def call_SU2_CFD(tag, parallel=False, processors=1):
"""This calls SU2 to perform an analysis according to the related .cfg file.
Assumptions:
None
Source:
N/A
Inputs:
tag <string> This determines what .cfg is used and what the output file is called.
parallel (optional) <boolean> This determines if SU2 will be run in parallel. This setting requires that SU2 has been built to allow this.
processors (optional) [-] The number of processors used for a parallel computation.
Outputs:
<tag>._forces_breakdown.dat This file has standard SU2 run information.
CL [-]
CD [-]
Properties Used:
N/A
"""
if parallel == True:
sys.path.append(os.environ['SU2_HOME'])
from parallel_computation import parallel_computation
parallel_computation(tag + '.cfg', processors)
pass
else:
subprocess.call(['SU2_CFD', tag + '.cfg'])
f = open(tag + '_forces_breakdown.dat')
SU2_results = Data()
# only the total forces have the ":"
for line in f:
if line.startswith('Total CL:'):
print 'CL:', line.split()[2]
SU2_results.coefficient_of_lift = float(line.split()[2])
elif line.startswith('Total CD:'):
print 'CD:', line.split()[2]
SU2_results.coefficient_of_drag = float(line.split()[2])
elif line.startswith('Total CMx:'):
print 'CMx:', line.split()[2]
SU2_results.moment_coefficient_x = float(line.split()[2])
elif line.startswith('Total CMy:'):
print 'CMy:', line.split()[2]
SU2_results.moment_coefficient_y = float(line.split()[2])
elif line.startswith('Total CMz:'):
print 'CMz:', line.split()[2]
SU2_results.moment_coefficient_z = float(line.split()[2])
CL = SU2_results.coefficient_of_lift
CD = SU2_results.coefficient_of_drag
return CL, CD
def call_SU2_CFD(tag, parallel=False, processors=1):
if parallel == True:
sys.path.append(os.environ['SU2_HOME'])
from parallel_computation import parallel_computation
parallel_computation(tag + '.cfg', processors)
pass
else:
subprocess.call(['SU2_CFD', tag + '.cfg'])
f = open(tag + '_forces_breakdown.dat')
SU2_results = Data()
# only the total forces have the ":"
for line in f:
if line.startswith('Total CL:'):
print 'CL:', line.split()[2]
SU2_results.coefficient_of_lift = float(line.split()[2])
elif line.startswith('Total CD:'):
print 'CD:', line.split()[2]
SU2_results.coefficient_of_drag = float(line.split()[2])
elif line.startswith('Total CMx:'):
print 'CMx:', line.split()[2]
SU2_results.moment_coefficient_x = float(line.split()[2])
elif line.startswith('Total CMy:'):
print 'CMy:', line.split()[2]
SU2_results.moment_coefficient_y = float(line.split()[2])
elif line.startswith('Total CMz:'):
print 'CMz:', line.split()[2]
SU2_results.moment_coefficient_z = float(line.split()[2])
CL = SU2_results.coefficient_of_lift
CD = SU2_results.coefficient_of_drag
return CL, CD
def call_SU2_CFD(tag, parallel=False, processors=1):
"""This calls SU2 to perform an analysis according to the related .cfg file.
Assumptions:
None
Source:
N/A
Inputs:
tag <string> This determines what .cfg is used and what the output file is called.
parallel (optional) <boolean> This determines if SU2 will be run in parallel. This setting requires that SU2 has been built to allow this.
processors (optional) [-] The number of processors used for a parallel computation.
Outputs:
<tag>_history.dat This file has the SU2 convergence history.
CL [-]
CD [-]
Properties Used:
N/A
"""
if parallel == True:
sys.path.append(os.environ['SU2_HOME'])
from parallel_computation import parallel_computation
parallel_computation(tag + '.cfg', processors)
pass
else:
subprocess.call(['SU2_CFD', tag + '.cfg'])
f = open(tag + '_history.dat')
SU2_results = Data()
lines = f.readlines()
final_state = lines[-1].split(',')
# Lift and Drag
CL = float(final_state[1])
CD = float(final_state[2])
SU2_results.coefficient_of_lift = CL
SU2_results.coefficient_of_drag = CD
print 'CL:', CL
print 'CD:', CD
# Moments
# Moments are currently not recorded since no
# reasonable reference length has been chosen
#CMx = float(final_state[4])
#CMy = float(final_state[5])
#CMz = float(final_state[6])
#SU2_results.moment_coefficient_x = CMx
#SU2_results.moment_coefficient_y = CMy
#SU2_results.moment_coefficient_z = CMz
#print 'CMx:',CMx
#print 'CMy:',CMy
#print 'CMz:',CMz
return CL, CD
def runCFD(self, config_file, bParallel=True):
if bParallel:
pc.parallel_computation(config_file, 8)
else:
subprocess.call(['SU2_CFD', config_file])
def mesh_adaptation(filename,
partitions=0,
cycles=1,
overwrite=False,
save_all=False):
# General and default parameters
Config_INP_filename = filename
Config_CFD_filename = "config_CFD_" + Config_INP_filename
Config_MAC_filename = "config_MAC_" + Config_INP_filename
#Mesh_MAC_filename = "mesh_MAC_" + filename.replace(".cfg",".su2")
finest_mesh_filename = "mesh_finest.su2"
finest_flow_filename = "restart_flow_finest.dat"
finest_lin_filename = "restart_lin_finest.dat"
finest_adj_filename = "restart_adj_finest.dat"
# assumes serial with partitions = 1
if partitions == 1: partitions = 0
# Get parameters
params_get = libSU2.Get_ConfigParams(Config_INP_filename)
kind_adapt = params_get['KIND_ADAPT']
objfunc = params_get['ADJ_OBJFUNC']
restart_flow_file = params_get['RESTART_FLOW_FILENAME']
restart_adj_file = params_get['RESTART_ADJ_FILENAME']
original_mesh_file = params_get['MESH_FILENAME']
#output_mesh_file = params_get['MESH_OUT_FILENAME']
Mesh_MAC_filename = params_get['MESH_OUT_FILENAME']
cadj_prefix = libSU2.get_AdjointPrefix(objfunc)
# Get solution file names
volume_flow_file = params_get['VOLUME_FLOW_FILENAME']
volume_adj_file = params_get['VOLUME_ADJ_FILENAME']
surface_flow_file = params_get['SURFACE_FLOW_FILENAME']
surface_adj_file = params_get['SURFACE_ADJ_FILENAME']
history_file = params_get['CONV_FILENAME']
# Get mesh filenames and filetypes
mesh_filetype = params_get['MESH_FORMAT']
if mesh_filetype == "CGNS":
error_str = "Currently cannot support mesh adaptation with CGNS grid files. Please convert your CGNS mesh to SU2 format using the CGNS_TO_SU2 flag in the configuration file, re-specify the mesh file to the native .su2 file and set the MESH_FORMAT flag to SU2."
