def sdc_spinup(self, water, ll, cwd, rl, lnc):
"""SOIL POOLS SPINUP"""
for x in range(100000):
s_out = soil_dec.carbon3(self.soil_temp, water / self.wmax_mm, ll,
cwd, rl, lnc, self.sp_csoil, self.sp_snc)
soil_out = catch_out_carbon3(s_out)
self.sp_csoil = soil_out['cs']
self.sp_snc = soil_out['snc']
def run_caete(self, start_date, end_date, spinup=0, fix_co2=None):
""" start_date [str] "yyyymmdd" Start model execution
end_date [str] "yyyymmdd" End model execution
spinup [int] Number of repetitions in spinup. 0 for no spinup
fix_co2 [Float] Fixed value for ATM [CO2]
[int] Fixed value for ATM [CO2]
[str] "yyyy" Corresponding year of an ATM [CO2]
This function run the fortran subroutines and manage data flux. It
is the proper CAETÊ-DVM execution in the start_date - end_date period
"""
assert self.filled, "The gridcell has no input data"
assert not fix_co2 or type(
fix_co2
) == str or fix_co2 > 0, "A fixed value for ATM[CO2] must be a positive number greater than zero or a proper string "
def find_co2(year):
for i in self.co2_data:
if int(i.split('\t')[0]) == year:
return float(i.split('\t')[1].strip())
def find_index(start, end):
result = []
num = np.arange(self.ssize)
ind = np.arange(self.sind, self.eind + 1)
for r, i in zip(num, ind):
if i == start:
result.append(r)
for r, i in zip(num, ind):
if i == end:
result.append(r)
return result
# Define start and end dates (read actual arguments)
start = cftime.real_datetime(int(start_date[:4]), int(start_date[4:6]),
int(start_date[6:]))
end = cftime.real_datetime(int(end_date[:4]), int(end_date[4:6]),
int(end_date[6:]))
# Check dates sanity
assert start < end, "start > end"
assert start >= self.start_date
assert end <= self.end_date
# Define time index
start_index = int(cftime.date2num(start, self.time_unit,
self.calendar))
end_index = int(cftime.date2num(end, self.time_unit, self.calendar))
lb, hb = find_index(start_index, end_index)
steps = np.arange(lb, hb + 1)
day_indexes = np.arange(start_index, end_index + 1)
spin = 1 if spinup == 0 else spinup
# Catch climatic input and make conversions
temp = self.tas[lb:hb + 1] - 273.15 # ! K to °C
prec = self.pr[lb:hb + 1] * 86400 # kg m-2 s-1 to mm/day
# transforamando de Pascal pra mbar (hPa)
p_atm = self.ps[lb:hb + 1] * 0.01
# W m-2 to mol m-2 s-1 ! 0.5 converts RSDS to PAR
ipar = self.rsds[lb:hb + 1] * 0.5 / 2.18e5
ru = self.rhs[lb:hb + 1] / 100.0
year0 = start.year
co2 = find_co2(year0)
count_days = start.dayofyr - 2
loop = 0
next_year = 0.0
fix_co2_p = False
if fix_co2 is None:
fix_co2_p = False
elif type(fix_co2) == int or type(fix_co2) == float:
co2 = fix_co2
fix_co2_p = True
elif type(fix_co2) == str:
assert type(
int(fix_co2)
) == int, "The string(\"yyyy\") for the fix_co2 argument must be an year between 1901-2016"
co2 = find_co2(int(fix_co2))
fix_co2_p = True
for s in range(spin):
self._allocate_output(steps.size)
for step in range(steps.size):
if fix_co2_p:
pass
else:
loop += 1
