def main(experiment_id):
# --- FILE PATHS, DIR NAMES ETC --- #
base_dir = ""
param_dir = os.path.join(base_dir, "params")
met_dir = os.path.join(base_dir, "forcing")
run_dir = os.path.join(base_dir, "runs")
# --- CHANGE PARAM VALUES ON THE FLY --- #
itag = experiment_id + "_example"
otag = experiment_id + "_example_sim"
mtag = "met_data.gin"
out_fn = "EXAMPLE.csv"
out_param_fname = os.path.join(param_dir, otag + ".cfg")
cfg_fname = os.path.join(param_dir, itag + ".cfg")
met_fname = os.path.join(met_dir, mtag)
out_fname = os.path.join(run_dir, out_fn)
replace_dict = {
"out_param_fname": '"%s"' % (out_param_fname),
"cfg_fname": '"%s"' % (cfg_fname),
"met_fname": '"%s"' % (met_fname),
"out_fname": '"%s"' % (out_fname),
"age": "12.0",
"print_options": '"daily"',
"co2_conc": '"AMB"',
"canht": "17.0", # m
}
ad.adjust_param_file(cfg_fname, replace_dict)
# --- RUN THE MODEL --- #
G = model.Gday(cfg_fname)
G.run_sim()
def main(experiment_id):
# --- FILE PATHS, DIR NAMES ETC --- #
base_dir = os.getcwd()
param_dir = os.path.join(base_dir, "params")
met_dir = os.path.join(base_dir, "forcing")
run_dir = os.path.join(base_dir, "runs")
# --- CHANGE PARAM VALUES ON THE FLY --- #
itag = experiment_id + "_dk_youngforest"
otag = experiment_id + "_dk_simulation"
mtag = "nceas_met_AMB.csv"
out_fn = "D1GDAYDKAMB.csv"
out_param_fname = os.path.join(param_dir, otag + ".cfg")
cfg_fname = os.path.join(param_dir, itag + ".cfg")
met_fname = os.path.join(met_dir, mtag)
out_fname = os.path.join(run_dir, out_fn)
replace_dict = {
# files
"out_param_fname": '"%s"' % (out_param_fname),
"cfg_fname": '"%s"' % (cfg_fname),
"met_fname": '"%s"' % (met_fname),
"out_fname": '"%s"' % (out_fname),
# state
"age": "12.0",
# control
"alloc_model": '"fixed"',
"assim_model": '"mate"',
"calc_sw_params": "1", #0 uses fwp values, 1= derive them
"deciduous_model": '"false"',
"fixed_stem_nc": "1",
"fixleafnc": '"false"',
"grazing": '"false"',
"model_optroot": '"false"',
"modeljm": '"true"',
"nuptake_model": "1",
"passiveconst": '"false"',
"print_options": '"daily"',
"ps_pathway": '"c3"',
"strfloat": "0",
"trans_model": "1",
"use_eff_nc": "0",
"use_leuning": "0",
"water_stress": '"true"',
"sw_stress_model": "1", # Landsberg
}
ad.adjust_param_file(cfg_fname, replace_dict)
# --- RUN THE MODEL --- #
G = model.Gday(cfg_fname)
G.run_sim()
# translate output to NCEAS style output
# add this directory to python search path so we can find the scripts!
sys.path.append(os.path.join(base_dir, "scripts"))
import translate_GDAY_output_to_NCEAS_format as tr
tr.translate_output(out_fname, met_fname)
def main(experiment_id):
# --- FILE PATHS, DIR NAMES ETC --- #
base_dir = os.getcwd()
param_dir = os.path.join(base_dir, "params")
met_dir = os.path.join(base_dir, "forcing")
run_dir = os.path.join(base_dir, "runs")
# --- CHANGE PARAM VALUES ON THE FLY --- #
itag = experiment_id + "_dk_youngforest"
otag = experiment_id + "_dk_simulation"
mtag = "nceas_met_AMB.csv"
out_fn = "D1GDAYDKAMB.csv"
out_param_fname = os.path.join(param_dir, otag + ".cfg")
cfg_fname = os.path.join(param_dir, itag + ".cfg")
met_fname = os.path.join(met_dir, mtag)
out_fname = os.path.join(run_dir, out_fn)
replace_dict = {
# files
"out_param_fname": '"%s"' % (out_param_fname),
"cfg_fname": '"%s"' % (cfg_fname),
"met_fname": '"%s"' % (met_fname),
"out_fname": '"%s"' % (out_fname),
# state
"age": "12.0",
# control
"alloc_model": '"fixed"',
"assim_model": '"mate"',
"calc_sw_params": "1", # 0 uses fwp values, 1= derive them
"deciduous_model": '"false"',
"fixed_stem_nc": "1",
"fixleafnc": '"false"',
"grazing": '"false"',
"model_optroot": '"false"',
"modeljm": '"true"',
"nuptake_model": "1",
"passiveconst": '"false"',
"print_options": '"daily"',
"ps_pathway": '"c3"',
"strfloat": "0",
"trans_model": "1",
"use_eff_nc": "0",
"use_leuning": "0",
"water_stress": '"true"',
"sw_stress_model": "1", # Landsberg
}
ad.adjust_param_file(cfg_fname, replace_dict)
# --- RUN THE MODEL --- #
G = model.Gday(cfg_fname)
G.run_sim()