print "\n*****\n" + error_str + "\n*****\n"
return 1
elif mesh_filetype == "NETCDF_ASCII":
error_str = "Currently cannot support mesh adaptation with NETCDF_ASCII grid files. Please convert your mesh to SU2 format, re-specify the mesh file to the native .su2 file and set the MESH_FORMAT flag to SU2."
print "\n*****\n" + error_str + "\n*****\n"
return 1
# Get output solution filetypes
output_filetype = params_get['OUTPUT_FORMAT']
if output_filetype == "TECPLOT":
vol_file_ext = ".plt"
elif output_filetype == "PARAVIEW":
vol_file_ext = ".vtk"
if ((kind_adapt == "ROBUST") or (kind_adapt == "COMPUTABLE_ROBUST")):
restart_lin_file = params_get['RESTART_LIN_FILENAME']
# Loop over number of adaptation cycles
for iAdaptCycle in range(cycles):
# Copy original input file to working files
shutil.copy(Config_INP_filename, Config_MAC_filename)
shutil.copy(Config_INP_filename, Config_CFD_filename)
# Run direct flow simulation
# For iAdaptCycle == 0, store restart file, objective function and original mesh file
params_set = {'MATH_PROBLEM': 'DIRECT'}
if iAdaptCycle > 0:
params_set.update({
'RESTART_SOL': 'YES',
'ADJ_OBJFUNC': objfunc,
'RESTART_FLOW_FILENAME': restart_flow_file,
'RESTART_ADJ_FILENAME': restart_adj_file,
'SOLUTION_FLOW_FILENAME': restart_flow_file,
'MESH_FILENAME': Mesh_MAC_filename
})
if ((kind_adapt == "ROBUST")
or kind_adapt == ("COMPUTABLE_ROBUST")):
params_set.update({'RESTART_LIN_FILENAME': restart_lin_file})
# Load the new config file options and run the direct problem
libSU2.Set_ConfigParams(Config_CFD_filename, params_set)
if partitions > 1:
parallel_computation(Config_CFD_filename, partitions)
else:
libSU2_run.SU2_CFD(Config_CFD_filename, partitions)
# Copy flow solution & history file
if save_all:
print "Saving cycle " + str(
iAdaptCycle) + " flow solution and history files..."
print "Saving " + volume_flow_file + "_cycle" + str(
iAdaptCycle) + vol_file_ext
print "Saving " + surface_flow_file + "_cycle" + str(
iAdaptCycle) + vol_file_ext
print "Saving " + history_file + "_flow_cycle" + str(
iAdaptCycle) + vol_file_ext
shutil.move(
volume_flow_file + vol_file_ext,
volume_flow_file + "_cycle" + str(iAdaptCycle) + vol_file_ext)
shutil.move(
surface_flow_file + vol_file_ext,
surface_flow_file + "_cycle" + str(iAdaptCycle) + vol_file_ext)
shutil.move(
surface_flow_file + ".csv",
surface_flow_file + "_cycle" + str(iAdaptCycle) + ".csv")
shutil.move(
history_file + vol_file_ext,
history_file + "_flow_cycle" + str(iAdaptCycle) + vol_file_ext)
# If needed, run the adjoint simulation
# For the first adaption cycle, use the filenames of the orignal .cfg file
if (kind_adapt == "GRAD_ADJOINT" or kind_adapt == "GRAD_FLOW_ADJ"
or kind_adapt == "ROBUST" or kind_adapt == "COMPUTABLE_ROBUST"
or kind_adapt == "COMPUTABLE" or kind_adapt == "REMAINING"):
params_set = {
'MATH_PROBLEM': 'ADJOINT',
'SOLUTION_FLOW_FILENAME': restart_flow_file
}
if iAdaptCycle > 0:
params_set.update({
'RESTART_SOL': 'YES',
'SOLUTION_ADJ_FILENAME': restart_adj_file,
'MESH_FILENAME': Mesh_MAC_filename
})
# Load the new config file options and run the adjoint problem
libSU2.Set_ConfigParams(Config_CFD_filename, params_set)
if partitions > 1:
parallel_computation(Config_CFD_filename, partitions)
else:
libSU2_run.SU2_CFD(Config_CFD_filename, partitions)
# Copy adjoint solution & history file
if save_all:
print "Saving cycle " + str(
iAdaptCycle) + " adjoint solution and history files..."