count_days += 1
# CAST CO2 ATM CONCENTRATION
days = 366 if m.leap(year0) == 1 else 365
if count_days == days:
count_days = 0
year0 = cftime.num2date(day_indexes[step],
self.time_unit,
self.calendar).year
co2 = find_co2(year0)
next_year = (find_co2(year0 + 1) - co2) / days
elif loop == 1 and count_days < days:
year0 = start.year
next_year = (find_co2(year0 + 1) - co2) / \
(days - count_days)
co2 += next_year
# if step == 0:
# #print('1st day')
# Update soil temperature
self.soil_temp = st.soil_temp(self.soil_temp, temp[step])
# INFLATe VARS
sto = np.zeros(shape=(3, npls), order='F')
cleaf = np.zeros(npls, order='F')
cwood = np.zeros(npls, order='F')
croot = np.zeros(npls, order='F')
dcl = np.zeros(npls, order='F')
dca = np.zeros(npls, order='F')
dcf = np.zeros(npls, order='F')
uptk_costs = np.zeros(npls, order='F')
sto[0, self.vp_lsid] = self.vp_sto[0, :]
sto[1, self.vp_lsid] = self.vp_sto[1, :]
sto[2, self.vp_lsid] = self.vp_sto[2, :]
# Just Check the integrity of the data
assert self.vp_lsid.size == self.vp_cleaf.size, 'different shapes'
c = 0
for n in self.vp_lsid:
cleaf[n] = self.vp_cleaf[c]
cwood[n] = self.vp_cwood[c]
croot[n] = self.vp_croot[c]
dcl[n] = self.vp_dcl[c]
dca[n] = self.vp_dca[c]
dcf[n] = self.vp_dcf[c]
uptk_costs[n] = self.sp_uptk_costs[c]
c += 1
ton = self.sp_organic_n + self.sp_sorganic_n
top = self.sp_organic_p + self.sp_sorganic_p
out = model.daily_budget(
self.pls_table, self.wp_water_upper_mm,
self.wp_water_lower_mm, self.soil_temp, temp[step],
p_atm[step], ipar[step], ru[step], self.sp_available_n,
self.sp_available_p, ton, top, self.sp_organic_p, co2, sto,
cleaf, cwood, croot, dcl, dca, dcf, uptk_costs,
self.wmax_mm, step)
del sto, cleaf, cwood, croot, dcl, dca, dcf, uptk_costs
# Create a dict with the function output
daily_output = catch_out_budget(out)
self.vp_lsid = np.where(daily_output['ocpavg'] > 0.0)[0]
self.vp_ocp = daily_output['ocpavg'][self.vp_lsid]
self.ls[step] = self.vp_lsid.size
# UPDATE STATE VARIABLES
# WATER CWM
self.runom[step] = self._update_pool(prec[step],
daily_output['evavg'])
# UPDATE vegetation pools ! ABLE TO USE SPARSE MATRICES
self.vp_cleaf = daily_output['cleafavg_pft'][self.vp_lsid]
self.vp_cwood = daily_output['cawoodavg_pft'][self.vp_lsid]
self.vp_croot = daily_output['cfrootavg_pft'][self.vp_lsid]
self.vp_dcl = daily_output['delta_cveg'][0][self.vp_lsid]
self.vp_dca = daily_output['delta_cveg'][1][self.vp_lsid]
self.vp_dcf = daily_output['delta_cveg'][2][self.vp_lsid]
self.vp_sto = daily_output['stodbg'][:, self.vp_lsid]
self.sp_uptk_costs = daily_output['npp2pay'][self.vp_lsid]
# Plant uptake and Carbon costs of nutrient uptake
self.nupt[:, step] = daily_output['nupt']
self.pupt[:, step] = daily_output['pupt']
for i in range(3):
self.storage_pool[i, step] = np.sum(self.vp_ocp *
self.vp_sto[i])
# OUTPUTS for SOIL CWM
self.litter_l[step] = daily_output['litter_l']
self.cwd[step] = daily_output['cwd']
