def calc_liveweight(site, herb_class, available_forage):
supp_available = 0
DOY = 150
prop_legume = 0
herb_class.calc_distance_walked(site.S, herb_class.stocking_density,
available_forage)
max_intake = herb_class.calc_max_intake()
ZF = herb_class.calc_ZF()
HR = forage_u.calc_relative_height(available_forage)
diet = forage_u.diet_selection_t2(ZF, HR, prop_legume, supp_available,
max_intake, herb_class.FParam,
available_forage)
diet_interm = forage_u.calc_diet_intermediates(diet, herb_class,
prop_legume, DOY, site)
reduced_max_intake = forage_u.check_max_intake(diet, diet_interm,
herb_class, max_intake)
if reduced_max_intake < max_intake:
diet = forage_u.diet_selection_t2(ZF, HR, prop_legume,
supp_available,
reduced_max_intake,
herb_class.FParam,
available_forage)
diet_interm = forage_u.calc_diet_intermediates(
diet, herb_class, prop_legume, DOY, site)
delta_W = forage_u.calc_delta_weight(diet_interm, herb_class)
return delta_W
def one_step(FParam,
DOY,
herd,
available_forage,
prop_legume,
supp_available,
supp,
intake=None):
"""One step of the forage model, if available forage does not change."""
row = []
max_intake = herd.calc_max_intake(FParam)
if herd.Z < FParam.CR7:
ZF = 1. + (FParam.CR7 - herd.Z)
else:
ZF = 1.
if intake is not None: # if forage intake should be forced
diet = forage.Diet()
diet.If = intake
diet.DMDf = available_forage[0].digestibility # this is super hack-y
diet.CPIf = intake * available_forage[
0].crude_protein # and only works with one type of available forage
diet.Is = supp.DMO # also force intake of all supplement offered
diet_interm = forage.calc_diet_intermediates(FParam, diet, supp, herd,
site, prop_legume, DOY)
else:
diet = forage.diet_selection_t2(ZF, prop_legume, supp_available, supp,
max_intake, FParam, available_forage,
force_supp)
diet_interm = forage.calc_diet_intermediates(FParam, diet, supp, herd,
site, prop_legume, DOY)
reduced_max_intake = forage.check_max_intake(FParam, diet, diet_interm,
herd, max_intake)
if reduced_max_intake < max_intake:
diet = forage.diet_selection_t2(ZF, prop_legume, supp_available,
supp, reduced_max_intake, FParam,
available_forage, force_supp)
diet_interm = forage.calc_diet_intermediates(
FParam, diet, supp, herd, site, prop_legume, DOY)
delta_W = forage.calc_delta_weight(FParam, diet, diet_interm, supp, herd)
#delta_W_step = forage.convert_daily_to_step(delta_W)
herd.update(FParam, delta_W, forage.find_days_per_step())
row.append(max_intake)
row.append(diet.If)
row.append(diet.Is)
row.append(diet.CPIf)
row.append(diet_interm.MEItotal)
row.append(delta_W)
return row
def one_step(FParam, DOY, herd, available_forage, prop_legume, supp_available,
supp):
"""One step of the forage model, if available forage does not change."""
row = []
row.append(available_forage[0].label)
max_intake = herd.calc_max_intake(FParam)
if herd.Z < FParam.CR7:
ZF = 1. + (FParam.CR7 - herd.Z)
else:
ZF = 1.