# translate output to NCEAS style output
# add this directory to python search path so we can find the scripts!
sys.path.append(os.path.join(base_dir, "scripts"))
import translate_GDAY_output_to_NCEAS_format as tr
tr.translate_output(out_fname, met_fname)
def main(experiment_id, site, SPIN_UP=None):
# dir names
base_param_name = "base_start"
base_dir = os.getcwd()
param_dir = os.path.join(base_dir, "params")
met_dir = os.path.join(base_dir, "met_data")
run_dir = os.path.join(base_dir, "outputs")
if SPIN_UP == True:
# copy base files to make two new experiment files
shutil.copy(os.path.join(param_dir, base_param_name + ".cfg"),
os.path.join(param_dir, "%s_%s_model_spinup.cfg" % \
(experiment_id, site)))
# Run model to equilibrium assuming forest, growing C pools from
# effectively zero
itag = "%s_%s_model_spinup" % (experiment_id, site)
otag = "%s_%s_model_spunup" % (experiment_id, site)
mtag = "%s_met_data_equilibrium_50_yrs.csv" % (site)
out_fn = itag + "_equilib.out"
out_param_fname = os.path.join(param_dir, otag + ".cfg")
cfg_fname = os.path.join(param_dir, itag + ".cfg")
met_fname = os.path.join(met_dir, mtag)
out_fname = os.path.join(run_dir, out_fn)
replace_dict = {
# files
"out_param_fname": '"%s"' % (out_param_fname),
"cfg_fname": '"%s"' % (cfg_fname),
"met_fname": '"%s"' % (met_fname),
"out_fname": '"%s"' % (out_fname),
# control - using Fixed allocation coeffs
"alloc_model": '"fixed"',
"assim_model": '"mate"',
"calc_sw_params": '"true"', #false=use fwp values, true=derive them
"deciduous_model": '"false"',
"disturbance": "0",
"fixed_stem_nc": '"true"',
"fixleafnc": '"false"',
"grazing": '"false"',
"gs_model": '"medlyn"',
"model_optroot": '"false"',
"modeljm": '"true"',
"nuptake_model": "1",
"passiveconst": '"false"',
"print_options": '"end"',
"ps_pathway": '"c3"',
"strfloat": "0",
"sw_stress_model": "1", # Sands and Landsberg
"trans_model": "1",
"use_eff_nc": "0",
"use_leuning": "0",
"water_stress": '"true"',
# state - default C:N 25.
"age": "0.0",
"canht": "17.0", # Canopy height increased from 16m in 2001 to 18m in 2004 at Duke
"activesoil": "0.001",
"activesoiln": "0.00004",
"age": "0.0",
"branch": "0.001",
"branchn": "0.00004",
"cstore": "0.001",
"inorgn": "0.00004",
"metabsoil": "0.0",
"metabsoiln": "0.0",
"metabsurf": "0.0",
"metabsurfn": "0.0",
"nstore": "0.00004",
"passivesoil": "0.001",
"passivesoiln": "0.0004",
"prev_sma": "1.0",
"root": "0.001",
"root_depth": "-9999.9",
"rootn": "0.00004",
"sapwood": "0.001",
"shoot": "0.001",
"shootn": "0.00004",
"slowsoil": "0.001",
"slowsoiln": "0.00004",
"stem": "0.001",
"stemn": "0.00004",
"stemnimm": "0.00004",
"stemnmob": "0.0",
"structsoil": "0.001",
"structsoiln": "0.00004",
"structsurf": "0.001",
"structsurfn": "0.00004",
# parameters
"latitude": "35.9",
"intercep_frac": "0.15",
"max_intercep_lai": "3.0",
"albedo": "0.123", # modis site avg
"finesoil": "0.5",
"slamax": "4.6", # Drake, 2010, PCE, 33, 1756-1766, fig5 (values are in DM and projected, i.e. one sided, what we need for GDAY). Take value for ~20 years. y=47.2-0.063*x
"sla": "4.6", # Drake, 2010, PCE, 33, 1756-1766, fig5 (values are in DM and projected, i.e. one sided, what we need for GDAY). Take value for ~20 years. y=47.2-0.063*x
"slazero": "4.6", # Drake, 2010, PCE, 33, 1756-1766, fig5 (values are in DM and projected, i.e. one sided, what we need for GDAY). Take value for ~20 years. y=47.2-0.063*x
"cfracts": "0.5",
"cfracts": "0.5",
"lai_cover": "0.5",
"jmaxn": "60.0", # Original values Belinda had, plus largely match scatter plot fig 7, pg 235 Ellsworth 2011
"vcmaxn": "30.61", # Original values Belinda had, plus largely match scatter plot fig 7, pg 235 Ellsworth 2011
"c_alloc_fmax": "0.25",
"c_alloc_fmin": "0.25",
"c_alloc_rmax": "0.05",
"c_alloc_rmin": "0.05",
"c_alloc_bmax": "0.2",
"c_alloc_bmin": "0.2",
"fretrans": "0.5",
"rretrans": "0.0",
"bretrans": "0.0",
"wretrans": "0.0",
"ncwnewz": "0.003",
"ncwnew": "0.003",
"ncwimmz": "0.003",
"ncwimm": "0.003",
"ncbnewz": "0.003",
"ncbnew": "0.003",
"ncrfac": "0.8",
"ncmaxfyoung": "0.06",
"ncmaxfold": "0.06",
"ncmaxr": "0.03",
"retransmob": "0.0",
"fdecay": "0.63", # 19 mth turnover * 1/30, McCarthy, 2007, GCB, 13, 2479-2497
"fdecaydry": "0.63", # 19 mth turnover * 1/30, McCarthy, 2007, GCB, 13, 2479-2497
"rdecay": "0.63",
"rdecaydry": "0.63",
"bdecay": "0.02",
"wdecay": "0.02",
"watdecaydry": "0.0",
"watdecaywet": "0.1",
"ligshoot": "0.25",
"ligroot": "0.25",
"brabove": "0.5",
"rateuptake": "3.0", # set somewhat (very) arbitarly to get an LAI ~ 4.
