def pe(avgfile, grdfile, gridid=None, maskfile='/media/Armadillo/bkp/lado/MSc/work/ROMS/plot_outputs3/msk_shelf.npy', normalize=False, verbose=True):
"""
USAGE
-----
t, pe = pe(avgfile, grdfile, gridid=None, maskfile='/media/Armadillo/bkp/lado/MSc/work/ROMS/plot_outputs3/msk_shelf.npy', normalize=False, verbose=True):
Calculates Potential Energy (PE) change integrated within a control volume
for each time record of a ROMS *.avg or *.his file. The change is computed relative to
the initial conditions, i.e., rhop(x,y,z,t=ti) = rho(x,y,z,t=ti) - rho(x,y,z,t=t0).
[-g*(rhop^2)]
PE = Integrated in a control volume V [-----------] # [J]
[ 2*drhodz ]
If 'normalize' is set to 'True', then PE/V (mean PE density [J/m3]) is returned instead.
Reference:
----------
Cushman-Roisin (1994): Introduction to Geophysical Fluid Dynamics, page 213,
Combination of Equations 15-29 and 15-30.
"""
print("Loading outputs and grid.")
## Get outputs.
avg = Dataset(avgfile)
## Load domain mask.
if maskfile:
mask = np.load(maskfile)
if type(mask[0,0])==np.bool_:
pass
else:
mask=mask==1.
## Getting mask indices.
ilon,ilat = np.where(mask)
## Get grid, time-dependent free-surface and topography.
zeta = avg.variables['zeta']
grd = pyroms.grid.get_ROMS_grid(gridid, zeta=zeta, hist_file=avgfile, grid_file=grdfile)
## Get time.
t = avg.variables['ocean_time'][:]
t = t - t[0]
nt = t.size
## Get grid coordinates at RHO-points.
lonr, latr = avg.variables['lon_rho'][:], avg.variables['lat_rho'][:]
## Get grid spacings at RHO-points.
## Find cell widths.
dx = grd.hgrid.dx # Cell width in the XI-direction.
dy = grd.hgrid.dy # Cell width in the ETA-direction.
if maskfile:
dA = dx[mask]*dy[mask]
else:
dA = dx*dy
## Get temp, salt.
temp = avg.variables['temp']
salt = avg.variables['salt']
## Find cell heights (at ti=0).
zw = grd.vgrid.z_w[0,:] # Cell depths (at ti=0).
if maskfile:
dz = zw[1:,ilat,ilon] - zw[:-1,ilat,ilon] # Cell height.
else:
dz = zw[1:,:] - zw[:-1,:]
dz = 0.5*(dz[1:,:] + dz[:-1,:]) # Cell heights at W-points.
## Get pres, g and pden (at ti=0).
p0 = -zw # Approximation, for computational efficiency.
p0 = 0.5*(p0[1:,:]+p0[:-1,:])
if maskfile:
rho0 = pden(salt[0,:,ilat,ilon],temp[0,:,ilat,ilon],p0[:,ilat,ilon],pr=0.)
else:
rho0 = pden(salt[0,:],temp[0,:],p0,pr=0.)
if maskfile:
g = grav(latr[mask])
else:
g = grav(latr)
drho0 = rho0[1:,:] - rho0[:-1,:]
rho0z = drho0/dz # Background potential density vertical gradient.
PE = np.array([])
for ti in range(nt):
tp = ti + 1
print("Processing time record %s of %s"%(tp,nt))
if maskfile:
rhoi = pden(salt[ti,:,ilat,ilon],temp[ti,:,ilat,ilon],p0[:,ilat,ilon],pr=0.)
else:
rhoi = pden(salt[ti,:],temp[ti,:],p0,pr=0.)
rhop = rhoi - rho0 # Density anomaly, i.e., rho(x,y,z,t=ti) - rho(x,y,z,t=0)
rhop = 0.5*(rhop[1:,:] + rhop[:-1,:])
## Find cell heights.
zw = grd.vgrid.z_w[ti,:] # Cell depths (at ti=0).
if maskfile:
dz = zw[1:,ilat,ilon] - zw[:-1,ilat,ilon] # Cell height.
