def run_simulation(filename, start_time, save_output, temp, RH, RO2_indices,
H2O, input_dict, simulation_time, batch_step):
from assimulo.solvers import RodasODE, CVode #Choose solver accoring to your need.
from assimulo.problem import Explicit_Problem
# In this function, we import functions that have been pre-compiled for use in the ODE solver
# The function that calculates the RHS of the ODE is also defined within this function, such
# that it can be used by the Assimulo solvers
# The variables passed to this function are defined as follows:
#-------------------------------------------------------------------------------------
# define the ODE function to be called
def dydt_func(t, y):
"""
This function defines the right-hand side [RHS] of the ordinary differential equations [ODEs] to be solved
input:
• t - time variable [internal to solver]
• y - array holding concentrations of all compounds in both gas and particulate [molecules/cc]
output:
dydt - the dy_dt of each compound in both gas and particulate phase [molecules/cc.sec]
"""
#pdb.set_trace()
# Calculate time of day
time_of_day_seconds = start_time + t
# make sure the y array is not a list. Assimulo uses lists
y_asnumpy = numpy.array(y)
#Calculate the concentration of RO2 species, using an index file created during parsing
RO2 = numpy.sum(y[RO2_indices])
#Calculate reaction rate for each equation.
# Note that H2O will change in parcel mode
# The time_of_day_seconds is used for photolysis rates - need to change this if want constant values
rates = evaluate_rates_fortran(RO2, H2O, temp, time_of_day_seconds)
#pdb.set_trace()
# Calculate product of all reactants and stochiometry for each reaction [A^a*B^b etc]
reactants = reactants_fortran(y_asnumpy)
#pdb.set_trace()
#Multiply product of reactants with rate coefficient to get reaction rate
reactants = numpy.multiply(reactants, rates)
#pdb.set_trace()
# Now use reaction rates with the loss_gain matri to calculate the final dydt for each compound
# With the assimulo solvers we need to output numpy arrays
dydt = loss_gain_fortran(reactants)
#pdb.set_trace()
return dydt
#-------------------------------------------------------------------------------------
#-------------------------------------------------------------------------------------
# define jacobian function to be called
def jacobian(t, y):
"""
This function defines Jacobian of the ordinary differential equations [ODEs] to be solved
input:
• t - time variable [internal to solver]
• y - array holding concentrations of all compounds in both gas and particulate [molecules/cc]
output:
dydt_dydt - the N_compounds x N_compounds matrix of Jacobian values
"""
# Different solvers might call jacobian at different stages, so we have to redo some calculations here
# Calculate time of day
time_of_day_seconds = start_time + t
# make sure the y array is not a list. Assimulo uses lists
y_asnumpy = numpy.array(y)
#Calculate the concentration of RO2 species, using an index file created during parsing
RO2 = numpy.sum(y[RO2_indices])
#Calculate reaction rate for each equation.
# Note that H2O will change in parcel mode
rates = evaluate_rates_fortran(RO2, H2O, temp, time_of_day_seconds)
#pdb.set_trace()
# Now use reaction rates with the loss_gain matrix to calculate the final dydt for each compound
# With the assimulo solvers we need to output numpy arrays
dydt_dydt = jacobian_fortran(rates, y_asnumpy)
#pdb.set_trace()
return dydt_dydt
#-------------------------------------------------------------------------------------
#import static compilation of Fortran functions for use in ODE solver
print("Importing pre-compiled Fortran modules")
from rate_coeff_f2py import evaluate_rates as evaluate_rates_fortran
from reactants_conc_f2py import reactants as reactants_fortran
from loss_gain_f2py import loss_gain as loss_gain_fortran
from jacobian_f2py import jacobian as jacobian_fortran
# 'Unpack' variables from input_dict
species_dict = input_dict['species_dict']
species_dict2array = input_dict['species_dict2array']
species_initial_conc = input_dict['species_initial_conc']
equations = input_dict['equations']
#Specify some starting concentrations [ppt]
Cfactor = 2.55e+10 #ppb-to-molecules/cc
# Create variables required to initialise ODE
num_species = len(species_dict.keys())
y0 = [0] * num_species #Initial concentrations, set to 0
t0 = 0.0 #T0
# Define species concentrations in ppb
# You have already set this in the front end script, and now we populate the y array with those concentrations
for specie in species_initial_conc.keys():
y0[species_dict2array[specie]] = species_initial_conc[
specie] * Cfactor #convert from pbb to molcules/cc
#Set the total_time of the simulation to 0 [havent done anything yet]
total_time = 0.0
# Now run through the simulation in batches.
# I do this to enable testing of coupling processes. Some initial investigations with non-ideality in
# the condensed phase indicated that even defining a maximum step was not enough for ODE solvers to
# overshoot a stable region. It also helps with in-simulation debugging. Its up to you if you want to keep this.
# To not run in batches, just define one batch as your total simulation time. This will reduce any overhead with
# initialising the solvers
# Set total simulation time and batch steps in seconds
# Note also that the current module outputs solver information after each batch step. This can be turned off and the
# the batch step change for increased speed
#simulation_time= 3600.0
#batch_step=100.0
t_array = []
time_step = 0
number_steps = int(
simulation_time /
batch_step) # Just cycling through 3 steps to get to a solution
# Define a matrix that stores values as outputs from the end of each batch step. Again, you can remove
# the need to run in batches. You can tell the Assimulo solvers the frequency of outputs.
y_matrix = numpy.zeros((int(number_steps), len(y0)))
print("Starting simulation")
# In the following, we can
while total_time < simulation_time:
if total_time == 0.0:
#Define an Assimulo problem
#Define an explicit solver
exp_mod = Explicit_Problem(dydt_func, y0, t0, name=filename)
else:
y0 = y_output[
-1, :] # Take the output from the last batch as the start of this
exp_mod = Explicit_Problem(dydt_func, y0, t0, name=filename)
# Define ODE parameters.
# Initial steps might be slower than mid-simulation. It varies.
#exp_mod.jac = dydt_jac
# Define which ODE solver you want to use
exp_sim = CVode(exp_mod)
tol_list = [1.0e-3] * num_species
exp_sim.atol = tol_list #Default 1e-6
exp_sim.rtol = 0.03 #Default 1e-6
exp_sim.inith = 1.0e-6 #Initial step-size
#exp_sim.discr = 'Adams'
exp_sim.maxh = 100.0
# Use of a jacobian makes a big differece in simulation time. This is relatively
# easy to define for a gas phase - not sure for an aerosol phase with composition
# dependent processes.
exp_sim.usejac = True # To be provided as an option in future update.