print "Saving " + volume_adj_file + "_cycle" + str(
iAdaptCycle) + vol_file_ext
print "Saving " + surface_adj_file + "_adj_cycle" + str(
iAdaptCycle) + vol_file_ext
print "Saving " + history_file + "_flow_cycle" + str(
iAdaptCycle) + vol_file_ext
shutil.move(
volume_adj_file + vol_file_ext, volume_adj_file +
"_cycle" + str(iAdaptCycle) + vol_file_ext)
shutil.move(
surface_adj_file + vol_file_ext, surface_adj_file +
"_cycle" + str(iAdaptCycle) + vol_file_ext)
shutil.move(
surface_adj_file + ".csv",
surface_adj_file + "_cycle" + str(iAdaptCycle) + ".csv")
shutil.move(
history_file + vol_file_ext, history_file + "_adj_cycle" +
str(iAdaptCycle) + vol_file_ext)
# If needed, change the parameters to run the first linear simulation
# For the first adaptation cycle, use the filenames from the original .cfg file
if kind_adapt == "COMPUTABLE_ROBUST":
params_set = {
'MATH_PROBLEM': 'LINEARIZED',
'SOLUTION_FLOW_FILENAME': restart_flow_file
}
if iAdaptCycle > 0:
params_set.update({
'RESTART_SOL': 'YES',
'RESTART_LIN_FILENAME': restart_lin_file,
'MESH_FILENAME': Mesh_MAC_filename
})
# Load the new config file options and run the linearized problem
libSU2.Set_ConfigParams(Config_CFD_filename, params_set)
if partitions > 1:
parallel_computation(Config_CFD_filename, partitions)
else:
libSU2_run.SU2_CFD(Config_CFD_filename, partitions)
# Change the parameters to do a direct and adjoint iteration over a fine grid
if ((kind_adapt == "ROBUST" or kind_adapt == "COMPUTABLE"
or kind_adapt == "COMPUTABLE_ROBUST" or kind_adapt == "REMAINING")
and (iAdaptCycle < cycles - 1 or cycles == 1)):
# Create the fine grid and interpolate the flow solution from coarse to refined grid
params_set = {
'KIND_ADAPT': "FULL_FLOW",
'SOLUTION_FLOW_FILENAME': restart_flow_file,
'RESTART_FLOW_FILENAME': finest_flow_filename,
'MESH_FILENAME': original_mesh_file,
'MESH_OUT_FILENAME': finest_mesh_filename
}
if iAdaptCycle > 0:
params_set.update({'MESH_FILENAME': Mesh_MAC_filename})
# Run the mesh adaptation module
libSU2.Set_ConfigParams(Config_MAC_filename, params_set)
libSU2_run.SU2_MAC(Config_MAC_filename, partitions)
# Create the fine grid and interpolate the adjoint solution from coarse to refined grid
params_set = {
'KIND_ADAPT': "FULL_ADJOINT",
'SOLUTION_FLOW_FILENAME': restart_flow_file,
'SOLUTION_ADJ_FILENAME': restart_adj_file,
'RESTART_FLOW_FILENAME': finest_flow_filename,
'RESTART_ADJ_FILENAME': finest_adj_filename,
'MESH_FILENAME': original_mesh_file,
'MESH_OUT_FILENAME': finest_mesh_filename
}
if iAdaptCycle > 0:
params_set.update({'MESH_FILENAME': Mesh_MAC_filename})
# Run the mesh adaptation module
libSU2.Set_ConfigParams(Config_MAC_filename, params_set)
libSU2_run.SU2_MAC(Config_MAC_filename, partitions)
# Create the fine grid and interpolate the linear solution from coarse to refined grid
if kind_adapt == "COMPUTABLE_ROBUST":
params_set = {
'KIND_ADAPT': "FULL_LINEAR",
'SOLUTION_FLOW_FILENAME': restart_flow_file,
'SOLUTION_LIN_FILENAME': restart_lin_file,
'RESTART_FLOW_FILENAME': finest_flow_filename,
'RESTART_ADJ_FILENAME': finest_lin_filename,
'MESH_FILENAME': original_mesh_file,
'MESH_OUT_FILENAME': finest_mesh_filename
}
if iAdaptCycle > 0:
params_set.update({'MESH_FILENAME': Mesh_MAC_filename})
# Run the mesh adaptation module
libSU2.Set_ConfigParams(Config_MAC_filename, params_set)
libSU2_run.SU2_MAC(Config_MAC_filename, partitions)
# Change the parameters to do one iteration of the flow solver on the finest grid
# Always start from the interpolated solution and store the residual in the solution file for finest grid
# No multigrid or convergence acceleration
params_set = {
'MATH_PROBLEM': 'DIRECT',
'EXT_ITER': 2,
'RESTART_SOL': 'YES',
'SOLUTION_FLOW_FILENAME': finest_flow_filename,
'STORE_RESIDUAL': 'YES',
'RESTART_FLOW_FILENAME': finest_flow_filename,
'MESH_FILENAME': finest_mesh_filename,
'FULLMG': 'NO',
'MGLEVEL': 0,
'MGCYCLE': 0,
'MG_PRE_SMOOTH': '( 0 )',
'MG_POST_SMOOTH': '( 0 )',
'MG_CORRECTION_SMOOTH': '( 0 )'
}
libSU2.Set_ConfigParams(Config_CFD_filename, params_set)
if partitions > 1:
parallel_computation(Config_CFD_filename, partitions)
else:
libSU2_run.SU2_CFD(Config_CFD_filename, partitions)
# Change the parameters to do one iteration of the adjoint solver on the finest grid
# Always start from the interpolated solution and store the residual in the solution file for finest grid
# No multigrid or convergence acceleration
params_set = {
'MATH_PROBLEM': 'ADJOINT',
'EXT_ITER': 2,
'RESTART_SOL': 'YES',
'SOLUTION_FLOW_FILENAME': finest_flow_filename,
'SOLUTION_ADJ_FILENAME': finest_adj_filename,
'MESH_FILENAME': finest_mesh_filename,
'FULLMG': 'NO',
'MGLEVEL': 0,
'MGCYCLE': 0,
'MG_PRE_SMOOTH': '( 0 )',
'MG_POST_SMOOTH': '( 0 )',
'MG_CORRECTION_SMOOTH': '( 0 )'
}
libSU2.Set_ConfigParams(Config_CFD_filename, params_set)
if partitions > 1:
parallel_computation(Config_CFD_filename, partitions)
else:
libSU2_run.SU2_CFD(Config_CFD_filename, partitions)
# Change the parameters to do one iteration of the linear solver on the finest grid
# Always start from the interpolated solution and store the residual in the solution file for finest grid
# No multigrid or convergence acceleration
if kind_adapt == "COMPUTABLE_ROBUST":
params_set = {
'MATH_PROBLEM': 'LINEARIZED',
'EXT_ITER': 2,
'RESTART_SOL': 'YES',
'SOLUTION_FLOW_FILENAME': finest_flow_filename,
'SOLUTION_LIN_FILENAME': finest_lin_filename,
'RESTART_LIN_FILENAME': finest_lin_filename,
'MESH_FILENAME': finest_mesh_filename,
'FULLMG': 'NO',
'MGLEVEL': 0,
'MGCYCLE': 0,
'MG_PRE_SMOOTH': '( 0 )',
'MG_POST_SMOOTH': '( 0 )',
'MG_CORRECTION_SMOOTH': '( 0 )'
}
libSU2.Set_ConfigParams(Config_CFD_filename, params_set)
if partitions > 1:
parallel_computation(Config_CFD_filename, partitions)
else:
libSU2_run.SU2_CFD(Config_CFD_filename, partitions)
# Perform adaptation using above solution files
if ((kind_adapt == "GRAD_FLOW") or (kind_adapt == "GRAD_ADJOINT")
or (kind_adapt == "GRAD_FLOW_ADJ")):
params_set = {
'SOLUTION_FLOW_FILENAME': restart_flow_file,
'SOLUTION_ADJ_FILENAME': restart_adj_file
}
elif ((kind_adapt == "COMPUTABLE") or (kind_adapt == "REMAINING")):
params_set = {
'SOLUTION_FLOW_FILENAME': finest_flow_filename,
'SOLUTION_ADJ_FILENAME': finest_adj_filename,
'RESTART_FLOW_FILENAME': restart_flow_file,
'RESTART_ADJ_FILENAME': restart_adj_file
}
elif ((kind_adapt == "ROBUST") or (kind_adapt == "COMPUTABLE_ROBUST")):
params_set = {
'SOLUTION_FLOW_FILENAME': finest_flow_filename,
'SOLUTION_ADJ_FILENAME': finest_adj_filename,
'SOLUTION_LIN_FILENAME': finest_lin_filename,
'RESTART_FLOW_FILENAME': restart_flow_file,
'RESTART_ADJ_FILENAME': restart_adj_file,
'RESTART_LIN_FILENAME': restart_lin_file
}
params_set.update({
'KIND_ADAPT': kind_adapt,
'MESH_OUT_FILENAME': Mesh_MAC_filename
})
if iAdaptCycle > 0:
params_set.update({'MESH_FILENAME': Mesh_MAC_filename})
# Run the mesh adaptation module
libSU2.Set_ConfigParams(Config_MAC_filename, params_set)
libSU2_run.SU2_MAC(Config_MAC_filename, partitions)
# Copy cycle mesh file
if save_all:
print "Saving cycle " + str(iAdaptCycle) + " mesh file..."
shutil.copy(
Mesh_MAC_filename,
Mesh_MAC_filename.replace(".su2", "_cycle" + str(iAdaptCycle) +
".su2"))
# Clean up
if overwrite: os.rename(Mesh_MAC_filename, original_mesh_file)
if ((kind_adapt == "ROBUST") or (kind_adapt == "COMPUTABLE")
or (kind_adapt == "COMPUTABLE_ROBUST")
or (kind_adapt == "REMAINING")):
os.remove(finest_mesh_filename)
os.remove(finest_flow_filename)
if kind_adapt == "COMPUTABLE_ROBUST":
os.remove(finest_lin_filename)
if save_all:
os.remove(Mesh_MAC_filename)
os.remove(Config_MAC_filename)
os.remove(Config_CFD_filename)
def call_SU2_CFD(tag,parallel=False,processors=1):
"""This calls SU2 to perform an analysis according to the related .cfg file.
Assumptions:
None
Source:
N/A
Inputs:
tag <string> This determines what .cfg is used and what the output file is called.
parallel (optional) <boolean> This determines if SU2 will be run in parallel. This setting requires that SU2 has been built to allow this.
processors (optional) [-] The number of processors used for a parallel computation.
Outputs:
<tag>_history.dat This file has the SU2 convergence history.