"rateloss": "0.5",
"topsoil_depth": "350.0", # Not needed as I have supplied the root zone water and topsoil water available
"rooting_depth": "750.0", # Not needed as I have supplied the root zone water and topsoil water available
"ctheta_topsoil": "0.5", # Derive based on soil type clay_loam
"ntheta_topsoil": "5.0", # Derive based on soil type clay_loam
"ctheta_root": "0.4", # Derive based on soil type clay
"ntheta_root": "3.0", # Derive based on soil type clay
"topsoil_type": '"clay_loam"',
"rootsoil_type": '"clay"',
"measurement_temp": "25.0",
"dz0v_dh": "0.075", # However I have used value from Jarvis, quoted in Jones 1992, pg. 67. Produces a value within the bounds of 3.5-1.1 mol m-2 s-1 Drake, 2010, GCB for canht=17
"displace_ratio": "0.78",
"g1": "2.74",
"jmaxna": "60.0", # Original values Belinda had, plus largely match scatter plot fig 7, pg 235 Ellsworth 2011
"jmaxnb": "0.0", # Original values Belinda had, plus largely match scatter plot fig 7, pg 235 Ellsworth 2011
"vcmaxna": "30.61",# Original values Belinda had, plus largely match scatter plot fig 7, pg 235 Ellsworth 2011
"vcmaxnb": "0.0", # Original values Belinda had, plus largely match scatter plot fig 7, pg 235 Ellsworth 2011
"sapturnover": "0.1",
"heighto": "4.826",
"htpower": "0.35",
"height0": "5.0",
"height1": "20.0",
"leafsap0": "8000.0",
"leafsap1": "3060.0", # Duke protocol
"branch0": "5.61",
"branch1": "0.346",
"targ_sens": "0.5",
"density": "420.0",
}
ad.adjust_param_file(cfg_fname, replace_dict)
G = model.Gday(cfg_fname, spin_up=True)
G.spin_up_pools()
def main(experiment_id, site, treatment, ascii=True):
# --- FILE PATHS, DIR NAMES ETC --- #
# base_dir = os.getcwd()
param_dir = "params"
met_dir = "met_data"
run_dir = "outputs"
# --- CHANGE PARAM VALUES ON THE FLY --- #
itag = "%s_%s_model_youngforest_%s" % (experiment_id, site, treatment)
otag = "%s_%s_model_simulation_%s" % (experiment_id, site, treatment)
mtag = "%s_met_data_%s_co2.csv" % (site, treatment)
out_fn = "D1GDAY%s%s" + (".csv" if ascii else ".bin")
# import pdb; pdb.set_trace()
out_fn = out_fn % (site, treatment.upper())
out_param_fname = os.path.join(param_dir, otag + ".cfg")
cfg_fname = os.path.join(param_dir, itag + ".cfg")
met_fname = os.path.join(met_dir, mtag)
out_fname = os.path.join(run_dir, out_fn)
replace_dict = {
"git_hash": str(git_revision),
"out_param_fname": "%s" % (out_param_fname),
"cfg_fname": "%s" % (cfg_fname),
"met_fname": "%s" % (met_fname),
"out_fname": "%s" % (out_fname),
# state
"age": "12.0",
# control
"alloc_model": "allometric",
"assim_model": "mate",
"calc_sw_params": "1", # 0 uses fwp values, 1= derive them
"deciduous_model": "false",
"fixed_stem_nc": "1",
"fixleafnc": "false",
"grazing": "false",
"model_optroot": "false",
"modeljm": "2",
"nuptake_model": "2",
"output_ascii": str(ascii),
"passiveconst": "false",
"print_options": "daily",
"ps_pathway": "c3",
"respiration_model": "fixed",
"strfloat": "0",
"trans_model": "1",
"use_eff_nc": "0",
"use_leuning": "0",
"water_stress": "true",
"sw_stress_model": "1", # Landsberg
}
ad.adjust_param_file(cfg_fname, replace_dict)
# --- RUN THE MODEL --- #
G = model.Gday(cfg_fname)
G.run_sim()
