mdwarf_hydro.py

"""
Dedalus script for full sphere anelastic convection,
using a Lane-Emden structure and internal heat source.
Designed for modelling fully-convective stars.

Usage:
    mdwarf_dynamo.py [options]

Options:
    --Ekman=<Ekman>                      Ekman number    [default: 1e-4]
    --ConvectiveRossbySq=<Co2>           Squared Convective Rossby = Ra*Ek**2/Pr [default: 1e-2]
    --Prandtl=<Prandtl>                  Prandtl number  [default: 1]
    --n_rho=<n_rho>                      Density scale heights [default: 3]

    --Ntheta=<Ntheta>                    Latitudinal modes [default: 32]
    --Nr=<Nr>                            Radial modes [default: 32]
    --dealias=<dealias>                  Degree of deailising   [default: 1.5]
    --mesh=<mesh>                        Processor mesh for 3-D runs; if not set a sensible guess will be made

    --benchmark                          Use benchmark initial conditions
    --spectrum                           Use a spectrum of benchmark perturbations
    --ell_benchmark=<ell_benchmark>      Integer value of benchmark perturbation m=+-ell [default: 3]

    --thermal_equilibrium                Start in thermal equilibrum

    --max_dt=<max_dt>                    Largest possible timestep [default: 0.25]
    --safety=<safety>                    CFL safety factor [default: 0.4]

    --run_time_sim=<run_time>            How long to run, in rotating time units
    --run_time_diffusion=<run_time_d>    How long to run, in diffusion time units
    --run_time_iter=<niter>              How long to run, in iterations

    --slice_dt=<slice_dt>                Cadence at which to output slices, in rotation times (P_rot = 4pi).  If not specified, a sensible guess based on sqrt(Co2) will be made.
    --scalar_dt=<scalar_dt>              Time between scalar outputs, in rotation times (P_rot = 4pi)

    --restart=<restart>                  Merged chechpoint file to restart from.
                                         Make sure "--label" is set to avoid overwriting the previous run.

    --violate_L_cons

    --label=<label>                      Additional label for run output directory

    --ncc_cutoff=<ncc_cutoff>            Amplitude to truncate NCC terms [default: 1e-10]
    --plot_sparse                        Plot sparsity structures for L+M and it's LU decomposition
"""
import logging
logger = logging.getLogger(__name__)
for system in ['matplotlib', 'h5py', 'evaluator', 'transposes', 'transforms']:
    dlog = logging.getLogger(system)
    dlog.setLevel(logging.WARNING)

import numpy as np
import sys
import h5py

from mpi4py import MPI

comm = MPI.COMM_WORLD
rank = comm.rank
ncpu = comm.size

from docopt import docopt
args = docopt(__doc__)

data_dir = sys.argv[0].split('.py')[0]
data_dir += '_Co{}_Ek{}_Pr{}'.format(args['--ConvectiveRossbySq'],args['--Ekman'],args['--Prandtl'])
data_dir += '_Th{}_R{}'.format(args['--Ntheta'], args['--Nr'])
if args['--thermal_equilibrium']:
    data_dir += '_therm'
if args['--violate_L_cons']:
    data_dir += '_badL'
if args['--benchmark']:
    data_dir += '_benchmark'
if args['--label']:
    data_dir += '_{:s}'.format(args['--label'])

import dedalus.tools.logging as dedalus_logging
dedalus_logging.add_file_handler(data_dir+'/logs/dedalus_log', 'DEBUG')

mesh = args['--mesh']
if mesh is not None:
    mesh = mesh.split(',')
    mesh = [int(mesh[0]), int(mesh[1])]
else:
    log2 = np.log2(ncpu)
    if log2 == int(log2):
        mesh = [int(2**np.ceil(log2/2)),int(2**np.floor(log2/2))]
logger.info("running on processor mesh={}".format(mesh))

Nθ = int(args['--Ntheta'])
Nr = int(args['--Nr'])
Nφ = Nθ*2

ncc_cutoff = float(args['--ncc_cutoff'])

n_rho = float(args['--n_rho'])
radius = 1

Ek = Ekman = float(args['--Ekman'])
Co2 = ConvectiveRossbySq = float(args['--ConvectiveRossbySq'])
Pr = Prandtl = float(args['--Prandtl'])

if args['--run_time_iter']:
    niter = int(float(args['--run_time_iter']))
else:
    niter = np.inf
if args['--run_time_sim']:
    run_time = float(args['--run_time_sim'])
elif args['--run_time_diffusion']:
    run_time = float(args['--run_time_diffusion'])*1/Ekman
else:
    run_time = np.inf