#exp_sim.fac1 = 0.05
#exp_sim.fac2 = 50.0
exp_sim.report_continuously = True
exp_sim.maxncf = 1000
#Sets the parameters
t_output, y_output = exp_sim.simulate(
batch_step) #Simulate 'batch' seconds
total_time += batch_step
t_array.append(
total_time
) # Save the output from the end step, of the current batch, to a matrix
y_matrix[time_step, :] = y_output[-1, :]
#now save this information into a matrix for later plotting.
time_step += 1
# Do you want to save the generated matrix of outputs?
if save_output:
numpy.save(filename + '_output', y_matrix)
df = pd.DataFrame(y_matrix)
df.to_csv(filename + "_output_matrix.csv")
w = csv.writer(open(filename + "_output_names.csv", "w"))
for specie, number in species_dict2array.items():
w.writerow([specie, number])
with_plots = True
#pdb.set_trace()
#Plot the change in concentration over time for a given specie. For the user to change / remove
#In a future release I will add this as a seperate module
if with_plots:
try:
P.plot(t_array,
numpy.log10(y_matrix[:, species_dict2array['APINENE']]),
marker='o',
label="APINENE")
P.plot(t_array,
numpy.log10(y_matrix[:, species_dict2array['PINONIC']]),
marker='o',
label="PINONIC")
P.title(exp_mod.name)
P.legend(loc='upper left')
P.ylabel("Concetration log10[molecules/cc]")
P.xlabel("Time [seconds] since start of simulation")
P.show()
except:
print(
"There is a problem using Matplotlib in your environment. If using this within a docker container, you will need to transfer the data to the host or configure your container to enable graphical displays. More information can be found at http://wiki.ros.org/docker/Tutorials/GUI "
)
def run_simulation(filename, save_output, start_time, temp, RH, RO2_indices,
H2O, PInit, y_cond, input_dict, simulation_time, batch_step,
plot_mass):
from assimulo.solvers import RodasODE, CVode, RungeKutta4, LSODAR #Choose solver accoring to your need.
from assimulo.problem import Explicit_Problem
# In this function, we import functions that have been pre-compiled for use in the ODE solver
# The function that calculates the RHS of the ODE is also defined within this function, such
# that it can be used by the Assimulo solvers
# The variables passed to this function are defined as follows:
#-------------------------------------------------------------------------------------
#-------------------------------------------------------------------------------------
# define the ODE function to be called
def dydt_func(t, y):
"""
This function defines the right-hand side [RHS] of the ordinary differential equations [ODEs] to be solved
input:
• t - time variable [internal to solver]
• y - array holding concentrations of all compounds in both gas and particulate [molecules/cc]
output:
dydt - the dy_dt of each compound in both gas and particulate phase [molecules/cc.sec]
"""
dy_dt = numpy.zeros((total_length_y, 1), )
#pdb.set_trace()
# Calculate time of day
time_of_day_seconds = start_time + t
#pdb.set_trace()
# make sure the y array is not a list. Assimulo uses lists
y_asnumpy = numpy.array(y)
Model_temp = temp
#pdb.set_trace()
#Calculate the concentration of RO2 species, using an index file created during parsing
RO2 = numpy.sum(y[RO2_indices])
#Calculate reaction rate for each equation.
# Note that H2O will change in parcel mode
# The time_of_day_seconds is used for photolysis rates - need to change this if want constant values
rates = evaluate_rates_fortran(RO2, H2O, Model_temp,
time_of_day_seconds)
#pdb.set_trace()
# Calculate product of all reactants and stochiometry for each reaction [A^a*B^b etc]
reactants = reactants_fortran(y_asnumpy[0:num_species - 1])
#pdb.set_trace()
#Multiply product of reactants with rate coefficient to get reaction rate
reactants = numpy.multiply(reactants, rates)
#pdb.set_trace()
# Now use reaction rates with the loss_gain matri to calculate the final dydt for each compound
# With the assimulo solvers we need to output numpy arrays
dydt_gas = loss_gain_fortran(reactants)
#pdb.set_trace()
dy_dt[0:num_species - 1, 0] = dydt_gas
# Change the saturation vapour pressure of water
# Need to re-think the change of organic vapour pressures with temperature.
# At the moment this is kept constant as re-calulation using UManSysProp very slow
sat_vap_water = numpy.exp((-0.58002206E4 / Model_temp) + 0.13914993E1 - \
(0.48640239E-1 * Model_temp) + (0.41764768E-4 * (Model_temp**2.0E0))- \
(0.14452093E-7 * (Model_temp**3.0E0)) + (0.65459673E1 * numpy.log(Model_temp)))
sat_vp[-1] = (numpy.log10(sat_vap_water * 9.86923E-6))
Psat = numpy.power(10.0, sat_vp)
# Convert the concentration of each component in the gas phase into a partial pressure using the ideal gas law
# Units are Pascals
Pressure_gas = (y_asnumpy[0:num_species, ] /
NA) * 8.314E+6 * Model_temp #[using R]
core_mass_array = numpy.multiply(ycore_asnumpy / NA, core_molw_asnumpy)
####### Calculate the thermal conductivity of gases according to the new temperature ########
K_water_vapour = (
5.69 + 0.017 *
(Model_temp - 273.15)) * 1e-3 * 4.187 #[W/mK []has to be in W/m.K]
