def write_script_output(fn_h5, grp_name, results, args):
'''Store the output of a script in an open HDF5 file
**Arguments:**
fn_h5
The HDF5 filename
grp_name
The name of the group where the results will be stored.
results
A dictionary with results.
args
The results of the command line parser. All arguments are stored
as attributes in the HDF5 output file.
'''
with LockedH5File(fn_h5) as f:
# Store results
grp = f.require_group(grp_name)
for key in grp.keys():
del grp[key]
dump_h5(grp, results)
# Store command-line arguments arguments
store_args(args, grp)
if log.do_medium:
log('Results written to %s:%s' % (fn_h5, grp_name))
def write_script_output(fn_h5, grp_name, results, args):
'''Store the output of a script in an open HDF5 file
**Arguments:**
fn_h5
The HDF5 filename
grp_name
The name of the group where the results will be stored.
results
A dictionary with results.
args
The results of the command line parser. All arguments are stored
as attributes in the HDF5 output file.
'''
with LockedH5File(fn_h5) as f:
# Store results
grp = f.require_group(grp_name)
for key in grp.keys():
del grp[key]
dump_h5(grp, results)
# Store command-line arguments arguments
store_args(args, grp)
if log.do_medium:
log('Results written to %s:%s' % (fn_h5, grp_name))
def to_file(self, filename):
'''Write data to a file
**Arguments:**
filename
The file to write the data to
This routine uses the extension or prefix of the filename to determine
the file format. For each file format, a specialized function is
called that does the real work.
'''
if isinstance(filename, h5.Group) or filename.endswith('.h5'):
data = vars(self).copy()
# get rid of leading underscores
for key in data.keys():
if key[0] == '_':
data[key[1:]] = data[key]
del data[key]
from horton.io.internal import dump_h5
dump_h5(filename, data)
elif filename.endswith('.xyz'):
from horton.io.xyz import dump_xyz
dump_xyz(filename, self)
elif filename.endswith('.cube'):
from horton.io.cube import dump_cube
dump_cube(filename, self)
elif filename.endswith('.cif'):
from horton.io.cif import dump_cif
dump_cif(filename, self)
elif filename.endswith('.molden.input') or filename.endswith(
'.molden'):
from horton.io.molden import dump_molden
dump_molden(filename, self)
elif os.path.basename(filename).startswith('POSCAR'):
from horton.io.vasp import dump_poscar
dump_poscar(filename, self)
elif 'FCIDUMP' in os.path.basename(filename):
from horton.io.molpro import dump_fcidump
dump_fcidump(filename, self)
else:
raise ValueError('Unknown file format for writing: %s' % filename)
def to_file(self, filename):
'''Write data to a file
**Arguments:**
filename
The file to write the data to
This routine uses the extension or prefix of the filename to determine
the file format. For each file format, a specialized function is
called that does the real work.
'''
if isinstance(filename, h5.Group) or filename.endswith('.h5'):
data = vars(self).copy()
# get rid of leading underscores
for key in data.keys():
if key[0] == '_':
data[key[1:]] = data[key]
del data[key]
from horton.io.internal import dump_h5
dump_h5(filename, data)
elif filename.endswith('.xyz'):
from horton.io.xyz import dump_xyz
dump_xyz(filename, self)
elif filename.endswith('.cube'):
from horton.io.cube import dump_cube
dump_cube(filename, self)
elif filename.endswith('.cif'):
from horton.io.cif import dump_cif
dump_cif(filename, self)
elif filename.endswith('.molden.input') or filename.endswith('.molden'):
from horton.io.molden import dump_molden
dump_molden(filename, self)
elif os.path.basename(filename).startswith('POSCAR'):
from horton.io.vasp import dump_poscar
dump_poscar(filename, self)
elif 'FCIDUMP' in os.path.basename(filename):
from horton.io.molpro import dump_fcidump
dump_fcidump(filename, self)
else:
raise ValueError('Unknown file format for writing: %s' % filename)
def write_part_output(fn_h5, grp_name, part, keys, args):
'''Write the output of horton-wpart.py
**Arguments:**
fn_h5
The filename for the HDF5 output file.
grp_name
the destination group
part
The partitioning object (instance of subclass of
horton.part.base.Part)
keys
The keys of the cached items that must go in the HDF5 outut file.
args
The results of the command line parser. All arguments are stored
as attributes in the HDF5 output file.
'''
def get_results(part, keys):
results = {}
for key in keys:
if isinstance(key, basestring):
results[key] = part[key]
elif isinstance(key, tuple):
assert len(key) == 2
index = key[1]
assert isinstance(index, int)
assert index >= 0
assert index < part.natom
atom_results = results.setdefault('atom_%05i' % index, {})
atom_results[key[0]] = part[key]
return results
# Store the results in an HDF5 file
with LockedH5File(fn_h5) as f:
# Transform results to a suitable dictionary structure
results = get_results(part, keys)
# Store results
grp = f.require_group(grp_name)
for key in grp.keys():
del grp[key]
dump_h5(grp, results)
# Store command line arguments
store_args(args, grp)
if args.debug:
# Collect debug results
debug_keys = [key for key in part.cache.iterkeys() if key not in keys]
debug_results = get_results(part, debug_keys)
# Store additional data for debugging
if 'debug' in grp:
del grp['debug']
debuggrp = f.create_group('debug')
dump_h5(debuggrp, debug_results)
if log.do_medium:
log('Results written to %s:%s' % (fn_h5, grp_name))
def write_part_output(fn_h5, grp_name, part, keys, args):
'''Write the output of horton-wpart.py
**Arguments:**
fn_h5
The filename for the HDF5 output file.
grp_name
the destination group
part
The partitioning object (instance of subclass of
horton.part.base.Part)
keys
The keys of the cached items that must go in the HDF5 outut file.
args
The results of the command line parser. All arguments are stored
as attributes in the HDF5 output file.
'''
def get_results(part, keys):
results = {}
for key in keys:
if isinstance(key, basestring):
results[key] = part[key]
elif isinstance(key, tuple):
assert len(key) == 2
index = key[1]
assert isinstance(index, int)
assert index >= 0
assert index < part.natom
atom_results = results.setdefault('atom_%05i' % index, {})
atom_results[key[0]] = part[key]
return results
# Store the results in an HDF5 file
with LockedH5File(fn_h5) as f:
# Transform results to a suitable dictionary structure
results = get_results(part, keys)
# Store results
grp = f.require_group(grp_name)
for key in grp.keys():
del grp[key]
dump_h5(grp, results)
# Store command line arguments
store_args(args, grp)
if args.debug:
# Collect debug results
debug_keys = [
key for key in part.cache.iterkeys() if key not in keys
]
debug_results = get_results(part, debug_keys)
# Store additional data for debugging
if 'debug' in grp:
del grp['debug']
debuggrp = f.create_group('debug')
dump_h5(debuggrp, debug_results)
if log.do_medium:
log('Results written to %s:%s' % (fn_h5, grp_name))
