def drive_zscroll_noTs(ZHIGH, ZLOW, DZ):
print "Now calling initialize"
initialize.run()
for z in np.arange(ZHIGH, ZLOW, DZ):
print z
perturb_field.run(z)
return
nzoom = int(sys.argv[3])
x, y, z, r = my.get_xyzr(nstop)
r = r * 2**nzoom
for i in range(nzoom):
nc = nstart + i * (nstop - nstart) / nzoom
folder = "output_" + str(nc).zfill(5)
xc, yc, zc, rc = my.get_xyzr(nc)
r = r / 2
xmi = str(xc - r)
xma = str(xc + r)
ymi = str(yc - r)
yma = str(yc + r)
zmi = str(zc - r / (i + 1))
zma = str(zc + r / (i + 1))
bndry = "-xmi " + xmi + " -xma " + xma
bndry = bndry + " -ymi " + ymi + " -yma " + yma
bndry = bndry + " -zmi " + zmi + " -zma " + zma
lma = 9 + i
stri = str(i)
cmd1 = "amr2map -typ 1 -lma " + str(
lma) + " -inp " + folder + " -out mov/gas/gas_zoomstep_" + stri
cmd1 = cmd1 + ".dat -dir z " + bndry
cmd2 = "map2img.py -l --colormap=hot mov/gas/gas_zoomstep_" + stri + ".dat "
cmd2 = cmd2 + "-o mov/gas/gas_zoomstep_" + stri + ".png"
my.run(cmd1, cmd2, calc, show, run)
import initialize
import train_seg
if __name__ == '__main__':
initialize.run()
train_seg.run()
def run_atm(self):
""" Program sequence """
#====================================================
# Initialization Process
#====================================================
print '==================='
print ' Initializing ATM'
print '==================='
read_control.read_control(self)
initialize.initialize(self)
read_layers.read_layers(self)
model_domain.model_domain(self)
create_attm_cohort_arrays.create_attm_cohort_arrays(self)
#=========================================
# Initializing Site Specific Information
#=========================================
if self.Simulation_area.lower() == 'barrow':
run_barrow.initialize_barrow(self)
elif self.Simulation_area.lower() == 'tanana':
run_tanana.initialize_tanana(self)
elif self.Simulation_area.lower() == 'yukon':
run_yukon.initialize_yukon(self)
#=======================================
# READ MET Data, Calculate Degree Days,
# and Calculate Climatic Data needed
# for ecotype changes.
#=======================================
initialize.Met(self)
#++++++++++++++++++++++++++++++++++++++++++++++
# ========================================
# INITIALIZE COHORT PROPERTIES
# ========================================
#++++++++++++++++++++++++++++++++++++++++++++++
print '======================================'
print ' Initializing Terrestrial Properties '
print '======================================'
if self.Simulation_area.lower() == 'barrow':
run_barrow.initialize_barrow_cohorts(self)
elif self.Simulation_area.lower() == 'tanana':
run_tanana.Terrestrial_Tanana(self)
print '=================================================='
print ' Starting the MAIN LOOP '
print '=================================================='
initialize.run(self)
if self.Simulation_area.lower() == 'barrow':
run_barrow.run_barrow(self, time)
elif self.Simulation_area.lower() == 'tanana':
run_tanana.run_tanana(self, time)
print '=================================================='
print ' Finished the MAIN LOOP '
print '=================================================='
# -------------------
# Simulation End Time
# -------------------
clock.finish(self)
#===========================
# Output Simulation Results
#===========================
if self.results_onscreen.lower() == 'yes':
results.on_screen(self)
if self.archive_simulation.lower() == 'yes':
results.on_file(self)
# ================
# Archive Results
# ================
if self.archive_simulation.lower() == 'yes':
archive.read_archive(self)
archive.archive(self)
#----------------------------------------------------------------------------------------------------------
# Create the tarfile
#----------------------------------------------------------------------------------------------------------
self.archive_file =tarfile.open(self.control['Run_dir']+self.Output_directory+str('/Archive/')+ \
self.archive_time+str('_')+self.simulation_name+".tar.gz", mode='w:gz')
#----------------------------------------------------------------------------------------------------------
if self.Simulation_area.lower() == 'barrow':
os.chdir(self.control['Run_dir'] + self.Input_directory +
'/Barrow/')
print '----------------------------------------'
print ' Simulation Complete '
