def merge(self, gswfk_file, dfpt_files, gkk_files, out_gkk, binascii=0, cwd=None):
"""Merge DDB file, return the absolute path of the new database."""
raise NotImplementedError("This method should be tested")
out_gkk = out_gkk if cwd is None else os.path.join(os.path.abspath(cwd), out_gkk)
# We work with absolute paths.
gswfk_file = absath(gswfk_file)
dfpt_files = [os.path.abspath(s) for s in list_strings(dfpt_files)]
gkk_files = [os.path.abspath(s) for s in list_strings(gkk_files)]
if self.verbose:
print("Will merge %d 1WF files, %d GKK file in output %s" %
(len(dfpt_nfiles), (len_gkk_files), out_gkk))
for (i, f) in enumerate(dfpt_files):
print(" [%d] 1WF %s" % (i, f))
for (i, f) in enumerate(gkk_files):
print(" [%d] GKK %s" % (i, f))
self.stdin_fname, self.stdout_fname, self.stderr_fname = (
"mrggkk.stdin", "mrggkk.stdout", "mrggkk.stderr")
if cwd is not None:
self.stdin_fname, self.stdout_fname, self.stderr_fname = \
map(os.path.join, 3 * [cwd], [self.stdin_fname, self.stdout_fname, self.stderr_fname])
inp = StringIO.StringIO()
inp.write(out_gkk + "\n") # Name of the output file
inp.write(str(binascii) + "\n") # Integer flag: 0 --> binary output, 1 --> ascii formatted output
inp.write(gswfk_file + "\n") # Name of the groud state wavefunction file WF
#dims = len(dfpt_files, gkk_files, ?)
dims = " ".join([str(d) for d in dims])
inp.write(dims + "\n") # Number of 1WF, of GKK files, and number of 1WF files in all the GKK files
# Names of the 1WF files...
for fname in dfpt_files:
inp.write(fname + "\n")
# Names of the GKK files...
for fname in gkk_files:
inp.write(fname + "\n")
inp.seek(0)
self.stdin_data = [s for s in inp]
with open(self.stdin_fname, "w") as fh:
fh.writelines(self.stdin_data)
try:
self.execute(cwd=cwd)
except self.Error:
raise
return out_gkk
def merge(self, workdir, gswfk_file, dfpt_files, gkk_files, out_gkk, binascii=0):
"""
Merge GGK files, return the absolute path of the new database.
Args:
gswfk_file: Ground-state WFK filename
dfpt_files: List of 1WFK files to merge.
gkk_files: List of GKK files to merge.
out_gkk: Name of the output GKK file
binascii: Integer flat. 0 --> binary output, 1 --> ascii formatted output
"""
raise NotImplementedError("This method should be tested")
#out_gkk = out_gkk if cwd is None else os.path.join(os.path.abspath(cwd), out_gkk)
# We work with absolute paths.
gswfk_file = absath(gswfk_file)
dfpt_files = [os.path.abspath(s) for s in list_strings(dfpt_files)]
gkk_files = [os.path.abspath(s) for s in list_strings(gkk_files)]
print("Will merge %d 1WF files, %d GKK file in output %s" %
(len(dfpt_nfiles), len_gkk_files, out_gkk))
if self.verbose:
for i, f in enumerate(dfpt_files): print(" [%d] 1WF %s" % (i, f))
for i, f in enumerate(gkk_files): print(" [%d] GKK %s" % (i, f))
self.stdin_fname, self.stdout_fname, self.stderr_fname = \
map(os.path.join, 3 * [workdir], ["mrggkk.stdin", "mrggkk.stdout", "mrggkk.stderr"])
inp = cStringIO()
inp.write(out_gkk + "\n") # Name of the output file
inp.write(str(binascii) + "\n") # Integer flag: 0 --> binary output, 1 --> ascii formatted output
inp.write(gswfk_file + "\n") # Name of the groud state wavefunction file WF
#dims = len(dfpt_files, gkk_files, ?)
dims = " ".join([str(d) for d in dims])
inp.write(dims + "\n") # Number of 1WF, of GKK files, and number of 1WF files in all the GKK files
# Names of the 1WF files...
for fname in dfpt_files:
inp.write(fname + "\n")
# Names of the GKK files...
for fname in gkk_files:
inp.write(fname + "\n")
self.stdin_data = [s for s in inp.getvalue()]
with open(self.stdin_fname, "w") as fh:
fh.writelines(self.stdin_data)
self.execute(workdir)
return out_gkk
def parse(self, filenames):
"""
Read and parse a filename or a list of filenames.