# translate output to NCEAS style output
# add this directory to python search path so we can find the scripts!
sys.path.append("scripts")
import translate_GDAY_output_to_NCEAS_format as tr
if ascii:
tr.translate_output(out_fname, met_fname, binary=False)
else:
tr.translate_output(out_fname, met_fname, binary=True)
def main(experiment_id, site, treatment, ascii=True):
# --- FILE PATHS, DIR NAMES ETC --- #
#base_dir = os.getcwd()
param_dir = "params"
met_dir = "met_data"
run_dir = "outputs"
# --- CHANGE PARAM VALUES ON THE FLY --- #
itag = "%s_%s_model_youngforest_%s" % (experiment_id, site, treatment)
otag = "%s_%s_model_simulation_%s" % (experiment_id, site, treatment)
mtag = "%s_met_data_%s_co2.csv" % (site, treatment)
out_fn = "D1GDAY%s%s" + (".csv" if ascii else ".bin")
#import pdb; pdb.set_trace()
out_fn = out_fn % (site, treatment.upper())
out_param_fname = os.path.join(param_dir, otag + ".cfg")
cfg_fname = os.path.join(param_dir, itag + ".cfg")
met_fname = os.path.join(met_dir, mtag)
out_fname = os.path.join(run_dir, out_fn)
replace_dict = {
"git_hash": str(git_revision),
"out_param_fname": "%s" % (out_param_fname),
"cfg_fname": "%s" % (cfg_fname),
"met_fname": "%s" % (met_fname),
"out_fname": "%s" % (out_fname),
# state
"age": "12.0",
# control
"alloc_model": "allometric",
"assim_model": "mate",
"calc_sw_params": "1", #0 uses fwp values, 1= derive them
"deciduous_model": "false",
"fixed_stem_nc": "1",
"fixleafnc": "false",
"grazing": "false",
"model_optroot": "false",
"modeljm": "2",
"nuptake_model": "2",
"output_ascii": str(ascii),
"passiveconst": "false",
"print_options": "daily",
"ps_pathway": "c3",
"respiration_model": "fixed",
"strfloat": "0",
"trans_model": "1",
"use_eff_nc": "0",
"use_leuning": "0",
"water_stress": "true",
"sw_stress_model": "1", # Landsberg
}
ad.adjust_param_file(cfg_fname, replace_dict)
# --- RUN THE MODEL --- #
G = model.Gday(cfg_fname)
G.run_sim()
# translate output to NCEAS style output
# add this directory to python search path so we can find the scripts!
sys.path.append("scripts")
import translate_GDAY_output_to_NCEAS_format as tr
if ascii:
tr.translate_output(out_fname, met_fname, binary=False)
else:
tr.translate_output(out_fname, met_fname, binary=True)
def main(experiment_id, site, SPIN_UP=True, POST_INDUST=True, SPIN_UP_SIMS=True):
base_dir = os.path.dirname(os.getcwd())
# dir names
base_param_name = "base_start"
base_dir = os.path.dirname(os.getcwd())
base_param_dir = "/Users/mq42056055/Documents/gdayFresh/example/params"
param_dir = os.path.join(base_dir, "params")
met_dir = os.path.join(base_dir, "met_data")
run_dir = os.path.join(base_dir, "outputs")
if SPIN_UP == True:
# copy base files to make two new experiment files
shutil.copy(os.path.join(base_param_dir, base_param_name + ".cfg"),
os.path.join(param_dir, "%s_%s_model_spinup.cfg" % \
(experiment_id, site)))
# Run model to equilibrium assuming forest, growing C pools from effectively
# zero
itag = "%s_%s_model_spinup" % (experiment_id, site)
otag = "%s_%s_model_spunup" % (experiment_id, site)
mtag = "%s_met_data_equilibrium_50_yrs.csv" % (site)
out_fn = itag + "_equilib.out"
out_param_fname = os.path.join(param_dir, otag + ".cfg")
cfg_fname = os.path.join(param_dir, itag + ".cfg")
met_fname = os.path.join(met_dir, mtag)
out_fname = os.path.join(run_dir, out_fn)
replace_dict = {
# git stuff
"git_hash": str(git_revision),
# files
"out_param_fname": "%s" % (out_param_fname),
"cfg_fname": "%s" % (cfg_fname),
"met_fname": "%s" % (met_fname),
"out_fname": "%s" % (out_fname),
# state - default C:N 25.
"age": "0.0",
"canht": "17.0", # Canopy height increased from 16m in 2001 to 18m in 2004 at Duke
"activesoil": "0.001",
"activesoiln": "0.00004",
"age": "0.0",
"branch": "0.001",
"branchn": "0.00004",
"cstore": "0.001",
"inorgn": "0.00004",
"metabsoil": "0.0",
"metabsoiln": "0.0",
"metabsurf": "0.0",
"metabsurfn": "0.0",
"nstore": "0.00004",
"passivesoil": "0.001",
"passivesoiln": "0.0004",
"prev_sma": "1.0",
"root": "0.001",
"root_depth": "-9999.9",
"rootn": "0.00004",
"sapwood": "0.001",
"shoot": "0.001",
"shootn": "0.00004",
"slowsoil": "0.001",
"slowsoiln": "0.00004",
"stem": "0.001",
"stemn": "0.00004",
"stemnimm": "0.00004",
"stemnmob": "0.0",
"structsoil": "0.001",
"structsoiln": "0.00004",
"structsurf": "0.001",
"structsurfn": "0.00004",
"croot": "0.0", # don't simulate coarse roots
"crootn": "0.0", # don't simulate coarse roots
# parameters
"latitude": "35.9",
"intercep_frac": "0.15",
"max_intercep_lai": "3.0",
"albedo": "0.123", # modis site avg
"finesoil": "0.51", # set based on silt+clay fractions of topsoil 0.42+0.09=0.5
"slamax": "4.4", # Protocol [m2 kg-1 DW]
"sla": "4.4", # Protocol [m2 kg-1 DW]
"slazero": "4.4", # Protocol [m2 kg-1 DW]
"cfracts": "0.5",
"lai_closed": "0.5", # I am effectively turning this feature off by setting it so low
#"c_alloc_fmax": "0.25",
#"c_alloc_fmin": "0.25",
#"c_alloc_rmax": "0.05",
#"c_alloc_rmin": "0.05",
#"c_alloc_bmax": "0.2",
#"c_alloc_bmin": "0.2",
#"c_alloc_fmax": "0.3",
#"c_alloc_fmin": "0.3",
#"c_alloc_rmax": "0.3",
#"c_alloc_rmin": "0.3",
#"c_alloc_bmax": "0.2",
#"c_alloc_bmin": "0.2",
#"c_alloc_cmax": "0.0", # turn off coarse roots!