# Use this value for all organics, for now. If you start using a non-zero enthalpy of
# vapourisation, this needs to change.
therm_cond_air = K_water_vapour
#----------------------------------------------------------------------------
#F2c) Extract the current gas phase concentrations to be used in pressure difference calculations
C_g_i_t = y_asnumpy[0:num_species, ]
#Set the values for oxidants etc to 0 as will force no mass transfer
#C_g_i_t[ignore_index]=0.0
C_g_i_t = C_g_i_t[include_index]
#pdb.set_trace()
total_SOA_mass,aw_array,size_array,dy_dt_calc = dydt_partition_fortran(y_asnumpy,ycore_asnumpy,core_dissociation, \
core_mass_array,y_density_array_asnumpy,core_density_array_asnumpy,ignore_index_fortran,y_mw,Psat, \
DStar_org_asnumpy,alpha_d_org_asnumpy,C_g_i_t,N_perbin,gamma_gas_asnumpy,Latent_heat_asnumpy,GRAV, \
Updraft,sigma,NA,kb,Rv,R_gas,Model_temp,cp,Ra,Lv_water_vapour)
#pdb.set_trace()
# Add the calculated gains/losses to the complete dy_dt array
dy_dt[0:num_species + (num_species_condensed * num_bins),
0] += dy_dt_calc[:]
#pdb.set_trace()
#----------------------------------------------------------------------------
#F4) Now calculate the change in water vapour mixing ratio.
#To do this we need to know what the index key for the very last element is
#pdb.set_trace()
#pdb.set_trace()
#print "elapsed time=", elapsedTime
dydt_func.total_SOA_mass = total_SOA_mass
dydt_func.size_array = size_array
dydt_func.temp = Model_temp
dydt_func.RH = Pressure_gas[-1] / (Psat[-1] * 101325.0)
dydt_func.water_activity = aw_array
#----------------------------------------------------------------------------
return dy_dt
#-------------------------------------------------------------------------------------
#-------------------------------------------------------------------------------------
#import static compilation of Fortran functions for use in ODE solver
print("Importing pre-compiled Fortran modules")
from rate_coeff_f2py import evaluate_rates as evaluate_rates_fortran
from reactants_conc_f2py import reactants as reactants_fortran
from loss_gain_f2py import loss_gain as loss_gain_fortran
from partition_f2py import dydt_partition as dydt_partition_fortran
# 'Unpack' variables from input_dict
species_dict = input_dict['species_dict']
species_dict2array = input_dict['species_dict2array']
species_initial_conc = input_dict['species_initial_conc']
equations = input_dict['equations']
num_species = input_dict['num_species']
num_species_condensed = input_dict['num_species_condensed']
y_density_array_asnumpy = input_dict['y_density_array_asnumpy']
y_mw = input_dict['y_mw']
sat_vp = input_dict['sat_vp']
Delta_H = input_dict['Delta_H']
Latent_heat_asnumpy = input_dict['Latent_heat_asnumpy']
DStar_org_asnumpy = input_dict['DStar_org_asnumpy']
alpha_d_org_asnumpy = input_dict['alpha_d_org_asnumpy']
gamma_gas_asnumpy = input_dict['gamma_gas_asnumpy']
Updraft = input_dict['Updraft']
GRAV = input_dict['GRAV']
Rv = input_dict['Rv']
Ra = input_dict['Ra']
R_gas = input_dict['R_gas']
R_gas_other = input_dict['R_gas_other']
cp = input_dict['cp']
sigma = input_dict['sigma']
NA = input_dict['NA']
kb = input_dict['kb']
Lv_water_vapour = input_dict['Lv_water_vapour']
ignore_index = input_dict['ignore_index']
ignore_index_fortran = input_dict['ignore_index_fortran']
ycore_asnumpy = input_dict['ycore_asnumpy']
core_density_array_asnumpy = input_dict['core_density_array_asnumpy']
y_cond = input_dict['y_cond_initial']
num_bins = input_dict['num_bins']
core_molw_asnumpy = input_dict['core_molw_asnumpy']
core_dissociation = input_dict['core_dissociation']
N_perbin = input_dict['N_perbin']
include_index = input_dict['include_index']
# pdb.set_trace()
#Specify some starting concentrations [ppt]
Cfactor = 2.55e+10 #ppb-to-molecules/cc
# Create variables required to initialise ODE
y0 = [0] * (num_species + num_species_condensed * num_bins
) #Initial concentrations, set to 0
t0 = 0.0 #T0
# Define species concentrations in ppb fr the gas phase
# You have already set this in the front end script, and now we populate the y array with those concentrations
for specie in species_initial_conc.keys():
if specie is not 'H2O':
y0[species_dict2array[specie]] = species_initial_conc[
specie] * Cfactor #convert from pbb to molcules/cc
elif specie is 'H2O':
y0[species_dict2array[specie]] = species_initial_conc[specie]
# Now add the initial condensed phase [including water]
#pdb.set_trace()
y0[num_species:num_species +
((num_bins) * num_species_condensed)] = y_cond[:]
#pdb.set_trace()
#Set the total_time of the simulation to 0 [havent done anything yet]
total_time = 0.0
# Define a 'key' that represents the end of the composition variables to track
total_length_y = len(y0)
key = num_species + ((num_bins) * num_species) - 1
#pdb.set_trace()
