def getGasDensity(grid=None, ppar=None):
"""Calculates the total gas density distribution
Parameters
----------
grid : radmc3dGrid
An instance of the radmc3dGrid class containing the spatial and wavelength grid
ppar : dictionary
Dictionary containing all parameters of the model
Returns
-------
Returns the gas volume density in g/cm^3
"""
rhogas = np.zeros([grid.nx, grid.ny, grid.nz], dtype=np.float64) + 1e-20
xaxis = grid.x
yaxis = grid.y
zaxis = grid.z
nx = grid.nx
ny = grid.ny
nz = grid.nz
# for spherical coordinates
if ppar['crd_sys'] == 'sph':
for xx in range(nx):
for yy in range(ny):
xii = xaxis[xx] * np.sin(yaxis[yy])
zii = xaxis[xx] * abs(np.cos(yaxis[yy]))
# hii = ppar['H0'] * (xii / ppar['Rt'])**(ppar['qheight'])
hii = fneq.eq_taperheight(xii, ppar['Rt'], ppar['H0'],
ppar['qheight'], ppar['Router'], ppar['Hd'])
sigii = fneq.eq_sig(xii,ppar['mdisk'],ppar['Rinner'],ppar['Rt'],
ppar['Router'],ppar['sigp'],ppar['sigma_type'])
gdensii = sigii / (2.0*np.pi)**0.5 / hii * np.e**(-0.5*zii**2 / hii**2)
if gdensii < ppar['cutgdens']:
rhogas[xx,yy,:] = ppar['cutgdens']
else:
rhogas[xx,yy,:] = gdensii
# for cartesian coordinates
if ppar['crd_sys'] == 'car':
for xx in range(nx):
for yy in range(ny):
for zz in range(nz):
xii = (xaxis[xx]**2 + yaxis[yy]**2)**0.5
zii = abs(zaxis[yy])
#hii = ppar['H0'] * (xii / ppar['Rt'])**(ppar['qheight'])
hii = fneq.eq_taperheight(xii, ppar['Rt'], ppar['H0'],
ppar['qheight'], ppar['Router'], ppar['Hd'])
sigii = fneq.eq_sig(xii,ppar['mdisk'], ppar['Rinner'], ppar['Rt'],
ppar['Router'], ppar['sigp'], ppar['sigma_type'])
gdensii = sigii / (2.0*np.pi)**0.5 / hii * np.e**(-0.5*zii**2 / hii**2)
if gdensii < ppar['cutgdens']:
rhogas[xx,yy,zz] = ppar['cutgdens']
else:
rhogas[xx,yy,zz] = gdensii
return rhogas
def getGasDensity(grid=None, ppar=None):
"""Calculates the total gas density distribution
Parameters
----------
grid : radmc3dGrid
An instance of the radmc3dGrid class containing the spatial and wavelength grid
ppar : dictionary
Dictionary containing all parameters of the model
Returns
-------
Returns the gas volume density in g/cm^3
"""
mesh = np.meshgrid(grid.x, grid.y, grid.z, indexing='ij')
if ppar['crd_sys'] == 'sph':
rr = mesh[0]
tt = mesh[1]
pp = mesh[2]
xx = rr * np.sin(tt) * np.cos(pp)
yy = rr * np.sin(tt) * np.sin(pp)
zz = rr * np.cos(tt)
cyrr = np.sqrt(xx**2. + yy**2.)