diet = forage.diet_selection_t2(ZF, prop_legume, supp_available, supp,
max_intake, FParam, available_forage)
diet_interm = forage.calc_diet_intermediates(FParam, diet, supp, herd, site,
prop_legume, DOY)
reduced_max_intake = forage.check_max_intake(FParam, diet, diet_interm, herd,
max_intake)
if reduced_max_intake < max_intake:
diet = forage.diet_selection_t2(ZF, prop_legume, supp_available, supp,
reduced_max_intake, FParam, available_forage)
diet_interm = forage.calc_diet_intermediates(FParam, diet, supp, herd, site,
prop_legume, DOY)
delta_W = forage.calc_delta_weight(FParam, diet, diet_interm, supp, herd)
row.append(herd.W)
row.append(max_intake)
row.append(reduced_max_intake)
row.append(diet.If)
row.append(diet.CPIf)
row.append(diet_interm.MEItotal)
row.append(delta_W)
#delta_W_step = forage.convert_daily_to_step(delta_W)
herd.update(FParam, delta_W, forage.find_days_per_step())
return row
def diet_selection(forage_args, live_gm2, dead_gm2):
"""Perform diet selection on forage, as a metric of forage quality. Return
diet selected by an individual animal from the forage available as
described by live_gm2 and dead_gm2. Assume that digestibility of forage
is calculated from crude protein, and crude protein is specified in the
grass csv (i.e. fixed)."""
forage_u.set_time_step('month')
herbivore_list = []
herbivore_input = (pd.read_csv(forage_args['herbivore_csv']).to_dict(
orient='records'))
for h_class in herbivore_input:
herd = forage_u.HerbivoreClass(h_class)
herd.update()
herbivore_list.append(herd)
stocking_density_dict = forage_u.populate_sd_dict(herbivore_list)
total_SD = forage_u.calc_total_stocking_density(herbivore_list)
grass_list = (pd.read_csv(forage_args['grass_csv'])).to_dict(orient='records')
assert len(grass_list) == 1, "Must be one grass type"
grass_list[0]['green_gm2'] = live_gm2
grass_list[0]['dead_gm2'] = dead_gm2
available_forage = forage_u.calc_feed_types(grass_list)
for feed_type in available_forage:
feed_type.calc_digestibility_from_protein(
forage_args['digestibility_flag']) # TODO n_mult??
assert len(herbivore_list) == 1, "must be one herbivore type"
herb_class = herbivore_list[0]
herb_class.calc_distance_walked(1., total_SD, available_forage)
max_intake = herb_class.calc_max_intake()
ZF = herb_class.calc_ZF()
HR = forage_u.calc_relative_height(available_forage)
diet = forage_u.diet_selection_t2(ZF, HR, 0., 0, max_intake,
herb_class.FParam,
available_forage,
herb_class.f_w, herb_class.q_w)
diet_interm = forage_u.calc_diet_intermediates(diet, herb_class,
0., 150)
reduced_max_intake = forage_u.check_max_intake(diet, diet_interm,
herb_class,
max_intake)
if reduced_max_intake < max_intake:
diet = forage_u.diet_selection_t2(ZF, HR, 0., 0, max_intake,
herb_class.FParam,
available_forage,
herb_class.f_w,
herb_class.q_w)
return diet
def different_diets(available_forage, herbivore_csv, weight_1):
"""Create different diets for two hypothetical animal types. The weight
ratio describes the ratio of """
time_step = 'month'
forage_u.set_time_step(time_step)
total_SD = 2
prop_legume = 0
DOY = 100
supp_available = 0
site = forage_u.SiteInfo(1., -3.25)
supp_csv = "C:/Users/Ginger/Dropbox/NatCap_backup/Forage_model/Forage_model/model_inputs/Shem_et_al_1995_supp.csv"
