def setup_landuse_folder(self, class_num, manningsn_value=1,
folder_name=None):
"""
Set up a single landuse with name landuse_class_num
:param int class_num: land classification number for this folder
:param int manningsn_value: Manning's *n* value for this land
classification
:param string folder_name: folder name relative to ``self.base_dir``
:rtype: string
:returns: file name of bash script for this land class
"""
if folder_name is None:
folder_name = 'landuse_'+'{:=02d}'.format(class_num)
print 'Setting up folder -- '+folder_name+'...'
# create a folder for this land-use classification
fm.mkdir(os.path.join(self.basis_dir, folder_name))
# cp self.file_name folder_name
fm.copy(os.path.join(self.basis_dir, self.file_name),
os.path.join(self.basis_dir, folder_name))
# create *.in files
self.create_griddata_input_files(folder_name)
# create *.sh files
script_name = self.create_bash_script(folder_name)
# create the *.table file needed for grid_all_data
self.setup_tables_single_value(class_num, manningsn_value,
os.path.join(self.basis_dir,
folder_name))
return script_name
def setup_rfdir(self, path, num_procs):
"""
Creates the directory path and copies required files from
``self.base_dir`` into path:type path: string
:param path: folder_name
:param num_procs: number of processors per :program:`ADCIRC` run
"""
mkdir(path)
copy(self.save_dir + '/fort.13', path)
# crete sybolic links from fort.* files to path
inputs1 = glob.glob(self.grid_dir + '/fort.1*')
inputs2 = glob.glob(self.grid_dir + '/fort.2*')
inputs0 = glob.glob(self.grid_dir + '/fort.01*')
inputs = inputs0 + inputs1 + inputs2
if self.grid_dir + '/fort.13' in inputs:
inputs.remove(self.grid_dir + '/fort.13')
if not self.grid_dir + '/fort.019' in inputs:
if self.grid_dir + '/fort.015' in inputs:
inputs.remove(self.grid_dir + '/fort.015')
for fid in inputs:
if os.path.exists(path + '/' + fid.rpartition('/')[-1]):
os.remove(path + '/' + fid.rpartition('/')[-1])
os.symlink(fid, path + '/' + fid.rpartition('/')[-1])
#copy(fid, path+'/'+fid.rpartition('/')[-1])
if not os.path.exists(path + '/adcprep'):
os.symlink(self.base_dir + '/adcprep', path + '/adcprep')
prep.write_1(path, num_procs)
prep.write_2(path, num_procs)
prep.write_5(path, num_procs)
def setup_rfdir(self, path, num_procs):
"""
Creates the directory path and copies required files from
``self.base_dir`` into path:type path: string
:param path: folder_name
:param num_procs: number of processors per :program:`ADCIRC` run
"""
mkdir(path)
copy(self.save_dir+'/fort.13', path)
# crete sybolic links from fort.* files to path
inputs1 = glob.glob(self.grid_dir+'/fort.1*')
inputs2 = glob.glob(self.grid_dir+'/fort.2*')
inputs0 = glob.glob(self.grid_dir+'/fort.01*')
inputs = inputs0 + inputs1 + inputs2
if self.grid_dir+'/fort.13' in inputs:
inputs.remove(self.grid_dir+'/fort.13')
if not self.grid_dir+'/fort.019' in inputs:
if self.grid_dir+'/fort.015' in inputs:
inputs.remove(self.grid_dir+'/fort.015')
for fid in inputs:
if os.path.exists(path+'/'+fid.rpartition('/')[-1]):
os.remove(path+'/'+fid.rpartition('/')[-1])
os.symlink(fid, path+'/'+fid.rpartition('/')[-1])
#copy(fid, path+'/'+fid.rpartition('/')[-1])
if not os.path.exists(path+'/adcprep'):
os.symlink(self.base_dir+'/adcprep', path+'/adcprep')
prep.write_1(path, num_procs)
prep.write_2(path, num_procs)
prep.write_5(path, num_procs)
def __init__(self,
grid_dir,
save_dir,
basis_dir,
num_of_parallel_runs=10,
base_dir=None,
script_name=None):
"""
Initialization
"""
#: string, directory containing ``fort.14``, ``fort.15``, and
# ``fort.22*``
self.grid_dir = grid_dir
self.save_dir = save_dir
"""
string, directory where ``RF_directory_*`` are saved, and
where ``fort.13`` is located
"""
if os.path.exists(save_dir) == False:
os.mkdir(save_dir)
fort13_file = save_dir.rpartition('/')[0] + '/fort.13'
copy(fort13_file, save_dir)
#: string, directory where ``landuse_*`` folders are located
self.basis_dir = basis_dir
if base_dir:
self.base_dir = base_dir
"""