CL [-]
CD [-]
Properties Used:
N/A
"""
if parallel==True:
sys.path.append(os.environ['SU2_HOME'])
from parallel_computation import parallel_computation
parallel_computation( tag+'.cfg', processors )
pass
else:
subprocess.call(['SU2_CFD',tag+'.cfg'])
f = open(tag + '_history.dat')
SU2_results = Data()
lines = f.readlines()
final_state = lines[-1].split(',')
# Lift and Drag
CL = float(final_state[1])
CD = float(final_state[2])
SU2_results.coefficient_of_lift = CL
SU2_results.coefficient_of_drag = CD
print('CL:',CL)
print('CD:',CD)
# Moments
# Moments are currently not recorded since no
# reasonable reference length has been chosen
#CMx = float(final_state[4])
#CMy = float(final_state[5])
#CMz = float(final_state[6])
#SU2_results.moment_coefficient_x = CMx
#SU2_results.moment_coefficient_y = CMy
#SU2_results.moment_coefficient_z = CMz
#print 'CMx:',CMx
#print 'CMy:',CMy
#print 'CMz:',CMz
return CL,CD
def mesh_adaptation( filename ,
partitions = 0 ,
cycles = 1 ,
overwrite = False ,
save_all = False ):
# General and default parameters
Config_INP_filename = filename
Config_CFD_filename = "config_CFD_" + Config_INP_filename
Config_MAC_filename = "config_MAC_" + Config_INP_filename
#Mesh_MAC_filename = "mesh_MAC_" + filename.replace(".cfg",".su2")
finest_mesh_filename = "mesh_finest.su2"
finest_flow_filename = "restart_flow_finest.dat"
finest_lin_filename = "restart_lin_finest.dat"
finest_adj_filename = "restart_adj_finest.dat"
# assumes serial with partitions = 1
if partitions == 1: partitions = 0
# Get parameters
params_get = libSU2.Get_ConfigParams( Config_INP_filename )
kind_adapt = params_get['KIND_ADAPT']
objfunc = params_get['ADJ_OBJFUNC']
restart_flow_file = params_get['RESTART_FLOW_FILENAME']
restart_adj_file = params_get['RESTART_ADJ_FILENAME']
original_mesh_file = params_get['MESH_FILENAME']
#output_mesh_file = params_get['MESH_OUT_FILENAME']
Mesh_MAC_filename = params_get['MESH_OUT_FILENAME']
cadj_prefix = libSU2.get_AdjointPrefix(objfunc)
# Get solution file names
volume_flow_file = params_get['VOLUME_FLOW_FILENAME']
volume_adj_file = params_get['VOLUME_ADJ_FILENAME']
surface_flow_file = params_get['SURFACE_FLOW_FILENAME']
surface_adj_file = params_get['SURFACE_ADJ_FILENAME']
history_file = params_get['CONV_FILENAME']
# Get mesh filenames and filetypes
mesh_filetype = params_get['MESH_FORMAT']
if mesh_filetype == "CGNS":
error_str = "Currently cannot support mesh adaptation with CGNS grid files. Please convert your CGNS mesh to SU2 format using the CGNS_TO_SU2 flag in the configuration file, re-specify the mesh file to the native .su2 file and set the MESH_FORMAT flag to SU2."
print "\n*****\n" + error_str + "\n*****\n"
return 1
elif mesh_filetype == "NETCDF_ASCII":
error_str ="Currently cannot support mesh adaptation with NETCDF_ASCII grid files. Please convert your mesh to SU2 format, re-specify the mesh file to the native .su2 file and set the MESH_FORMAT flag to SU2."
print "\n*****\n" + error_str + "\n*****\n"
return 1
# Get output solution filetypes
output_filetype = params_get['OUTPUT_FORMAT']
if output_filetype == "TECPLOT":
vol_file_ext = ".plt"
elif output_filetype == "PARAVIEW":
vol_file_ext = ".vtk"
if( (kind_adapt == "ROBUST") or (kind_adapt == "COMPUTABLE_ROBUST") ):
restart_lin_file = params_get['RESTART_LIN_FILENAME']
# Loop over number of adaptation cycles
for iAdaptCycle in range(cycles):
# Copy original input file to working files
shutil.copy( Config_INP_filename, Config_MAC_filename )
shutil.copy( Config_INP_filename, Config_CFD_filename )
# Run direct flow simulation
# For iAdaptCycle == 0, store restart file, objective function and original mesh file
params_set = { 'MATH_PROBLEM' : 'DIRECT'}
if iAdaptCycle > 0:
params_set.update({'RESTART_SOL' : 'YES' ,
'ADJ_OBJFUNC' : objfunc,
'RESTART_FLOW_FILENAME' : restart_flow_file,
'RESTART_ADJ_FILENAME' : restart_adj_file,
'SOLUTION_FLOW_FILENAME' : restart_flow_file,
'MESH_FILENAME' : Mesh_MAC_filename })
if( (kind_adapt == "ROBUST") or kind_adapt == ("COMPUTABLE_ROBUST") ):
params_set.update( {'RESTART_LIN_FILENAME' : restart_lin_file} )
# Load the new config file options and run the direct problem
libSU2.Set_ConfigParams( Config_CFD_filename, params_set )
if partitions > 1:
parallel_computation( Config_CFD_filename, partitions )
else:
libSU2_run.SU2_CFD( Config_CFD_filename, partitions )
# Copy flow solution & history file
if save_all:
print "Saving cycle " + str(iAdaptCycle) + " flow solution and history files..."
print "Saving " + volume_flow_file + "_cycle" + str(iAdaptCycle) + vol_file_ext
print "Saving " + surface_flow_file + "_cycle" + str(iAdaptCycle) + vol_file_ext
print "Saving " + history_file + "_flow_cycle" + str(iAdaptCycle) + vol_file_ext
shutil.move( volume_flow_file + vol_file_ext , volume_flow_file + "_cycle"+str(iAdaptCycle)+vol_file_ext )
shutil.move( surface_flow_file + vol_file_ext , surface_flow_file + "_cycle"+str(iAdaptCycle)+vol_file_ext )
shutil.move( surface_flow_file + ".csv" , surface_flow_file + "_cycle"+str(iAdaptCycle)+".csv" )
shutil.move( history_file + vol_file_ext , history_file + "_flow_cycle"+str(iAdaptCycle)+vol_file_ext )
# If needed, run the adjoint simulation
# For the first adaption cycle, use the filenames of the orignal .cfg file
if ( kind_adapt == "GRAD_ADJOINT" or kind_adapt == "GRAD_FLOW_ADJ" or kind_adapt == "ROBUST" or kind_adapt == "COMPUTABLE_ROBUST" or kind_adapt == "COMPUTABLE" or kind_adapt == "REMAINING" ):
params_set = { 'MATH_PROBLEM' : 'ADJOINT',
'SOLUTION_FLOW_FILENAME' : restart_flow_file }
if iAdaptCycle > 0:
params_set.update({ 'RESTART_SOL' : 'YES' ,
'SOLUTION_ADJ_FILENAME' : restart_adj_file ,
'MESH_FILENAME' : Mesh_MAC_filename })
# Load the new config file options and run the adjoint problem
libSU2.Set_ConfigParams( Config_CFD_filename, params_set )
if partitions > 1:
parallel_computation( Config_CFD_filename, partitions )
else:
libSU2_run.SU2_CFD( Config_CFD_filename, partitions )
# Copy adjoint solution & history file
if save_all:
print "Saving cycle " + str(iAdaptCycle) + " adjoint solution and history files..."