else:
dz = zw[1:,:] - zw[:-1,:]
## Find cell volumes.
print(dx.shape,dy.shape,dz.shape)
dV = dA*dz # [m3]
dV = 0.5*(dV[1:,:]+dV[:-1,:])
## Gravitational Available Potential Energy density (energy/volume).
print(g.shape)
print(rhop.shape)
print(rho0z.shape)
pe = -g*(rhop**2)/(2*rho0z) # [J/m3]
## Do volume integral to calculate Gravitational Available Potential Energy of the control volume.
Pe = np.sum(pe*dV) # [J]
if normalize:
V = dV.sum()
Pe = Pe/V
print("")
print("Total volume of the control volume is %e m3."%V)
print("Normalizing PE by this volume, i.e., mean PE density [J/m3].")
print("")
if verbose:
if normalize:
print("PE = %e J/m3"%Pe)
else:
print("PE = %e J"%Pe)
PE = np.append(PE, Pe)
return t, PE
def pe(avgfile,
grdfile,
gridid=None,
maskfile='/media/Armadillo/bkp/lado/MSc/work/ROMS/plot_outputs3/msk_shelf.npy',
normalize=False,
verbose=True):
"""
USAGE
-----
t, pe = pe(avgfile, grdfile, gridid=None, maskfile='/media/Armadillo/bkp/lado/MSc/work/ROMS/plot_outputs3/msk_shelf.npy', normalize=False, verbose=True):
Calculates Potential Energy (PE) change integrated within a control volume
for each time record of a ROMS *.avg or *.his file. The change is computed relative to
the initial conditions, i.e., rhop(x,y,z,t=ti) = rho(x,y,z,t=ti) - rho(x,y,z,t=t0).
[-g*(rhop^2)]
PE = Integrated in a control volume V [-----------] # [J]
[ 2*drhodz ]
If 'normalize' is set to 'True', then PE/V (mean PE density [J/m3]) is returned instead.
Reference:
----------
Cushman-Roisin (1994): Introduction to Geophysical Fluid Dynamics, page 213,
Combination of Equations 15-29 and 15-30.
"""
print("Loading outputs and grid.")
## Get outputs.
avg = Dataset(avgfile)
## Load domain mask.
if maskfile:
mask = np.load(maskfile)
if type(mask[0, 0]) == np.bool_:
pass
else:
mask = mask == 1.
## Getting mask indices.
ilon, ilat = np.where(mask)
## Get grid, time-dependent free-surface and topography.
zeta = avg.variables['zeta']
grd = pyroms.grid.get_ROMS_grid(gridid,
zeta=zeta,
hist_file=avgfile,
grid_file=grdfile)
## Get time.
t = avg.variables['ocean_time'][:]
t = t - t[0]
nt = t.size
## Get grid coordinates at RHO-points.
lonr, latr = avg.variables['lon_rho'][:], avg.variables['lat_rho'][:]
## Get grid spacings at RHO-points.
## Find cell widths.
dx = grd.hgrid.dx # Cell width in the XI-direction.
dy = grd.hgrid.dy # Cell width in the ETA-direction.
if maskfile:
dA = dx[mask] * dy[mask]
else:
dA = dx * dy
## Get temp, salt.
temp = avg.variables['temp']
salt = avg.variables['salt']
## Find cell heights (at ti=0).
zw = grd.vgrid.z_w[0, :] # Cell depths (at ti=0).
if maskfile:
dz = zw[1:, ilat, ilon] - zw[:-1, ilat, ilon] # Cell height.
else:
dz = zw[1:, :] - zw[:-1, :]
dz = 0.5 * (dz[1:, :] + dz[:-1, :]) # Cell heights at W-points.
## Get pres, g and pden (at ti=0).
p0 = -zw # Approximation, for computational efficiency.
p0 = 0.5 * (p0[1:, :] + p0[:-1, :])
if maskfile:
rho0 = pden(salt[0, :, ilat, ilon],
temp[0, :, ilat, ilon],
p0[:, ilat, ilon],
pr=0.)
else:
rho0 = pden(salt[0, :], temp[0, :], p0, pr=0.)
if maskfile:
g = grav(latr[mask])
else:
g = grav(latr)
drho0 = rho0[1:, :] - rho0[:-1, :]
rho0z = drho0 / dz # Background potential density vertical gradient.