print '----------------------------------------'
#!/usr/bin/python
# shrink_spheres.py
# invoke shrink_sphere.py for all halos on stellar part
import os
import sys
import threading
import initialize as my
d = sys.argv[1]+"/"
os.nice(10)
halo = open(d+"halo","r")
os.system("rm "+d+"halosp")
i = 0
for line in halo:
i = i + 1
si = str(i)
cmd = "shrink_sphere.py "+d+"stars/stars_"+si+".dat >>"+d+"halosp"
print cmd
my.run(cmd)
# this is not done for the stars
# we want to center only on dm particles
import sys
import initialize as my
import mys
brute = True; loop=True;
os.nice(1)
my.print_usage()
# get parameters
# no parameter: run all
# one param: run specified
i = len(sys.argv)
if(i==1):
for k in range(18):
my.run("master.py "+str(k))
sys.exit(0)
action = int(sys.argv[1])
if(action==-1):
mys.clear()
if(action==0):
print "prepare output folder structure, MySQL structure"
# mys.setup()
# mys.fill_sim(simdir,num,nstart,nstop)
for ncounter in range(nstop-nstart+1):
d=mys.d(nstart+ncounter)
# d=simdir+"/output_"+str(ncounter+nstart).zfill(5)+"/";
my.mkdir(d+'amr')
def run_atm(self):
""" Program sequence """
#====================================================
# Initialization Process
#====================================================
print '==================='
print ' Initializing ATM'
print '==================='
read_control.read_control(self)
initialize.initialize(self)
read_layers.read_layers(self)
model_domain.model_domain(self)
create_attm_cohort_arrays.create_attm_cohort_arrays(self)
#=========================================
# Initializing Site Specific Information
#=========================================
if self.Simulation_area.lower() == 'barrow':
run_barrow.initialize_barrow(self)
elif self.Simulation_area.lower() == 'tanana':
run_tanana.initialize_tanana(self)
#=======================================
# READ MET Data, Calculate Degree Days,
# and Calculate Climatic Data needed
# for ecotype changes.
#=======================================
initialize.Met(self)
#++++++++++++++++++++++++++++++++++++++++++++++
# ========================================
# INITIALIZE COHORT PROPERTIES
# ========================================
#++++++++++++++++++++++++++++++++++++++++++++++
print '======================================'
print ' Initializing Terrestrial Properties '
print '======================================'
if self.Simulation_area.lower() == 'barrow':
run_barrow.initialize_barrow_cohorts(self)
elif self.Simulation_area.lower() == 'tanana':
run_tanana.Terrestrial_Tanana(self)
print '=================================================='
print ' Starting the MAIN LOOP '
print '=================================================='
initialize.run(self)
if self.Simulation_area.lower() == 'barrow':
run_barrow.run_barrow(self, time)
elif self.Simulation_area.lower() == 'tanana':
run_tanana.run_tanana(self, time)
print '=================================================='
print ' Finished the MAIN LOOP '
print '=================================================='
# -------------------
# Simulation End Time
# -------------------
clock.finish(self)
#===========================
# Output Simulation Results
#===========================
if self.results_onscreen.lower() == 'yes':
results.on_screen(self)
if self.archive_simulation.lower() == 'yes':
results.on_file(self)
# ================
# Archive Results
# ================
if self.archive_simulation.lower() == 'yes':
#----------------------------------------------------------------------------------------------------------
# Create the tarfile
#----------------------------------------------------------------------------------------------------------
self.archive_file =tarfile.open(self.control['Run_dir']+self.Output_directory+str('/Archive/')+ \
self.archive_time+str('_')+self.simulation_name+".tar.gz", mode='w:gz')
#----------------------------------------------------------------------------------------------------------
archive.read_archive(self)
archive.archive(self)
print '----------------------------------------'
print ' Simulation Complete '
print '----------------------------------------'
import initialize as my
import mys
brute = True
loop = True
os.nice(1)
my.print_usage()
# get parameters
# no parameter: run all
# one param: run specified
i = len(sys.argv)
if (i == 1):