print "Saving " + volume_adj_file + "_cycle" + str(iAdaptCycle) + vol_file_ext
print "Saving " + surface_adj_file + "_adj_cycle" + str(iAdaptCycle) + vol_file_ext
print "Saving " + history_file + "_flow_cycle" + str(iAdaptCycle) + vol_file_ext
shutil.move( volume_adj_file + vol_file_ext , volume_adj_file + "_cycle"+str(iAdaptCycle)+vol_file_ext )
shutil.move( surface_adj_file + vol_file_ext , surface_adj_file + "_cycle"+str(iAdaptCycle)+vol_file_ext )
shutil.move( surface_adj_file + ".csv" , surface_adj_file + "_cycle"+str(iAdaptCycle)+".csv" )
shutil.move( history_file + vol_file_ext , history_file + "_adj_cycle"+str(iAdaptCycle)+vol_file_ext )
# If needed, change the parameters to run the first linear simulation
# For the first adaptation cycle, use the filenames from the original .cfg file
if kind_adapt == "COMPUTABLE_ROBUST":
params_set = {'MATH_PROBLEM' : 'LINEARIZED' ,
'SOLUTION_FLOW_FILENAME' : restart_flow_file }
if iAdaptCycle > 0:
params_set.update({'RESTART_SOL' : 'YES' ,
'RESTART_LIN_FILENAME' : restart_lin_file ,
'MESH_FILENAME' : Mesh_MAC_filename })
# Load the new config file options and run the linearized problem
libSU2.Set_ConfigParams(Config_CFD_filename, params_set)
if partitions > 1:
parallel_computation( Config_CFD_filename, partitions )
else:
libSU2_run.SU2_CFD( Config_CFD_filename, partitions )
# Change the parameters to do a direct and adjoint iteration over a fine grid
if ( (kind_adapt == "ROBUST" or kind_adapt == "COMPUTABLE" or
kind_adapt == "COMPUTABLE_ROBUST" or kind_adapt == "REMAINING")
and (iAdaptCycle < cycles-1 or cycles == 1) ):
# Create the fine grid and interpolate the flow solution from coarse to refined grid
params_set = { 'KIND_ADAPT' : "FULL_FLOW" ,
'SOLUTION_FLOW_FILENAME' : restart_flow_file ,
'RESTART_FLOW_FILENAME' : finest_flow_filename ,
'MESH_FILENAME' : original_mesh_file ,
'MESH_OUT_FILENAME' : finest_mesh_filename }
if iAdaptCycle > 0:
params_set.update( {'MESH_FILENAME' : Mesh_MAC_filename} )
# Run the mesh adaptation module
libSU2.Set_ConfigParams( Config_MAC_filename, params_set )
libSU2_run.SU2_MAC(Config_MAC_filename,partitions)
# Create the fine grid and interpolate the adjoint solution from coarse to refined grid
params_set = { 'KIND_ADAPT' : "FULL_ADJOINT" ,
'SOLUTION_FLOW_FILENAME' : restart_flow_file ,
'SOLUTION_ADJ_FILENAME' : restart_adj_file ,
'RESTART_FLOW_FILENAME' : finest_flow_filename ,
'RESTART_ADJ_FILENAME' : finest_adj_filename ,
'MESH_FILENAME' : original_mesh_file ,
'MESH_OUT_FILENAME' : finest_mesh_filename }
if iAdaptCycle > 0:
params_set.update( {'MESH_FILENAME' : Mesh_MAC_filename} )
# Run the mesh adaptation module
libSU2.Set_ConfigParams( Config_MAC_filename, params_set )
libSU2_run.SU2_MAC(Config_MAC_filename,partitions)
# Create the fine grid and interpolate the linear solution from coarse to refined grid
if kind_adapt == "COMPUTABLE_ROBUST":
params_set = { 'KIND_ADAPT' : "FULL_LINEAR" ,
'SOLUTION_FLOW_FILENAME' : restart_flow_file ,
'SOLUTION_LIN_FILENAME' : restart_lin_file ,
'RESTART_FLOW_FILENAME' : finest_flow_filename ,
'RESTART_ADJ_FILENAME' : finest_lin_filename ,
'MESH_FILENAME' : original_mesh_file ,
'MESH_OUT_FILENAME' : finest_mesh_filename }
if iAdaptCycle > 0:
params_set.update( {'MESH_FILENAME' : Mesh_MAC_filename} )
# Run the mesh adaptation module
libSU2.Set_ConfigParams( Config_MAC_filename, params_set )
libSU2_run.SU2_MAC( Config_MAC_filename, partitions )
# Change the parameters to do one iteration of the flow solver on the finest grid
# Always start from the interpolated solution and store the residual in the solution file for finest grid
# No multigrid or convergence acceleration
params_set = { 'MATH_PROBLEM' : 'DIRECT' ,
'EXT_ITER' : 2 ,
'RESTART_SOL' : 'YES' ,
'SOLUTION_FLOW_FILENAME' : finest_flow_filename ,
'STORE_RESIDUAL' : 'YES' ,
'RESTART_FLOW_FILENAME' : finest_flow_filename ,
'MESH_FILENAME' : finest_mesh_filename ,
'FULLMG' : 'NO' ,
'MGLEVEL' : 0 ,
'MGCYCLE' : 0 ,
