def dgdxi(i, node, atom_coords, excl_inds,
control=control, coord=coord,
eps=eps, srun=srun_command, dscf=dscf_command,
grad=grad_command):
if node.occupied is None:
node.occupied = i
# wait
while(node.occupied != i):
if node.occupied is None:
node.occupied = i
yield (False, None)
# wait
while(node.update_status() != Node.IDLE):
yield (False, None)
my_coord = node.node_dir+'/'+coord
my_control = node.node_dir+'/'+control
node.restore_files()
# wait
while(node.update_status() != Node.IDLE):
yield (False, None)
changed = update_coord(i, eps, atom_coords, my_coord)
print "node {} coord {} dscf+".format(node.node_dir, i)
node.run(srun + dscf)
while(node.update_status() != Node.IDLE):
yield (False, None)
print "node {} coord {} grad+".format(node.node_dir, i)
node.run(srun + grad)
# wait
while(node.update_status() != Node.IDLE):
yield (False, None)
grads, en = read_control(my_control, changed)
print "{}-th + Energy {}".format(i,en)
res = exclude_grads_and_flatten(grads, excl_inds)
node.make_log(out_files=(coord, control), prefix='task_p')
node.restore_files()
update_coord(i, -eps, atom_coords, my_coord)
print "node {} coord {} dscf-".format(node.node_dir, i)
node.run(srun + dscf)
# wait
while(node.update_status() != Node.IDLE):
yield (False, None)
print "node {} coord {} grad-".format(node.node_dir, i)
node.run(srun + grad)
# wait
while(node.update_status() != Node.IDLE):
yield (False, None)
grads, en = read_control(my_control, changed)
print "{}-th - Energy {}".format(i, en)
node.make_log(out_files=(coord, control), prefix='task_m')
res = res - exclude_grads_and_flatten(grads,
excl_inds)
res = res/(2*eps)
node.occupied = None
yield (True, (res, p_res))
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 '----------------------------------------'
import sys
sys.path.insert(0,"./modules")
from read_control import read_control
from read_rmc6f import read_rmc6f
from j2j0_calc import j2j0_calc
try:
contr_file = sys.argv[1]
except:
print "Usage: python mc_main.py CONTROL_FILE_NAME"
sys.exit(0)
print "------------------------------------------------------------------------>"
print "First, we read in the main control file.\n"
config_name,j2j0Min,j2j0Max,j2j0binNum,EFermi,out_file,j2j0WinAnalysis,j2j0WinMin,\
j2j0WinMax,rbinsNum,distHistOutFile = read_control(contr_file)
print "<------------------------------------------------------------------------\n"
print "------------------------------------------------------------------------>"
print "Next, we proceed to read in the structure configuration.\n"
metric,atomList = read_rmc6f(config_name)
print "<------------------------------------------------------------------------\n"
print "------------------------------------------------------------------------>"
print "Next, we move to the main body of the J/J0 statistics calculation.\n"
if j2j0WinAnalysis=="T":
print "J/J0 window analysis will be carried out.\n"
j2j0Out,rbinsOut = j2j0_calc(j2j0Min,j2j0Max,j2j0binNum,EFermi,metric,\
atomList,j2j0WinAnalysis,j2j0WinMin,j2j0WinMax,rbinsNum)
else:
j2j0Out = j2j0_calc(j2j0Min,j2j0Max,j2j0binNum,EFermi,metric,atomList,\
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 '----------------------------------------'
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 '----------------------------------------'
f_gaus.write(" A \n")
f_gaus.write("Frequencies -- {}\n ".format(omega))
f_gaus.write("Atom AN X Y Z \n")
for jj in range(len(vectors[:,ii1])/3):
f_gaus.write(("{:3d} {:3d} "+"{:.2f} "*3+'\n').format(jj+1, at_numbers[labels[jj]],*vectors[jj:jj+3,ii1]))
kk+=1
f_gaus.write(" {} \n".format(kk))
f_gaus.write(" A \n")
f_gaus.write("Frequencies -- {}\n ".format(omega))
f_gaus.write("Atom AN X Y Z \n")
for jj in range(len(vectors[:,ii2])/3):
f_gaus.write(("{:3d} {:3d} "+"{:.2f} "*3+'\n').format(jj+1, at_numbers[labels[jj]],*vectors[jj:jj+3,ii2]))
kk+=1
atoms = labels[::3]
grads, en = read_control(control, atoms)
fs = sc.ravel(grads)
drs = sc.dot(scl.inv(hessian), fs)
print 'delta_coords'
drs_formatted = drs.view()
drs_formatted.shape= (len(drs)/3, 3)
print drs_formatted
delta_e = -sc.dot(drs, fs)
print "dE = {:.4f} a.u.".format(delta_e)
with open(delta_coord, 'w') as fout:
fout.write('$coord_delta\n')
for dr, at in zip(drs_formatted, atoms):
fout.write('{} {} {} {at}\n'.format(*dr, at=at))
fout.write('$end\n N={}\n'.format(len(drs)))
fout.write(('{} '*len(drs)).format(*drs))
fout.write('\n')
from read_control import read_control
from read_rmc6f import read_rmc6f
from calc_neigh import calc_neigh
from read_mag_cfg import read_mag_cfg
from mag_cluster_average import mag_cluster_average
try:
contr_file = sys.argv[1]
except:
print "Usage: python mc_main.py CONTROL_FILE_NAME"
sys.exit(0)
print "------------------------------------------------------------------------>"
print "First, we read in the main control file.\n"
nuc_config_name,mag_config_name,magAtmType,\
mclusterR,outFile = read_control(contr_file)
print "<------------------------------------------------------------------------\n"
print "------------------------------------------------------------------------>"
print "Next, we proceed to read in the magnetic atoms list.\n"
metric, magAtmList = read_rmc6f(nuc_config_name)
print "<------------------------------------------------------------------------\n"
print "------------------------------------------------------------------------>"
print "Next, we move on to calculate the neighbour list.\n"
magAtmNeigh = calc_neigh(metric, magAtmList, mclusterR)
print "<------------------------------------------------------------------------\n"
print "------------------------------------------------------------------------>"
print "Next, we move on to read in the magnetic moments.\n"
mag_mom = read_mag_cfg(mag_config_name)