supp_list = (pandas.read_csv(supp_csv)).to_dict(orient='records')
supp_info = supp_list[0]
supp = forage_u.Supplement(FreerParam.FreerParamCattle('indicus'),
supp_info['digestibility'],
supp_info['kg_per_day'], supp_info['M_per_d'],
supp_info['ether_extract'],
supp_info['crude_protein'],
supp_info['rumen_degradability'])
herbivore_input = (pandas.read_csv(herbivore_csv)).to_dict(
orient='records')
herbivore_list = []
for h_class in herbivore_input:
herd = forage_u.HerbivoreClass(h_class)
herd.update()
herbivore_list.append(herd)
avail_weights = [weight_1, 0]
qual_weights = [0, weight_1]
diet_dict = {}
for idx in xrange(len(herbivore_list)):
herb_class = herbivore_list[idx]
f_w = avail_weights[idx]
rq_w = qual_weights[idx]
herb_class.calc_distance_walked(total_SD, site.S, available_forage)
max_intake = herb_class.calc_max_intake()
ZF = herb_class.calc_ZF()
HR = forage_u.calc_relative_height(available_forage)
diet = diet_selection_t2(ZF, HR, prop_legume, supp_available, supp,
max_intake, herb_class.FParam,
available_forage, idx, f_w, rq_w)
diet_interm = forage_u.calc_diet_intermediates(diet, supp, herb_class,
site, prop_legume, DOY)
# if herb_class.type != 'hindgut_fermenter':
# reduced_max_intake = forage_u.check_max_intake(diet,
# diet_interm,
# herb_class,
# max_intake)
# if reduced_max_intake < max_intake:
# diet = forage_u.diet_selection_t2(ZF, HR,
# args[u'prop_legume'],
# supp_available, supp,
# reduced_max_intake,
# herb_class.FParam,
# available_forage)
diet_dict[herb_class.label] = diet
return diet_dict
# forage_u.reduce_demand(diet_dict, stocking_density_dict,
# available_forage)
diet_interm = forage_u.calc_diet_intermediates(diet, supp, herb_class,
site, prop_legume, DOY)
delta_W = forage_u.calc_delta_weight(diet_interm, herb_class)
delta_W_step = forage_u.convert_daily_to_step(delta_W)
herb_class.update(delta_weight=delta_W_step,
delta_time=forage_u.find_days_per_step())
def launch_model(herb_csv, grass_list, outdir):
f_args = {
'latitude': 0.02759,
'prop_legume': 0.0,
'steepness': 1.,
'DOY': 1,
'start_year': 2015,
'start_month': 1,
'num_months': 1,
'mgmt_threshold': 0.,
'century_dir':
'C:/Users/Ginger/Dropbox/NatCap_backup/Forage_model/CENTURY4.6/Century46_PC_Jan-2014',
'outdir': outdir,
'template_level': 'GH',
'fix_file': 'drytrpfi.100',
'user_define_protein': 1,
'user_define_digestibility': 0,
'herbivore_csv': herb_csv,
'supp_csv':
"C:/Users/Ginger/Dropbox/NatCap_backup/Forage_model/Forage_model/model_inputs/Rubanza_et_al_2005_supp.csv",
'restart_yearly': 0,
'diet_verbose': 1,
}
now_str = datetime.now().strftime("%Y-%m-%d--%H_%M_%S")
if not os.path.exists(f_args['outdir']):
os.makedirs(f_args['outdir'])
forage.write_inputs_log(f_args, now_str)
forage.set_time_step('month') # current default, enforced by CENTURY
add_event = 1 # TODO should this ever be 0?
steps_per_year = forage.find_steps_per_year()
if f_args['diet_verbose']:
master_diet_dict = {}
diet_segregation_dict = {'step': [], 'segregation': []}
herbivore_list = []
if f_args[u'herbivore_csv'] is not None:
herbivore_input = (pandas.read_csv(
f_args[u'herbivore_csv'])).to_dict(orient='records')
for h_class in herbivore_input:
herd = forage.HerbivoreClass(h_class)
herd.update()
BC = 1 # TODO get optional BC from user