Files that cannot be opened are ignored. A single filename may also be given.
Return list of successfully read files.
"""
filenames = list_strings(filenames)
read_ok = []
for fname in filenames:
try:
fh = open(fname)
except IOError:
logger.warning("Cannot open file %s" % fname)
continue
try:
self._read(fh, fname)
read_ok.append(fname)
except self.Error as e:
logger.warning("exception while parsing file %s :\n%s" % (fname, str(e)))
continue
finally:
fh.close()
# Add read_ok to the list of files that have been parsed.
self._filenames.extend(read_ok)
return read_ok
def parse(self, filenames):
"""
Read and parse a filename or a list of filenames.
Files that cannot be opened are ignored. A single filename may also be given.
Return list of successfully read files.
"""
filenames = list_strings(filenames)
read_ok = []
for fname in filenames:
try:
fh = open(fname)
except IOError:
logger.warning("Cannot open file %s" % fname)
continue
try:
self._read(fh, fname)
read_ok.append(fname)
except self.Error as e:
logger.warning("exception while parsing file %s :\n%s" % (fname, str(e)))
continue
finally:
fh.close()
# Add read_ok to the list of files that have been parsed.
self._filenames.extend(read_ok)
return read_ok
def merge_qpoints(self, workdir, files_to_merge, out_prefix):
"""
Execute mrgscr inside directory `workdir` to merge `files_to_merge`.
Produce new file with prefix `out_prefix`
"""
# We work with absolute paths.
files_to_merge = [os.path.abspath(s) for s in list_strings(files_to_merge)]
nfiles = len(files_to_merge)
if self.verbose:
print("Will merge %d files with output_prefix %s" % (nfiles, out_prefix))
for (i, f) in enumerate(files_to_merge):
print(" [%d] %s" % (i, f))
if nfiles == 1:
raise self.Error("merge_qpoints does not support nfiles == 1")
self.stdin_fname, self.stdout_fname, self.stderr_fname = \
map(os.path.join, 3 * [workdir], ["mrgscr.stdin", "mrgscr.stdout", "mrgscr.stderr"])
inp = cStringIO()
inp.write(str(nfiles) + "\n") # Number of files to merge.
inp.write(out_prefix + "\n") # Prefix for the final output file:
for filename in files_to_merge:
inp.write(filename + "\n") # List with the files to merge.
inp.write("1\n") # Option for merging q-points.
self.stdin_data = [s for s in inp.getvalue()]
with open(self.stdin_fname, "w") as fh:
fh.writelines(self.stdin_data)
self.execute(workdir)
def find_file(files, ext, prefix=None, dataset=None, image=None):
"""
Given a list of file names, return the file with extension "_" + ext, None if not found.
The prefix, the dataset index and the image index can be specified
.. warning::
There are some border cases that will confuse the algorithm
since the order of dataset and image is not tested.
Solving this problem requires the knowledge of ndtset and nimages
This code, however should work in 99.9% of the cases.
"""
separator = "_"
for filename in list_strings(files):
# Remove Netcdf extension (if any)
f = filename[:-3] if filename.endswith(".nc") else filename
if separator not in f: continue
tokens = f.split(separator)
if tokens[-1] == ext:
found = True
if prefix is not None:
found = found and filename.startswith(prefix)
if dataset is not None:
found = found and "DS" + str(dataset) in tokens
if image is not None:
found = found and "IMG" + str(image) in tokens
if found: return filename
else:
return None
def __init__(self, pseudos):
"""
Args:
pseudos:
List of pseudopotentials or filepaths
"""
# Store pseudos in a default dictionary with z as key.
# Note that we can have more than one pseudo for given z.
# hence the values are lists of pseudos.
if not isinstance(pseudos, collections.Iterable):
pseudos = [pseudos]
if is_string(pseudos[0]):
pseudos = list_strings(pseudos)
self._pseudos_with_z = collections.defaultdict(list)
for pseudo in pseudos:
p = pseudo
if not isinstance(pseudo, Pseudo):
p = Pseudo.from_file(pseudo)
self._pseudos_with_z[p.Z].append(p)
for z in self.zlist:
pseudo_list = self._pseudos_with_z[z]
symbols = [p.symbol for p in pseudo_list]
symbol = symbols[0]
if any(symb != symbol for symb in symbols):
raise ValueError(
"All symbols must be equal while they are: %s" %
str(symbols))
setattr(self, symbol, pseudo_list)
def find_file(files, ext, prefix=None, dataset=None, image=None):
"""
Given a list of file names, return the file with extension "_" + ext, None if not found.
