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Slope_Tracer.py
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Slope_Tracer.py
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"""
Dedalus scripts for 2D tracer advection-diffusion on a slope
This code uses a Fourier basis in the y direction with periodic boundary
conditions.
The functions can be ran serially or in parallel, and uses the built-in analysis
framework to save data snapshots in HDF5 files.
"""
import numpy as np
import h5py
import matplotlib
import shutil
import time
import matplotlib.pyplot as plt
from mpi4py import MPI
from scipy.special import erf
import os
from IPython import display
from dedalus import public as de
from dedalus.extras import flow_tools
from dedalus.tools import post
import pathlib
from dedalus.extras import plot_tools
import obsfit1d
import logging
logger = logging.getLogger(__name__)
# Default parameters ------------------------------------------------------------------------
# Input Grids
Ly, Lz = (1500000., 3000.) # units = 1m
ny, nz = (384, 192)
# Physical parameters
N2 = 1.0e-6
slope = 1/400.0
Prv0 = 1.0 # upslope Pr (in q0)
SPru0i = 0.0 # across-slope (S*Pru0)^(-1) (interior db/dz reduction)
Kinf = 1.0e-5
K0 = 1.0e-3
d = 500.0
Kred = 0 # 1 = reduce to zero at bottom with scale Kreds, 0 = don't.
Kreds = 0.5 # scale of exponential reduction (units of q0^{-1}).
AH = 0.0
AHvar = 1 # 1 = Reduced in BBL, 0 = Constant
AHfull = 0 # 0 = horizontal diffusion, 1 = along-isopycnal diffusion
# Initial tracer parameters
trItype = 1 # 1 = point, 2 = layer
z0 = 0.5 # units of d
sz0 = 3. # units of Lz/nz
c0 = 0.5 # units of Ly (point only)
sy0 = 3. # units of Ly/ny (point only)
mny0 = 0. # units of Ly (layer only)
mxy0 = 1. # units of Ly (layer only)
# Advection type
ADV = 2
# Timing information
lday = 1.0e5 # A "long-day" unit (86400 ~= 100000)
dt=8*lday
Ttot = 3200
sfreq = 2
accept_list = ['Ly','Lz','ny','nz','N2','slope','Prv0','SPru0i',
'Kinf','K0','d','AH','AHvar','AHfull','trItype','z0','sz0',
'c0','sy0','mxy0','mny0','ADV','lday','dt',
'Ttot','sfreq','Kred','Kreds']
default_input_dict = {}
for i in accept_list:
exec('default_input_dict[i] = %s' % i)
# Run a simulation -----------------------------------------------------------------------------------------
def run_sim(rundir,Ly,Lz,ny,nz,N2,slope,Prv0,SPru0i,
Kinf,K0,d,AH,AHvar,AHfull,trItype,z0,sz0,
c0,sy0,mxy0,mny0,ADV,lday,dt,
Ttot,sfreq,Kred,Kreds,plot):
# Create bases and domain
y_basis = de.Fourier('y', ny, interval=(0, Ly))#, dealias=3/2)
z_basis = de.Chebyshev('z', nz, interval=(0, Lz))#, dealias=3/2)
domain = de.Domain([y_basis, z_basis], grid_dtype=np.float64)
y = domain.grid(0)
z = domain.grid(1)