"c_alloc_fmax": "0.35",
"c_alloc_fmin": "0.15",
"c_alloc_rmax": "0.35",
"c_alloc_rmin": "0.05",
"c_alloc_bmax": "0.1",
"c_alloc_bmin": "0.1",
"c_alloc_cmax": "0.0", # turn off coarse roots!
"fretrans": "0.5",
"rretrans": "0.0",
"bretrans": "0.0",
"wretrans": "0.0",
"ncwnewz": "0.003",
"ncwnew": "0.003",
"ncwimmz": "0.003",
"ncwimm": "0.003",
"ncbnewz": "0.003",
"ncbnew": "0.003",
"ncrfac": "0.8",
"ncmaxfyoung": "0.04",
"ncmaxfold": "0.04",
"ncmaxr": "0.03",
"retransmob": "0.0",
"fdecay": "0.59988", # Protocol [years-1]
"fdecaydry": "0.59988", # Protocol
"rdecay": "0.33333", # Protocol
"rdecaydry": "0.33333", # Protocol
"bdecay": "0.02", # No data, assuming 50 years
"wdecay": "0.02",
"crdecay": "0.00", # turn off coarse roots!
"watdecaydry": "0.0",
"watdecaywet": "0.1",
"ligshoot": "0.24", # Based on White et al. 2000 for ENF
"ligroot": "0.22", # Based on White et al. 2000
"rateuptake": "3.0", # set somewhat (very) arbitarly to get an LAI ~ 4.
"rateloss": "0.5",
"wcapac_root": "96.75", # [mm] (FC (m3/m-3)-WP (m3/m-3)) * rooting_depth (mm) using derived values and depth from protocol, 750 mm (FC=0.164 - WP=0.035)
"wcapac_topsoil": "25.8", # [mm] (FC (m3/m-3)-WP (m3/m-3)) * rooting_depth (mm) using derived values and depth from protocol, assuming 200 mm top soil following Corbeels 2005a (FC=0.164 - WP=0.035)
"ctheta_topsoil": "0.5", # Derive based on soil type clay_loam
"ntheta_topsoil": "5.0", # Derive based on soil type clay_loam
"ctheta_root": "0.4", # Derive based on soil type clay
"ntheta_root": "3.0", # Derive based on soil type clay
"topsoil_type": "clay_loam",
"rootsoil_type": "clay",
"measurement_temp": "25.0",
"dz0v_dh": "0.075", # However I have used value from Jarvis, quoted in Jones 1992, pg. 67. Produces a value within the bounds of 3.5-1.1 mol m-2 s-1 Drake, 2010, GCB for canht=17
"displace_ratio": "0.78",
"g1": "2.74",
#"jmaxna": "60.0", # Original values Belinda had, I think based on Crous 2008, fig 2. Although those values I think are measured at 28 and 30 deg, the assumption being here that this is the same as 25 deg!
#"jmaxnb": "0.0", # Original values Belinda had, I think based on Crous 2008, fig 2. Although those values I think are measured at 28 and 30 deg, the assumption being here that this is the same as 25 deg!
#"vcmaxna": "30.61",# Original values Belinda had, I think based on Crous 2008, fig 2. Although those values I think are measured at 28 and 30 deg, the assumption being here that this is the same as 25 deg!
#"vcmaxnb": "0.0", # Original values Belinda had, I think based on Crous 2008, fig 2. Although those values I think are measured at 28 and 30 deg, the assumption being here that this is the same as 25 deg!