The prefix, the dataset index and the image index can be specified
.. warning::
There are some border cases that will confuse the algorithm
since the order of dataset and image is not tested.
Solving this problem requires the knowledge of ndtset and nimages
This code, however should work in 99.9% of the cases.
"""
separator = "_"
for filename in list_strings(files):
# Remove Netcdf extension (if any)
f = filename[:-3] if filename.endswith(".nc") else filename
if separator not in f: continue
tokens = f.split(separator)
if tokens[-1] == ext:
found = True
if prefix is not None: found = found and filename.startswith(prefix)
if dataset is not None: found = found and "DS" + str(dataset) in tokens
if image is not None: found = found and "IMG" + str(image) in tokens
if found: return filename
else:
return None
def __init__(self, pseudos):
"""
Args:
pseudos:
List of pseudopotentials or filepaths
"""
# Store pseudos in a default dictionary with z as key.
# Note that we can have more than one pseudo for given z.
# hence the values are lists of pseudos.
if not isinstance(pseudos, collections.Iterable):
pseudos = [pseudos]
if is_string(pseudos[0]):
pseudos = list_strings(pseudos)
self._pseudos_with_z = collections.defaultdict(list)
for pseudo in pseudos:
p = pseudo
if not isinstance(pseudo, Pseudo):
p = Pseudo.from_file(pseudo)
self._pseudos_with_z[p.Z].append(p)
for z in self.zlist:
pseudo_list = self._pseudos_with_z[z]
symbols = [p.symbol for p in pseudo_list]
symbol = symbols[0]
if any(symb != symbol for symb in symbols):
raise ValueError("All symbols must be equal while they are: %s" % str(symbols))
setattr(self, symbol, pseudo_list)
def merge(self, ddb_files, out_ddb, description, cwd=None):
"""Merge DDB file, return the absolute path of the new database."""
# We work with absolute paths.
ddb_files = [os.path.abspath(s) for s in list_strings(ddb_files)]
out_ddb = out_ddb if cwd is None else os.path.join(
os.path.abspath(cwd), out_ddb)
if self.verbose:
print("Will merge %d files into output DDB %s" %
(len(ddb_files), out_ddb))
for (i, f) in enumerate(ddb_files):
print(" [%d] %s" % (i, f))
# Handle the case of a single file since mrgddb uses 1 to denote GS files!
if len(ddb_files) == 1:
with open(ddb_files[0], "r") as inh, open(out_ddb, "w") as out:
for line in inh:
out.write(line)
return out_ddb
self.stdin_fname, self.stdout_fname, self.stderr_fname = (
"mrgddb.stdin", "mrgddb.stdout", "mrgddb.stderr")
if cwd is not None:
self.stdin_fname, self.stdout_fname, self.stderr_fname = \
map(os.path.join, 3 * [cwd], [self.stdin_fname, self.stdout_fname, self.stderr_fname])
inp = StringIO.StringIO()
inp.write(out_ddb + "\n") # Name of the output file.
inp.write(str(description) + "\n") # Description.
inp.write(str(len(ddb_files)) + "\n") # Number of input DDBs.
# Names of the DDB files.
for fname in ddb_files:
inp.write(fname + "\n")
inp.seek(0)
self.stdin_data = [s for s in inp]
with open(self.stdin_fname, "w") as fh:
fh.writelines(self.stdin_data)
try:
self.execute(cwd=cwd)
except self.Error:
raise
return out_ddb
def merge(self, ddb_files, out_ddb, description, cwd=None):
"""Merge DDB file, return the absolute path of the new database."""
# We work with absolute paths.
ddb_files = [os.path.abspath(s) for s in list_strings(ddb_files)]
out_ddb = out_ddb if cwd is None else os.path.join(os.path.abspath(cwd), out_ddb)
if self.verbose:
print("Will merge %d files into output DDB %s" % (len(ddb_files), out_ddb))
for (i, f) in enumerate(ddb_files):
print(" [%d] %s" % (i, f))
# Handle the case of a single file since mrgddb uses 1 to denote GS files!
if len(ddb_files) == 1:
with open(ddb_files[0], "r") as inh, open(out_ddb, "w") as out:
for line in inh:
out.write(line)
return out_ddb
self.stdin_fname, self.stdout_fname, self.stderr_fname = (
"mrgddb.stdin", "mrgddb.stdout", "mrgddb.stderr")
if cwd is not None:
self.stdin_fname, self.stdout_fname, self.stderr_fname = \
map(os.path.join, 3 * [cwd], [self.stdin_fname, self.stdout_fname, self.stderr_fname])
inp = StringIO.StringIO()
inp.write(out_ddb + "\n") # Name of the output file.
inp.write(str(description) + "\n") # Description.
inp.write(str(len(ddb_files)) + "\n") # Number of input DDBs.