# Notes: dealias (n+1)/2 where n is the RHS non-linearity order (e.g. n2).
# so dealias = 1 if no non-linearities
# Create input fields
# Isotropic Diffusivity
K = domain.new_field()
K.meta['y']['constant'] = True
Kz = domain.new_field()
Kz.meta['y']['constant'] = True
K['g'] = Kinf + (K0-Kinf)*np.exp(-z/d)
# K.set_scales(domain.dealias)
K.differentiate('z',out=Kz)
# Upslope Velocity
PSI = domain.new_field()
PSI.meta['y']['constant'] = True
V = domain.new_field()
V.meta['y']['constant'] = True
PSIbbl = domain.new_field()
PSIbbl.meta['y']['constant'] = True
Vbbl = domain.new_field()
Vbbl.meta['y']['constant'] = True
theta = np.arctan(slope)
q0 = (N2*np.sin(theta)*np.sin(theta)/4.0/Prv0/K0/K0*(1.+SPru0i))**(1.0/4.0)
PSI['g'] = np.cos(theta)/np.sin(theta)/(1.+SPru0i)*(1.0-np.exp(-q0*z)*(np.cos(q0*z)+np.sin(q0*z)))
PSIbbl['g'] = PSI['g']*(K0+SPru0i*Kinf)
if ADV == 2:
PSI['g'] = PSI['g']*(K['g']+SPru0i*Kinf) # SML + BBL
elif ADV == 1:
PSI['g'] = PSI['g']*(K0+SPru0i*Kinf) # BBL
else:
PSI['g'] = 0.0 # No ADV
PSIbbl['g'] = 0.0
PSIbbl.differentiate('z',out=Vbbl)
PSI.differentiate('z',out=V)
# Depth-dependent horizontal diffusivity
AHdd = domain.new_field()
AHdd.meta['y']['constant'] = True
if AHvar == 1:
AHdd['g'] = AH*(1.-np.exp(-q0*z))
else:
AHdd['g'] = AH
# BBL fluxes from thickness criteria:
hvs = np.ones_like(z);
hvs[z > np.pi/q0] = 0.
Hbbl = domain.new_field()
Hbbl.meta['y']['constant'] = True
Hbbl['g'] = hvs
# Buoyancy field:
By = N2*np.sin(theta)
Bz = domain.new_field();Bz.meta['y']['constant'] = True
Bzp = domain.new_field();Bzp.meta['y']['constant'] = True
BzpSML = domain.new_field();BzpSML.meta['y']['constant'] = True
BzpSMLz = domain.new_field();BzpSMLz.meta['y']['constant'] = True
B = domain.new_field()
B['g'] = N2*np.sin(theta)*y + N2*np.cos(theta)/(1.+SPru0i)*(z +
np.exp(-q0*z)*np.cos(q0*z)/q0*(1.+SPru0i*Kinf/K0) +
SPru0i*d*np.log(1.+Kinf/K0*(np.exp(z/d)-1.)))
f = domain.new_field();f.meta['y']['constant'] = True
f['g'] = np.exp(-q0*z)*(np.cos(q0*z)+np.sin(q0*z))
Bzp['g'] = -N2*np.cos(theta)/(1+SPru0i)*f['g']
Bz['g'] = (N2*np.cos(theta)/(1+SPru0i) + Bzp['g'])*(1+SPru0i*Kinf/K['g'])
BzpSML['g'] = -N2*np.cos(theta)*(K0-Kinf)*np.exp(-z/d)*SPru0i/((1+SPru0i)*K['g'])
BzpSML.differentiate('z',out=BzpSMLz)
# NOTE: SPru0i non-zero case only works with Kinf not equal to 0.
# Artifically reduce K through BBL:
if Kred == 1:
K['g'] = K['g']*(1.-np.exp(-q0*z/Kreds))
K.differentiate('z',out=Kz)
# Equations and Solver
problem = de.IVP(domain, variables=['tr','trz'], ncc_cutoff=1e-20)
problem.meta[:]['z']['dirichlet'] = True
problem.parameters['N2'] = N2
problem.parameters['K'] = K
problem.parameters['Kz'] = Kz
problem.parameters['AHdd'] = AHdd
problem.parameters['V'] = V
problem.parameters['Vbbl'] = Vbbl
problem.parameters['By'] = By
problem.parameters['Bz'] = Bz
problem.parameters['Bzp'] = Bzp
problem.parameters['BzpSML'] = BzpSML
problem.parameters['BzpSMLz'] = BzpSMLz
problem.parameters['B'] = B
problem.parameters['Hbbl'] = Hbbl
problem.parameters['costh'] = np.cos(theta)
problem.parameters['sinth'] = np.sin(theta)
problem.parameters['SPru0i'] = SPru0i
problem.parameters['f'] = f
# Flux-formulation:
# Advection and isotropic diffusion fluxes:
problem.substitutions['Fy'] = "V*tr - K*dy(tr)"
problem.substitutions['Fz'] = " - K*trz"
# LHS K-tensor terms:
if AHfull == 1: # Full along-isopycnal diffusion
problem.substitutions['GB2'] = "Bz**2.+By**2."
problem.substitutions['KHyy'] = "Bz**2./GB2"
problem.substitutions['KHyz'] = "-By*Bz/GB2"
problem.substitutions['KHzz'] = "By**2./GB2"
else: # Horizontal diffusion
problem.substitutions['KHyy'] = "costh**2"
problem.substitutions['KHyz'] = "-costh*sinth"
problem.substitutions['KHzz'] = "sinth**2."