# if BC:
# herd.check_BC(BC)
herbivore_list.append(herd)
results_dict = {'step': [], 'year': [], 'month': []}
for h_class in herbivore_list:
results_dict[h_class.label + '_kg'] = []
results_dict[h_class.label + '_gain_kg'] = []
results_dict[h_class.label + '_intake_forage_per_indiv_kg'] = []
if h_class.sex == 'lac_female':
results_dict['milk_prod_kg'] = []
results_dict['total_offtake'] = []
supp_available = 0
if 'supp_csv' in f_args.keys():
supp_list = (pandas.read_csv(
f_args[u'supp_csv'])).to_dict(orient='records')
assert len(supp_list) == 1, "Only one supplement type is allowed"
supp_info = supp_list[0]
supp = forage.Supplement(FreerParam.FreerParamCattle('indicus'),
supp_info['digestibility'],
supp_info['kg_per_day'], supp_info['M_per_d'],
supp_info['ether_extract'],
supp_info['crude_protein'],
supp_info['rumen_degradability'])
if supp.DMO > 0.:
supp_available = 1
stocking_density_dict = forage.populate_sd_dict(herbivore_list)
total_SD = forage.calc_total_stocking_density(herbivore_list)
site = forage.SiteInfo(f_args[u'steepness'], f_args[u'latitude'])
threshold_exceeded = 0
try:
for step in xrange(f_args[u'num_months']):
step_month = f_args[u'start_month'] + step
if step_month > 12:
mod = step_month % 12
if mod == 0:
month = 12
else:
month = mod
else:
month = step_month
year = (step / 12) + f_args[u'start_year']
if month == 1 and f_args['restart_yearly'] and \
f_args[u'herbivore_csv'] is not None:
threshold_exceeded = 0
herbivore_list = []
for h_class in herbivore_input:
herd = forage.HerbivoreClass(h_class)
herd.update()
herbivore_list.append(herd)
# get biomass and crude protein for each grass type
available_forage = forage.calc_feed_types(grass_list)
results_dict['step'].append(step)
results_dict['year'].append(year)
results_dict['month'].append(month)
if not f_args[u'user_define_digestibility']:
for feed_type in available_forage:
feed_type.calc_digestibility_from_protein()
total_biomass = forage.calc_total_biomass(available_forage)
if step == 0:
# threshold biomass, amount of biomass required to be left
# standing (kg per ha)
threshold_biomass = total_biomass * float(
f_args[u'mgmt_threshold'])
diet_dict = {}
for herb_class in herbivore_list:
herb_class.calc_distance_walked(total_SD, site.S,
available_forage)
max_intake = herb_class.calc_max_intake()
ZF = herb_class.calc_ZF()
HR = forage.calc_relative_height(available_forage)
diet = forage.diet_selection_t2(ZF, HR, f_args[u'prop_legume'],
supp_available, supp,
max_intake, herb_class.FParam,
available_forage,
herb_class.f_w, herb_class.q_w)
diet_interm = forage.calc_diet_intermediates(
diet, supp, herb_class, site, f_args[u'prop_legume'],
f_args[u'DOY'])
if herb_class.type != 'hindgut_fermenter':
reduced_max_intake = forage.check_max_intake(
diet, diet_interm, herb_class, max_intake)
if reduced_max_intake < max_intake:
diet = forage.diet_selection_t2(
ZF, HR, f_args[u'prop_legume'], supp_available,
supp, reduced_max_intake, herb_class.FParam,
available_forage)
diet_dict[herb_class.label] = diet
forage.reduce_demand(diet_dict, stocking_density_dict,
available_forage)
if f_args['diet_verbose']:
# save diet_dict across steps to be written out later
master_diet_dict[step] = diet_dict