# Now run through the simulation in batches.
# I do this to enable testing of coupling processes. Some initial investigations with non-ideality in
# the condensed phase indicated that even defining a maximum step was not enough for ODE solvers to
# overshoot a stable region. It also helps with in-simulation debugging. Its up to you if you want to keep this.
# To not run in batches, just define one batch as your total simulation time. This will reduce any overhead with
# initialising the solvers
# Set total simulation time and batch steps in seconds
# Note also that the current module outputs solver information after each batch step. This can be turned off and the
# the batch step change for increased speed
# simulation_time= 3600.0
# batch_step=300.0
t_array = []
time_step = 0
number_steps = int(
simulation_time /
batch_step) # Just cycling through 3 steps to get to a solution
# Define a matrix that stores values as outputs from the end of each batch step. Again, you can remove
# the need to run in batches. You can tell the Assimulo solvers the frequency of outputs.
y_matrix = numpy.zeros((int(number_steps), len(y0)))
# Also define arrays and matrices that hold information such as total SOA mass
SOA_matrix = numpy.zeros((int(number_steps), 1))
size_matrix = numpy.zeros((int(number_steps), num_bins))
print("Starting simulation")
# In the following, we can
while total_time < simulation_time:
if total_time == 0.0:
#Define an Assimulo problem
#Define an explicit solver
exp_mod = Explicit_Problem(dydt_func, y0, t0, name=filename)
else:
y0 = y_output[
-1, :] # Take the output from the last batch as the start of this
exp_mod = Explicit_Problem(dydt_func, y0, t0, name=filename)
# Define ODE parameters.
# Initial steps might be slower than mid-simulation. It varies.
#exp_mod.jac = dydt_jac
# Define which ODE solver you want to use
exp_sim = CVode(exp_mod)
tol_list = [1.0e-2] * len(y0)
exp_sim.atol = tol_list #Default 1e-6
exp_sim.rtol = 1.0e-4 #Default 1e-6
exp_sim.inith = 1.0e-6 #Initial step-size
#exp_sim.discr = 'Adams'
exp_sim.maxh = 100.0
# Use of a jacobian makes a big differece in simulation time. This is relatively
# easy to define for a gas phase - not sure for an aerosol phase with composition
# dependent processes.
exp_sim.usejac = False # To be provided as an option in future update.
#exp_sim.fac1 = 0.05
#exp_sim.fac2 = 50.0
exp_sim.report_continuously = True
exp_sim.maxncf = 1000
#Sets the parameters
t_output, y_output = exp_sim.simulate(
batch_step) #Simulate 'batch' seconds
total_time += batch_step
t_array.append(
total_time
) # Save the output from the end step, of the current batch, to a matrix
y_matrix[time_step, :] = y_output[-1, :]
SOA_matrix[time_step, 0] = dydt_func.total_SOA_mass
size_matrix[time_step, :] = dydt_func.size_array
print("SOA [micrograms/m3] = ", dydt_func.total_SOA_mass)
#now save this information into a matrix for later plotting.
time_step += 1
if save_output is True:
print(
"Saving the model output as a pickled object for later retrieval")
# save the dictionary to a file for later retrieval - have to do each seperately.
with open(filename + '_y_output.pickle', 'wb') as handle:
pickle.dump(y_matrix, handle, protocol=pickle.HIGHEST_PROTOCOL)
with open(filename + '_t_output.pickle', 'wb') as handle:
pickle.dump(t_array, handle, protocol=pickle.HIGHEST_PROTOCOL)
with open(filename + '_SOA_output.pickle', 'wb') as handle:
pickle.dump(SOA_matrix, handle, protocol=pickle.HIGHEST_PROTOCOL)
with open(filename + '_size_output.pickle', 'wb') as handle:
pickle.dump(size_matrix, handle, protocol=pickle.HIGHEST_PROTOCOL)
with open(filename + 'include_index.pickle', 'wb') as handle:
pickle.dump(include_index,
handle,
protocol=pickle.HIGHEST_PROTOCOL)
#pdb.set_trace()
#Plot the change in concentration over time for a given specie. For the user to change / remove
#In a future release I will add this as a seperate module
if plot_mass is True:
try:
P.plot(t_array, SOA_matrix[:, 0], marker='o')
P.title(exp_mod.name)
P.ylabel("SOA mass [micrograms/m3]")
P.xlabel("Time [seconds] since start of simulation")
P.show()
except:
print(
"There is a problem using Matplotlib in your environment. If using this within a docker container, you will need to transfer the data to the host or configure your container to enable graphical displays. More information can be found at http://wiki.ros.org/docker/Tutorials/GUI "
)
def run_sim(Y, time, Y_AER1, YICE):
def dy_dt_func(t, Y):
dy_dt = np.zeros(len(Y))
# add condensed semi-vol mass into bins
if n.SV_flag:
MBIN2[-1 * n.n_sv:, :] = np.reshape(Y[INDSV1:INDSV2],