# LHS fluxes:
problem.substitutions['FHy'] = "-AHdd*(KHyy*dy(tr) + KHyz*trz)"
problem.substitutions['FHz'] = "-AHdd*(KHyz*dy(tr) + KHzz*trz)"
problem.add_equation("dt(tr) + dy(Fy + FHy) + dz(Fz + FHz) = 0.")
problem.add_equation("trz - dz(tr) = 0")
problem.add_bc("left(trz) = 0")
problem.add_bc("right(trz) = 0")
# Build solver
solver = problem.build_solver(de.timesteppers.RK222)
logger.info('Solver built')
# Initial condition:
tr = solver.state['tr']
trz = solver.state['trz']
cz = d*z0;sy = Ly/ny*sy0;sz = Lz/nz*sz0;cy = Ly*c0;
if (trItype == 1):
# Gaussian blob:
tr['g'] = np.exp(-(z-cz)**2/2/sz**2 -(y-cy)**2/2/sy**2)
elif (trItype == 2):
# Function of buoyancy:
hvs = np.ones_like(y);hvs[y <= mny0*Ly] = 0.;hvs[y >= mxy0*Ly] = 0.
tr['g'] = 0*z
tr['g'] = np.exp(-(B['g']/N2/np.cos(theta) - cz)**2/2/sz**2)*hvs
else:
"ERROR: Must pick a valid initial tracer distribution"
return
tr.differentiate('z',out=trz)
# Integration parameters
solver.stop_sim_time = np.inf
solver.stop_wall_time = np.inf
solver.stop_iteration = Ttot*lday/dt
Itot = solver.stop_iteration
# Save parameters:
np.savez(rundir + 'runparams',Ly=Ly,Lz=Lz,N2=N2,slope=slope,theta=theta,Prv0=Prv0,SPru0i=SPru0i,Kinf=Kinf,K0=K0,d=d,AH=AH,AHvar=AHvar,AHfull=AHfull,
q0=q0,By=By,sy=sy,sz=sz,cy=cy,cz=cz,lday=lday,dt=dt,sfreq=sfreq,Itot=Itot,Ttot=Ttot,mxy0=mxy0,mny0=mny0,Kred=Kred,Kreds=Kreds)
## Analysis
# Input fields file:
ifields = solver.evaluator.add_file_handler(rundir + 'ifields', iter=5000000000000, max_writes=20000)
ifields.add_task("B", layout='g', name = 'B')
ifields.add_task("K", layout='g', name = 'K')
ifields.add_task("AHdd", layout='g', name = 'AHdd')
ifields.add_task("V", layout='g', name = 'V')
ifields.add_task("Bz", layout='g', name = 'Bz')
ifields.add_task("Bzp", layout='g', name = 'Bzp')
ifields.add_task("BzpSML", layout='g', name = 'BzpSML')
# Snapshots file:
snapshots = solver.evaluator.add_file_handler(rundir + 'snapshots', iter=sfreq, max_writes=20000)
snapshots.add_system(solver.state, layout='g')
snapshots.add_task("tr*V", layout='g', name = 'advFy')
snapshots.add_task("integ(tr,'y')", layout='g', name = 'ym0')
snapshots.add_task("integ(tr*y,'y')", layout='g', name = 'ym1')
snapshots.add_task("integ(tr*y*y,'y')", layout='g', name = 'ym2')
snapshots.add_task("integ(tr,'z')", layout='g', name = 'zm0')
snapshots.add_task("integ(tr*z,'z')", layout='g', name = 'zm1')
snapshots.add_task("integ(tr*z*z,'z')", layout='g', name = 'zm2')
snapshots.add_task("integ(integ(tr,'y'),'z')", layout = 'g', name = 'trT')
snapshots.add_task("integ(integ(tr*y,'y'),'z')", layout='g', name = 'ym1i')
snapshots.add_task("integ(integ(tr*z,'z'),'y')", layout='g', name = 'zm1i')
# Moment time series file:
moments = solver.evaluator.add_file_handler(rundir + 'moments', iter=1, max_writes=20000)
moments.add_task("integ(integ(tr,'y'),'z')", layout = 'g', name = 'trT')