PE = np.array([])
for ti in range(nt):
tp = ti + 1
print("Processing time record %s of %s" % (tp, nt))
if maskfile:
rhoi = pden(salt[ti, :, ilat, ilon],
temp[ti, :, ilat, ilon],
p0[:, ilat, ilon],
pr=0.)
else:
rhoi = pden(salt[ti, :], temp[ti, :], p0, pr=0.)
rhop = rhoi - rho0 # Density anomaly, i.e., rho(x,y,z,t=ti) - rho(x,y,z,t=0)
rhop = 0.5 * (rhop[1:, :] + rhop[:-1, :])
## Find cell heights.
zw = grd.vgrid.z_w[ti, :] # Cell depths (at ti=0).
if maskfile:
dz = zw[1:, ilat, ilon] - zw[:-1, ilat, ilon] # Cell height.
else:
dz = zw[1:, :] - zw[:-1, :]
## Find cell volumes.
print(dx.shape, dy.shape, dz.shape)
dV = dA * dz # [m3]
dV = 0.5 * (dV[1:, :] + dV[:-1, :])
## Gravitational Available Potential Energy density (energy/volume).
print(g.shape)
print(rhop.shape)
print(rho0z.shape)
pe = -g * (rhop**2) / (2 * rho0z) # [J/m3]
## Do volume integral to calculate Gravitational Available Potential Energy of the control volume.
Pe = np.sum(pe * dV) # [J]
if normalize:
V = dV.sum()
Pe = Pe / V
print("")
print("Total volume of the control volume is %e m3." % V)
print(
"Normalizing PE by this volume, i.e., mean PE density [J/m3].")
print("")
if verbose:
if normalize:
print("PE = %e J/m3" % Pe)
else:
print("PE = %e J" % Pe)
PE = np.append(PE, Pe)
return t, PE
def energy_diagnostics(avgfile, grdfile, rho0=1025., gridid=None, maskfile='msk_shelf.npy', normalize=True, verbose=True):
"""
USAGE
-----
t, HKE, TPE = energy_diagnostics(avgfile, grdfile, rho0=1025., gridid=None, maskfile='msk_shelf.npy', normalize=True, verbose=True)
Calculates volume-integrated Horizontal Kinetic Energy (HKE) and Total Potential Energy (TPE)
within a control volume for each time record of a ROMS *.avg or *.his file.
"""
avg = Dataset(avgfile)
print("Loading outputs and grid.")
## Load domain mask.
if maskfile:
mask = np.load(maskfile)
if type(mask[0,0])==np.bool_:
pass
else:
mask=mask==1.
## Getting mask indices.
ilon,ilat = np.where(mask)
## Getting velocity field.
try:
U = avg.variables['u']
V = avg.variables['v']
uvrho3 = False
except KeyError:
U = avg.variables['u_eastward']
V = avg.variables['v_northward']
uvrho3 = True
## Get temp, salt.
temp = avg.variables['temp']
salt = avg.variables['salt']
## Get grid, time-dependent free-surface and topography.
zeta = avg.variables['zeta']
grd = pyroms.grid.get_ROMS_grid(gridid, zeta=zeta, hist_file=avgfile, grid_file=grdfile)
## Find cell widths at RHO-points.
dx = grd.hgrid.dx # Cell width in the XI-direction.
dy = grd.hgrid.dy # Cell width in the ETA-direction.
if maskfile:
dA = dx[mask]*dy[mask]
else:
dA = dx*dy
## Get pres, g and pden (at ti=0).
p0 = -grd.vgrid.z_r[0,:] # Approximation, for computational efficiency.
if maskfile:
g = grav(avg.variables['lat_rho'][:][mask])
else:
g = grav(avg.variables['lat_rho'][:])
## Get time.
t = avg.variables['ocean_time'][:]
t = t - t[0]
nt = t.size
KE = np.array([])
PE = np.array([])
for ti in range(nt):
tp = ti + 1
print("")
print("Processing time record %s of %s"%(tp,nt))
print("Calculating density.")