[n.n_sv, nbins * nmodes])
# calculate saturation vapour pressure over liquid
svp1 = f.svp_liq(Y[ITEMP])
# saturation ratio
SL = svp1 * Y[IRH] / (Y[IPRESS] - svp1)
SL = (SL * Y[IPRESS] / (1 + SL)) / svp1
# water vapour mixing ratio
WV = c.eps * Y[IRH] * svp1 / (Y[IPRESS] - svp1)
WL = np.sum(Y[IND1:IND2] * Y[:IND1]) # LIQUID MIXING RATIO
WI = np.sum(YICE[IND1:IND2] * YICE[:IND1]) # ice mixing ratio
RM = c.RA + WV * c.RV
CPM = c.CP + WV * c.CPV + WL * c.CPW + WI * c.CPI
if simulation_type.lower() == 'chamber':
# CHAMBER MODEL - pressure change
dy_dt[IPRESS] = -100 * PRESS1 * PRESS2 * np.exp(-PRESS2 *
(time + t))
elif simulation_type.lower() == 'parcel':
# adiabatic parcel
dy_dt[IPRESS] = -Y[IPRESS] / RM / Y[
ITEMP] * c.g * w #! HYDROSTATIC EQUATION
else:
print('simulation type unknown')
return
# ----------------------------change in vapour content: -----------------------
# 1. equilibruim size of particles
if n.kappa_flag:
#if n.SV_flag:
# need to recalc kappa taking into acount the condensed semi-vols
Kappa = np.sum(
(MBIN2[:, :] / RHOBIN2[:, :]) * KAPPABIN2[:, :],
axis=0) / np.sum(MBIN2[:, :] / RHOBIN2[:, :], axis=0)
# print(Kappa)
# print(MBIN2/RHOBIN2)
KK01 = f.kk01(Y[0:IND1], Y[ITEMP], MBIN2, RHOBIN2, Kappa)
else:
KK01 = f.K01(Y[0:IND1], Y[ITEMP], MBIN2, n.n_sv, RHOBIN2,
NUBIN2, MOLWBIN2)
# print(KK01[0])
Dw = KK01[2] # wet diameter
RHOAT = KK01[1] # density of particles inc water and aerosol mass
RH_EQ = KK01[0] # equilibrium RH
# print(MBIN2/MOLWBIN2)
# 2. growth rate of particles, Jacobson p455
# rate of change of radius
growth_rate = f.DROPGROWTHRATE(Y[ITEMP], Y[IPRESS], SL, RH_EQ,
RHOAT, Dw)
growth_rate[np.isnan(growth_rate)] = 0 # get rid of nans
growth_rate = np.where(Y[IND1:IND2] < 1e-9, 0.0, growth_rate)
# 3. Mass of water condensing
# change in mass of water per particle
dy_dt[:IND1] = (np.pi * RHOAT * Dw**2) * growth_rate
# 4. Change in vapour content
# change in water vapour mixing ratio
dwv_dt = -1 * np.sum(
Y[IND1:IND2] *
dy_dt[:IND1]) # change to np.sum for speed # mass
# -----------------------------------------------------------------------------
if simulation_type.lower() == 'chamber':
# CHAMBER MODEL - temperature change
dy_dt[ITEMP] = -Temp1 * Temp2 * np.exp(-Temp2 * (time + t))
elif simulation_type.lower() == 'parcel':
# adiabatic parcel
dy_dt[ITEMP] = RM / Y[IPRESS] * dy_dt[IPRESS] * Y[
ITEMP] / CPM # TEMPERATURE CHANGE: EXPANSION
dy_dt[ITEMP] = dy_dt[ITEMP] - c.LV / CPM * dwv_dt
else:
print('simulation type unknown')
return
# --------------------------------RH change------------------------------------
dy_dt[IRH] = svp1 * dwv_dt * (Y[IPRESS] - svp1)
dy_dt[IRH] = dy_dt[IRH] + svp1 * WV * dy_dt[IPRESS]
dy_dt[IRH] = (
dy_dt[IRH] - WV * Y[IPRESS] *
derivative(f.svp_liq, Y[ITEMP], dx=1.0) * dy_dt[ITEMP])
dy_dt[IRH] = dy_dt[IRH] / (c.eps * svp1**2)
# -----------------------------------------------------------------------------
# ------------------------------ SEMI-VOLATILES -------------------------------
if n.SV_flag:
# SV_mass = np.reshape(Y[INDSV1:INDSV2],[n.n_sv,n.nmodes*n.nbins])
# SV_mass = np.where(SV_mass == 0.0,1e-30,SV_mass)
# MBIN2[n.n_sv*-1:,:] = SV_mass
RH_EQ_SV = f.K01SV(Y[:IND1], Y[ITEMP], MBIN2, n.n_sv, RHOBIN2,
NUBIN2, MOLWBIN2)
RH_EQ = RH_EQ_SV[0]
RHOAT = RH_EQ_SV[1]
DW = RH_EQ_SV[2]
SVP_ORG = f.SVP_GASES(n.semi_vols, Y[ITEMP],
n.n_sv) #C-C equation
#RH_ORG = [x*Y[IPRESS]/c.RA/Y[ITEMP] for x in Y[IRH_SV]]
RH_ORG = [x for x in Y[IRH_SV]]
RH_ORG = [(x / c.aerosol_dict[key][0]) * c.R * Y[ITEMP]
for x, key in zip(RH_ORG, n.semi_vols[:n.n_sv])
] # just for n_sv keys in dictionary
RH_ORG = [RH_ORG[x] / SVP_ORG[x] for x in range(n.n_sv)]
dy_dt[INDSV1:INDSV2] = f.SVGROWTHRATE(Y[ITEMP], Y[IPRESS],
SVP_ORG, RH_ORG, RH_EQ,
DW, n.n_sv, n.nbins,
n.nmodes, MOLWBIN2)
dy_dt[IRH_SV] = -np.sum(np.reshape(
dy_dt[INDSV1:INDSV2], [n.n_sv, IND1]) * Y[IND1:IND2],
axis=1) #see line 137
return dy_dt
#--------------------- SET-UP solver ------------------------------------------
y0 = Y
t0 = 0.0
#define assimulo problem
exp_mod = Explicit_Problem(dy_dt_func, y0, t0)
# define an explicit solver
exp_sim = CVode(exp_mod)
exp_sim.iter = 'Newton'
exp_sim.discr = 'BDF'
#set parameters
tol_list = np.zeros_like(Y)
tol_list[0:IND1] = 1e-40 # this is now different to ACPIM (1e-25)
tol_list[IND1:IND2] = 10 # number
tol_list[IND2:IND3] = 1e-30 # capacitance
tol_list[IND3:INDSV2] = 1e-26 #condendensed semi-vol mass
tol_list[IRH_SV] = 1e-26 # RH of each semi-vol compound
tol_list[IPRESS] = 10
tol_list[ITEMP] = 1e-4
tol_list[IRH] = 1e-8 # set tolerance for each dydt function
exp_sim.atol = tol_list