self.litter_fr[step] = daily_output['litter_fr']
self.lnc[:, step] = daily_output['lnc']
wtot = self.wp_water_upper_mm + self.wp_water_lower_mm
s_out = soil_dec.carbon3(self.soil_temp, wtot / self.wmax_mm,
self.litter_l[step], self.cwd[step],
self.litter_fr[step], self.lnc[:,
step],
self.sp_csoil, self.sp_snc)
soil_out = catch_out_carbon3(s_out)
# Organic C N & P
self.sp_csoil = soil_out['cs']
self.sp_snc = soil_out['snc']
# INCLUDE MINERALIZED NUTRIENTS
self.sp_available_p += soil_out['pmin']
self.sp_available_n += soil_out['nmin']
# NUTRIENT DINAMICS
# Inorganic N
self.sp_in_n += self.sp_available_n + self.sp_so_n
self.sp_so_n = soil_dec.sorbed_n_equil(self.sp_in_n)
self.sp_available_n = soil_dec.solution_n_equil(self.sp_in_n)
self.sp_in_n -= self.sp_so_n + self.sp_available_n
# Inorganic P
self.sp_in_p += self.sp_available_p + self.sp_so_p
self.sp_so_p = soil_dec.sorbed_p_equil(self.sp_in_p)
self.sp_available_p = soil_dec.solution_p_equil(self.sp_in_p)
self.sp_in_p -= self.sp_so_p + self.sp_available_p
# Sorbed P
if self.pupt[1, step] > 0.05:
rwarn(
f"Puptk_SO > soP_max - 729 | in spin{s}, step{step} - {self.pupt[1, step]}"
)
self.pupt[1, step] = 0.0
if self.pupt[1, step] > self.sp_so_p:
rwarn(
f"Puptk_SO > soP_pool - 731 | in spin{s}, step{step} - {self.pupt[1, step]}"
)
self.sp_so_p -= self.pupt[1, step]
t1 = np.all(self.sp_snc > 0.0)
if not t1:
self.snc[np.where(self.snc < 0)] = 0.0
# ORGANIC nutrients uptake
# N
if self.nupt[1, step] < 0.0:
rwarn(
f"NuptkO < 0 - 745 | in spin{s}, step{step} - {self.nupt[1, step]}"
)
self.nupt[1, step] = 0.0
if self.nupt[1, step] > 0.8:
rwarn(
f"NuptkO > max - 749 | in spin{s}, step{step} - {self.nupt[1, step]}"
)
self.nupt[1, step] = 0.0
total_on = self.sp_snc[:4].sum()
frsn = [i / total_on for i in self.sp_snc[:4]]
for i, fr in enumerate(frsn):
self.sp_snc[i] -= self.nupt[1, step] * fr
self.sp_organic_n = self.sp_snc[:2].sum()
self.sp_sorganic_n = self.sp_snc[2:4].sum()
# P
if self.pupt[2, step] < 0.0:
rwarn(
f"PuptkO < 0 - 759 | in spin{s}, step{step} - {self.pupt[2, step]}"
)
self.pupt[2, step] = 0.0
if self.pupt[2, step] > 0.1:
rwarn(
f"PuptkO < max - 763 | in spin{s}, step{step} - {self.pupt[2, step]}"
)
self.pupt[2, step] = 0.0
total_op = self.sp_snc[4:].sum()
frsp = [i / total_op for i in self.sp_snc[4:]]
for i, fr in enumerate(frsp):
self.sp_snc[i + 4] -= self.pupt[2, step] * fr
self.sp_organic_p = self.sp_snc[4:6].sum()
self.sp_sorganic_p = self.sp_snc[6:].sum()
# Raise some warnings
if self.sp_organic_n < 0.0:
rwarn(f"ON negative in spin{s}, step{step}")
if self.sp_sorganic_n < 0.0:
rwarn(f"SON negative in spin{s}, step{step}")
if self.sp_organic_p < 0.0:
rwarn(f"OP negative in spin{s}, step{step}")
if self.sp_sorganic_p < 0.0:
rwarn(f"SOP negative in spin{s}, step{step}")
# CALCULATE THE EQUILIBTIUM IN SOIL POOLS
# Soluble and inorganic pools
if self.pupt[0, step] > 2.5:
rwarn(
f"Puptk > max - 786 | in spin{s}, step{step} - {self.pupt[0, step]}"