moments.add_task("integ(integ(trz,'y'),'z')", layout = 'g', name = 'trzT')
moments.add_task("integ(integ(abs(trz),'y'),'z')", layout = 'g', name = 'atrzT')
moments.add_task("integ(integ(trz*z,'y'),'z')", layout = 'g', name = 'trzzT')
moments.add_task("integ(integ(trz*y,'y'),'z')", layout = 'g', name = 'trzyT')
moments.add_task("integ(integ(tr*B,'y'),'z')", layout = 'g', name = 'bm1i')
moments.add_task("integ(integ(tr*B*B,'y'),'z')", layout = 'g', name = 'bm2i')
moments.add_task("integ(integ(tr*B*B*B,'y'),'z')", layout = 'g', name = 'bm3i')
moments.add_task("integ(integ(tr*B*B*B*B,'y'),'z')", layout = 'g', name = 'bm4i')
moments.add_task("integ(integ(tr*y,'y'),'z')", layout='g', name = 'ym1i')
moments.add_task("integ(integ(tr*y*y,'y'),'z')", layout='g', name = 'ym2i')
moments.add_task("integ(integ(tr*z,'z'),'y')", layout='g', name = 'zm1i')
moments.add_task("integ(integ(tr*z*z,'z'),'y')", layout='g', name = 'zm2i')
moments.add_task("integ(integ(tr*z*y,'z'),'y')", layout='g', name = 'yzmi')
moments.add_task("integ(integ(tr*K,'z'),'y')", layout='g', name = 'Ktr')
moments.add_task("integ(integ(trz*K,'z'),'y')", layout='g', name = 'Ktrz')
moments.add_task("integ(integ(abs(trz)*K,'z'),'y')", layout='g', name = 'Katrz')
moments.add_task("integ(integ(trz*K*y,'z'),'y')", layout='g', name = 'Kytrz')
moments.add_task("integ(integ(tr*V*y,'z'),'y')", layout='g', name = 'Vytr')
moments.add_task("integ(integ(tr*V*z,'z'),'y')", layout='g', name = 'Vztr')
# Z VAR terms:
moments.add_task("integ(integ(z*Kz*tr,'z'),'y')", layout='g', name = 'zKztr')
# B COM terms:
moments.add_task("integ(integ(tr*V*By,'z'),'y')", layout='g', name = 'VtrBy')
moments.add_task("integ(integ(tr*Vbbl*By,'z'),'y')", layout='g', name = 'VbbltrBy')
moments.add_task("integ(integ(tr*V*Hbbl*By,'z'),'y')", layout='g', name = 'VbblTtrBy')
moments.add_task("integ(integ(K*dy(tr)*By,'z'),'y')", layout='g', name = 'KtryBy')
moments.add_task("integ(integ(K*Hbbl*dy(tr)*By,'z'),'y')", layout='g', name = 'KbblTtryBy')
moments.add_task("integ(integ(Kz*tr*N2*costh,'z'),'y')", layout='g', name = 'KztrBZ')
moments.add_task("integ(integ(K*trz*Bz,'z'),'y')", layout='g', name = 'KtrzBz')
moments.add_task("integ(integ(K*trz*Bzp,'z'),'y')", layout='g', name = 'KtrzBzp')
moments.add_task("integ(integ(K*trz*BzpSML,'z'),'y')", layout='g', name = 'KtrzBzpSML')
moments.add_task("integ(integ(Kz*tr*BzpSML,'z'),'y')", layout='g', name = 'KztrBzpSML')
moments.add_task("integ(integ(K*tr*BzpSMLz,'z'),'y')", layout='g', name = 'KtrBzpSMLz')
moments.add_task("integ(integ(K*trz*N2*costh,'z'),'y')", layout='g', name = 'KtrzBZ')
moments.add_task("integ(integ(K*Hbbl*trz*Bz,'z'),'y')", layout='g', name = 'KbblTtrzBz')
moments.add_task("integ(integ(trz*Bzp,'z'),'y')", layout='g', name = 'trzBzp')
moments.add_task("integ(integ(trz*BzpSML,'z'),'y')", layout='g', name = 'trzBzpSML')
# B VAR terms:
moments.add_task("integ(integ(tr*K*(BzpSML+N2*costh)*(BzpSML+N2*costh),'z'),'y')", layout='g', name = 'KtrBzpSMLBzpSML')