directory that contains ADCIRC executables, and machine
specific ``in.prep#`` files
"""
else:
self.base_dir = basis_dir.rpartition('/')[0]
self.prep_dir = basis_dir.rpartition('/')[0]
#: int, size of batch of jobs to be submitted to queue
self.num_of_parallel_runs = num_of_parallel_runs
#: dict() of :class:`np.ndarray`, timeseries data
self.ts_data = None
#: dict() of :class:`np.ndarray`, non-timeseries data
self.nts_data = None
#: list(), list of ``RF_directory_*/`` names
self.rf_dirs = None
#: dict() of :class:`np.array`, time in (s) of observations
self.time_obs = None
if script_name:
#: string, name of the batch bash script
self.script_name = script_name
else:
self.script_name = "run_job_batch.sh"
super(runSet, self).__init__()
def __init__(self, grid_dir, save_dir, basis_dir, num_of_parallel_runs=10,
base_dir=None, script_name=None):
"""
Initialization
"""
#: string, directory containing ``fort.14``, ``fort.15``, and
# ``fort.22*``
self.grid_dir = grid_dir
self.save_dir = save_dir
"""
string, directory where ``RF_directory_*`` are saved, and
where ``fort.13`` is located
"""
if os.path.exists(save_dir) == False:
os.mkdir(save_dir)
fort13_file = save_dir.rpartition('/')[0]+'/fort.13'
copy(fort13_file, save_dir)
#: string, directory where ``landuse_*`` folders are located
self.basis_dir = basis_dir
if base_dir:
self.base_dir = base_dir
"""
directory that contains ADCIRC executables, and machine
specific ``in.prep#`` files
"""
else:
self.base_dir = basis_dir.rpartition('/')[0]
self.prep_dir = basis_dir.rpartition('/')[0]
#: int, size of batch of jobs to be submitted to queue
self.num_of_parallel_runs = num_of_parallel_runs
#: dict() of :class:`np.ndarray`, timeseries data
self.ts_data = None
#: dict() of :class:`np.ndarray`, non-timeseries data
self.nts_data = None
#: list(), list of ``RF_directory_*/`` names
self.rf_dirs = None
#: dict() of :class:`np.array`, time in (s) of observations
self.time_obs = None
if script_name:
#: string, name of the batch bash script
self.script_name = script_name
else:
self.script_name = "run_job_batch.sh"
super(runSet, self).__init__()
def setup_rfdir(self, path, num_procs):
"""
Creates the directory path and copies required files from
``self.base_dir`` into
:param string path: folder_name
:param int num_procs: number of processors per :program:`ADCIRC` run
"""
mkdir(path)
copy(os.path.join(self.save_dir, 'fort.13'), path)
# crete sybolic links from fort.* files to path
inputs1 = glob.glob(os.path.join(self.grid_dir, 'fort.1*'))
inputs2 = glob.glob(os.path.join(self.grid_dir, 'fort.2*'))
inputs0 = glob.glob(os.path.join(self.grid_dir, 'fort.01*'))
inputs = inputs0 + inputs1 + inputs2
if os.path.join(self.grid_dir, 'fort.13') in inputs:
inputs.remove(os.path.join(self.grid_dir, 'fort.13'))
if not os.path.join(self.grid_dir, 'fort.019') in inputs:
if os.path.join(self.grid_dir, 'fort.015') in inputs:
inputs.remove(os.path.join(self.grid_dir, 'fort.015'))
else:
sub_files = ['bv.nodes', 'py.140', 'py.141']
sub_files = [os.path.join(self.grid_dir, sf) for sf in sub_files]
inputs.extend(sub_files)
for fid in inputs:
rf_fid = os.path.join(path, fid.rpartition('/')[-1])
if os.path.exists(rf_fid):
if os.path.islink(rf_fid):
os.unlink(rf_fid)
else:
os.remove(rf_fid)
os.symlink(fid, rf_fid)
if not os.path.exists(os.path.join(path, 'padcirc')):
os.symlink(os.path.join(self.base_dir, 'padcirc'),
os.path.join(path, 'padcirc'))
if not os.path.exists(os.path.join(path, 'adcprep')):
os.symlink(os.path.join(self.base_dir, 'adcprep'),
os.path.join(path, 'adcprep'))
prep.write_1(path, num_procs)
prep.write_2(path, num_procs)
prep.write_5(path, num_procs)
def setup_rfdir(self, path, num_procs):
"""
Creates the directory path and copies required files from
``self.base_dir`` into
:param string path: folder_name
:param int num_procs: number of processors per :program:`ADCIRC` run
"""
mkdir(path)
copy(os.path.join(self.save_dir, 'fort.13'), path)