exp_sim.rtol = 1.0e-8
exp_sim.inith = 0 # initial time step-size
exp_sim.usejac = False
exp_sim.maxncf = 100 # max number of convergence failures allowed by solver
exp_sim.verbosity = 40
t_output, y_output = exp_sim.simulate(1)
return y_output[-1, :], t_output[:]
def run_sim_ice(Y, YLIQ):
def dy_dt_func(t, Y):
dy_dt = np.zeros(len(Y))
svp = f.svp_liq(Y[ITEMP])
svp_ice = f.svp_ice(Y[ITEMP])
# vapour mixing ratio
WV = c.eps * Y[IRH_ICE] * svp / (Y[IPRESS_ICE] - svp)
# liquid mixing ratio
WL = sum(YLIQ[IND1:IND2] * YLIQ[0:IND1])
# ice mixing ratio
WI = sum(Y[IND1:IND2] * Y[0:IND1])
Cpm = c.CP + WV * c.CPV + WL * c.CPW + WI * c.CPI
# RH with respect to ice
RH_ICE = WV / (c.eps * svp_ice / (Y[IPRESS_ICE] - svp_ice))
# ------------------------- growth rate of ice --------------------------
RH_EQ = 1e0 # from ACPIM, FPARCELCOLD - MICROPHYSICS.f90
CAP = f.CAPACITANCE01(Y[0:IND1], np.exp(Y[IND2:IND3]))
growth_rate = f.ICEGROWTHRATE(Y[ITEMP_ICE], Y[IPRESS_ICE],
RH_ICE, RH_EQ, Y[0:IND1],
np.exp(Y[IND2:IND3]), CAP)
growth_rate[np.isnan(growth_rate)] = 0 # get rid of nans
growth_rate = np.where(Y[IND1:IND2] < 1e-6, 0.0, growth_rate)
# Mass of water condensing
dy_dt[:IND1] = growth_rate
#---------------------------aspect ratio---------------------------------------
DELTA_RHO = c.eps * svp / (Y[IPRESS_ICE] - svp)
DELTA_RHOI = c.eps * svp_ice / (Y[IPRESS_ICE] - svp_ice)
DELTA_RHO = Y[IRH_ICE] * DELTA_RHO - DELTA_RHOI
DELTA_RHO = DELTA_RHO * Y[IPRESS_ICE] / Y[ITEMP_ICE] / c.RA
RHO_DEP = f.DEP_DENSITY(DELTA_RHO, Y[ITEMP_ICE])
# this is the rate of change of LOG of the aspect ratio
dy_dt[IND2:IND3] = (dy_dt[0:IND1] *
((f.INHERENTGROWTH(Y[ITEMP_ICE]) - 1) /
(f.INHERENTGROWTH(Y[ITEMP_ICE]) + 2)) /
(Y[0:IND1] * c.rhoi * RHO_DEP))
#------------------------------------------------------------------------------
# Change in vapour content
dwv_dt = -1 * sum(Y[IND1:IND2] * dy_dt[0:IND1])
# change in water vapour mixing ratio
DRI = -1 * dwv_dt
dy_dt[ITEMP_ICE] = 0.0 #+c.LS/Cpm*DRI
# if n.Simulation_type.lower() == 'parcel':
# dy_dt[ITEMP_ICE]=dy_dt[ITEMP_ICE] + c.LS/Cpm*DRI
#---------------------------RH change------------------------------------------
dy_dt[IRH_ICE] = (Y[IPRESS_ICE] - svp) * svp * dwv_dt
dy_dt[IRH_ICE] = (
dy_dt[IRH_ICE] - WV * Y[IPRESS_ICE] *
derivative(f.svp_liq, Y[ITEMP_ICE], dx=1.0) * dy_dt[ITEMP_ICE])
dy_dt[IRH_ICE] = dy_dt[IRH_ICE] / (c.eps * svp**2)
#------------------------------------------------------------------------------
return dy_dt
#--------------------- SET-UP solver --------------------------------------
y0 = Y
t0 = 0.0
#define assimulo problem
exp_mod = Explicit_Problem(dy_dt_func, y0, t0)
# define an explicit solver
exp_sim = CVode(exp_mod)
exp_sim.iter = 'Newton'
exp_sim.discr = 'BDF'
# set tolerance for each dydt function
tol_list = np.zeros_like(Y)
tol_list[0:IND1] = 1e-30 # mass
tol_list[IND1:IND2] = 10 # number
tol_list[IND2:IND3] = 1e-30 # aspect ratio
# tol_list[IND3:IRH_SV_ICE] = 1e-26
#tol_list[IRH_SV_ICE] = 1e-26
tol_list[IPRESS_ICE] = 10
tol_list[ITEMP_ICE] = 1e-4
tol_list[IRH_ICE] = 1e-8
exp_sim.atol = tol_list
exp_sim.rtol = 1.0e-8
exp_sim.inith = 1.0e-2 # initial time step-size
exp_sim.usejac = False
exp_sim.maxncf = 100 # max number of convergence failures allowed by solver
exp_sim.verbosity = 40
t_output, y_output = exp_sim.simulate(1)
return y_output[-1, :]
def func_set_system():
##############################################
#% initial conditions
P_0 = depth*9.8*2600. #; % initial chamber pressure (Pa)
T_0 = 1200 #; % initial chamber temperature (K)
eps_g0 = 0.04 #; % initial gas volume fraction
rho_m0 = 2600 #; % initial melt density (kg/m^3)
rho_x0 = 3065 #; % initial crystal density (kg/m^3)
a = 2000. #; % initial radius of the chamber (m)
V_0 = (4.*np.pi/3.)*a**3. #; % initial volume of the chamber (m^3)
##############################################
##############################################
IC = np.array([P_0, T_0, eps_g0, V_0, rho_m0, rho_x0]) # % store initial conditions
## Gas (eps_g = zero), eps_x is zero, too many crystals, 50 % crystallinity,eruption (yes/no)
sw0 = [False,False,False,False,False]
##############################################
#% error tolerances used in ode method
dt = 3e7*10.
begin_time = 0 # ; % initialize time
N = int(round((end_time-begin_time)/dt))
##############################################
#Define an Assimulo problem
exp_mod = Chamber_Problem(depth=depth,t0=begin_time,y0=IC,sw0=sw0)
exp_mod.param['T_S'] = 500.#+273.
exp_mod.param['T_in'] = 1200.
exp_mod.param['eps_g_in'] = 0.0 # Gas fraction of incoming melt - gas phase ..