if maskfile:
rho = pden(salt[ti,:,ilat,ilon],temp[ti,:,ilat,ilon],p0[:,ilat,ilon],pr=0.)
else:
rho = pden(salt[ti,:],temp[ti,:],p0,pr=0.)
print("Loading velocities.")
uu = U[ti,:]
vv = V[ti,:]
if not uvrho3:
# Calculate u and v at PSI-points.
u = 0.5*(uu[:,1:,:] + uu[:,:-1,:])
v = 0.5*(vv[:,:,1:] + vv[:,:,:-1])
# Calculate rho at PSI-points.
rhop = 0.5*(rho[:,1:,:] + rho[:,:-1,:])
rhop = 0.5*(rhop[:,:,1:] + rhop[:,:,:-1])
if maskfile:
u = u[:,ilat+1,ilon+1]
v = v[:,ilat+1,ilon+1]
rhop = rhop[:,ilat+1,ilon+1]
else:
pass
else:
# U and V both at RHO-points, no reshaping necessary.
if maskfile:
u = uu[:,ilat,ilon]
v = vv[:,ilat,ilon]
else:
u = uu
v = vv
## Find cell depths, invert z-axis direction (downward).
if maskfile:
z = -grd.vgrid.z_r[ti,:,ilat,ilon]
else:
z = -grd.vgrid.z_r[ti,:]
## Find cell heights.
zw = grd.vgrid.z_w[ti,:]
if maskfile:
dz = zw[1:,ilat,ilon] - zw[:-1,ilat,ilon] # Cell height.
else:
dz = zw[1:,:] - zw[:-1,:]
## Find cell volumes.
dV = dA*dz # [m3]
print("Squaring velocities.")
u2v2 = u*u + v*v
## Total Potential Energy (TPE) density relative to z=0 (energy/volume).
pe = rho*g*z # [J/m3]
## Horizontal Kinetic Energy (HKE) density (energy/volume).
if not uvrho3:
ke = 0.5*rhop*u2v2 # [J/m3]
else:
ke = 0.5*rho*u2v2 # [J/m3]
## Do volume integral to calculate TPE/HKE of the control volume.
Pe = np.sum(pe*dV) # [J]
Ke = np.sum(ke*dV) # [J]
if normalize:
Vol = dV.sum()
Pe = Pe/Vol
Ke = Ke/Vol
if verbose and tp==1:
print("")
print("Total volume of the control volume is %e m3."%Vol)
print("Normalizing TPE/HKE by this volume, i.e., mean TPE/HKE density [J/m3].")
print("")
if verbose:
print("")
if normalize:
print("TPE/vol = %e J/m3"%Pe)
print("HKE/vol = %e J/m3"%Ke)
else:
print("TPE = %e J"%Pe)
print("HKE = %e J"%Ke)
PE = np.append(PE, Pe)
KE = np.append(KE, Ke)
return t, KE, PE
def energy_diagnostics(avgfile,
grdfile,
rho0=1025.,
gridid=None,
maskfile='msk_shelf.npy',
normalize=True,
verbose=True):
"""
USAGE
-----
t, HKE, TPE = energy_diagnostics(avgfile, grdfile, rho0=1025., gridid=None, maskfile='msk_shelf.npy', normalize=True, verbose=True)
Calculates volume-integrated Horizontal Kinetic Energy (HKE) and Total Potential Energy (TPE)
within a control volume for each time record of a ROMS *.avg or *.his file.
"""
avg = Dataset(avgfile)
print("Loading outputs and grid.")
## Load domain mask.
if maskfile:
mask = np.load(maskfile)
if type(mask[0, 0]) == np.bool_:
pass
else:
mask = mask == 1.