for k in range(18):
my.run("master.py " + str(k))
sys.exit(0)
action = int(sys.argv[1])
if (action == -1):
mys.clear()
if (action == 0):
print "prepare output folder structure, MySQL structure"
# mys.setup()
# mys.fill_sim(simdir,num,nstart,nstop)
for ncounter in range(nstop - nstart + 1):
d = mys.d(nstart + ncounter)
# d=simdir+"/output_"+str(ncounter+nstart).zfill(5)+"/";
my.mkdir(d + 'amr')
def run_attm(self):
""" Program sequence """
#====================================================
# Initialization Process
#====================================================
print '==================='
print ' Initializing ATTM'
print '==================='
read_control.read_control(self)
initialize.initialize(self)
read_layers.read_layers(self)
model_domain.model_domain(self)
create_attm_cohort_arrays.create_attm_cohort_arrays(self)
if self.Simulation_area.lower() == 'barrow':
initial_cohort_population.barrow_initial_cohort_population(self)
initial_cohort_check.barrow_initial_cohort_check(self)
cohort_present.barrow_cohort_present(self)
elif self.Simulation_area.lower() == 'tanana':
initial_cohort_population.tanana_initial_cohort_population(self)
initial_cohort_check.tanana_initial_cohort_check(self)
cohort_present.tanana_cohort_present(self)
#=======================================
# READ MET Data & Calculate Degree Days
#=======================================
initialize.Met(self)
#++++++++++++++++++++++++++++++++++++++++++++++
# ========================================
# INITIALIZE BARROW COHORT PROPERTIES
# ========================================
#++++++++++++++++++++++++++++++++++++++++++++++
if self.Simulation_area.lower() == 'barrow':
print '=================================== '
print ' Initializing Lake & Pond Properties'
print '===================================='
initialize.LakePond(self)
set_lake_pond_depth.set_lake_pond_depth(self)
set_lake_ice_depth_constant.set_lake_ice_depth_constant(self)
set_ice_thickness_array.set_ice_thickness_array(self)
climate_expansion_arrays.set_climate_expansion_arrays(self)
set_pond_growth_array.set_pond_growth_array(self)
print '====================================='
print ' Initializing Terrestrial Properties'
print '====================================='
initialize.Terrestrial_Barrow(self)
read_ice_content.read_ice_content(self)
read_drainage_efficiency.read_drainage_efficiency(self)
read_initial_ALD.read_initial_ALD(self)
set_ALD_constant.set_ALD_constant(self)
set_ALD_array.set_ALD_array(self)
set_protective_layer.set_protective_layer(self)
set_initial_cumulative_probability.set_initial_cumulative_probability(self)
# Initializing Terrestrial Cohort Properties
initialize.Wet_NPG(self)
initialize.Wet_LCP(self)
initialize.Wet_CLC(self)
initialize.Wet_FCP(self)
initialize.Wet_HCP(self)
# Other needed information [in the future]
initial_cohort_age.initial_cohort_age(self)
elif self.Simulation_area.lower() == 'tanana':
print '======================================'
print ' Initializing Terrestrial Properties '
print '======================================'
initialize.Terrestrial_Tanana(self)
print '=================================================='
print ' Starting the MAIN LOOP '
print '=================================================='
initialize.run(self)
for time in range(0, self.stop):
if time == 0:
if self.Simulation_area.lower() == 'barrow':
cohorts.initial_barrow(self)
elif self.Simulation_area.lower() == 'tanana':
cohorts.initial_tanana(self)
print ' at time step: ', time
# ++++++++++++++++++++++++++++++++++++++
# Check for significant climatic event
# ++++++++++++++++++++++++++++++++++++++
check_climate_event.check_climate_event(self)
# ----------------------------------------------------------
# Looping over elements
# ----------------------------------------------------------
for element in range(0, self.ATTM_nrows * self.ATTM_ncols):
# ----------------------------------------------------
# Define the total fractional area of cohorts for
# each element
# ----------------------------------------------------
cohort_start = cohort_check.cohort_start(self, element, time)
# ----------------------------------------------------
# Expand/Infill lake & ponds by prescribed rates
# ----------------------------------------------------
lake_pond_expansion.lake_pond_expansion(self, element)