import dedalus.public as de
from dedalus.extras import flow_tools


logger.debug(sys.argv)
logger.debug('-'*40)
logger.info("saving data in {}".format(data_dir))
logger.info("Run parameters")
logger.info("Ek = {}, Co2 = {}, Pr = {}".format(Ek,Co2,Pr))

dealias = float(args['--dealias'])

c = de.SphericalCoordinates('phi', 'theta', 'r')
d = de.Distributor(c, mesh=mesh, dtype=np.float64)
b = de.BallBasis(c, shape=(Nφ,Nθ,Nr), radius=radius, dealias=dealias, dtype=np.float64)
b_S2 = b.S2_basis()
bk2 = b.clone_with(k=2)
bk1 = b.clone_with(k=1)

b_ncc = de.BallBasis(c, shape=(1,1,Nr), radius=radius, dealias=dealias, dtype=np.float64)
b_ncc_k2 = b_ncc.clone_with(k=2)
b_ncc_k1 = b_ncc.clone_with(k=1)

phi, theta, r = b.local_grids()

p = d.Field(name='p', bases=bk1)
s = d.Field(name='s', bases=b)
u = d.VectorField(c, name='u', bases=b)
τ_p = d.Field(name='τ_p')
τ_s = d.Field(name='τ_s', bases=b_S2)
τ_u = d.VectorField(c, name='τ_u', bases=b_S2)

# Parameters and operators
div = lambda A: de.Divergence(A, index=0)
lap = lambda A: de.Laplacian(A, c)
grad = lambda A: de.Gradient(A, c)
curl = lambda A: de.Curl(A)
dot = lambda A, B: de.DotProduct(A, B)
cross = lambda A, B: de.CrossProduct(A, B)
ddt = lambda A: de.TimeDerivative(A)
trans = lambda A: de.TransposeComponents(A)
radial = lambda A: de.RadialComponent(A)
angular = lambda A: de.AngularComponent(A, index=1)
trace = lambda A: de.Trace(A)
power = lambda A, B: de.Power(A, B)
lift_basis = b.clone_with(k=2)
lift = lambda A, n: de.Lift(A,lift_basis,n)
integ = lambda A: de.Integrate(A, c)
azavg = lambda A: de.Average(A, c.coords[0])
shellavg = lambda A: de.Average(A, c.S2coordsys)
avg = lambda A: de.Integrate(A, c)/(4/3*np.pi*radius**3)

# NCCs and variables of the problem
ex = d.VectorField(c, bases=b, name='ex')
ex['g'][2] = np.sin(theta)*np.cos(phi)
ex['g'][1] = np.cos(theta)*np.cos(phi)
ex['g'][0] = -np.sin(phi)
ey = d.VectorField(c, bases=b, name='ey')
ey['g'][2] = np.sin(theta)*np.sin(phi)
ey['g'][1] = np.cos(theta)*np.sin(phi)
ey['g'][0] = np.cos(phi)
ez = d.VectorField(c, name='ez', bases=b)
ez['g'][1] = -np.sin(theta)
ez['g'][2] =  np.cos(theta)
ez_g = de.Grid(ez).evaluate()
ez_g.name='ez_g'

x = d.Field(name='x', bases=b)
y = d.Field(name='y', bases=b)
z = d.Field(name='z', bases=b)
x['g'] = r*np.sin(theta)*np.cos(phi)
y['g'] = r*np.sin(theta)*np.sin(phi)
z['g'] = r*np.cos(theta)

r_cyl = d.VectorField(c, name='r_cyl', bases=b)
r_cyl['g'][2] =  r*np.sin(theta)
r_cyl['g'][1] = -r*np.cos(theta)

r_vec = d.VectorField(c, name='r_vec', bases=b)
r_vec['g'][2] = r
r_vec_g = de.Grid(r_vec).evaluate()

from structure import lane_emden
structure = lane_emden(Nr, n_rho=n_rho, m=1.5, comm=MPI.COMM_SELF)

T = d.Field(name='T', bases=b_ncc)
lnρ = d.Field(name='lnρ', bases=b_ncc)

if T['g'].size > 0 :
    # TO-DO: clean this up and make work for lane-emden solve in np.float64 rather than np.complex128
    for i, r_i in enumerate(r[0,0,:]):
         T['g'][:,:,i] = structure['T'](r=r_i).evaluate()['g'].real
         lnρ['g'][:,:,i] = structure['lnρ'](r=r_i).evaluate()['g'].real