elif ppar['crd_sys'] == 'car':
xx = mesh[0]
yy = mesh[1]
zz = mesh[2]
rr = np.sqrt(xx**2 + yy * 2 + zz**2)
cyrr = np.sqrt(xx**2 + yy**2)
else:
raise ValueError('crd_sys not specified')
hh = ppar['Ht'] * (cyrr / ppar['Rt'])**(ppar['qheight'])
sig_cyrr = fneq.eq_sig(cyrr, ppar['mdisk'], xx.min(), ppar['Rsig'],
xx.max(), ppar['sigp'], 1)
# armpart = getSpiral(cyrr, pp, ppar['Rspir'], ppar['bspir'], ppar['wspir'])
armpart = getSpiral(cyrr, grid.x, grid.y, grid.z, ppar['Rspir'],
ppar['bspir'], ppar['wspir'], ppar['pspir'],
ppar['Rend'])
gappart = getGap(cyrr, ppar['Rgap'], ppar['wgap'])
rhogas = sig_cyrr * armpart * gappart / np.sqrt(2. * np.pi) / hh * np.exp(
-0.5 * (zz / hh)**2)
vol = grid.getCellVolume()
sumd = rhogas * vol
rat = ppar['mdisk'] / sumd.sum()
rhogas = rhogas * rat
return rhogas
def getDustDensity(grid=None, ppar=None):
"""Calculates the dust density distribution
if given 2 dust grain species, then first one is for envelope, second one is for disk
if only 1 dust grain species, then used for both
Parameters
----------
grid : radmc3dGrid
An instance of the radmc3dGrid class containing the spatial and wavelength grid
ppar : dictionary
Dictionary containing all parameters of the model
Returns
-------
Returns the dust volume density in g/cm^3
"""
mesh = np.meshgrid(grid.x, grid.y, grid.z, indexing='ij')
if ppar['crd_sys'] == 'sph':
rr = mesh[0]
tt = mesh[1]
pp = mesh[2]
xx = rr * np.sin(tt) * np.cos(pp)
yy = rr * np.sin(tt) * np.sin(pp)
zz = rr * np.cos(tt)
cyrr = np.sqrt(xx**2. + yy**2.)
elif ppar['crd_sys'] == 'car':
xx = mesh[0]
yy = mesh[1]
zz = mesh[2]
rr = np.sqrt(xx**2 + yy*2 + zz**2)
cyrr = np.sqrt(xx**2 + yy**2)
else:
raise ValueError('crd_sys not specified')
# read dust grain information
op = dustopac.radmc3dDustOpac()
dinfo = op.readDustInfo()
ngs = len(dinfo['gsize'])
dweights = dinfo['dweights']
# create dust distribution
rhodust = np.zeros([grid.nx, grid.ny, grid.nz, ngs], dtype=np.float64)
# cavity
cavfac = DiskEqs.eqCavity(cyrr, zz, ppar)
# envelope component
rho_env3d = cyrr * 0
if ppar['envmode'] == 0: # Ulrich model
r2d = rr[:,:,0]
t2d = tt[:,:,0]
if ppar['dMenv'] >= 0:
GMR3 = natconst.gg * ppar['mstar'][0] * ppar['Rc']**3
dMenv = ppar['dMenv'] * natconst.ms / natconst.year
rhoRc = dMenv / (8.*np.pi) / np.sqrt(GMR3)
else:
rhoRc = ppar['rhoRc']
envdens2d = DiskEqs.eqEnvelopeDens(r2d, t2d, ppar['Rc'], rhoRc)
for ip in range(grid.nz):
rho_env3d[:,:,ip] = envdens2d
elif ppar['envmode'] == 1: # oblate model
rho_env3d = DiskEqs.eqOblateDens(cyrr, zz, ppar['rhoRc'], ppar['Rc'], ppar['eta'], ppar['envq_1'])
rho_env3d = rho_env3d * ppar['g2d'] * cavfac
# disk component
hh = fn_scaleheight(cyrr, ppar['Rt'], ppar['H0'], ppar['qheight'],
ppar['Rhouter'], 5., mode=ppar['hmode'])
sig_cyrr = fneq.eq_sig(cyrr, ppar['mdisk'], ppar['Rinner'], ppar['Rsig'],
ppar['Router'], ppar['sigp'], ppar['sigma_type'],
sigp2=ppar['sigp2'], sig0=ppar['sig0'])
rho_disk = sig_cyrr * 0
reg = hh > 0
rho_disk[reg] = sig_cyrr[reg] / np.sqrt(2.*np.pi) / hh[reg] * np.exp(-0.5*(zz[reg]/hh[reg])**2.)