)
self.pupt[0, step] = 0.0
self.sp_available_p -= self.pupt[0, step]
if self.nupt[0, step] > 2.5:
rwarn(
f"Nuptk > max - 792 | in spin{s}, step{step} - {self.nupt[0, step]}"
)
self.nupt[0, step] = 0.0
self.sp_available_n -= self.nupt[0, step]
# END SOIL NUTRIENT DYNAMICS
# # # Process (cwm) & store (np.array) outputs
self.carbon_costs[self.vp_lsid, step] = self.sp_uptk_costs
self.emaxm.append(daily_output['epavg'])
self.tsoil.append(self.soil_temp)
self.photo[step] = daily_output['phavg']
self.aresp[step] = daily_output['aravg']
self.npp[step] = daily_output['nppavg']
self.lai[step] = daily_output['laiavg']
self.rcm[step] = daily_output['rcavg']
self.f5[step] = daily_output['f5avg']
self.evapm[step] = daily_output['evavg']
self.wsoil[step] = self.wp_water_upper_mm
self.swsoil[step] = self.wp_water_lower_mm
self.rm[step] = daily_output['rmavg']
self.rg[step] = daily_output['rgavg']
self.wue[step] = daily_output['wueavg']
self.cue[step] = daily_output['cueavg']
self.cdef[step] = daily_output['c_defavg']
self.vcmax[step] = daily_output['vcmax']
self.specific_la[step] = daily_output['specific_la']
self.cleaf[step] = daily_output['cp'][0]
self.cawood[step] = daily_output['cp'][1]
self.cfroot[step] = daily_output['cp'][2]
self.hresp[step] = soil_out['hr']
self.csoil[:, step] = soil_out['cs']
self.inorg_n[step] = self.sp_in_n
self.inorg_p[step] = self.sp_in_p
self.sorbed_n[step] = self.sp_so_n
self.sorbed_p[step] = self.sp_so_p
self.snc[:, step] = soil_out['snc']
self.nmin[step] = self.sp_available_n
self.pmin[step] = self.sp_available_p
self.area[self.vp_lsid, step] = self.vp_ocp
self.lim_status[:, self.vp_lsid, step] = daily_output[
'limitation_status'][:, self.vp_lsid]
self.uptake_strategy[:, self.vp_lsid, step] = daily_output[
'uptk_strat'][:, self.vp_lsid]
if s > 0:
while True:
if sv.is_alive():
sleep(0.5)
else:
break
self.flush_data = self._flush_output('spin',
(start_index, end_index))
sv = Thread(target=self._save_output, args=(self.flush_data, ))
sv.start()
while True:
if sv.is_alive():
sleep(0.5)
else:
break
return None
from caete_module import soil_dec as funcs
from caete_module import global_par as gp
def zeroes(*args):
return np.zeros(shape=args, dtype=np.float32)
cl = zeroes(2) + 0.01
cs = zeroes(3) + 0.01
nmin = zeroes(1) + 0.02
plab = zeroes(1) + 0.003
lnr = zeroes(6) + np.random.random(6, ) * 0.001
header = ['hr', 'cl1', 'cl2', 'cs1', 'cs2', 'cs3']
# subroutine carbon3(tsoil,leaf_l,cwd,root_l,lnr,cl,cs,cl_out,cs_out,hr)
# tsoil, leaf_l, cwd, root_l, lnr, cl, cs, cl_out, cs_out, hr
with open('carbon3_test.csv', 'w') as fh:
CSV_WRITER = csv.writer(fh, delimiter=',')
CSV_WRITER.writerow(header)
for x in range(100000):
df = funcs.carbon3(20, 0.1, 0.1, 0.1, lnr, cl, cs)
line = [df[-1], df[0][0], df[0][1], df[1][0], df[1][1], df[1][2]]
CSV_WRITER.writerow(line)
cl = df[0][:]
cs = df[1][:]
data = pd.read_csv('carbon3_test.csv')
os.system('rm -rf carbon3_test.csv')