'MG_PRE_SMOOTH' : '( 0 )' ,
'MG_POST_SMOOTH' : '( 0 )' ,
'MG_CORRECTION_SMOOTH' : '( 0 )' }
libSU2.Set_ConfigParams( Config_CFD_filename, params_set )
if partitions > 1:
parallel_computation( Config_CFD_filename, partitions )
else:
libSU2_run.SU2_CFD( Config_CFD_filename, partitions )
# Change the parameters to do one iteration of the adjoint solver on the finest grid
# Always start from the interpolated solution and store the residual in the solution file for finest grid
# No multigrid or convergence acceleration
params_set = { 'MATH_PROBLEM' : 'ADJOINT' ,
'EXT_ITER' : 2 ,
'RESTART_SOL' : 'YES' ,
'SOLUTION_FLOW_FILENAME' : finest_flow_filename ,
'SOLUTION_ADJ_FILENAME' : finest_adj_filename ,
'MESH_FILENAME' : finest_mesh_filename ,
'FULLMG' : 'NO' ,
'MGLEVEL' : 0 ,
'MGCYCLE' : 0 ,
'MG_PRE_SMOOTH' : '( 0 )' ,
'MG_POST_SMOOTH' : '( 0 )' ,
'MG_CORRECTION_SMOOTH' : '( 0 )' }
libSU2.Set_ConfigParams( Config_CFD_filename, params_set )
if partitions > 1:
parallel_computation( Config_CFD_filename, partitions )
else:
libSU2_run.SU2_CFD( Config_CFD_filename, partitions )
# Change the parameters to do one iteration of the linear solver on the finest grid
# Always start from the interpolated solution and store the residual in the solution file for finest grid
# No multigrid or convergence acceleration
if kind_adapt == "COMPUTABLE_ROBUST":
params_set = { 'MATH_PROBLEM' : 'LINEARIZED' ,
'EXT_ITER' : 2 ,
'RESTART_SOL' : 'YES' ,
'SOLUTION_FLOW_FILENAME' : finest_flow_filename ,
'SOLUTION_LIN_FILENAME' : finest_lin_filename ,
'RESTART_LIN_FILENAME' : finest_lin_filename ,
'MESH_FILENAME' : finest_mesh_filename ,
'FULLMG' : 'NO' ,
'MGLEVEL' : 0 ,
'MGCYCLE' : 0 ,
'MG_PRE_SMOOTH' : '( 0 )' ,
'MG_POST_SMOOTH' : '( 0 )' ,
'MG_CORRECTION_SMOOTH' : '( 0 )' }
libSU2.Set_ConfigParams( Config_CFD_filename, params_set )
if partitions > 1:
parallel_computation( Config_CFD_filename, partitions )
else:
libSU2_run.SU2_CFD( Config_CFD_filename, partitions )
# Perform adaptation using above solution files
if( (kind_adapt == "GRAD_FLOW") or (kind_adapt == "GRAD_ADJOINT") or (kind_adapt == "GRAD_FLOW_ADJ")):
params_set = { 'SOLUTION_FLOW_FILENAME' : restart_flow_file,
'SOLUTION_ADJ_FILENAME' : restart_adj_file }
elif( (kind_adapt == "COMPUTABLE") or (kind_adapt == "REMAINING") ):
params_set = { 'SOLUTION_FLOW_FILENAME' : finest_flow_filename,
'SOLUTION_ADJ_FILENAME' : finest_adj_filename ,
'RESTART_FLOW_FILENAME' : restart_flow_file ,
'RESTART_ADJ_FILENAME' : restart_adj_file }
elif( (kind_adapt == "ROBUST") or (kind_adapt == "COMPUTABLE_ROBUST") ):
params_set = { 'SOLUTION_FLOW_FILENAME' : finest_flow_filename,
'SOLUTION_ADJ_FILENAME' : finest_adj_filename ,
'SOLUTION_LIN_FILENAME' : finest_lin_filename ,
'RESTART_FLOW_FILENAME' : restart_flow_file ,
'RESTART_ADJ_FILENAME' : restart_adj_file ,
'RESTART_LIN_FILENAME' : restart_lin_file }
params_set.update({'KIND_ADAPT' : kind_adapt, 'MESH_OUT_FILENAME' : Mesh_MAC_filename})
if iAdaptCycle > 0:
params_set.update({'MESH_FILENAME' : Mesh_MAC_filename})
# Run the mesh adaptation module
libSU2.Set_ConfigParams( Config_MAC_filename, params_set )
libSU2_run.SU2_MAC( Config_MAC_filename, partitions )
# Copy cycle mesh file
if save_all:
print "Saving cycle " + str(iAdaptCycle) + " mesh file..."
shutil.copy( Mesh_MAC_filename, Mesh_MAC_filename.replace(".su2", "_cycle"+str(iAdaptCycle)+".su2"))
# Clean up
if overwrite : os.rename( Mesh_MAC_filename, original_mesh_file )
if( (kind_adapt == "ROBUST") or (kind_adapt == "COMPUTABLE") or
(kind_adapt == "COMPUTABLE_ROBUST") or (kind_adapt == "REMAINING") ):
os.remove(finest_mesh_filename)
os.remove(finest_flow_filename)
if kind_adapt == "COMPUTABLE_ROBUST":
os.remove(finest_lin_filename)
if save_all:
os.remove(Mesh_MAC_filename)
os.remove(Config_MAC_filename)
os.remove(Config_CFD_filename)
def generate_data(model, inputdir, outputdir, cluster_type="pp", pp_cpus=2, runs=1):
"""
The first pipeline step: data generation.
