density):
ws.write_block(f, "MASS", 0, dens_gas)
else:
ws.write_block(f, "MASS", 0, mass)
ws.write_block(f, "ID ", 0, ids)
if not (ExternalPotential):
print "Adding central star..."
if(add_background):
ws.write_block(f, "POS ", 4, np.array([BOX_WIDTH * 0.5, BOX_WIDTH * 0.5, BOX_HEIGHT * 0.5]).T)
else:
accel = 1.0 / radius**2
if (mesh_type == "polar"):
cellsize = 2.0*np.pi*radius/Ntheta
elif (mesh_type == "rings"):
cellsize = 2.0*np.pi*inner_rad/N_in
timestep = np.minimum(CourantFac*cellsize/csnd,ErrTolIntAccuracy*np.sqrt(cellsize/accel))
timestep_nbin=np.log10(MaxSizeTimestep/MinSizeTimestep)/np.log10(2.0)
timestep_bins = 2.0**np.linspace(np.log10(MinSizeTimestep)/np.log10(2.0),np.log10(MaxSizeTimestep)/np.log10(2.0),timestep_nbin)
hist=np.histogram(timestep,bins=timestep_bins)
print hist
Ngas = pos.shape[0]
print "shape",pos.shape, vel.shape,dens.shape,ids.shape
f=ws.openfile("disk.dat.hdf5")
npart=np.array([Ngas,0,0,0,0,0], dtype="uint32")
massarr=np.array([0,0,0,0,0,0], dtype="float64")
header=ws.snapshot_header(npart=npart, nall=npart, massarr=massarr,
boxsize=BoxX, double = np.array([1], dtype="int32"))
ws.writeheader(f, header)
ws.write_block(f, "POS ", 0, pos)
ws.write_block(f, "VEL ", 0, vel)
ws.write_block(f, "MASS", 0, dens)
ws.write_block(f, "U ", 0, u)
ws.write_block(f, "ID ", 0, ids)
ws.closefile(f)
R_edge=2.5
#plt.plot(radius,dens,'ro',ms=0.8,mew=0.0)
#plt.plot(radius[np.argsort(radius)],densprofile,color='b',ms=0.8,mew=0.0)
#plt.axis([0,20,0,0.001])
#plt.plot(radius,vphi,'ro',ms=0.8,mew=0.0)
#plt.plot(radius[np.argsort(radius)],np.sqrt(vphiprofilesq),color='b',ms=0.8,mew=0.0)
#plt.axis([0,20,0,1.5])
#plt.show()
#write to disk the "fixed" snapshot
Ngas = pos.shape[0]
filename_fixed = base + "snap_fixed_" + str(num).zfill(3) + ".hdf5"
f = ws.openfile(filename_fixed)
npart = np.array([Ngas, 0, 0, 0, 0, 0], dtype="uint32")
massarr = np.array([0, 0, 0, 0, 0, 0], dtype="float64")
header = ws.snapshot_header(npart=npart,
nall=npart,
massarr=massarr,
time=time,
boxsize=BoxX,
double=np.array([1], dtype="int32"))
ws.writeheader(f, header)
ws.write_block(f, "POS ", 0, pos)
ws.write_block(f, "VEL ", 0, vel)
ws.write_block(f, "MASS", 0, mass)
ws.write_block(f, "RHO ", 0, dens)
ws.write_block(f, "U ", 0, u)
#plt.plot(radius,dens,'ro',ms=0.8,mew=0.0)
#plt.plot(radius[np.argsort(radius)],densprofile,color='b',ms=0.8,mew=0.0)
#plt.axis([0,20,0,0.001])
#plt.plot(radius,vphi,'ro',ms=0.8,mew=0.0)
#plt.plot(radius[np.argsort(radius)],np.sqrt(vphiprofilesq),color='b',ms=0.8,mew=0.0)
#plt.axis([0,20,0,1.5])
#plt.show()
#write to disk the "fixed" snapshot
Ngas = pos.shape[0]
filename_fixed =base+"snap_fixed_"+str(num).zfill(3)+".hdf5"
f=ws.openfile(filename_fixed)
npart=np.array([Ngas,0,0,0,0,0], dtype="uint32")
massarr=np.array([0,0,0,0,0,0], dtype="float64")
header=ws.snapshot_header(npart=npart, nall=npart, massarr=massarr,time=time,
boxsize=BoxX, double = np.array([1], dtype="int32"))
ws.writeheader(f, header)
ws.write_block(f, "POS ", 0, pos)
ws.write_block(f, "VEL ", 0, vel)
ws.write_block(f, "MASS", 0, mass)
ws.write_block(f, "RHO ", 0, dens)
ws.write_block(f, "U ", 0, u)
ws.write_block(f, "ID ", 0, ids)
ws.write_block(f, "VOL ", 0, vol)
ws.closefile(f)