# Names of the DDB files.
for fname in ddb_files:
inp.write(fname + "\n")
inp.seek(0)
self.stdin_data = [s for s in inp]
with open(self.stdin_fname, "w") as fh:
fh.writelines(self.stdin_data)
try:
self.execute(cwd=cwd)
except self.Error:
raise
return out_ddb
def merge_qpoints(self, files_to_merge, out_prefix, cwd=None):
"""
Execute mrgscr in a subprocess to merge files_to_merge. Produce new file with prefix out_prefix
If cwd is not None, the child's current directory will be changed to cwd before it is executed.
"""
# We work with absolute paths.
files_to_merge = [
os.path.abspath(s) for s in list_strings(files_to_merge)
]
nfiles = len(files_to_merge)
if self.verbose:
print("Will merge %d files with output_prefix %s" %
(nfiles, out_prefix))
for (i, f) in enumerate(files_to_merge):
print(" [%d] %s" % (i, f))
if nfiles == 1:
raise self.Error("merge_qpoints does not support nfiles == 1")
self.stdin_fname, self.stdout_fname, self.stderr_fname = (
"mrgscr.stdin", "mrgscr.stdout", "mrgscr.stderr")
if cwd is not None:
self.stdin_fname, self.stdout_fname, self.stderr_fname = \
map(os.path.join, 3 * [cwd], [self.stdin_fname, self.stdout_fname, self.stderr_fname])
inp = StringIO.StringIO()
inp.write(str(nfiles) + "\n") # Number of files to merge.
inp.write(out_prefix + "\n") # Prefix for the final output file:
for filename in files_to_merge:
inp.write(filename + "\n") # List with the files to merge.
inp.write("1\n") # Option for merging q-points.
inp.seek(0)
self.stdin_data = [s for s in inp]
with open(self.stdin_fname, "w") as fh:
fh.writelines(self.stdin_data)
try:
self.execute(cwd=cwd)
except self.Error:
raise
def merge(self, workdir, ddb_files, out_ddb, description):
"""Merge DDB file, return the absolute path of the new database in workdir."""
# We work with absolute paths.
ddb_files = [os.path.abspath(s) for s in list_strings(ddb_files)]
out_ddb = os.path.join(os.path.abspath(workdir), os.path.basename(out_ddb))
if self.verbose:
print("Will merge %d files into output DDB %s" % (len(ddb_files), out_ddb))
for i, f in enumerate(ddb_files):
print(" [%d] %s" % (i, f))
# Handle the case of a single file since mrgddb uses 1 to denote GS files!
if len(ddb_files) == 1:
with open(ddb_files[0], "r") as inh, open(out_ddb, "w") as out:
for line in inh:
out.write(line)
return out_ddb
self.stdin_fname, self.stdout_fname, self.stderr_fname = \
map(os.path.join, 3 * [workdir], ["mrgddb.stdin", "mrgddb.stdout", "mrgddb.stderr"])
inp = cStringIO()
inp.write(out_ddb + "\n") # Name of the output file.
inp.write(str(description) + "\n") # Description.
inp.write(str(len(ddb_files)) + "\n") # Number of input DDBs.
# Names of the DDB files.
for fname in ddb_files:
inp.write(fname + "\n")
self.stdin_data = [s for s in inp.getvalue()]
with open(self.stdin_fname, "w") as fh:
fh.writelines(self.stdin_data)
retcode = self.execute(workdir)
if retcode == 0:
# Remove ddb files.
for f in ddb_files:
try:
os.remove(f)
except IOError:
pass
return out_ddb
def merge_qpoints(self, files_to_merge, out_prefix, cwd=None):
"""
Execute mrgscr in a subprocess to merge files_to_merge. Produce new file with prefix out_prefix
If cwd is not None, the child's current directory will be changed to cwd before it is executed.