lake_pond_expansion.pond_infill(self, element, time)
# ----------------------------------------------------------
# Set active layer depth
# ---------------------------------------------------------
active_layer_depth.active_layer_depth(self, time, element)
# ----------------------------------
# Cycle through terrestrial cohorts
# ----------------------------------
check_Wet_NPG.check_Wet_NPG(self, element, time)
check_Wet_LCP.check_Wet_LCP(self, element, time)
check_Wet_CLC.check_Wet_CLC(self, element, time)
check_Wet_FCP.check_Wet_FCP(self, element, time)
check_Wet_HCP.check_Wet_HCP(self, element, time)
# ----------------------------------
# Set pond/lake ice thickness depth
# ----------------------------------
ice_thickness.ice_thickness(self, time, element)
# ------------------------------
# Cycle through ponds and lakes
# ------------------------------
check_Ponds.check_Ponds(self, element, time)
check_Lakes.check_Lakes(self, element, time)
# -------------------------------------------------
# Cohort Fraction Check (mass balance of cohorts)
# -------------------------------------------------
cohort_check.cohort_check(self, element, time, cohort_start)
if time == self.stop-1:
if self.Simulation_area.lower() == 'barrow':
cohorts.final_barrow(self)
elif self.Simulation_area.lower() == 'tanana':
cohorts.final_tanana(self)
# ========================================================================
# END MAIN LOOP
# ========================================================================
# ========================================================================
# OUTPUT RESULTS (if requested)
# ========================================================================
# - - - - - - - - -
# Fractional Areas
# - - - - - - - - -
Output_cohorts_by_year.Output_cohorts_by_year(self, time)
# - - - - - - - - - - - - -
# Dominant Fractional Area
# - - - - - - - - - - - - -
Output_cohorts_by_year.dominant_cohort(self) # Terrestrial_Control
Output_cohorts_by_year.dominant_fractional_plot(self, time) # Terrestrial_Control
# =================================
# OUTPUT ANIMATIONS (if requested)
# =================================
# - - - - - - - - - - - - - - -
# Fractional Area of Cohorts
# - - - - - - - - - - - - - - - -
Output_cohorts_by_year.write_Fractions_avi(self)
Output_cohorts_by_year.write_Dominant_Cohort_avi(self) # Terrestrial_Control
# -------------------
# Simulation End Time
# -------------------
clock.finish(self)
#===========================
# Output Simulation Results
#===========================
if self.results_onscreen.lower() == 'yes':
results.on_screen(self)
if self.archive_simulation.lower() == 'yes':
results.on_file(self)
# ================
# Archive Results
# ================
if self.archive_simulation.lower() == 'yes':
#----------------------------------------------------------------------------------------------------------
# Create the tarfile
#----------------------------------------------------------------------------------------------------------
self.archive_file =tarfile.open(self.control['Run_dir']+self.Output_directory+str('/Archive/')+ \
self.archive_time+str('_')+self.simulation_name+".tar.gz", mode='w:gz')
#----------------------------------------------------------------------------------------------------------
archive.read_archive(self)
archive.archive(self)
print '----------------------------------------'
print ' Simulation Complete '
print '----------------------------------------'
nstart = int(sys.argv[1])
nstop = int(sys.argv[2])
nzoom = int(sys.argv[3])
x,y,z,r= my.get_xyzr(nstop)
r = r*2**nzoom
for i in range(nzoom):
nc = nstart+i*(nstop-nstart)/nzoom
folder = "output_"+str(nc).zfill(5)
xc,yc,zc,rc=my.get_xyzr(nc)
r = r/2
xmi= str(xc-r); xma = str(xc+r)
ymi= str(yc-r); yma = str(yc+r)
zmi= str(zc-r/(i+1)); zma = str(zc+r/(i+1))
bndry="-xmi "+xmi+" -xma "+xma
bndry=bndry+" -ymi "+ymi+" -yma "+yma
bndry=bndry+" -zmi "+zmi+" -zma "+zma
lma = 9+i
stri = str(i)
cmd1 = "amr2map -typ 1 -lma "+str(lma)+" -inp "+folder+" -out mov/gas/gas_zoomstep_"+stri
cmd1 = cmd1 +".dat -dir z "+bndry
cmd2 = "map2img.py -l --colormap=hot mov/gas/gas_zoomstep_"+stri+".dat "
cmd2 = cmd2+"-o mov/gas/gas_zoomstep_"+stri+".png"
my.run(cmd1,cmd2,calc,show,run)