## Getting mask indices.
ilon, ilat = np.where(mask)
## Getting velocity field.
try:
U = avg.variables['u']
V = avg.variables['v']
uvrho3 = False
except KeyError:
U = avg.variables['u_eastward']
V = avg.variables['v_northward']
uvrho3 = True
## Get temp, salt.
temp = avg.variables['temp']
salt = avg.variables['salt']
## Get grid, time-dependent free-surface and topography.
zeta = avg.variables['zeta']
grd = pyroms.grid.get_ROMS_grid(gridid,
zeta=zeta,
hist_file=avgfile,
grid_file=grdfile)
## Find cell widths at RHO-points.
dx = grd.hgrid.dx # Cell width in the XI-direction.
dy = grd.hgrid.dy # Cell width in the ETA-direction.
if maskfile:
dA = dx[mask] * dy[mask]
else:
dA = dx * dy
## Get pres, g and pden (at ti=0).
p0 = -grd.vgrid.z_r[0, :] # Approximation, for computational efficiency.
if maskfile:
g = grav(avg.variables['lat_rho'][:][mask])
else:
g = grav(avg.variables['lat_rho'][:])
## Get time.
t = avg.variables['ocean_time'][:]
t = t - t[0]
nt = t.size
KE = np.array([])
PE = np.array([])
for ti in range(nt):
tp = ti + 1
print("")
print("Processing time record %s of %s" % (tp, nt))
print("Calculating density.")
if maskfile:
rho = pden(salt[ti, :, ilat, ilon],
temp[ti, :, ilat, ilon],
p0[:, ilat, ilon],
pr=0.)
else:
rho = pden(salt[ti, :], temp[ti, :], p0, pr=0.)
print("Loading velocities.")
uu = U[ti, :]
vv = V[ti, :]
if not uvrho3:
# Calculate u and v at PSI-points.
u = 0.5 * (uu[:, 1:, :] + uu[:, :-1, :])
v = 0.5 * (vv[:, :, 1:] + vv[:, :, :-1])
# Calculate rho at PSI-points.
rhop = 0.5 * (rho[:, 1:, :] + rho[:, :-1, :])
rhop = 0.5 * (rhop[:, :, 1:] + rhop[:, :, :-1])
if maskfile:
u = u[:, ilat + 1, ilon + 1]
v = v[:, ilat + 1, ilon + 1]
rhop = rhop[:, ilat + 1, ilon + 1]
else:
pass
else:
# U and V both at RHO-points, no reshaping necessary.
if maskfile:
u = uu[:, ilat, ilon]
v = vv[:, ilat, ilon]
else:
u = uu
v = vv
## Find cell depths, invert z-axis direction (downward).
if maskfile:
z = -grd.vgrid.z_r[ti, :, ilat, ilon]
else:
z = -grd.vgrid.z_r[ti, :]
## Find cell heights.
zw = grd.vgrid.z_w[ti, :]
if maskfile:
dz = zw[1:, ilat, ilon] - zw[:-1, ilat, ilon] # Cell height.
else:
dz = zw[1:, :] - zw[:-1, :]
## Find cell volumes.
dV = dA * dz # [m3]
print("Squaring velocities.")
u2v2 = u * u + v * v
## Total Potential Energy (TPE) density relative to z=0 (energy/volume).
pe = rho * g * z # [J/m3]
## Horizontal Kinetic Energy (HKE) density (energy/volume).
if not uvrho3:
ke = 0.5 * rhop * u2v2 # [J/m3]
else:
ke = 0.5 * rho * u2v2 # [J/m3]
## Do volume integral to calculate TPE/HKE of the control volume.
Pe = np.sum(pe * dV) # [J]
Ke = np.sum(ke * dV) # [J]
if normalize:
Vol = dV.sum()
Pe = Pe / Vol
Ke = Ke / Vol
if verbose and tp == 1:
print("")
print("Total volume of the control volume is %e m3." % Vol)
print(
"Normalizing TPE/HKE by this volume, i.e., mean TPE/HKE density [J/m3]."
)
print("")
if verbose:
print("")
if normalize:
print("TPE/vol = %e J/m3" % Pe)
print("HKE/vol = %e J/m3" % Ke)
else:
print("TPE = %e J" % Pe)
print("HKE = %e J" % Ke)
PE = np.append(PE, Pe)
KE = np.append(KE, Ke)
return t, KE, PE