# crete sybolic links from fort.* files to path
inputs1 = glob.glob(os.path.join(self.grid_dir, 'fort.1*'))
inputs2 = glob.glob(os.path.join(self.grid_dir, 'fort.2*'))
inputs0 = glob.glob(os.path.join(self.grid_dir, 'fort.01*'))
inputs = inputs0 + inputs1 + inputs2
if os.path.join(self.grid_dir, 'fort.13') in inputs:
inputs.remove(os.path.join(self.grid_dir, 'fort.13'))
if not os.path.join(self.grid_dir, 'fort.019') in inputs:
if os.path.join(self.grid_dir, 'fort.015') in inputs:
inputs.remove(os.path.join(self.grid_dir, 'fort.015'))
else:
sub_files = ['bv.nodes', 'py.140', 'py.141']
sub_files = [os.path.join(self.grid_dir, sf) for sf in sub_files]
inputs.extend(sub_files)
for fid in inputs:
rf_fid = os.path.join(path, fid.rpartition('/')[-1])
if os.path.exists(rf_fid):
if os.path.islink(rf_fid):
os.unlink(rf_fid)
else:
os.remove(rf_fid)
os.symlink(fid, rf_fid)
if not os.path.exists(os.path.join(path, 'padcirc')):
os.symlink(os.path.join(self.base_dir, 'padcirc'),
os.path.join(path, 'padcirc'))
if not os.path.exists(os.path.join(path, 'adcprep')):
os.symlink(os.path.join(self.base_dir, 'adcprep'),
os.path.join(path, 'adcprep'))
prep.write_1(path, num_procs)
prep.write_2(path, num_procs)
prep.write_5(path, num_procs)
def setup_folder(self, folder_name = 'temp'):
"""
Set up a single folder with name folder_name
:param string folder_name: folder name relative to ``self.base_dir``
:rtype: string
:returns: file name of bash script for this land class
"""
print 'Setting up folder -- '+folder_name+'...'
# create a folder for this land-use classification
fm.mkdir(self.basis_dir+'/'+folder_name)
# cp self.file_name folder_name
fm.copy(self.basis_dir+'/'+self.file_name, self.basis_dir+'/'+folder_name)
# create *.in files
self.create_griddata_input_files(folder_name)
# create *.sh files
script_name = self.create_bash_script(folder_name)
# create the *.table file needed for grid_all_data
self.setup_tables(self.basis_dir+'/'+folder_name)
return script_name
import polyadcirc.pyADCIRC.fort13_management as f13
import glob
# Specify run parameter folders
adcirc_dir = '/h1/lgraham/workspace'
grid_dir = adcirc_dir + '/ADCIRC_landuse/Katrina_small/inputs'
save_dir = adcirc_dir + '/ADCIRC_landuse/Katrina_small/runs/output_test'
basis_dir = adcirc_dir + '/ADCIRC_landuse/Katrina_small/landuse_basis/gap/shelf_test'
# load in the small katrina mesh
domain = dom.domain(grid_dir)
domain.update()
# load in basis vectors for domain
bv_dict = tmm.get_basis_vectors(basis_dir)
# create the shelf basis vector dictonary
shelf_limits = [0, 50]
shelf_bv = tmm.create_shelf(domain, shelf_limits, bv_dict)
# write this out to an appropriately numbered basis vector mesh in the correct
# basis_dir
# get list of landuse folder names
folders = glob.glob(basis_dir + '/landuse_*')
# create new folder
folder_name = basis_dir + '/landuse_' + '{:=02d}'.format(len(folders))
fm.mkdir(folder_name)
# copy a fort.13 file to that folder
fm.copy(save_dir + '/fort.13', folder_name + '/fort.13')
f13.update_mann(shelf_bv, folder_name)
# Specify run parameter folders
adcirc_dir = '/h1/lgraham/workspace'
grid_dir = adcirc_dir + '/ADCIRC_landuse/Katrina_small/inputs'
save_dir = adcirc_dir + '/ADCIRC_landuse/Katrina_small/runs/output_test'
basis_dir = adcirc_dir +'/ADCIRC_landuse/Katrina_small/landuse_basis/gap/shelf_test'
# load in the small katrina mesh
domain = dom.domain(grid_dir)
domain.update()
# load in basis vectors for domain
bv_dict = tmm.get_basis_vectors(basis_dir)
# create the shelf basis vector dictonary
shelf_limits = [0, 50] #[0, 100] [50, 100]
shelf_bv = tmm.create_shelf(domain, shelf_limits, bv_dict)
# write this out to an appropriately numbered basis vector mesh in the correct
# basis_dir
# get list of landuse folder names
folders = glob.glob(basis_dir+'/landuse_*')
# create new folder
folder_name = basis_dir+'/landuse_'+'{:=02d}'.format(len(folders))
fm.mkdir(folder_name)
# copy a fort.13 file to that folder
fm.copy(save_dir+'/fort.13', folder_name+'/fort.13')
f13.update_mann(shelf_bv, folder_name)
