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 run(self, num_procs, base_dir, input_dir=None, global_dir=None,
write_option=None, num_writers=None, LorS=None, R=False):
"""
Preprocess and run ADCIRC on this domain
.. seealso:: `Generic ADCIRC Command Line Options <http://adcirc.org/home/documentation/generic-adcirc-command-line-options/>`_
:param int num_procs: number of processors for this ADCIRC run
:param string base_dir: directory containing the padcirc executables
:param string input_dir: directory containing the input files
:param string global_dir: directory to write fulldomain output files to
:param string write_option: (optional) specifiy ``W`` or ``Ws`` flag
:param int num_writers: number of MPI process to dedicate soley to the
task of writing ascii files
:param string LorS: (optional) specify ``L`` or ``S`` flag
:param string R: (optional) specify ``R`` flag
"""
if base_dir is None:
base_dir = self.path
if input_dir is None:
input_dir = self.path
if global_dir is None:
global_dir = self.path
if not os.path.exists(os.path.join(self.path, 'adcprep')):
os.symlink(os.path.join(base_dir, 'adcprep'),
os.path.join(self.path, 'adcprep'))
prep.write_1(self.path, num_procs)
prep.write_2(self.path, num_procs)
subprocess.call('./adcprep < in.prep1 > prep_o.txt', shell=True,
cwd=self.path)
subprocess.call('./adcprep < in.prep2 > prep_o.txt', shell=True,
cwd=self.path)
command = ['ibrun', 'padcirc', '-I', input_dir, '-O', global_dir]
if LorS:
command.append('-'+LorS)
if R:
command.append('-'+R)
if write_option:
command.append('-'+write_option)
command.append(str(num_writers))
subprocess.call(command, cwd=base_dir)
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)