T2 = d.Field(name='T2', bases=b_ncc_k2)
T.change_scales(1)
T2['g'] = T['g']

lnT = np.log(T).evaluate()
lnT.name='lnT'
grad_lnT = grad(lnT).evaluate()
grad_lnT.name='grad_lnT'
grad_lnT1 = d.VectorField(c,name='grad_lnT1', bases=b_ncc_k1)
grad_lnT.change_scales(1)
grad_lnT1['g'] = grad_lnT['g']
ρ = np.exp(lnρ).evaluate()
ρ.name='ρ'
ρ2 = d.Field(name='ρ2', bases=b_ncc_k2)
ρ.change_scales(1)
ρ2['g'] = ρ['g']
ρ1 = d.Field(name='ρ1', bases=b_ncc_k1)
ρ1['g'] = ρ['g']
grad_lnρ = grad(lnρ).evaluate()
grad_lnρ.name='grad_lnρ'
ρT = (ρ*T).evaluate()
ρT.name='ρT'
ρT2 = d.Field(name='ρT2', bases=b_ncc_k2)
ρT.change_scales(1)
ρT2['g'] = ρT['g']
ρT1 = d.Field(name='ρT1', bases=b_ncc_k1)
ρT1['g'] = ρT['g']

# Entropy source function, inspired from MESA model
def source_function(r):
    # from fits to MESA profile on r = [0,0.85]
    σ = 0.11510794072958948
    Q0_over_Q1 = 10.969517734412433
    # normalization from Brown et al 2020
    Q1 = σ**-2/(Q0_over_Q1 + 1) # normalize to σ**-2 at r=0
    logger.info("Source function: Q0/Q1 = {:}, σ = {:}, Q1 = {:}".format(Q0_over_Q1, σ, Q1))
    return (Q0_over_Q1*np.exp(-r**2/(2*σ**2)) + 1)*Q1

source_func = d.Field(name='S', bases=b)
source_func['g'] = source_function(r)
source = de.Grid(Ek/Pr*ρT*source_func).evaluate()
source.name='source'

#e = 0.5*(grad(u) + trans(grad(u)))
e = grad(u) + trans(grad(u))

ω = curl(u)
viscous_terms = (div(e) - 2/3*grad(div(u)))
trace_e = trace(e)
Phi = trace(dot(e, e)) - 1/3*(trace_e*trace_e)

m, ell, n = d.coeff_layout.local_group_arrays(b.domain, scales=1)
mask = (ell==1)*(n==0)
if args['--violate_L_cons']:
    mask = False

τ_L = d.VectorField(c, bases=b, name='τ_L')
τ_L.valid_modes[2] *= mask
τ_L.valid_modes[0] = False
τ_L.valid_modes[1] = False

#Problem
problem = de.IVP([p, u, s, τ_p, τ_u, τ_s, τ_L])
problem.add_equation((ρ*ddt(u) + ρ*grad(p) - Co2*ρT*grad(s) - Ek*viscous_terms + τ_L + lift(τ_u,-1),
                      -(ρ*dot(u, e)) + ρ*cross(u, ez_g) ) )
problem.add_equation((ρ*u, 0))
eq = problem.equations[-1]
eq['LHS'].valid_modes[2] *= mask
eq['LHS'].valid_modes[0] = False
eq['LHS'].valid_modes[1] = False

problem.add_equation((T*dot(grad_lnρ, u) + T*div(u) + τ_p, 0))
problem.add_equation((ρT*ddt(s) - Ek/Pr*T*(lap(s)+ dot(grad_lnT, grad(s))) + lift(τ_s,-1),
                      -(ρT*dot(u, grad(s))) + source + 1/2*Ek/Co2*Phi))
# Boundary conditions
problem.add_equation((radial(u(r=radius)), 0))
problem.add_equation((radial(angular(e(r=radius))), 0))
problem.add_equation((integ(p), 0))
problem.add_equation((s(r=radius), 0))
logger.info("Problem built")

logger.info("NCC expansions:")
for ncc in [ρ2, T, ρT, (T*grad_lnρ).evaluate(), (T*grad_lnT1).evaluate()]:
    logger.info("{}: {}".format(ncc, np.where(np.abs(ncc['c']) >= ncc_cutoff)[0].shape))

if args['--thermal_equilibrium']:
    logger.info("solving for thermal equilbrium")
    equilibrium = de.LBVP([s, τ_s])
    equilibrium.add_equation((-Ek/Pr*T*(lap(s)+ dot(grad_lnT1, grad(s))) + lift(τ_s,-1), source))
    equilibrium.add_equation((s(r=radius), 0))
    eq_solver = equilibrium.build_solver(ncc_cutoff=ncc_cutoff)
    eq_solver.solve()