:param model: the model to process
:param inputdir: the directory containing the model
:param outputdir: the directory containing the output files
:param cluster_type: pp for local Parallel Python, lsf for Load Sharing Facility, sge for Sun Grid Engine.
:param pp_cpus: the number of CPU used by Parallel Python.
:param runs: the number of model simulation
:return: no output
"""
if runs < 1:
logger.error("variable " + str(runs) + " must be greater than 0. Please, check your configuration file.")
return
if not os.path.isfile(os.path.join(inputdir, model)):
logger.error(os.path.join(inputdir, model) + " does not exist.")
return
copasi = get_copasi()
if copasi is None:
logger.error(
"CopasiSE not found! Please check that CopasiSE is installed and in the PATH environmental variable.")
return
# folder preparation
refresh_directory(outputdir, model[:-4])
# execute runs simulations.
logger.info("Simulating model " + model + " for " + str(runs) + " time(s)")
# Replicate the copasi file and rename its report file
groupid = "_" + get_rand_alphanum_str(20) + "_"
group_model = model[:-4] + groupid
for i in xrange(1, runs + 1):
shutil.copyfile(os.path.join(inputdir, model), os.path.join(inputdir, group_model) + str(i) + ".cps")
replace_string_in_file(os.path.join(inputdir, group_model) + str(i) + ".cps",
model[:-4] + ".csv",
group_model + str(i) + ".csv")
# run copasi in parallel
# To make things simple, the last 10 character of groupid are extracted and reversed.
# This string will be likely different from groupid and is the string to replace with
# the iteration number.
str_to_replace = groupid[10::-1]
command = copasi + " " + os.path.join(inputdir, group_model + str_to_replace + ".cps")
parallel_computation(command, str_to_replace, cluster_type, runs, outputdir, pp_cpus)
# move the report files
report_files = [f for f in os.listdir(inputdir) if
re.match(group_model + '[0-9]+.*\.csv', f) or re.match(group_model + '[0-9]+.*\.txt', f)]
for file in report_files:
# Replace some string in the report file
replace_str_copasi_sim_report(os.path.join(inputdir, file))
# rename and move the output file
shutil.move(os.path.join(inputdir, file), os.path.join(outputdir, file.replace(groupid, "_")[:-4] + ".csv"))
# removed repeated copasi files
repeated_copasi_files = [f for f in os.listdir(inputdir) if re.match(group_model + '[0-9]+.*\.cps', f)]
for file in repeated_copasi_files:
os.remove(os.path.join(inputdir, file))
def generate_data(model, inputdir, cluster_type, pp_cpus, nfits, outputdir, sim_data_dir, updated_models_dir):
"""
The first pipeline step: data generation.
:param model: the model to process
:param inputdir: the directory containing the model
:param cluster_type: pp for parallel python, lsf for load sharing facility, sge for sun grid engine
:param pp_cpus: the number of cpu for parallel python
:param nfits: the number of fits to perform
:param outputdir: the directory to store the results
:param sim_data_dir: the directory containing the simulation data sets
:param updated_models_dir: the directory containing the Copasi models with updated parameters for
each estimation
:return: no output
"""
if int(nfits) < 1:
logger.error("variable " + nfits + " must be greater than 0. Please, check your configuration file.")
return
if not os.path.isfile(os.path.join(inputdir, model)):
logger.error(os.path.join(inputdir, model) + " does not exist.")
return
# folder preparation
refresh_directory(sim_data_dir, model[:-4])
refresh_directory(updated_models_dir, model[:-4])
copasi = get_copasi()
if copasi is None:
logger.error(
"CopasiSE not found! Please check that CopasiSE is installed and in the PATH environmental variable."
)
return
logger.info("Configure Copasi:")
logger.info(
"Replicate a Copasi file configured for parameter estimation and randomise the initial parameter values"
)
groupid = "_" + get_rand_alphanum_str(20) + "_"
group_model = model[:-4] + groupid
pre_param_estim = RandomiseParameters(inputdir, model)
pre_param_estim.print_parameters_to_estimate()
pre_param_estim.generate_instances_from_template(nfits, groupid)
logger.info("\n")
logger.info("Parallel parameter estimation:")
# To make things simple, the last 10 character of groupid are extracted and reversed.
# This string will be likely different from groupid and is the string to replace with
# the iteration number.
str_to_replace = groupid[10::-1]
command = (
copasi
+ " -s "
+ os.path.join(inputdir, group_model + str_to_replace + ".cps")
+ " "
+ os.path.join(inputdir, group_model + str_to_replace + ".cps")
)
parallel_computation(command, str_to_replace, cluster_type, nfits, outputdir, pp_cpus)
# Move the report files to the outputdir
report_files = [
f
for f in os.listdir(inputdir)
if re.match(group_model + "[0-9]+.*\.csv", f) or re.match(group_model + "[0-9]+.*\.txt", f)
]
for file in report_files:
# copy report and remove the groupid
shutil.move(os.path.join(inputdir, file), os.path.join(sim_data_dir, file.replace(groupid, "_")))
# removed repeated copasi files
repeated_copasi_files = [f for f in os.listdir(inputdir) if re.match(group_model + "[0-9]+.*\.cps", f)]
for file in repeated_copasi_files:
# os.remove(os.path.join(inputdir, file))
shutil.move(os.path.join(inputdir, file), os.path.join(updated_models_dir, file.replace(groupid, "_")))