moments.add_task("integ(integ(B*K*tr*BzpSMLz,'z'),'y')", layout='g', name = 'KtrBBzpSMLz')
moments.add_task("integ(integ(tr*B*V*By,'z'),'y')", layout='g', name = 'VtrBBy')
moments.add_task("integ(integ(tr*B*Vbbl*By,'z'),'y')", layout='g', name = 'VbbltrBBy')
moments.add_task("integ(integ(tr*B*V*Hbbl*By,'z'),'y')", layout='g', name = 'VbblTtrBBy')
moments.add_task("integ(integ(B*K*dy(tr)*By,'z'),'y')", layout='g', name = 'KtryBBy')
moments.add_task("integ(integ(B*K*trz*Bz,'z'),'y')", layout='g', name = 'KtrzBBz')
moments.add_task("integ(integ(B*K*trz*Bzp,'z'),'y')", layout='g', name = 'KtrzBBzp')
moments.add_task("integ(integ(tr*K*Bzp*N2*costh,'z'),'y')", layout='g', name = 'KtrBZBzp')
moments.add_task("integ(integ(tr*K*Bzp*(BzpSML+N2*costh),'z'),'y')", layout='g', name = 'KtrBBzpBzpSML')
moments.add_task("integ(integ(B*K*trz*BzpSML,'z'),'y')", layout='g', name = 'KtrzBBzpSML')
moments.add_task("integ(integ(tr*K*BzpSML*N2*costh,'z'),'y')", layout='g', name = 'KtrBZBzpSML')
moments.add_task("integ(integ(B*Kz*tr*N2*costh,'z'),'y')", layout='g', name = 'KztrBBZ')
moments.add_task("integ(integ(B*K*Hbbl*dy(tr)*By,'z'),'y')", layout='g', name = 'KbblTtryBBy')
moments.add_task("integ(integ(B*K*Hbbl*trz*Bz,'z'),'y')", layout='g', name = 'KbblTtrzBBz')
# Approximation check terms:
moments.add_task("integ(integ(AHdd*sinth*Bzp*(trz*sinth-dy(tr)*costh),'z'),'y')", layout='g', name = 'AHbm1')
moments.add_task("integ(integ(AHdd*sinth*B*Bzp*(trz*sinth-dy(tr)*costh),'z'),'y')", layout='g', name = 'AHbm2')
# Plotting:
if plot:
f, ax = plt.subplots(figsize=(10,5))
f.set_facecolor('white')
ax.set_xlabel('true y (km)');ax.set_ylabel('true z (m)')
y = domain.grid(0,scales=domain.dealias)
z = domain.grid(1,scales=domain.dealias)
ym, zm = np.meshgrid(y,z)
zt = np.cos(theta)*zm + np.sin(theta)*ym
yt = -np.sin(theta)*zm + np.cos(theta)*ym
p = ax.pcolormesh(yt/1.0e3, zt, tr['g'].T/np.max(tr['g']), cmap='RdBu_r', vmin=-1., vmax=1.);
Buo = N2*np.sin(theta)*ym + N2*np.cos(theta)*(zm + np.exp(-q0*zm)*np.cos(q0*zm)/q0)
# NOTE: This plotting only works with SPru0i=0
ax.contour(yt/1.0e3, zt, Buo, 30, colors='k')
ax.plot(y/1.0e3, slope*y,'k-', linewidth=4)
plt.colorbar(p, ax = ax)
ax.set_xlim([0,Ly/1.e3]);ax.set_ylim([0.,Lz + slope*Ly]);
ax.set_facecolor('k')
ax.set_title('Normalized Tracer Concentration')
# Main loop
try:
logger.info('Starting loop')
start_time = time.time()
while solver.ok:
# dt = CFL.compute_dt()
solver.step(dt)
if (plot and (solver.iteration-1) % 5 == 0):
p.set_array(np.ravel(tr['g'][:-1,:-1].T/np.max(tr['g'])))
display.clear_output()
display.display(f)
if (solver.iteration-1) % 2 == 0:
logger.info('Iteration: %i, Time: %e, dt: %e' %(solver.iteration, solver.sim_time, dt))
assert (np.max(tr['g'][:,:])<10.),'blow-up'
except:
logger.error('Exception raised, triggering end of main loop.')