"vcmaxna": "22.29",
"vcmaxnb": "8.45",
"jv_slope": "1.86",
"jv_intercept": "0.0",
"sapturnover": "0.1",
"heighto": "4.826",
"htpower": "0.35",
"height0": "5.0",
"height1": "20.0",
"leafsap0": "8000.0",
"leafsap1": "3060.0", # Duke protocol
"branch0": "5.61",
"branch1": "0.346",
"targ_sens": "0.5",
"density": "420.0",
# control
"adjust_rtslow": "false", # priming, off
"alloc_model": "allometric",
"assim_model": "mate",
"calc_sw_params": "false", #false=use fwp values, true=derive them
"deciduous_model": "false",
"disturbance": "0",
"exudation": "false",
"fixed_stem_nc": "true",
"fixleafnc": "false",
"grazing": "false",
"gs_model": "medlyn",
"model_optroot": "false",
"modeljm": "2",
"ncycle": "true",
"nuptake_model": "2",
"passiveconst": "false",
"print_options": "end",
"ps_pathway": "c3",
"respiration_model": "fixed",
"strfloat": "0",
"sw_stress_model": "1", # Sands and Landsberg
"trans_model": "1",
"use_eff_nc": "0",
"use_leuning": "0",
"water_stress": "true",
}
ad.adjust_param_file(cfg_fname, replace_dict)
G = model.Gday(cfg_fname, spin_up=True)
G.spin_up_pools()
if POST_INDUST == True:
# run for 200 odd years post industrial with increasing co2/ndep
# we are swapping forest params for grass params now
# copy spunup base files to make two new experiment files
shutil.copy(os.path.join(param_dir, "%s_%s_model_spunup.cfg" % (experiment_id, site)),
os.path.join(param_dir, "%s_%s_model_spunup_adj.cfg" % (experiment_id, site)))
itag = "%s_%s_model_spunup_adj" % (experiment_id, site)
otag = "%s_%s_model_indust" % (experiment_id, site)
mtag = "%s_met_data_industrial_to_present_1850_1983.csv" % (site)
out_fn = itag + "_indust.out"
out_param_fname = os.path.join(param_dir, otag + ".cfg")
cfg_fname = os.path.join(param_dir, itag + ".cfg")
print cfg_fname
met_fname = os.path.join(met_dir, mtag)
out_fname = os.path.join(run_dir, out_fn)
replace_dict = {
# git stuff
"git_hash": str(git_revision),
# files
"out_param_fname": "%s" % (out_param_fname),
"cfg_fname": "%s" % (cfg_fname),
"met_fname": "%s" % (met_fname),
"out_fname": "%s" % (out_fname),
# state - default C:N 25.
"age": "0.0",
"branch": "0.0",
"branchn": "0.0",
"canht": "0.79", # Taken default C3grass value from JULES
"cstore": "0.001",
"nstore": "0.00004",
"croot": "0.0", # don't simulate coarse roots
"crootn": "0.0", # don't simulate coarse roots
"root": "0.001",
"rootn": "0.00004",
"sapwood": "0.0",
"shoot": "0.001",
"shootn": "0.00004",
"stem": "0.0",
"stemn": "0.0",
"stemnimm": "0.0",
"stemnmob": "0.0",
"nepsum": "0.0",
"nppsum": "0.0",
# parameters
"ligshoot": "0.09", # Smith et al. 2000, GRASS
"ligroot": "0.22", # Smith et al. 2000
"age": "1.0",
"slamax": "6.0",
"sla": "6.0",
"slazero": "6.0",
"cfracts": "0.5",
"lai_closed": "0.5", # I am effectively turning this feature off by setting it so low
"c_alloc_fmax": "0.8",
"c_alloc_fmin": "0.2",
"c_alloc_rmax": "0.8",
"c_alloc_rmin": "0.2",
"c_alloc_bmax": "0.0",
"c_alloc_bmin": "0.0",
"c_alloc_cmax": "0.0", # turn off coarse roots!
"fretrans": "0.4",
"rretrans": "0.0",
"bretrans": "0.0",
"wretrans": "0.0",
"ncwnewz": "0.0",
"ncwnew": "0.0",
"ncwimmz": "0.0",
"ncwimm": "0.0",
"ncbnewz": "0.0",
"ncbnew": "0.0",
"ncrfac": "0.7",
"ncmaxfyoung": "0.035",
"ncmaxfold": "0.035",
"ncmaxr": "0.0287",
"retransmob": "0.0",
"fdecay": "1.0",
"fdecaydry": "1.0",
"rdecay": "1.0",
"rdecaydry": "1.0",
"bdecay": "0.0",
"wdecay": "0.0",
"watdecaydry": "0.0",
"watdecaywet": "0.1",
"crdecay": "0.00", # turn off coarse roots!
"dz0v_dh": "0.10", # Taken default C3grass value from JULES
"displace_ratio": "0.64", #Jones 1992, pg. 67.
"z0h_z0m": "1.0", # Assume z0m = z0h, probably a big assumption [as z0h often < z0m.], see comment in code!!
"jmaxna": "62.0", # assuming j = v * 2
"jmaxnb": "0.0", # assuming no intercept
"vcmaxna": "31.0", # C3 grasses - CLM4 tech doc, table 8.2, Oleson et al 2010, page 176
"vcmaxnb": "0.0", # assuming no intercept
# control
"adjust_rtslow": "false", # priming, off
"alloc_model": "grasses",
"assim_model": "mate",
"calc_sw_params": "false", #false=use fwp values, true=derive them
"deciduous_model": "false",
"disturbance": "0",
"exudation": "false",
"fixed_stem_nc": "true",
"fixleafnc": "false",
"grazing": "false",
"gs_model": "medlyn",
"model_optroot": "false",
"modeljm": "1",
"nuptake_model": "2",
"ncycle": "true",
"passiveconst": "false",
"print_options": "end",
"ps_pathway": "c3",
"respiration_model": "fixed",
"strfloat": "0",
"sw_stress_model": "1", # Sands and Landsberg
"trans_model": "1",
"use_eff_nc": "0",
"use_leuning": "0",
"water_stress": "true",
}
ad.adjust_param_file(cfg_fname, replace_dict)
G = model.Gday(cfg_fname)
G.run_sim()
if SPIN_UP_SIMS:
#
## Equilib
#
# copy spunup base files to make two new experiment files
shutil.copy(os.path.join(param_dir, "%s_%s_model_spunup.cfg" % (experiment_id, site)),
os.path.join(param_dir, "%s_%s_model_spunup_trace.cfg" % (experiment_id, site)))
itag = "%s_%s_model_spunup_trace" % (experiment_id, site)
otag = "%s_%s_model_indust" % (experiment_id, site)
mtag = "%s_met_data_preindust_traceability_equilib.csv" % (site)
out_fn = "D1GDAY%sSU280.csv" % (site)
out_param_fname = os.path.join(param_dir, otag + ".cfg")
cfg_fname = os.path.join(param_dir, itag + ".cfg")
met_fname = os.path.join(met_dir, mtag)
out_fname = os.path.join(run_dir, out_fn)
replace_dict = {
# git stuff
"git_hash": str(git_revision),
# files
"out_param_fname": "%s" % (out_param_fname),
"cfg_fname": "%s" % (cfg_fname),
"met_fname": "%s" % (met_fname),
"out_fname": "%s" % (out_fname),
"print_options": "daily",
}
ad.adjust_param_file(cfg_fname, replace_dict)
G = model.Gday(cfg_fname)
G.run_sim()