# diet_segregation = forage.calc_diet_segregation(diet_dict)
# diet_segregation_dict['step'].append(step)
# diet_segregation_dict['segregation'].append(diet_segregation)
total_intake_step = forage.calc_total_intake(
diet_dict, stocking_density_dict)
if (total_biomass - total_intake_step) < threshold_biomass:
print "Forage consumed violates management threshold"
threshold_exceeded = 1
total_intake_step = 0
for herb_class in herbivore_list:
if threshold_exceeded:
diet_dict[herb_class.label] = forage.Diet()
diet = diet_dict[herb_class.label]
# if herb_class.type != 'hindgut_fermenter':
diet_interm = forage.calc_diet_intermediates(
diet, supp, herb_class, site, f_args[u'prop_legume'],
f_args[u'DOY'])
if herb_class.sex == 'lac_female':
milk_production = forage.check_milk_production(
herb_class.FParam, diet_interm)
milk_kg_day = herb_class.calc_milk_yield(milk_production)
if threshold_exceeded:
delta_W = -(forage.convert_step_to_daily(herb_class.W))
else:
delta_W = forage.calc_delta_weight(diet_interm, herb_class)
delta_W_step = forage.convert_daily_to_step(delta_W)
herb_class.update(delta_weight=delta_W_step,
delta_time=forage.find_days_per_step())
results_dict[herb_class.label + '_kg'].append(herb_class.W)
results_dict[herb_class.label +
'_gain_kg'].append(delta_W_step)
results_dict[herb_class.label +
'_intake_forage_per_indiv_kg'].append(
forage.convert_daily_to_step(diet.If))
if herb_class.sex == 'lac_female':
results_dict['milk_prod_kg'].append(
forage.convert_daily_to_step(milk_kg_day))
results_dict['total_offtake'].append(total_intake_step)
finally:
if f_args['diet_verbose']:
# df = pandas.DataFrame(diet_segregation_dict)
# save_as = os.path.join(f_args['outdir'], 'diet_segregation.csv')
# df.to_csv(save_as, index=False)
for h_label in master_diet_dict[0].keys():
new_dict = {}
new_dict['step'] = master_diet_dict.keys()
new_dict['DMDf'] = [
master_diet_dict[step][h_label].DMDf
for step in master_diet_dict.keys()
]
new_dict['CPIf'] = [
master_diet_dict[step][h_label].CPIf
for step in master_diet_dict.keys()
]
grass_labels = master_diet_dict[0][h_label].intake.keys()
for g_label in grass_labels:
new_dict['intake_' + g_label] = \
[master_diet_dict[step][h_label].intake[g_label] for
step in master_diet_dict.keys()]
df = pandas.DataFrame(new_dict)
save_as = os.path.join(f_args['outdir'], h_label + '_diet.csv')
df.to_csv(save_as, index=False)
filled_dict = forage.fill_dict(results_dict, 'NA')
df = pandas.DataFrame(filled_dict)
df.to_csv(os.path.join(f_args['outdir'], 'summary_results.csv'))
def run_simulations():
century_dir = 'C:/Users/Ginger/Dropbox/NatCap_backup/Forage_model/CENTURY4.6/Century46_PC_Jan-2014'
fix_file = 'drytrpfi.100'
graz_file = os.path.join(century_dir, "graz.100")
site_list = ['Research', 'Loidien'] #, 'Rongai', 'Kamok']
input_dir = "C:/Users/Ginger/Dropbox/NatCap_backup/Forage_model/CENTURY4.6/Kenya/input"
outer_dir = "C:/Users/Ginger/Dropbox/NatCap_backup/Forage_model/CENTURY4.6/Output/Stocking_density_test"
prop_legume = 0
template_level = 'GL'
herb_class_weights = "C:/Users/Ginger/Dropbox/NatCap_backup/Forage_model/CENTURY4.6/Kenya/Boran_weights.csv"
sd_dir = 'C:/Users/Ginger/Dropbox/NatCap_backup/Forage_model/CENTURY4.6/Kenya/OPC_stocking_density'
breed = 'Boran'
steepness = 1.