rho_disk = rho_disk * ppar['g2d'] * cavfac
# decide on how to add it together
if ngs == 1:
rhodust[:,:,:,0] = rho_env3d + rho_disk
elif ngs == 2:
ig = 0 # first one for envelope
rhodust[:,:,:,ig] = rho_env3d
ig = 1 # second one for disk
rhodust[:,:,:,ig] = rho_disk
else:
# same for all?
# for ig in range(ngs):
# rhodust[:,:,:,ig] = (rho_env3d + rho_disk) * dweights[ig]
raise ValueError('number of grains can only be less than 2 for this model')
# flag out regions lower than cutgdens
reg = rhodust < (ppar['cutgdens'] * ppar['g2d'])
rhodust[reg] = ppar['cutgdens'] * ppar['g2d']
return rhodust
def getGasDensity(grid=None, ppar=None):
"""Calculates the total gas density distribution
Parameters
----------
grid : radmc3dGrid
An instance of the radmc3dGrid class containing the spatial and wavelength grid
ppar : dictionary
Dictionary containing all parameters of the model
Returns
-------
Returns the gas volume density in g/cm^3
"""
mesh = np.meshgrid(grid.x, grid.y, grid.z, indexing='ij')
if ppar['crd_sys'] == 'sph':
rr = mesh[0]
tt = mesh[1]
pp = mesh[2]
xx = rr * np.sin(tt) * np.cos(pp)
yy = rr * np.sin(tt) * np.sin(pp)
zz = rr * np.cos(tt)
cyrr = np.sqrt(xx**2. + yy**2.)
elif ppar['crd_sys'] == 'car':
xx = mesh[0]
yy = mesh[1]
zz = mesh[2]
rr = np.sqrt(xx**2 + yy*2 + zz**2)
cyrr = np.sqrt(xx**2 + yy**2)
else:
raise ValueError('crd_sys not specified')
rhogas = np.zeros([grid.nx, grid.ny, grid.nz], dtype=np.float64) + 1e-30
hh = fn_scaleheight(cyrr, ppar['Rt'], ppar['H0'], ppar['qheight'],
ppar['Rhouter'], 5., mode=ppar['hmode'])
sig_cyrr = fneq.eq_sig(cyrr, ppar['mdisk'], ppar['Rinner'], ppar['Rsig'],
ppar['Router'], ppar['sigp'], ppar['sigma_type'],
sigp2=ppar['sigp2'], sig0=ppar['sig0'])
reg = hh > 0
rhogas[reg] = sig_cyrr[reg] / np.sqrt(2.*np.pi) / hh[reg] * np.exp(-0.5*(zz[reg]/hh[reg])**2.)
# flag out regions with 0 scale height
reg = hh <= 0.
rhogas[reg] = ppar['cutgdens']
# include envelope
if ppar['envmode'] == 0: # Ulrich model
r2d = rr[:,:,0]
t2d = tt[:,:,0]
if ppar['dMenv'] >= 0:
GMR3 = natconst.gg * ppar['mstar'][0] * ppar['Rc']**3
dMenv = ppar['dMenv'] * natconst.ms / natconst.year
rhoRc = dMenv / (8.*np.pi) / np.sqrt(GMR3)
else:
rhoRc = ppar['rhoRc']
envdens2d = DiskEqs.eqEnvelopeDens(r2d, t2d, ppar['Rc'], rhoRc, envq_1=ppar['envq_1'])
for ip in range(grid.nz):
rhoin = rhogas[:,:,ip]
rhogas[:,:,ip] = rhogas[:,:,ip] + envdens2d
elif ppar['envmode'] == 1: # oblate model
rhogas = DiskEqs.eqOblateDens(cyrr, zz, ppar['rhoRc'], ppar['Rc'], ppar['eta'], ppar['envq_1'])
# cavity
fac = DiskEqs.eqCavity(cyrr, zz, ppar)
rhogas = rhogas * fac
# flag out regions lower than cutgdens
reg = rhogas < ppar['cutgdens']
rhogas[reg] = ppar['cutgdens']
return rhogas
def getDustDensity(grid=None, ppar=None):
"""Calculates the dust density distribution
Parameters