raise
finally:
end_time = time.time()
if plot:
p.set_array(np.ravel(tr['g'][:-1,:-1].T/np.max(tr['g'])))
display.clear_output()
display.display(f)
logger.info('Iterations: %i' %solver.iteration)
logger.info('Sim end time: %f' %solver.sim_time)
logger.info('Run time: %.2f sec' %(end_time-start_time))
logger.info('Run time: %f cpu-hr' %((end_time-start_time)/60/60*domain.dist.comm_cart.size))
def merge_move(rundir,outdir):
# Merge snapshots from different processes:
post.merge_process_files(rundir + "snapshots", cleanup=True)
set_paths = list(pathlib.Path(rundir + "snapshots").glob("snapshots_s*.h5"))
post.merge_sets(rundir + "snapshots/snapshots.h5", set_paths, cleanup=True)
# ifields
post.merge_process_files(rundir + "ifields", cleanup=True)
set_paths = list(pathlib.Path(rundir + "ifields").glob("ifields_s*.h5"))
post.merge_sets(rundir + "ifields/ifields.h5", set_paths, cleanup=True)
# moments
post.merge_process_files(rundir + "moments", cleanup=True)
set_paths = list(pathlib.Path(rundir + "moments").glob("moments_s*.h5"))
post.merge_sets(rundir + "moments/moments.h5", set_paths, cleanup=True)
if __name__ == "__main__":
comm = MPI.COMM_WORLD
nprocs = comm.Get_size()
rank = comm.Get_rank()
rundir = '/short/e14/rmh561/dedalus/Slope_Tracer/rundir/';
outbase = '/g/data/e14/rmh561/Slope_Tracer/saveRUNS/';
# outfold = outbase + 'prodruns_layer30-08-18/'
outfold = outbase + 'prodruns24-08-18/'