latitude = 0
supp_available = 0
FParam = FreerParam.FreerParam(forage.get_general_breed(breed))
supp = forage.Supplement(FParam, 0, 0, 0, 0, 0, 0)
forage.set_time_step('month')
add_event = 1
grass_file = "C:/Users/ginge/Dropbox/NatCap_backup/Forage_model/Forage_model/model_inputs/grass.csv"
grass = (pandas.read_csv(grass_file)).to_dict(orient='records')[0]
grass['DMD_green'] = 0.64
grass['DMD_dead'] = 0.64
grass['cprotein_green'] = 0.1
grass['cprotein_dead'] = 0.1
for site in site_list:
spin_up_outputs = [site + '_hist_log.txt', site + '_hist.lis']
century_outputs = [site + '_log.txt', site + '.lis', site + '.bin']
filename = 'average_animals_%s_2km_per_ha.csv' % site
stocking_density_file = os.path.join(sd_dir, filename)
sd_df = pandas.read_table(stocking_density_file, sep=',')
outdir = os.path.join(outer_dir, site)
if not os.path.exists(outdir):
os.makedirs(outdir)
# write CENTURY bat for spin-up simulation
hist_bat = os.path.join(input_dir, (site + '_hist.bat'))
hist_schedule = site + '_hist.sch'
hist_output = site + '_hist'
cent.write_century_bat(input_dir, hist_bat, hist_schedule, hist_output,
fix_file, 'outvars.txt')
# write CENTURY bat for extend simulation
extend_bat = os.path.join(input_dir, site + '.bat')
schedule = site + '.sch'
output = site
extend = site + '_hist'
cent.write_century_bat(century_dir, extend_bat, schedule, output,
fix_file, 'outvars.txt', extend)
# move CENTURY run files to CENTURY dir
site_file = os.path.join(input_dir, site + '.100')
weather_file = os.path.join(input_dir, site + '.wth')
e_schedule = os.path.join(input_dir, site + '.sch')
h_schedule = os.path.join(input_dir, site + '_hist.sch')
file_list = [
hist_bat, extend_bat, e_schedule, h_schedule, site_file,
weather_file
]
for file in file_list:
shutil.copyfile(file,
os.path.join(century_dir, os.path.basename(file)))
# make a copy of the original graz params and schedule file
shutil.copyfile(graz_file, os.path.join(century_dir, 'graz_orig.100'))
label = os.path.basename(e_schedule)[:-4]
copy_name = label + '_orig.sch'
shutil.copyfile(e_schedule, os.path.join(input_dir, copy_name))
# run CENTURY for spin-up up to start_year and start_month
hist_bat = os.path.join(century_dir, site + '_hist.bat')
century_bat = os.path.join(century_dir, site + '.bat')
p = Popen(["cmd.exe", "/c " + hist_bat], cwd=century_dir)
stdout, stderr = p.communicate()
p = Popen(["cmd.exe", "/c " + century_bat], cwd=century_dir)
stdout, stderr = p.communicate()
# save copies of CENTURY outputs, but remove from CENTURY dir
intermediate_dir = os.path.join(outdir, 'CENTURY_outputs_spin_up')
if not os.path.exists(intermediate_dir):
os.makedirs(intermediate_dir)
to_move = century_outputs + spin_up_outputs
for file in to_move:
shutil.copyfile(os.path.join(century_dir, file),
os.path.join(intermediate_dir, file))
os.remove(os.path.join(century_dir, file))
grass_list = [grass]
results_dict = {'year': [], 'month': []}
herbivore_input = (pandas.read_csv(herb_class_weights).to_dict(
orient='records'))
herbivore_list = []
for h_class in herbivore_input:
results_dict[h_class['label'] + '_gain_kg'] = []
results_dict[h_class['label'] + '_offtake'] = []
results_dict['milk_prod_kg'] = []
for grass in grass_list:
results_dict[grass['label'] + '_green_kgha'] = []
results_dict[grass['label'] + '_dead_kgha'] = []
results_dict['total_offtake'] = []
results_dict['stocking_density'] = []
try:
for row in xrange(len(sd_df)):
herbivore_list = []
for h_class in herbivore_input:
herd = forage.HerbivoreClass(FParam,
breed,
h_class['weight'],
h_class['sex'],
h_class['age'],
h_class['stocking_density'],
h_class['label'],
Wbirth=24)
herd.update(FParam, 0, 0)
herbivore_list.append(herd)
for h_class in herbivore_list:
h_class.stocking_density = sd_df.iloc[row][h_class.label]
total_SD = forage.calc_total_stocking_density(herbivore_list)
results_dict['stocking_density'].append(total_SD)
siteinfo = forage.SiteInfo(total_SD, steepness, latitude)
month = sd_df.iloc[row].month
year = sd_df.iloc[row].year
suf = '%d-%d' % (month, year)
DOY = month * 30
# get biomass and crude protein for each grass type from CENTURY
output_file = os.path.join(intermediate_dir, site + '.lis')
outputs = cent.read_CENTURY_outputs(output_file, year,
year + 2)
target_month = cent.find_prev_month(year, month)
grass['prev_g_gm2'] = grass['green_gm2']
grass['prev_d_gm2'] = grass['dead_gm2']
grass['green_gm2'] = outputs.loc[target_month, 'aglivc']
grass['dead_gm2'] = outputs.loc[target_month, 'stdedc']
grass['cprotein_green'] = (
outputs.loc[target_month, 'aglive1'] /
outputs.loc[target_month, 'aglivc'])
grass['cprotein_dead'] = (
outputs.loc[target_month, 'stdede1'] /
outputs.loc[target_month, 'stdedc'])
if row == 0:
available_forage = forage.calc_feed_types(grass_list)
else:
available_forage = forage.update_feed_types(
grass_list, available_forage)
results_dict['year'].append(year)
results_dict['month'].append(month)
for feed_type in available_forage:
results_dict[feed_type.label + '_' +
feed_type.green_or_dead + '_kgha'].append(
feed_type.biomass)
siteinfo.calc_distance_walked(FParam, available_forage)
for feed_type in available_forage:
feed_type.calc_digestibility_from_protein()
total_biomass = forage.calc_total_biomass(available_forage)
# Initialize containers to track forage consumed across herbivore
# classes
total_intake_step = 0.