# Solver
solver = problem.build_solver(de.SBDF2, ncc_cutoff=ncc_cutoff)

if args['--benchmark']:
    amp = 1e-1
    𝓁 = int(args['--ell_benchmark'])
    norm = 1/(2**𝓁*np.math.factorial(𝓁))*np.sqrt(np.math.factorial(2*𝓁+1)/(4*np.pi))
    s['g'] += amp*norm*r**𝓁*(1-r**2)*(np.cos(𝓁*phi)+np.sin(𝓁*phi))*np.sin(theta)**𝓁
    logger.info("benchmark run with perturbations at ell={} with norm={}".format(𝓁, norm))
elif args['--spectrum']:
    𝓁_min = 1
    for 𝓁 in np.arange(𝓁_min, int(args['--ell_benchmark'])+1):
        norm = 1/(2**𝓁*np.math.factorial(𝓁))*np.sqrt(np.math.factorial(2*𝓁+1)/(4*np.pi))
        s['g'] += amp*norm*r**𝓁*(1-r**2)*(np.cos(𝓁*phi)+np.sin(𝓁*phi))*np.sin(theta)**𝓁
    logger.info("bandwide run with perturbations at ell={}--{}".format(𝓁_min, 𝓁))
else:
    amp = 1e-5
    noise = d.Field(name='noise', bases=b)
    noise.fill_random('g', seed=42, distribution='standard_normal')
    noise.low_pass_filter(scales=0.25)
    noise.high_pass_filter(scales=0.125)
    s['g'] += amp*noise['g']*(1-r**2)

max_dt = float(args['--max_dt'])
dt = max_dt/10
if not args['--restart']:
    mode = 'overwrite'
else:
    write, dt = solver.load_state(args['--restart'])
    mode = 'append'

solver.stop_iteration = niter
solver.stop_sim_time = run_time

# Analysis
eφ = d.VectorField(c, bases=b)
eφ['g'][0] = 1
eθ = d.VectorField(c, bases=b)
eθ['g'][1] = 1
er = d.VectorField(c, bases=b)
er['g'][2] = 1

ur = dot(u, er)
uθ = dot(u, eθ)
uφ = dot(u, eφ)

ρ_cyl = d.Field(bases=b)
ρ_cyl['g'] = r*np.sin(theta)
Ωz = uφ/ρ_cyl # this is not ω_z; misses gradient terms; this is angular differential rotation.

u_fluc = u - azavg(ur)*er - azavg(uθ)*eθ - azavg(uφ)*eφ

KE = 0.5*ρ*dot(u,u)
DRKE = 0.5*ρ*(azavg(uφ)**2)
MCKE = 0.5*ρ*(azavg(ur)**2 + azavg(uθ)**2)
FKE = KE - DRKE - MCKE #0.5*dot(u_fluc, u_fluc)

PE = Co2*ρ*T*s
PE.name = 'PE'

L = cross(r_vec,ρ*u)
L.name='L'

enstrophy = dot(curl(u),curl(u))
enstrophy_fluc = dot(curl(u_fluc),curl(u_fluc))

Re2 = dot(u,u)*(ρ/Ek)**2
Re2_fluc = dot(u_fluc,u_fluc)*(ρ/Ek)**2

if args['--slice_dt']:
    slice_dt = float(args['--slice_dt'])
else:
    slice_dt = 10/np.sqrt(Co2)

if args['--scalar_dt']:
    scalar_dt = float(args['--scalar_dt'])
else:
    scalar_dt = 1/np.sqrt(Co2)

logger.debug('output cadences: slices = {:}, scalar_dt = {:}'.format(slice_dt, scalar_dt))

traces = solver.evaluator.add_file_handler(data_dir+'/traces', sim_dt=scalar_dt, max_writes=None, mode=mode)
traces.add_task(avg(KE), name='KE')
traces.add_task(avg(DRKE), name='DRKE')
traces.add_task(avg(MCKE), name='MCKE')
traces.add_task(avg(FKE), name='FKE')
traces.add_task(np.sqrt(avg(enstrophy)), name='Ro')
traces.add_task(np.sqrt(avg(Re2)), name='Re')
traces.add_task(np.sqrt(avg(enstrophy_fluc)), name='Ro_fluc')
traces.add_task(np.sqrt(avg(Re2_fluc)), name='Re_fluc')
traces.add_task(avg(PE), name='PE')
traces.add_task(integ(dot(L,ex)), name='Lx')
traces.add_task(integ(dot(L,ey)), name='Ly')
traces.add_task(integ(dot(L,ez)), name='Lz')
traces.add_task(integ(-x*div(L)), name='Λx')
traces.add_task(integ(-y*div(L)), name='Λy')
traces.add_task(integ(-z*div(L)), name='Λz')
traces.add_task(np.abs(τ_p), name='τ_p')
traces.add_task(shellavg(np.abs(τ_s)), name='τ_s')
traces.add_task(shellavg(np.sqrt(dot(τ_u,τ_u))), name='τ_u')
traces.add_task(shellavg(np.sqrt(dot(τ_L,τ_L))), name='τ_L')

