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ReferenceState.pyx
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#!python
# cython: boundscheck=False
# cython: wraparound=True
# cython: initializedcheck=False
# cython: cdivision=True
cimport Grid
cimport Restart
cimport numpy as np
import numpy as np
from NetCDFIO cimport NetCDFIO_Stats
cimport ParallelMPI
from scipy.integrate import odeint
include 'parameters.pxi'
cdef extern from "thermodynamic_functions.h":
inline double qt_from_pv(double p0, double pv)
cdef class ReferenceState:
def __init__(self, Grid.Grid Gr ):
self.p0 = np.zeros(Gr.dims.nlg[2], dtype=np.double, order='c')
self.p0_half = np.zeros(Gr.dims.nlg[2], dtype=np.double, order='c')
self.alpha0 = np.zeros(Gr.dims.nlg[2], dtype=np.double, order='c')
self.alpha0_half = np.zeros(Gr.dims.nlg[2], dtype=np.double, order='c')
self.rho0 = np.zeros(Gr.dims.nlg[2], dtype=np.double, order='c')
self.rho0_half = np.zeros(Gr.dims.nlg[2], dtype=np.double, order='c')
self.p0_global = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
self.p0_half_global = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
self.alpha0_global = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
self.alpha0_half_global = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
self.rho0_global = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
self.rho0_half_global = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
return
def initialize(self, Grid.Grid Gr, Thermodynamics, NetCDFIO_Stats NS, ParallelMPI.ParallelMPI Pa):
'''
Initilize the reference profiles. The function is typically called from the case specific initialization
fucntion defined in Initialization.pyx
:param Gr: Grid class
:param Thermodynamics: Thermodynamics class
:param NS: StatsIO class
:param Pa: ParallelMPI class
:return:
'''
self.sg = Thermodynamics.entropy(self.Pg, self.Tg, self.qtg, 0.0, 0.0)
# Form a right hand side for integrating the hydrostatic equation to
# determine the reference pressure
def rhs(p, z):
T, ql, qi = Thermodynamics.eos(np.exp(p), self.sg, self.qtg)
return -g / (Rd * T * (1.0 - self.qtg + eps_vi * (self.qtg - ql - qi)))
# Construct arrays for integration points
z = np.array(Gr.z[Gr.dims.gw - 1:-Gr.dims.gw + 1])
z_half = np.append([0.0], np.array(Gr.z_half[Gr.dims.gw:-Gr.dims.gw]))
# We are integrating the log pressure so need to take the log of the
# surface pressure
p0 = np.log(self.Pg)
p = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
p_half = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
# Perform the integration
p[Gr.dims.gw - 1:-Gr.dims.gw +1] = odeint(rhs, p0, z, hmax=1.0)[:, 0]
p_half[Gr.dims.gw:-Gr.dims.gw] = odeint(rhs, p0, z_half, hmax=1.0)[1:, 0]
# Set boundary conditions
p[:Gr.dims.gw - 1] = p[2 * Gr.dims.gw - 2:Gr.dims.gw - 1:-1]
p[-Gr.dims.gw + 1:] = p[-Gr.dims.gw - 1:-2 * Gr.dims.gw:-1]
p_half[:Gr.dims.gw] = p_half[2 * Gr.dims.gw - 1:Gr.dims.gw - 1:-1]
p_half[-Gr.dims.gw:] = p_half[-Gr.dims.gw - 1:-2 * Gr.dims.gw - 1:-1]
p = np.exp(p)
p_half = np.exp(p_half)
self.p0_global = p
self.p0_half_global = p_half
cdef double[:] p_ = p
cdef double[:] p_half_ = p_half
cdef double[:] temperature = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
cdef double[:] temperature_half = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
cdef double[:] alpha = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
cdef double[:] alpha_half = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
cdef double[:] ql = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
cdef double[:] qi = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
cdef double[:] qv = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
cdef double[:] ql_half = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
cdef double[:] qi_half = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
cdef double[:] qv_half = np.zeros(Gr.dims.ng[2], dtype=np.double, order='c')
# Compute reference state thermodynamic profiles
for k in xrange(Gr.dims.ng[2]):
temperature[k], ql[k], qi[k] = Thermodynamics.eos(p_[k], self.sg, self.qtg)
qv[k] = self.qtg - (ql[k] + qi[k])
alpha[k] = Thermodynamics.alpha(p_[k], temperature[k], self.qtg, qv[k])
temperature_half[k], ql_half[k], qi_half[k] = Thermodynamics.eos(p_half_[k], self.sg, self.qtg)
qv_half[k] = self.qtg - (ql_half[k] + qi_half[k])
alpha_half[k] = Thermodynamics.alpha(p_half_[k], temperature_half[k], self.qtg, qv_half[k])
# Now do a sanity check to make sure that the Reference State entropy profile is uniform following
# saturation adjustment
cdef double s
for k in xrange(Gr.dims.ng[2]):
s = Thermodynamics.entropy(p_half[k],temperature_half[k],self.qtg,ql_half[k],qi_half[k])
if np.abs(s - self.sg)/self.sg > 0.01:
Pa.root_print('Error in reference profiles entropy not constant !')