exp_mod.param['m_eq_in'] = 0.03 # Volatile fraction of incoming melt
exp_mod.param['Mdot_in'] = mdot
exp_mod.param['eta_x_max'] = 0.55 # Locking fraction
exp_mod.param['delta_Pc'] = 20e6
exp_mod.allow_diffusion_init = True
exp_mod.radius = a
exp_mod.permeability = perm_val
exp_mod.R_steps = 1500
exp_mod.dt_init = dt
inp_func1 = inp.Input_functions_Degruyer()
exp_mod.set_input_functions(inp_func1)
exp_mod.get_constants()
exp_mod.set_init_crust(material = 'Westerly_Granite')
#################
begin_time = exp_mod.set_init_crust_profile(T_0)
exp_mod.tcurrent = begin_time
P_0 = exp_mod.plith
exp_mod.t0 = begin_time
exp_mod.param['heat_cond'] = 1. # Turn on/off heat conduction
exp_mod.param['visc_relax'] = 1. # Turn on/off viscous relaxation
exp_mod.param['press_relax'] = 1. ## Turn on/off pressure diffusion
exp_mod.param['frac_rad_Temp'] =0.75
exp_mod.param['vol_degass'] = 1.
exp_mod.param['outflow_model'] = None # 'huppert'
IC = np.array([P_0, T_0, eps_g0, V_0, rho_m0, rho_x0]) # % store initial conditions
exp_mod.y0 = IC
#Define an explicit solver
exp_sim = CVode(exp_mod) #Create a CVode solver
# exp_sim = LSODAR(exp_mod) #Create a CVode solver
#Sets the parameters
exp_sim.store_event_points = True
#exp_sim.iter = 'Newton'
#exp_sim.discr = 'BDF'
exp_sim.inith = 1e2
#exp_sim.display_progress = True
exp_sim.rtol = 1.e-7
#exp_sim.maxh = 3e8*5. # 10 years
exp_sim.atol = 1e-7
#exp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitvity method used
#exp_sim.suppress_sens = True #Dont suppress the sensitivity variables in the error test.
#exp_sim.usesens = True
#exp_sim.report_continuously = True
return exp_mod,exp_sim,N
mod_pen = Explicit_Problem(rhs, y0, t0)
mod_pen.name = 'Elastic Pendulum with CVode'
"""
Run simulation
"""
#Create solver object
sim_pen = CVode(mod_pen)
#Simulation parameters
#atol = 1.e-6*ones(shape(y0))
atol = rtol * N.array([1, 1, 1, 1]) #default 1e-06
sim_pen.atol = atol
sim_pen.rtol = rtol
sim_pen.maxh = hmax
sim_pen.maxord = maxord
sim_pen.inith = h0
#Simulate
t, y = sim_pen.simulate(tf)
"""
Plot results
"""
#Plot
#P.plot(t,y)
#P.legend(['$x$','$y$','$\dot{x}$','$\dot{y}$'])
#P.title('Elastic pendulum with k = ' + str(k) + ', stretch = ' + str(stretch))
#P.xlabel('time')
#P.ylabel('state')
#show()
P.plot(y[:, 0], y[:, 1])
P.plot(y[0, 0], y[0, 1], 'ro')
def run_simulation(filename, save_output, start_time, temp, RH, RO2_indices,
H2O, input_dict, simulation_time, batch_step):
from assimulo.solvers import RodasODE, CVode #Choose solver accoring to your need.
from assimulo.problem import Explicit_Problem
# In this function, we import functions that have been pre-compiled for use in the ODE solver
# The function that calculates the RHS of the ODE is also defined within this function, such
# that it can be used by the Assimulo solvers
# In the standard Python version [not using Numba] I use Sparse matrix operations in calculating loss/gain of each compound.
# This function loads the matrix created at the beginning of the module.
def load_sparse_csr(filename):
loader = numpy.load('loss_gain_' + filename + '.npz')
return csr_matrix(
(loader['data'], loader['indices'], loader['indptr']),
shape=loader['shape'])
def load_sparse_csr_reactants(filename):
loader = numpy.load('reactants_indices_sparse_' + filename + '.npz')
return csr_matrix(
(loader['data'], loader['indices'], loader['indptr']),
shape=loader['shape'])
#-------------------------------------------------------------------------------------
# define the ODE function to be called
def dydt_func(t, y):
"""
This function defines the right-hand side [RHS] of the ordinary differential equations [ODEs] to be solved
input:
• t - time variable [internal to solver]
• y - array holding concentrations of all compounds in both gas and particulate [molecules/cc]
output:
dydt - the dy_dt of each compound in both gas and particulate phase [molecules/cc.sec]
"""
#pdb.set_trace()
#Here we use the pre-created Numba based functions to arrive at our value for dydt
# Calculate time of day
time_of_day_seconds = start_time + t
# make sure the y array is not a list. Assimulo uses lists
y_asnumpy = numpy.array(y)
#pdb.set_trace()
# reactants=numpy.zeros((equations),)
#pdb.set_trace()
#Calculate the concentration of RO2 species, using an index file created during parsing
RO2 = numpy.sum(y[RO2_indices])
#Calculate reaction rate for each equation.
# Note that H2O will change in parcel mode [to be changed in the full aerosol mode]
# The time_of_day_seconds is used for photolysis rates - need to change this if want constant values
#pdb.set_trace()
rates = evaluate_rates(time_of_day_seconds, RO2, H2O, temp,
numpy.zeros((equations)), numpy.zeros((63)))
# Calculate product of all reactants and stochiometry for each reaction [A^a*B^b etc]
reactants = reactant_product(y_asnumpy, equations,
numpy.zeros((equations)))
#Multiply product of reactants with rate coefficient to get reaction rate
#pdb.set_trace()
reactants = numpy.multiply(reactants, rates)
# Now use reaction rates with the loss_gain information in a pre-created Numba file to calculate the final dydt for each compound
dydt = dydt_eval(numpy.zeros((len(y_asnumpy))), reactants)
#pdb.set_trace()
############ Development place-holder ##############
# ----------------------------------------------------------------------------------
# The following demonstrates the same procedure but using only Numpy and pure python
# For the full MCM this is too slow, but is useful for demonstrations and testing
#Calculate reaction rate for each equation.
