def heatcond(src, dst, key, par, gd, l1, l2, m1, m2, n1, n2, nghost):
if key == "hcond":
n1shift,n2shift,m1shift,m2shift,l1shift,l2shift=der_limits(
n1,n2,m1,m2,l1,l2,nghost)
if "tt" in dst["data"].keys():
tt = dst["data/tt"][n1shift,n2shift,m1shift,m2shift,l1shift,l2shift]
else:
calc_derived_data(src["data"], dst["data"], "tt", par,
gd, l1, l2, m1, m2, n1, n2, nghost)
tt = dst["data/tt"][n1shift,n2shift,m1shift,m2shift,l1shift,l2shift]
lntt = np.log(dst["data/tt"][n1shift,n2shift,m1shift,m2shift,l1shift,l2shift])
gradlnT = grad(lntt,grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
del2T = del2(tt,grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
if "rho" in src["data"].keys():
lnrho = np.log(src["rho"][n1shift,n2shift,m1shift,m2shift,l1shift,l2shift])
gradlnrho = grad(lnrho,grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
lrho = True
elif "lnrho" in src["data"].keys():
lnrho = src["lnrho"][n1shift,n2shift,m1shift,m2shift,l1shift,l2shift]
gradlnrho = grad(lnrho,grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
lrho = True
else:
lrho = False
var = par.cp*par.chi*del2T/tt
if lrho:
var += par.cp*par.chi*dot(gradlnrho,gradlnT)
n1r,m1r,l1r = under_limits(n1,m1,l1,n1shift,m1shift,l1shift,nghost)
return var[n1r:n2-n1+n1r,m1r:m2-m1+m1r,l1r:l2-l1+l1r]
def advec_heat(src, dst, key, par, gd, l1, l2, m1, m2, n1, n2, nghost):
if key == "hadvec":
n1shift,n2shift,m1shift,m2shift,l1shift,l2shift=der_limits(
n1,n2,m1,m2,l1,l2,nghost)
uu = np.array([
src["data/ux"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift],
src["data/uy"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift],
src["data/uz"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift]
])
if "ss" in dst["data"].keys():
ss = src["ss"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift]
sgrad = grad(ss,grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
if "tt" in dst["data"].keys():
tt = dst["tt"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift]
else:
calc_derived_data(src["data"], dst["data"], "tt", par,
gd, l1, l2, m1, m2, n1, n2, nghost)
tt = dst["data/tt"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift]
if "rho" in dst["data"].keys():
rho = src["data/rho"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift]
elif "lnrho" in dst["data"].keys():
rho = np.exp(src["data/lnrho"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift])
else:
rho=1
advec = -dot(uu,sgrad)/(rho*tt)
n1r,m1r,l1r = under_limits(n1,m1,l1,n1shift,m1shift,l1shift,nghost)
return advec[n1r:n2-n1+n1r,m1r:m2-m1+m1r,l1r:l2-l1+l1r]
def visc_heat(src, dst, key, par, gd, l1, l2, m1, m2, n1, n2, nghost):
if key == "hvisc":
th1 = 1./3
n1shift,n2shift,m1shift,m2shift,l1shift,l2shift=der_limits(
n1,n2,m1,m2,l1,l2,nghost)
uu = np.array([
src["data/ux"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift],
src["data/uy"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift],
src["data/uz"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift]
])
tmp0 = grad(uu[0],grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
tmp1 = grad(uu[1],grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
tmp2 = grad(uu[2],grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
var = tmp0[1]**2
var += tmp0[2]**2
var += tmp1[2]**2
if "tt" in dst["data"].keys():
tt = dst["tt"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift]
else:
calc_derived_data(src["data"], dst["data"], "tt", par,
gd, l1, l2, m1, m2, n1, n2, nghost)
tt = dst["data/tt"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift]
var *= 2*par.nu*var/tt
n1r,m1r,l1r = under_limits(n1,m1,l1,n1shift,m1shift,l1shift,nghost)
return var[n1r:n2-n1+n1r,m1r:m2-m1+m1r,l1r:l2-l1+l1r]
def resistive(src, dst, key, par, gd, l1, l2, m1, m2, n1, n2, nghost):
if key == "etadel2a":
n1shift,n2shift,m1shift,m2shift,l1shift,l2shift=der_limits(
n1,n2,m1,m2,l1,l2,nghost)
if "ax" in src["data"].keys():
aa = np.array([
src["data/ax"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift],
src["data/ay"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift],
src["data/az"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift]
])
if par.eta == 0.:
print("no resistivity used setting etadel2a=0 in resistive")
var = np.zeros_like(aa)
else:
var = par.eta*del2(aa, gd.dx, gd.dy, gd.dz,x=gd.x[l1shift:l2shift],y=gd.y[m1shift:m2shift],coordinate_system=par.coord_system)
else:
print("no vector potential for resistive calculation")
for key in src["data"].keys():
if len(src["data"][key].shape) == 3:
var = np.zeros([3,src["data"][key].shape[0],
src["data"][key].shape[1],
src["data"][key].shape[2] ])
break