plot = False
# # Production runs Point-Release -------------------
# # AH=0:
# ADVs = [0,0,0,1,1,1,2,2,2]
# Kinfs = [1.e-5,1.e-4,1.e-3] *3
# z0s = [0.5] * 9
# slopes = [1./400.] * 9
# slopes.extend([1./200.]* 3 + [1./100.]*3)
# ADVs.extend([0,1,2] * 2)
# Kinfs.extend([1.e-5] * 6)
# z0s.extend([0.5] * 6)
# z0s.extend([0.125,0.25,1.,2.])
# ADVs.extend([2]*4)
# Kinfs.extend([1.e-5]*4)
# slopes.extend([1./400.]*4)
# AHs = [0.] * len(ADVs)
# More z0 runs Point-Release -------------------
# z0s = [0.0625, 0.375, 0.75, 1.5]
# AHs = [0.] * len(z0s)
# z0s = [0.0625, 0.125, 0.25, 0.375, 0.5, 0.75, 1.5, 2.]
# AHs = [100.] * 8
# ADVs = [2] * len(z0s)
# Kinfs = [1.e-5] * len(z0s)
# slopes = [1./400.] * len(z0s)
# Production runs Layer-Release -----------------
# if end spacing is dz (e.g. 500m), then mny0 = (z0*d-dz)/(slope*Ly)
# mny0s = [1.4/3.,1.6/3.]
# AHs = [10.,10.]
# AHs = [0.,20.,30.,40.,50.,60.,70.,80.,90.]
# mny0s = [1.6/3.] * len(AHs)
# # Larger Ly runs:
# AHs = [100.,125.,150.,175.,200.]
# mny0s = [1.6/3.] * len(AHs)
# for ii in range(len(AHs)):
for ii in range(1):#len(AHs)):
input_dict = default_input_dict.copy()
# # Production isoAH (true along-isopycnal) point-release runs:
# input_dict['dt'] = 4*lday
# input_dict['sfreq'] = 4
# input_dict['nz'] = 768
# input_dict['ny'] = 576
# input_dict['sz0'] = 3.*768./192.
# input_dict['sy0'] = 3.*576./384.
# input_dict['AH'] = AHs[ii]
# input_dict['AHvar'] = 0
# input_dict['AHfull'] = 1
# outdir = outfold + 'z0_0p5000_AH_%03d_ADV_2_Kinf_m5_slope_400_isoAH/' % (AHs[ii])
# # Production isoAH (true along-isopycnal) layer-release runs:
# input_dict['dt'] = 4*lday
# input_dict['sfreq'] = 4
# # input_dict['nz'] = 768
# input_dict['ny'] = 576
# input_dict['AHvar'] = 0
# input_dict['AHfull'] = 1
# input_dict['slope'] = 1/200.
# input_dict['AH'] = AHs[ii]
# input_dict['mny0'] = mny0s[ii]
# input_dict['z0'] = 10.
# input_dict['trItype'] = 2
# input_dict['sz0'] = 3.*768./192.
# input_dict['Lz'] = 4000.
# input_dict['nz'] = 1024
# mny0str = ('%0.4f' % mny0s[ii]).replace('.','p')
# outdir = outfold + 'AH_%03d_ADV_2_Kinf_m5_mny0_%s_slope_200_isoAH_Lz4000/' % (AHs[ii],mny0str)
# BBTRE run:
input_dict['dt'] = 4*lday
input_dict['Ttot'] = 6400
input_dict['sfreq'] = 4
input_dict['ny'] = 768
input_dict['nz'] = 1024
input_dict['Lz'] = 4000.
input_dict['Ly'] = 2000000.
input_dict['AHvar'] = 0
input_dict['AHfull'] = 1
input_dict['slope'] = 1/500.
input_dict['AH'] = 100.
input_dict['N2'] = 1.69e-6
input_dict['d'] = 230.
input_dict['SPru0i'] = 1.95
input_dict['K0'] = 1.8e-3
input_dict['Kinf'] = 5.2e-5
input_dict['z0'] = 4.3
input_dict['sz0'] = 3.*1024./192.
input_dict['sy0'] = 3.*576./384.
outdir = outfold + 'BBTRE/'
# # K BBL variation testing:
# input_dict['dt'] = 4*lday
# input_dict['sfreq'] = 4
# input_dict['ny'] = 384
# input_dict['nz'] = 768
# input_dict['sz0'] = 3.*2.
# input_dict['sy0'] = 3.*2.
# input_dict['Kred'] = 1
# outdir = outfold + 'Kredtest_Kred_Kreds_0p5/'
# z0str = ('%1.4f' % z0s[ii]).replace('.','p')
# Kinfstr = ('%01d' % np.log10(Kinfs[ii])).replace('-','m')
# slopestr = '%03d' % (1./slopes[ii])
run_sim(rundir,plot=plot,**input_dict)
print(outdir)
merge_move(rundir,outdir)
if rank == 0:
os.makedirs(outdir, exist_ok=True)
shutil.move(rundir + 'snapshots/snapshots.h5',outdir + 'snapshots.h5');
shutil.move(rundir + 'moments/moments.h5',outdir + 'moments.h5');
shutil.move(rundir + 'ifields/ifields.h5',outdir + 'ifields.h5');
shutil.move(rundir + 'runparams.npz',outdir + 'runparams.npz');
shutil.rmtree(rundir + 'snapshots/');
shutil.rmtree(rundir + 'ifields/');
shutil.rmtree(rundir + 'moments/');