Pa.root_print('Likely error in saturation adjustment')
Pa.root_print('Kill Simulation Now!')
Pa.kill()
self.alpha0_global = alpha
self.alpha0_half_global = alpha_half
self.rho0_global = 1.0/np.array(self.alpha0_global)
self.rho0_half_global = 1.0/np.array(self.alpha0_half_global)
# print(np.array(Gr.extract_local_ghosted(alpha_half,2)))
self.alpha0_half = Gr.extract_local_ghosted(alpha_half, 2)
self.alpha0 = Gr.extract_local_ghosted(alpha, 2)
self.p0 = Gr.extract_local_ghosted(p_, 2)
self.p0_half = Gr.extract_local_ghosted(p_half, 2)
self.rho0 = 1.0 / np.array(self.alpha0)
self.rho0_half = 1.0 / np.array(self.alpha0_half)
# Write reference profiles to StatsIO
NS.add_reference_profile('alpha0', Gr, Pa)
NS.write_reference_profile('alpha0', alpha_half[Gr.dims.gw:-Gr.dims.gw], Pa)
NS.add_reference_profile('p0', Gr, Pa)
NS.write_reference_profile('p0', p_half[Gr.dims.gw:-Gr.dims.gw], Pa)
NS.add_reference_profile('rho0', Gr, Pa)
NS.write_reference_profile('rho0', 1.0 / np.array(alpha_half[Gr.dims.gw:-Gr.dims.gw]), Pa)
NS.add_reference_profile('temperature0', Gr, Pa)
NS.write_reference_profile('temperature0', temperature_half[Gr.dims.gw:-Gr.dims.gw], Pa)
NS.add_reference_profile('ql0', Gr, Pa)
NS.write_reference_profile('ql0', ql_half[Gr.dims.gw:-Gr.dims.gw], Pa)
NS.add_reference_profile('qv0', Gr, Pa)
NS.write_reference_profile('qv0', qv_half[Gr.dims.gw:-Gr.dims.gw], Pa)
NS.add_reference_profile('qi0', Gr, Pa)
NS.write_reference_profile('qi0', qi_half[Gr.dims.gw:-Gr.dims.gw], Pa)
return
cpdef restart(self, Grid.Grid Gr, Restart.Restart Re):
Re.restart_data['Ref'] = {}
Re.restart_data['Ref']['p0'] = np.array(self.p0)
Re.restart_data['Ref']['p0_half'] = np.array(self.p0_half)
Re.restart_data['Ref']['alpha0'] = np.array(self.alpha0)
Re.restart_data['Ref']['alpha0_half'] = np.array(self.alpha0_half)
Re.restart_data['Ref']['p0_global'] = np.array(self.p0_global)
Re.restart_data['Ref']['p0_half_global'] = np.array(self.p0_half_global)
Re.restart_data['Ref']['alpha0_global'] = np.array(self.alpha0_global)
Re.restart_data['Ref']['alpha0_half_global'] = np.array(self.alpha0_half_global)
Re.restart_data['Ref']['Tg'] = self.Tg
Re.restart_data['Ref']['Pg'] = self.Pg
Re.restart_data['Ref']['sg'] = self.sg
Re.restart_data['Ref']['qtg'] = self.qtg
Re.restart_data['Ref']['u0'] = self.u0
Re.restart_data['Ref']['v0'] = self.v0
return
cpdef init_from_restart(self, Grid.Grid Gr, Restart.Restart Re):
self.Tg = Re.restart_data['Ref']['Tg']
self.Pg = Re.restart_data['Ref']['Pg']
self.sg = Re.restart_data['Ref']['sg']
self.qtg = Re.restart_data['Ref']['qtg']
self.u0 = Re.restart_data['Ref']['u0']
self.v0 = Re.restart_data['Ref']['v0']
self.p0 = Re.restart_data['Ref']['p0']
self.p0_half = Re.restart_data['Ref']['p0_half']
self.alpha0 = Re.restart_data['Ref']['alpha0']
self.alpha0_half = Re.restart_data['Ref']['alpha0_half']
self.rho0 = 1.0 / Re.restart_data['Ref']['alpha0']
self.rho0_half = 1.0 / Re.restart_data['Ref']['alpha0_half']
self.p0_global = Re.restart_data['Ref']['p0_global']
self.p0_half_global = Re.restart_data['Ref']['p0_half_global']
self.alpha0_global = Re.restart_data['Ref']['alpha0_global']
self.alpha0_half_global = Re.restart_data['Ref']['alpha0_half_global']
self.rho0_global = 1.0 / Re.restart_data['Ref']['alpha0_global']
self.rho0_half_global = 1.0 / Re.restart_data['Ref']['alpha0_half_global']
return