## rates=test(time_of_day_seconds,RO2,H2O,temp)
# Calculate product of all reactants and stochiometry for each reaction [A^a*B^b etc]
# Take the approach of using sparse matrix operations from a python perspective
# This approach uses the rule of logarithms and sparse matrix multiplication
##temp_array=reactants_indices_sparse @ numpy.log(y_asnumpy)
##indices=numpy.where(temp_array > 0.0)
##reactants[indices]=numpy.exp(temp_array[indices])
#Multiply product of reactants with rate coefficient to get reaction rate
## reactants = numpy.multiply(reactants,rates)
# Now use reaction rates with the loss_gain matri to calculate the final dydt for each compound
# With the assimulo solvers we need to output numpy arrays
##dydt=numpy.array(loss_gain @ reactants)
# ----------------------------------------------------------------------------------
return dydt
#-------------------------------------------------------------------------------------
print(
"Importing Numba modules [compiling if first import or clean build...please be patient]"
)
#import Numba functions for use in ODE solver
from Rate_coefficients_numba import evaluate_rates
from Reactants_conc_numba import reactants as reactant_product
from Loss_Gain_numba import dydt as dydt_eval
# 'Unpack' variables from input_dict
species_dict = input_dict['species_dict']
species_dict2array = input_dict['species_dict2array']
species_initial_conc = input_dict['species_initial_conc']
equations = input_dict['equations']
# Set dive by zero to ignore for use of any sparse matrix multiplication
numpy.errstate(divide='ignore')
# --- For Numpy and pure Python runs ----
# Load the sparse matrix used in calculating the reactant products and dydt function
## reactants_indices_sparse = load_sparse_csr_reactants(filename)
## loss_gain = load_sparse_csr(filename)
#Specify some starting concentrations [ppt]
Cfactor = 2.55e+10 #ppb-to-molecules/cc
# Create variables required to initialise ODE
num_species = len(species_dict.keys())
y0 = [0] * num_species #Initial concentrations, set to 0
t0 = 0.0 #T0
# Define species concentrations in ppb
# You have already set this in the front end script, and now we populate the y array with those concentrations
for specie in species_initial_conc.keys():
y0[species_dict2array[specie]] = species_initial_conc[
specie] * Cfactor #convert from pbb to molcules/cc
#Set the total_time of the simulation to 0 [havent done anything yet]
total_time = 0.0
# Now run through the simulation in batches.
# I do this to enable testing of coupling processes. Some initial investigations with non-ideality in
# the condensed phase indicated that even defining a maximum step was not enough for ODE solvers to
# overshoot a stable region. It also helps with in-simulation debugging. Its up to you if you want to keep this.
# To not run in batches, just define one batch as your total simulation time. This will reduce any overhead with
# initialising the solvers
# Set total simulation time and batch steps in seconds
# Note also that the current module outputs solver information after each batch step. This can be turned off and the
# the batch step change for increased speed
# simulation_time= 3600.0 # seconds
# batch_step=100.0 # seconds
t_array = []
time_step = 0
number_steps = int(
simulation_time /
batch_step) # Just cycling through 3 steps to get to a solution
# Define a matrix that stores values as outputs from the end of each batch step. Again, you can remove
# the need to run in batches. You can tell the Assimulo solvers the frequency of outputs.
y_matrix = numpy.zeros((int(number_steps), len(y0)))
print("Starting simulation")
#pdb.set_trace()
while total_time < simulation_time:
if total_time == 0.0:
#Define an Assimulo problem
#Define an explicit solver
#pdb.set_trace()
exp_mod = Explicit_Problem(dydt_func, y0, t0, name=filename)
else:
y0 = y_output[
-1, :] # Take the output from the last batch as the start of this
exp_mod = Explicit_Problem(dydt_func, y0, t0, name=filename)
# Define ODE parameters.
# Initial steps might be slower than mid-simulation. It varies.
#exp_mod.jac = dydt_jac
# Define which ODE solver you want to use
exp_sim = CVode(exp_mod)
tol_list = [1.0e-3] * num_species
exp_sim.atol = tol_list #Default 1e-6
exp_sim.rtol = 1e-6 #Default 1e-6
exp_sim.inith = 1.0e-6 #Initial step-size
#exp_sim.discr = 'Adams'
exp_sim.maxh = 100.0
# Use of a jacobian makes a big differece in simulation time. This is relatively
# easy to define for a gas phase - not sure for an aerosol phase with composition
# dependent processes.
exp_sim.usejac = False # To be provided as an option in future update. See Fortran variant for use of Jacobian
#exp_sim.fac1 = 0.05
#exp_sim.fac2 = 50.0
exp_sim.report_continuously = True
exp_sim.maxncf = 1000
#Sets the parameters
t_output, y_output = exp_sim.simulate(
batch_step) #Simulate 'batch' seconds
total_time += batch_step
t_array.append(
total_time
) # Save the output from the end step, of the current batch, to a matrix
y_matrix[time_step, :] = y_output[-1, :]
#pdb.set_trace()
#now save this information into a matrix for later plotting.
time_step += 1
# Do you want to save the generated matrix of outputs?
if save_output:
numpy.save(filename + '_output', y_matrix)
df = pd.DataFrame(y_matrix)
df.to_csv(filename + "_output_matrix.csv")
w = csv.writer(open(filename + "_output_names.csv", "w"))
for specie, number in species_dict2array.items():
w.writerow([specie, number])
with_plots = True
#pdb.set_trace()
#Plot the change in concentration over time for a given specie. For the user to change / remove
#In a future release I will add this as a seperate module
if with_plots:
try:
P.plot(t_array,
numpy.log10(y_matrix[:, species_dict2array['APINENE']]),
marker='o',
label="APINENE")
P.plot(t_array,
numpy.log10(y_matrix[:, species_dict2array['PINONIC']]),
marker='o',
label="PINONIC")
P.title(exp_mod.name)
P.legend(loc='upper left')
P.ylabel("Concetration log10[molecules/cc]")
P.xlabel("Time [seconds] since start of simulation")
P.show()
except:
print(
"There is a problem using Matplotlib in your environment. If using this within a docker container, you will need to transfer the data to the host or configure your container to enable graphical displays. More information can be found at http://wiki.ros.org/docker/Tutorials/GUI "
)