----------
grid : radmc3dGrid
An instance of the radmc3dGrid class containing the spatial and wavelength grid
ppar : dictionary
Dictionary containing all parameters of the model
Returns
-------
Returns the dust volume density in g/cm^3
"""
op = dustopac.radmc3dDustOpac()
dinfo = op.readDustInfo()
ngs = len(dinfo['gsize'])
rhodust = np.zeros([grid.nx, grid.ny, grid.nz, ngs], dtype=np.float64)
rhogas = getGasDensity(grid=grid, ppar=ppar)
if ppar['dosettle'] == 0:
for gg in range(ngs):
rhodust[:, :, :, gg] = rhogas * dinfo['dweights'][gg] * ppar['g2d']
else: # if we want to do dust settling
tgas = getGasTemperature(grid=grid, ppar=ppar)
if ppar['crd_sys'] == 'sph':
# need to interpolate the temperature to cartesian first
res = crd_trans.contSph2Cart(contSph=tgas[:,:,0], raxis=grid.x, ttaaxis=grid.y,
log=True, pad=ppar['cuttemp'], midplane=False)
tgas_xz = res['contCart']
tgas_x = res['xaxis']
tgas_z = res['zaxis']
tgas_zi = np.zeros([len(tgas_z)+1], dtype=np.float64)
tgas_zi[1:-1] = 0.5*(tgas_z[1:] + tgas_z[0:-1])
tgas_zi[0] = tgas_zi[1] - abs(tgas_zi[2]-tgas_zi[1])
tgas_zi[-1] = tgas_zi[-2] + abs(tgas_zi[-3]-tgas_zi[-2])
tgas_dz = tgas_zi[1:] - tgas_zi[0:-1]
res = crd_trans.contSph2Cart(contSph=rhogas[:,:,0], raxis=grid.x, ttaaxis=grid.y,
log=True, pad=ppar['cutgdens'], midplane=False)
rhogas_xz = res['contCart']
if ppar['crd_sys'] == 'car':
inx = np.argmin(yaxis)
reg = grid.x >= 0.0
tgas_xz = tgas[reg,inx,:]
tgas_x = grid.x[reg]
tgas_z = grid.z
tgas_zi = grid.zi
tgas_dz = tgas_zi[1:] - tgas_zi[0:-1]
rhogas_xz = rhogas[reg, inx, :]
sig_x = fneq.eq_sig(tgas_x,ppar['mdisk'], ppar['Rinner'], ppar['Rsig'],
ppar['Router'], ppar['sigp'], ppar['sigma_type'])
alphaxz = ppar['alpha'] + np.zeros(list(tgas_xz.shape), dtype=np.float64)
print('--calculating dust density--')
for gg in range(ngs):
print('.')
matdens = dinfo['matdens'][gg]
gsize = dinfo['gsize'][gg]
gam = ppar['gam']
dsig_x = sig_x * ppar['g2d'] * dinfo['dweights'][gg]
dustgg = dubrulle_settle(tgas_x, tgas_z, tgas_dz, tgas_xz, rhogas_xz, ppar['mstar'], dsig_x,
alphaxz, gam, matdens, gsize, cutdens=ppar['cutgdens']*ppar['g2d']*dinfo['dweights'][gg])
if ppar['crd_sys'] == 'sph':
dust_slice = crd_trans.contCart2Sph(contCart=dustgg, xaxis=tgas_x, zaxis=tgas_z, raxis=grid.x,
ttaaxis=grid.y, log=True, pad=ppar['cutgdens']*ppar['g2d']*dinfo['dweights'][gg])
for zz in range(grid.nz):
rhodust[:,:,zz,gg] = dust_slice['contSph']
if ppar['crd_sys'] == 'car':
finterp = interpolate.interp2d(tgas_x, tgas_z, np.log(dustgg), kind='cubic',
fill_value=np.log(ppar['cutgdens']))
for xx in range(grid.nx):
for yy in range(grid.ny):
rii = np.sqrt(xaxis[xx]**2 + yaxis[yy]**2)
rhodust[xx,yy,:,gg] = np.exp(finterp(np.array([rii]), zaxis))
return rhodust
def getGasDensity(grid=None, ppar=None, walls=False):
"""Calculates the total gas density distribution