# translate output to NCEAS style output
# add this directory to python search path so we can find the scripts!
sys.path.append(os.path.join(base_dir, "scripts"))
import translate_GDAY_output_to_NCEAS_format as tr
tr.translate_output(out_fname, met_fname)
#
## Equilib - amb
#
# copy spunup base files to make two new experiment files
shutil.copy(os.path.join(param_dir, "%s_%s_model_spunup.cfg" % (experiment_id, site)),
os.path.join(param_dir, "%s_%s_model_spunup_trace.cfg" % (experiment_id, site)))
itag = "%s_%s_model_spunup_trace" % (experiment_id, site)
otag = "%s_%s_model_indust" % (experiment_id, site)
mtag = "%s_met_data_amb_traceability_equilib.csv" % (site)
out_fn = "D1GDAY%sSUAMB.csv" % (site)
out_param_fname = os.path.join(param_dir, otag + ".cfg")
cfg_fname = os.path.join(param_dir, itag + ".cfg")
met_fname = os.path.join(met_dir, mtag)
out_fname = os.path.join(run_dir, out_fn)
replace_dict = {
# git stuff
"git_hash": str(git_revision),
# files
"out_param_fname": "%s" % (out_param_fname),
"cfg_fname": "%s" % (cfg_fname),
"met_fname": "%s" % (met_fname),
"out_fname": "%s" % (out_fname),
"print_options": "daily",
}
ad.adjust_param_file(cfg_fname, replace_dict)
G = model.Gday(cfg_fname)
G.run_sim()
# translate output to NCEAS style output
# add this directory to python search path so we can find the scripts!
sys.path.append(os.path.join(base_dir, "scripts"))
import translate_GDAY_output_to_NCEAS_format as tr
tr.translate_output(out_fname, met_fname)
#
## Equilib - ele
#
# copy spunup base files to make two new experiment files
shutil.copy(os.path.join(param_dir, "%s_%s_model_spunup.cfg" % (experiment_id, site)),
os.path.join(param_dir, "%s_%s_model_spunup_trace.cfg" % (experiment_id, site)))
itag = "%s_%s_model_spunup_trace" % (experiment_id, site)
otag = "%s_%s_model_indust" % (experiment_id, site)
mtag = "%s_met_data_ele_traceability_equilib.csv" % (site)
out_fn = "D1GDAY%sSUELE.csv" % (site)
out_param_fname = os.path.join(param_dir, otag + ".cfg")
cfg_fname = os.path.join(param_dir, itag + ".cfg")
met_fname = os.path.join(met_dir, mtag)
out_fname = os.path.join(run_dir, out_fn)
replace_dict = {
# git stuff
"git_hash": str(git_revision),
# files
"out_param_fname": "%s" % (out_param_fname),
"cfg_fname": "%s" % (cfg_fname),
"met_fname": "%s" % (met_fname),
"out_fname": "%s" % (out_fname),
"print_options": "daily",
}
ad.adjust_param_file(cfg_fname, replace_dict)
G = model.Gday(cfg_fname)
G.run_sim()