slices = solver.evaluator.add_file_handler(data_dir+'/slices', sim_dt = slice_dt, max_writes = 10, mode=mode)
slices.add_task(s(theta=np.pi/2), name='s')
slices.add_task(enstrophy(theta=np.pi/2), name='enstrophy')
slices.add_task(azavg(Ωz), name='<Ωz>')
slices.add_task(azavg(s), name='<s>')
slices.add_task(shellavg(s), name='s(r)')
slices.add_task(shellavg(ρ*dot(er, u)*(p+0.5*dot(u,u))), name='F_h(r)')
slices.add_task(shellavg(ρ*dot(er, u)*dot(u,u)), name='F_KE(r)')
slices.add_task(shellavg(-Co2*Ek/Pr*T*dot(er, grad(s))), name='F_κ(r)')
slices.add_task(shellavg(Co2*source), name='F_source(r)')

coeffs = solver.evaluator.add_file_handler(data_dir+'/coeffs', sim_dt = slice_dt, max_writes = 10, mode=mode)
coeffs.add_task(ρ*u, name='ρu', layout='c')

report_cadence = 100
flow = flow_tools.GlobalFlowProperty(solver, cadence=report_cadence)
flow.add_property(Re2, name='Re2')
flow.add_property(enstrophy, name='Ro2')
flow.add_property(Re2_fluc, name='Re2_fluc')
flow.add_property(enstrophy_fluc, name='Ro2_fluc')
flow.add_property(KE, name='KE')
flow.add_property(PE, name='PE')
flow.add_property(dot(L,ez), name='Lz')
flow.add_property(np.abs(τ_s), name='|τ_s|')
flow.add_property(np.abs(τ_p), name='|τ_p|')
flow.add_property(np.sqrt(dot(τ_u,τ_u)), name='|τ_u|')
flow.add_property(np.sqrt(dot(τ_L,τ_L)), name='|τ_L|')

# CFL
cfl_safety_factor = float(args['--safety'])
CFL = flow_tools.CFL(solver, initial_dt=dt, cadence=1, safety=cfl_safety_factor, max_dt=max_dt, threshold=0.1)
CFL.add_velocity(u)

good_solution = True
vol = 4*np.pi/3
while solver.proceed and good_solution:
    dt = CFL.compute_timestep()
    if solver.iteration % report_cadence == 0 and solver.iteration > 0:
        KE_avg = flow.volume_integral('KE')/vol # volume average needs a defined volume
        E0 = flow.volume_integral('KE')/Ek**2 # integral rather than avg
        Re_avg = np.sqrt(flow.volume_integral('Re2')/vol)
        Ro_avg = np.sqrt(flow.volume_integral('Ro2')/vol)
        Re_fluc_avg = np.sqrt(flow.volume_integral('Re2_fluc')/vol)
        Ro_fluc_avg = np.sqrt(flow.volume_integral('Ro2_fluc')/vol)
        PE_avg = flow.volume_integral('PE')/vol
        Lz_avg = flow.volume_integral('Lz')/vol
        max_τ = np.max([flow.max('|τ_u|'), flow.max('|τ_s|'), flow.max('|τ_p|'), flow.max('|τ_L|')])
        max_τ_L = flow.max('|τ_L|')

        log_string = "iter: {:d}, dt={:.1e}, t={:.3e} ({:.2e})".format(solver.iteration, dt, solver.sim_time, solver.sim_time*Ek)
        log_string += ", KE={:.2e}, PE={:.2e}".format(KE_avg, PE_avg)
        log_string += ", Re={:.1e}/{:.1e}, Ro={:.1e}/{:.1e}".format(Re_avg, Re_fluc_avg, Ro_avg, Ro_fluc_avg)
        log_string += ", Lz={:.1e}, τ={:.1e},{:.1e}".format(Lz_avg, max_τ, max_τ_L)
        logger.info(log_string)
        good_solution = np.isfinite(E0)
    solver.step(dt)

solver.log_stats()
logger.debug("mode-stages/DOF = {}".format(solver.total_modes/(Nφ*Nθ*Nr)))