total_consumed = {}
for feed_type in available_forage:
label_string = ';'.join(
[feed_type.label, feed_type.green_or_dead])
total_consumed[label_string] = 0.
for herb_class in herbivore_list:
max_intake = herb_class.calc_max_intake(FParam)
if herb_class.Z < FParam.CR7:
ZF = 1. + (FParam.CR7 - herb_class.Z)
else:
ZF = 1.
if herb_class.stocking_density > 0:
adj_forage = forage.calc_adj_availability(
available_forage, herb_class.stocking_density)
else:
adj_forage = list(available_forage)
diet = forage.diet_selection_t2(ZF, prop_legume,
supp_available, supp,
max_intake, FParam,
adj_forage)
diet_interm = forage.calc_diet_intermediates(
FParam, diet, supp, herb_class, siteinfo, prop_legume,
DOY)
reduced_max_intake = forage.check_max_intake(
FParam, diet, diet_interm, herb_class, max_intake)
if reduced_max_intake < max_intake:
diet = forage.diet_selection_t2(
ZF, prop_legume, supp_available, supp,
reduced_max_intake, FParam, adj_forage)
diet_interm = forage.calc_diet_intermediates(
FParam, diet, supp, herb_class, siteinfo,
prop_legume, DOY)
total_intake_step += (
forage.convert_daily_to_step(diet.If) *
herb_class.stocking_density)
if herb_class.sex == 'lac_female':
milk_production = forage.check_milk_production(
FParam, diet_interm)
milk_kg_day = forage.calc_milk_yield(
FParam, milk_production)
delta_W = forage.calc_delta_weight(FParam, diet,
diet_interm, supp,
herb_class)
delta_W_step = forage.convert_daily_to_step(delta_W)
herb_class.update(FParam, delta_W_step,
forage.find_days_per_step())
if herb_class.stocking_density > 0:
results_dict[herb_class.label +
'_gain_kg'].append(delta_W_step)
results_dict[herb_class.label + '_offtake'].append(
diet.If)
else:
results_dict[herb_class.label +
'_gain_kg'].append('NA')
results_dict[herb_class.label +
'_offtake'].append('NA')
if herb_class.sex == 'lac_female':
results_dict['milk_prod_kg'].append(milk_kg_day * 30.)