Parameters
----------
grid : radmc3dGrid
An instance of the radmc3dGrid class containing the spatial and wavelength grid
ppar : dictionary
Dictionary containing all parameters of the model
Returns
-------
Returns the gas volume density in g/cm^3
"""
if walls is False:
xaxis = grid.x; nx = grid.nx
yaxis = grid.y; ny = grid.ny
zaxis = grid.z; nz = grid.nz
else:
xaxis = grid.xi; nx = grid.nxi
yaxis = grid.yi; ny = grid.nyi
zaxis = grid.zi; nz = grid.nzi
rhogas = np.zeros([nx, ny, nz], dtype=np.float64) + 1e-30
if ppar['dohydroeq'] == 0:
if ppar['crd_sys'] == 'sph':
for xx in range(nx):
for yy in range(ny):
xii = xaxis[xx] * np.sin(yaxis[yy])
zii = xaxis[xx] * abs(np.cos(yaxis[yy]))
# hii = ppar['H0'] * (xii / ppar['Rt'])**(ppar['qheight'])
hii = fneq.eq_taperheight(xii, ppar['Rt'], ppar['H0'],
ppar['qheight'], ppar['Router'], ppar['Hd'])
sigii = fneq.eq_sig(xii,ppar['mdisk'],ppar['Rinner'],ppar['Rsig'],
ppar['Router'],ppar['sigp'],ppar['sigma_type'])
gdensii = sigii / (2.0*np.pi)**0.5 / hii * np.exp(-0.5*(zii/hii)**2)
if gdensii < ppar['cutgdens']:
rhogas[xx,yy,:] = ppar['cutgdens']
else:
rhogas[xx,yy,:] = gdensii
if ppar['crd_sys'] == 'car':
for xx in range(nx):
for yy in range(ny):
for zz in range(nz):
xii = (xaxis[xx]**2 + yaxis[yy]**2)**0.5
zii = abs(zaxis[yy])
#hii = ppar['H0'] * (xii / ppar['Rt'])**(ppar['qheight'])
hii = fneq.eq_taperheight(xii, ppar['Rt'], ppar['H0'],
ppar['qheight'], ppar['Router'], ppar['Hd'])
sigii = fneq.eq_sig(xii,ppar['mdisk'], ppar['Rinner'], ppar['Rsig'],
ppar['Router'], ppar['sigp'], ppar['sigma_type'])
gdensii = sigii / (2.0*np.pi)**0.5 / hii * np.exp(-0.5*(zii/hii)**2)
if gdensii < ppar['cutgdens']:
rhogas[xx,yy,zz] = ppar['cutgdens']
else:
rhogas[xx,yy,zz] = gdensii
else: #if want to do hydo equilibrium
tgas = getGasTemperature(grid=grid, ppar=ppar)
if ppar['crd_sys'] == 'sph':
# need to interpolate the temperature to cartesian first
res = crd_trans.contSph2Cart(contSph=tgas[:,:,0], raxis=grid.x, ttaaxis=grid.y,
log=True, pad=ppar['cuttemp'], midplane=False)
tgas_xz = res['contCart']
tgas_x = res['xaxis']
tgas_z = res['zaxis']
tgas_zi = np.zeros([len(tgas_z)+1], dtype=np.float64)
tgas_zi[1:-1] = 0.5*(tgas_z[1:] + tgas_z[0:-1])
tgas_zi[0] = tgas_zi[1] - abs(tgas_zi[2]-tgas_zi[1])
tgas_zi[-1] = tgas_zi[-2] + abs(tgas_zi[-3]-tgas_zi[-2])
if ppar['crd_sys'] == 'car':
inx = np.argmin(yaxis)
reg = grid.x >= 0.0
tgas_xz = tgas[reg,inx,:]
tgas_x = grid.x[reg]
tgas_z = grid.z
tgas_zi = grid.zi
sig_x = fneq.eq_sig(tgas_x,ppar['mdisk'], ppar['Rinner'], ppar['Rsig'],
ppar['Router'], ppar['sigp'], ppar['sigma_type'])
rhogasxz = hydro_xz(tgas_x, tgas_zi, tgas_z, sig_x, tgas_xz, ppar['mstar'], ppar['cutgdens'])
if ppar['crd_sys'] == 'sph':
rhogas_slice = crd_trans.contCart2Sph(contCart=rhogasxz, xaxis=tgas_x, zaxis=tgas_z, raxis=xaxis, ttaaxis=yaxis,