"""
# We work with absolute paths.
files_to_merge = [os.path.abspath(s) for s in list_strings(files_to_merge)]
nfiles = len(files_to_merge)
if self.verbose:
print("Will merge %d files with output_prefix %s" % (nfiles, out_prefix))
for (i, f) in enumerate(files_to_merge):
print(" [%d] %s" % (i, f))
if nfiles == 1:
raise self.Error("merge_qpoints does not support nfiles == 1")
self.stdin_fname, self.stdout_fname, self.stderr_fname = (
"mrgscr.stdin", "mrgscr.stdout", "mrgscr.stderr")
if cwd is not None:
self.stdin_fname, self.stdout_fname, self.stderr_fname = \
map(os.path.join, 3 * [cwd], [self.stdin_fname, self.stdout_fname, self.stderr_fname])
inp = StringIO.StringIO()
inp.write(str(nfiles) + "\n") # Number of files to merge.
inp.write(out_prefix + "\n") # Prefix for the final output file:
for filename in files_to_merge:
inp.write(filename + "\n") # List with the files to merge.
inp.write("1\n") # Option for merging q-points.
inp.seek(0)
self.stdin_data = [s for s in inp]
with open(self.stdin_fname, "w") as fh:
fh.writelines(self.stdin_data)
try:
self.execute(cwd=cwd)
except self.Error:
raise
def fix_paths(self, paths):
"""
Fix the filenames in the iterable paths
Returns:
old2new:
Mapping old_path --> new_path
"""
old2new, fixed_exts = {}, []
for path in list_strings(paths):
newpath, ext = self._fix_path(path)
if newpath is not None:
assert ext not in fixed_exts
fixed_exts.append(ext)
old2new[path] = newpath
return old2new
def fix_paths(self, paths):
"""
Fix the filenames in the iterable paths
Returns:
old2new:
Mapping old_path --> new_path
"""
old2new, fixed_exts = {}, []
for path in list_strings(paths):
newpath, ext = self._fix_path(path)
if newpath is not None:
assert ext not in fixed_exts
fixed_exts.append(ext)
old2new[path] = newpath
return old2new
def merge(self,
gswfk_file,
dfpt_files,
gkk_files,
out_gkk,
binascii=0,
cwd=None):
"""
Merge GGK files, return the absolute path of the new database.
Args:
gswfk_file: Ground-state WFK filename
dfpt_files: List of 1WFK files to merge.
gkk_files: List of GKK files to merge.
out_gkk: Name of the output GKK file
binascii: Integer flat. 0 --> binary output, 1 --> ascii formatted output
cwd: Directory where the subprocess will be executed.
"""
raise NotImplementedError("This method should be tested")
out_gkk = out_gkk if cwd is None else os.path.join(
os.path.abspath(cwd), out_gkk)
# We work with absolute paths.
gswfk_file = absath(gswfk_file)
dfpt_files = [os.path.abspath(s) for s in list_strings(dfpt_files)]
gkk_files = [os.path.abspath(s) for s in list_strings(gkk_files)]
if self.verbose:
print("Will merge %d 1WF files, %d GKK file in output %s" %
(len(dfpt_nfiles), len_gkk_files, out_gkk))
for (i, f) in enumerate(dfpt_files):
print(" [%d] 1WF %s" % (i, f))
for (i, f) in enumerate(gkk_files):
print(" [%d] GKK %s" % (i, f))
self.stdin_fname, self.stdout_fname, self.stderr_fname = (
"mrggkk.stdin", "mrggkk.stdout", "mrggkk.stderr")
if cwd is not None:
self.stdin_fname, self.stdout_fname, self.stderr_fname = \
map(os.path.join, 3 * [cwd], [self.stdin_fname, self.stdout_fname, self.stderr_fname])
inp = cStringIO()
inp.write(out_gkk + "\n") # Name of the output file
inp.write(
str(binascii) + "\n"
) # Integer flag: 0 --> binary output, 1 --> ascii formatted output
inp.write(gswfk_file +
"\n") # Name of the groud state wavefunction file WF
#dims = len(dfpt_files, gkk_files, ?)
dims = " ".join([str(d) for d in dims])
inp.write(
dims + "\n"
) # Number of 1WF, of GKK files, and number of 1WF files in all the GKK files
# Names of the 1WF files...
for fname in dfpt_files:
inp.write(fname + "\n")
# Names of the GKK files...
for fname in gkk_files:
inp.write(fname + "\n")
self.stdin_data = [s for s in inp.getvalue()]
with open(self.stdin_fname, "w") as fh:
fh.writelines(self.stdin_data)
try:
self.execute(cwd=cwd)
except self.Error:
raise
return out_gkk