# translate output to NCEAS style output
# add this directory to python search path so we can find the scripts!
sys.path.append(os.path.join(base_dir, "scripts"))
import translate_GDAY_output_to_NCEAS_format as tr
tr.translate_output(out_fname, met_fname)
def main(experiment_id, GROW_FOREST=False, RUN_SIM=True):
# dir names
base_dir = "/Users/mdekauwe/src/python/pygday/example/"
param_dir = os.path.join(base_dir, "params")
met_dir = os.path.join(base_dir, "forcing")
run_dir = os.path.join(base_dir, "runs")
if GROW_FOREST == True:
# Grow forest from 1984 to start of FACE experiment
# we are swapping grass params for forest params now
itag = experiment_id + "_example"
otag = experiment_id + "_example_sim"
mtag = "met_data.gin"
out_fn = "EXAMPLE.csv"
out_param_fname = os.path.join(param_dir, otag + ".cfg")
cfg_fname = os.path.join(param_dir, itag + ".cfg")
# copy base files to make two new experiment files
shutil.copy(os.path.join(cfg_fname),
os.path.join(param_dir, itag + "_run" + ".cfg"))
cfg_fname = os.path.join(param_dir, itag + "_run" + ".cfg")
met_fname = os.path.join(met_dir, mtag)
out_fname = os.path.join(run_dir, out_fn)
replace_dict = {
"out_param_fname": '"%s"' % (out_param_fname),
"cfg_fname": '"%s"' % (cfg_fname),
"met_fname": '"%s"' % (met_fname),
"out_fname": '"%s"' % (out_fname),
"age": "0.0",
"ageold": "1000",
"print_options": "1",
"albedo": "0.123", # modis site avg
"finesoil": "0.5",
"n_crit": "0.04",
"slamax": "4.6", #Drake, 2010, PCE, 33, 1756-1766, fig5
"slainit": "4.6", #Drake, 2010, PCE, 33, 1756-1766, fig5
"slazero": "4.6", #Drake, 2010, PCE, 33, 1756-1766, fig5
"cfracts": "0.5",
"lai_cover": "0.5",
"callocf": "0.25",
"callocfz": "0.25",
"callocrx": "0.0",
"callocr": "0.05",
"callocrz": "0.05",
"callocb": "0.2",
"callocbz": "0.2",
"fretrans": "0.5",
"rretrans": "0.0",
"bretrans": "0.0",
"wretrans": "0.0",
"ncwnewz": "0.003",
"ncwnew": "0.003",
"ncwimmz": "0.003",
"ncwimm": "0.003",
"ncbnewz": "0.003",
"ncbnew": "0.003",
"ncrfac": "0.8",
"ncmaxfyoung": "0.04",
"ncmaxfold": "0.04",
"ncmaxr": "0.03",
"retransmob": "0.0",
"fdecay": "0.63", # 19 mth turnover * 1/30, McCarthy, 2007, GCB, 13, 2479-2497
"fdecaydry": "0.63", # 19 mth turnover * 1/30, McCarthy, 2007, GCB, 13, 2479-2497
"rdecay": "0.63",
"rdecaydry": "0.63",
"bdecay": "0.02",
"wdecay": "0.02",
"watdecaydry": "0.0",
"watdecaywet": "0.1",
"ligshoot": "0.25",
"ligroot": "0.25",
"brabove": "0.5",
"branch": "0.01",
"shoot": "0.01",
"root": "0.01",
"stem": "0.01",
"metabsurf": "0.0",
#"metabsoil": "0.0",
"metabsurfn": "0.0",
#"metabsoiln": "0.0",
"branchn": "0.001",
"shootn": "0.001",
"rootn": "0.001",
"stemn": "2E-03",
"stemnimm": "0.001",
"stemnmob": "0.001",
"wcapac_root": "67.387", # [mm] (FC-WP)*rooting_depth using derived values and depth from Oren et al 1998
"wcapac_topsoil": "6.045", # [mm] (FC-WP)*rooting_depth using derived values and depth from Oren et al 1998
"fwpmax_tsoil": "0.52", # this is the saturation point so this is wrong, derive value
"fwpmin_tsoil": "0.2",
"fwpmax_root": "0.52", # this is the saturation point so this is wrong, derive value
"fwpmin_root": "0.2",
"topsoil_type": '"clay_loam"',
"rootsoil_type": '"clay"',
"calc_sw_params": "1", #0 uses fwp values, 1= derive them
"co2_conc": "0",
"trans_model": "1",
"rateuptake": "5.7",
"rateloss": "0.5",
"g1": "2.74", # used to be 4.8
"deciduous_model": "0",
"canht": "17.0", # Canopy height increased from 16m in 2001 to 18m in 2004 at Duke
"dz0v_dh": "0.075", # However I have used value from Jarvis, quoted in Jones 1992, pg. 67. Produces a value within the bounds of 3.5-1.1 mol m-2 s-1 Drake, 2010, GCB for canht=17
"displace_ratio": "0.78",
"z0h_z0m": "1.0", # Assume z0m = z0h, probably a big assumption [as z0h often < z0m.], see comment in code!!
"callocrx": "0.0",
"vxfix": "5.0e-9", # N fixation per unit rhizodeposition 5g/1000g -> tonnes
"modeljm": "1",
"jmaxna": "60.0", # Original values Belinda had, plus largely match scatter plot fig 7, pg 235 Ellsworth 2011
"jmaxnb": "0.0", # Original values Belinda had, plus largely match scatter plot fig 7, pg 235 Ellsworth 2011
"vcmaxna": "30.61",# Original values Belinda had, plus largely match scatter plot fig 7, pg 235 Ellsworth 2011
"vcmaxnb": "0.0", # Original values Belinda had, plus largely match scatter plot fig 7, pg 235 Ellsworth 2011
"model_optroot": "0",
}
ad.adjust_param_file(cfg_fname, replace_dict)
#print cfg_fname
G = model.Gday(cfg_fname)
G.run_sim()
if RUN_SIM == True:
# Run Duke simulation
itag = experiment_id + "_example"
otag = experiment_id + "_example_sim"
mtag = "met_data.gin"
out_fn = "EXAMPLE.csv"
out_param_fname = os.path.join(param_dir, otag + ".cfg")
cfg_fname = os.path.join(param_dir, itag + ".cfg")
met_fname = os.path.join(met_dir, mtag)
out_fname = os.path.join(run_dir, out_fn)
replace_dict = {
"out_param_fname": '"%s"' % (out_param_fname),
"cfg_fname": '"%s"' % (cfg_fname),
"met_fname": '"%s"' % (met_fname),
"out_fname": '"%s"' % (out_fname),
"age": "12.0",
"print_options": "0",
"co2_conc": "0",
"water_stress": "1",
"model_optroot": "0",
}
ad.adjust_param_file(cfg_fname, replace_dict)
G = model.Gday(cfg_fname)
G.run_sim()