log=True, pad=ppar['cutgdens'])
for zz in range(nz):
rhogas[:,:,zz] = rhogas_slice['contSph']
if ppar['crd_sys'] == 'car':
finterp = interpolate.interp2d(tgas_x, tgas_z, np.log(rhogasxz), kind='cubic', fill_value=np.log(ppar['cutgdens']))
for xx in range(nx):
for yy in range(ny):
rii = np.sqrt(xaxis[xx]**2 + yaxis[yy]**2)
rhogas[xx,yy,:] = np.exp(finterp(np.array([rii]), zaxis))
return rhogas
def getGasDensity(grid=None, ppar=None):
"""Calculates the total gas density distribution
Parameters
----------
grid : radmc3dGrid
An instance of the radmc3dGrid class containing the spatial and wavelength grid
ppar : dictionary
Dictionary containing all parameters of the model
Returns
-------
Returns the gas volume density in g/cm^3
"""
mesh = np.meshgrid(grid.x, grid.y, grid.z, indexing='ij')
if ppar['crd_sys'] == 'sph':
rr = mesh[0]
tt = mesh[1]
pp = mesh[2]
xx = rr * np.sin(tt) * np.cos(pp)
yy = rr * np.sin(tt) * np.sin(pp)
zz = rr * np.cos(tt)
cyrr = np.sqrt(xx**2. + yy**2.)
elif ppar['crd_sys'] == 'car':
xx = mesh[0]
yy = mesh[1]
zz = mesh[2]
rr = np.sqrt(xx**2 + yy*2 + zz**2)
cyrr = np.sqrt(xx**2 + yy**2)
else:
raise ValueError('crd_sys not specified')
rhogas = np.zeros([grid.nx, grid.ny, grid.nz], dtype=np.float64) + 1e-30
hh = fn_scaleheight(cyrr, ppar['Rt'], ppar['H0'], ppar['qheight'],
ppar['Router'], ppar['Hd'], mode=ppar['hmode'])
sig_cyrr = fneq.eq_sig(cyrr, ppar['mdisk'], ppar['Rinner'], ppar['Rsig'],
ppar['Router'], ppar['sigp'], ppar['sigma_type'])
reg = hh > 0
rhogas[reg] = sig_cyrr[reg] / np.sqrt(2.*np.pi) / hh[reg] * np.exp(-0.5*(zz[reg]/hh[reg])**2.)
# flag out regions with 0 scale height
reg = hh <= 0.
rhogas[reg] = ppar['cutgdens']
# include envelope
if ppar['envrho0'] > 0:
r2d = rr[:,:,0]
t2d = tt[:,:,0]
# envdens2d = DiskEqs.eqEnvelopeDens(r2d, t2d, ppar['Rrot'], ppar['envrho0'])
envdens2d = ppar['envrho0'] / (1. + (r2d/ppar['Rrot'])**(ppar['envalph']))
for ip in range(grid.nz):
rhogas[:,:,ip] = rhogas[:,:,ip] + envdens2d
# flag out regions lower than cutgdens
reg = rhogas < ppar['cutgdens']
rhogas[reg] = ppar['cutgdens']
""" old stuff
# for spherical coordinates
if ppar['crd_sys'] == 'sph':
for xx in range(nx):
for yy in range(ny):
xii = xaxis[xx] * np.sin(yaxis[yy])
zii = xaxis[xx] * abs(np.cos(yaxis[yy]))
# hii = ppar['H0'] * (xii / ppar['Rt'])**(ppar['qheight'])
hii = fneq.eq_taperheight(xii, ppar['Rt'], ppar['H0'],
ppar['qheight'], ppar['Router'], ppar['Hd'])
sigii = fneq.eq_sig(xii,ppar['mdisk'],ppar['Rinner'],ppar['Rt'],
ppar['Rsig'],ppar['sigp'],ppar['sigma_type'])
if hii > 1e-90:
gdensii = sigii / (2.0*np.pi)**0.5 / hii * np.exp(-0.5*(zii/hii)**2)
else:
gdensii = ppar['cutgdens']
if gdensii < ppar['cutgdens']:
rhogas[xx,yy,:] = ppar['cutgdens']
else:
rhogas[xx,yy,:] = gdensii
"""
return rhogas