# after have performed max intake check, we have the final diet
# selected
# calculate percent live and dead removed for each grass type
consumed_by_class = forage.calc_percent_consumed(
available_forage, diet, herb_class.stocking_density)
forage.sum_percent_consumed(total_consumed,
consumed_by_class)
results_dict['total_offtake'].append(total_intake_step)
# send to CENTURY for this month's scheduled grazing event
date = year + float('%.2f' % (month / 12.))
schedule = os.path.join(century_dir, site + '.sch')
target_dict = cent.find_target_month(add_event, schedule, date,
1)
if target_dict == 0:
er = "Error: no opportunities exist to add grazing event"
raise Exception(er)
new_code = cent.add_new_graz_level(grass, total_consumed,
graz_file, template_level,
outdir, suf)
cent.modify_schedule(schedule, add_event, target_dict,
new_code, outdir, suf)
# call CENTURY from the batch file
century_bat = os.path.join(century_dir, site + '.bat')
p = Popen(["cmd.exe", "/c " + century_bat], cwd=century_dir)
stdout, stderr = p.communicate()
# save copies of CENTURY outputs, but remove from CENTURY dir
intermediate_dir = os.path.join(
outdir, 'CENTURY_outputs_m%d_y%d' % (month, year))
if not os.path.exists(intermediate_dir):
os.makedirs(intermediate_dir)
for file in century_outputs:
shutil.copyfile(os.path.join(century_dir, file),
os.path.join(intermediate_dir, file))
os.remove(os.path.join(century_dir, file))
# remove files from CENTURY directory
finally:
# replace graz params used by CENTURY with original file
os.remove(graz_file)
shutil.copyfile(os.path.join(century_dir, 'graz_orig.100'),
graz_file)
os.remove(os.path.join(century_dir, 'graz_orig.100'))
files_to_remove = [
os.path.join(century_dir, os.path.basename(f))
for f in file_list
]
for file in files_to_remove:
os.remove(file)
os.remove(os.path.join(century_dir, site + '_hist.bin'))
filled_dict = forage.fill_dict(results_dict, 'NA')
df = pandas.DataFrame(filled_dict)
df.to_csv(os.path.join(outdir, 'summary_results.csv'))
def one_step(site,
DOY,
herb_class,
available_forage,
prop_legume,
supp_available,
supp,
intake=None,
force_supp=None):
"""One step of the forage model, if available forage does not change."""
row = []
row.append(supp.DMO)
herb_class.calc_distance_walked(herb_class.stocking_density, site.S,
available_forage)
max_intake = herb_class.calc_max_intake()
ZF = herb_class.calc_ZF()
HR = forage.calc_relative_height(available_forage)
if intake is not None: # if forage intake should be forced
diet = forage.Diet()
diet.If = intake
diet.DMDf = available_forage[0].digestibility # this is super hack-y
diet.CPIf = intake * available_forage[
0].crude_protein # and only works with one type of available forage
diet.Is = supp.DMO # also force intake of all supplement offered
diet_interm = forage.calc_diet_intermediates(diet, supp, herb_class,
site, prop_legume, DOY)
row.append('NA')
else:
diet = forage.diet_selection_t2(ZF, HR, prop_legume, supp_available,
supp, max_intake, herb_class.FParam,
available_forage, force_supp)
diet_interm = forage.calc_diet_intermediates(diet, supp, herb_class,
site, prop_legume, DOY)
if herb_class.type != 'hindgut_fermenter':
reduced_max_intake = forage.check_max_intake(
diet, diet_interm, herb_class, max_intake)
row.append(reduced_max_intake)
if reduced_max_intake < max_intake:
diet = forage.diet_selection_t2(ZF, HR, prop_legume,
supp_available, supp,
reduced_max_intake,
herb_class.FParam,
available_forage, force_supp)
diet_interm = forage.calc_diet_intermediates(
diet, supp, herb_class, site, prop_legume, DOY)
delta_W = forage.calc_delta_weight(diet_interm, herb_class)
delta_W_step = forage.convert_daily_to_step(delta_W)
herd_t1 = forage.HerdT1(herb_class.W, 297)
maint_t1 = herd_t1.e_maintenance()
delta_W_t1 = herd_t1.e_allocate(diet_interm.MEItotal, maint_t1, 'moderate')
herb_class.update(delta_weight=delta_W_step,
delta_time=forage.find_days_per_step())
row.append(max_intake)
row.append(diet.If)
row.append(diet.Is)
row.append(diet.CPIf)
row.append(diet_interm.MEItotal)
row.append(delta_W)
row.append(delta_W_t1)
return row