n1r,m1r,l1r = under_limits(n1,m1,l1,n1shift,m1shift,l1shift,nghost)
return var[:,n1r:n2-n1+n1r,m1r:m2-m1+m1r,l1r:l2-l1+l1r]
def curletadel2a(src, dst, key, par, gd, l1, l2, m1, m2, n1, n2, nghost):
if key == "curletadel2a":
n1shift,n2shift,m1shift,m2shift,l1shift,l2shift=der_limits(
n1,n2,m1,m2,l1,l2,nghost)
if "etadel2a" in dst["calc"].keys():
tmp = dst["calc/etadel2a"][:,n1shift:n2shift,
m1shift:m2shift,
l1shift:l2shift]
else:
tmp = induction(src, dst, "etadel2a", par, gd, n1shift, n2shift,
m1shift, m2shift, l1shift, l2shift, nghost)
var = curl(tmp, gd.dx, gd.dy, gd.dz,x=gd.x[l1shift:l2shift],y=gd.y[m1shift:m2shift],coordinate_system=par.coord_system)
n1r,m1r,l1r = under_limits(n1,m1,l1,n1shift,m1shift,l1shift,nghost)
return var[:,n1r:n2-n1+n1r,m1r:m2-m1+m1r,l1r:l2-l1+l1r]
def rostrain(src, dst, key, par, gd, l1, l2, m1, m2, n1, n2, nghost):
if key == "fvisc":
n1shift,n2shift,m1shift,m2shift,l1shift,l2shift=der_limits(
n1,n2,m1,m2,l1,l2,nghost)
if par.nu > 0:
uu = np.array([
src["data/ux"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift],
src["data/uy"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift],
src["data/uz"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift]
])
#viscous forces
th2 = 2./3
th1 = 1./3
fvisc = np.zeros_like(uu)
del2u = np.zeros_like(uu)
for j in range(0,3):
del2u[j] = del2(uu[j],gd.dx,gd.dy,gd.dz,x=gd.x[l1shift:l2shift],y=gd.y[m1shift:m2shift],coordinate_system=par.coord_system)
fvisc += param.nu*del2u
del(del2u)
divu = div(uu,grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
graddivu = grad(divu,grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
fvisc += th1*par.nu*graddivu
del(graddivu)
if "rho" in src["data"].keys():
lnrho = np.log(src["data/rho"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift])
lrho = True
elif "lnrho" in src["data"].keys():
lnrho = src["data/lnrho"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift]
lrho = True
else:
lrho = False
if lrho:
tmp0 = grad(uu[0],grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
tmp1 = grad(uu[1],grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
tmp2 = grad(uu[2],grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
gradlnrho = grad(lnrho,grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
Sglnrho = np.zeros_like(uu)
Sglnrho[0] = dot(tmp0,gradlnrho) +\
(tmp0[0]+tmp1[0]+tmp2[0]-th2*divu)*gradlnrho[0]
Sglnrho[1] = dot(tmp1,gradlnrho) +\
(tmp0[1]+tmp1[1]+tmp2[1]-th2*divu)*gradlnrho[1]
Sglnrho[2] = dot(tmp2,gradlnrho) +\
(tmp0[2]+tmp1[2]+tmp2[2]-th2*divu)*gradlnrho[2]
fvisc += par.nu*Sglnrho
del(gradlnrho,Sglnrho)
del(divu)
n1r,m1r,l1r = under_limits(n1,m1,l1,n1shift,m1shift,l1shift,nghost)
return fvisc[:,n1r:n2-n1+n1r,m1r:m2-m1+m1r,l1r:l2-l1+l1r]
def advec_force(src, dst, key, par, gd, l1, l2, m1, m2, n1, n2, nghost):
if key == "uadvec":
n1shift,n2shift,m1shift,m2shift,l1shift,l2shift=der_limits(
n1,n2,m1,m2,l1,l2,nghost)
uu = np.array([
src["data/ux"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift],
src["data/uy"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift],
src["data/uz"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift]
])
tmp0 = grad(uu[0],grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
tmp1 = grad(uu[1],grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
tmp2 = grad(uu[2],grid.dx,grid.dy,grid.dz,x=grid.x[l1shift:l2shift],y=grid.y[m1shift:m2shift],coordinate_system=param.coord_system)
advec = np.zeros_like(uu)
advec[0] = -dot(uu,tmp0)
advec[1] = -dot(uu,tmp1)
advec[2] = -dot(uu,tmp2)
del(tmp0,tmp1,tmp2)
n1r,m1r,l1r = under_limits(n1,m1,l1,n1shift,m1shift,l1shift,nghost)
return advec[:,n1r:n2-n1+n1r,m1r:m2-m1+m1r,l1r:l2-l1+l1r]
def gradp(src, dst, key, par, gd, l1, l2, m1, m2, n1, n2, nghost):
if key == "gradp":
n1shift,n2shift,m1shift,m2shift,l1shift,l2shift=der_limits(
n1,n2,m1,m2,l1,l2,nghost)
if "pp" in dst["data"].keys():
pp = dst["data/pp"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift]
else:
calc_derived_data(src["data"], dst["data"], "pp", par,
gd, l1, l2, m1, m2, n1, n2, nghost)
pp = dst["data/pp"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift]
var = -grad(pp, gd.dx, gd.dy, gd.dz,x=gd.x[l1shift:l2shift],y=gd.y[m1shift:m2shift],coordinate_system=par.coord_system)
if "rho" in src["data"].keys():
rho = dst["data/rho"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift]
elif "lnrho" in src["data"].keys():
rho = np.exp(dst["data/lnrho"][n1shift:n2shift,m1shift:m2shift,l1shift:l2shift])
else:
rho = 1.
var /= rho
n1r,m1r,l1r = under_limits(n1,m1,l1,n1shift,m1shift,l1shift,nghost)
return var[:,n1r:n2-n1+n1r,m1r:m2-m1+m1r,l1r:l2-l1+l1r]