def check_generated(calc_root, machine_dct, params_lst, revision):
"""Check consistency of calc database values, replacement params in
`params_lst` and all written files.
"""
dbfn = pj(calc_root, 'calc.db')
db = sql.SQLiteDB(dbfn, table='calc')
print("database content:")
print(db.get_dict("select * from calc"))
db_colnames = [x[0] for x in db.get_header()]
for idx, hostname_str in db.execute(
"select idx,hostname from calc \
where revision==?",
(revision, )).fetchall():
for hostname in hostname_str.split(','):
machine = machine_dct[hostname]
calc_dir = pj(calc_root, 'calc_%s' % machine.hostname, str(idx))
for base in ['pw.in', machine.get_jobfile_basename()]:
fn = pj(calc_dir, base)
assert os.path.exists(fn)
lines = common.file_readlines(fn)
# assemble all possible replacements in one list of SQLEntry
# instances, some things are redundantely checked twice ...
sql_lst = params_lst[idx] + list(
machine.get_sql_record().values())
for db_key in db_colnames:
db_val = db.get_single(
"select %s from calc "
"where idx==?" % db_key, (idx, ))
if db_val is not None:
sql_lst.append(sql.SQLEntry(key=db_key, sqlval=db_val))
# for each replacement key, check if they are correctly placed
# in the database (if applicable) and in the written files
for sqlentry in sql_lst:
if sqlentry.key in db_colnames:
db_val = db.get_single("select %s from calc "
"where idx==?" \
%sqlentry.key, (idx,))
assert_all_types_equal(db_val, sqlentry.sqlval)
else:
db_val = 'NOT_DEFINED_IN_DB'
print("check_generated: idx={0}, sqlentry.key={1}, "
"sqlentry.sqlval={2}, db_val={3}".format(
idx, sqlentry.key, sqlentry.sqlval, db_val))
check_key_in_file(lines, sqlentry.key, sqlentry.sqlval)
db.finish()
def check_generated(calc_root, machine_dct, params_lst, revision):
"""Check consistency of calc database values, replacement params in
`params_lst` and all written files.
"""
db = sql.SQLiteDB(pj(calc_root, 'calc.db'), table='calc')
db_colnames = [x[0] for x in db.get_header()]
for idx,hostname_str in db.execute("select idx,hostname from calc \
where revision==?", (revision,)).fetchall():
for hostname in hostname_str.split(','):
machine = machine_dct[hostname]
calc_dir = pj(calc_root, 'calc_%s' %machine.hostname, str(idx))
for base in ['pw.in', machine.get_jobfile_basename()]:
fn = pj(calc_dir, base)
assert os.path.exists(fn)
lines = common.file_readlines(fn)
# assemble all possible replacements in one list of SQLEntry
# instances, some things are redundantely checked twice ...
sql_lst = params_lst[idx] + machine.get_sql_record().values()
for db_key in db_colnames:
db_val = db.get_single("select %s from calc "
"where idx==?" %db_key,
(idx,))
if db_val is not None:
sql_lst.append(sql.SQLEntry(key=db_key, sqlval=db_val))
# for each replacement key, check if they are correctly placed
# in the database (if applicable) and in the written files
for sqlentry in sql_lst:
if sqlentry.key in db_colnames:
db_val = db.get_single("select %s from calc "
"where idx==?" \
%sqlentry.key, (idx,))
assert_all_types_equal(db_val, sqlentry.sqlval)
else:
db_val = 'NOT_DEFINED_IN_DB'
print("check_generated: idx={0}, sqlentry.key={1}, "
"sqlentry.sqlval={2}, db_val={3}".format(idx, sqlentry.key,
sqlentry.sqlval,
db_val))
check_key_in_file(lines, sqlentry.key, sqlentry.sqlval)
db.finish()
def read_matdyn_freq(filename):
"""Parse frequency file produced by QE's matdyn.x ("flfrq" in matdyn.x
input, usually "matdyn.freq" or so) when calculating a phonon dispersion on
a grid (ldisp=.true., used for phonon dos) or a pre-defined k-path in the
BZ.
In QE 5.x, a file with suffix ".gp" (e.g. "matdyn.freq.gp") is now written,
where::
>>> import numpy as np
>>> from pwtools import kpath, pwscf
>>> d = np.loadtxt("matdyn.freq.gp")
>>> kpoints,freqs = pwscf.read_matdyn_freq("matdyn.freq")
>>> allclose(d[:,0], kpath.get_path_norm(kpoints))
>>> allclose(d[:,1:], freqs)
Parameters
----------
filename : file with k-points and phonon frequencies
Returns
-------
kpoints : array (nks, 3)
Array with `nks` k-points. AFAIK the unit is always ``2*pi/alat`` with
``alat = celldm(1)``.
freqs : array (nks, nbnd)
Array with `nbnd` energies/frequencies at each of the `nks` k-points.
For phonon DOS, nbnd == 3*natoms.
Notes
-----
`matdyn.in`::
&input
asr='simple',
amass(1)=26.981538,
amass(2)=14.00674,
flfrc='fc',
flfrq='matdyn.freq.disp'
/
101 | nks
0.000000 0.000000 0.000000 |
0.037500 0.037500 0.000000 | List of nks = 101 k-points
.... |
`filename` has the form::
<header>
<k-point, (3,)>
<frequencies,(nbnd,)
<k-point, (3,)>
<frequencies,(nbnd,)
...
for example::
&plot nbnd= 6, nks= 101 /
0.000000 0.000000 0.000000
0.0000 0.0000 0.0000 456.2385 456.2385 871.5931
0.037500 0.037500 0.000000
23.8811 37.3033 54.3776 455.7569 457.2338 869.8832
.....
See Also
--------
bin/plot_dispersion.py, :func:`pwtools.kpath.plot_dis`,
:func:`pwtools.kpath.get_path_norm`
"""
lines = file_readlines(filename)
# Read number of bands (nbnd) and k-points (nks). OK, Fortran's namelists
# win here :)
# nbnd: number of bands = number of frequencies per k-point = 3*natoms for
# phonons
# nks: number of k-points
pat = r'.*\s+nbnd\s*=\s*([0-9]+)\s*,\s*nks\s*=\s*([0-9]+)\s*/'
match = re.match(pat, lines[0])
assert (match is not None), "match is None"
nbnd = int(match.group(1))
nks = int(match.group(2))
kpoints = np.empty((nks, 3), dtype=float)
freqs = np.empty((nks, nbnd), dtype=float)
step = 3 + nbnd
# nasty trick: join all lines containing data into one 1d array: " ".join()
# does "1 2\n3 4" -> "1 2\n 3 4" and split() splits at \n + whitespace.
items = np.array(' '.join(lines[1:]).split(), dtype=float)
for ii in range(len(items) / step):
kpoints[ii,:] = items[ii*step:(ii*step+3)]
freqs[ii,:] = items[(ii*step+3):(ii*step+step)]
return kpoints, freqs
def read_matdyn_freq(filename):
"""Parse frequency file produced by QE's matdyn.x ("flfrq" in matdyn.x
input, usually "matdyn.freq" or so) when calculating a phonon dispersion on
a grid (ldisp=.true., used for phonon dos) or a pre-defined k-path in the
BZ.
In QE 5.x, a file with suffix ".gp" (e.g. "matdyn.freq.gp") is now written,
where::
>>> import numpy as np
>>> from pwtools import kpath, pwscf
>>> d = np.loadtxt("matdyn.freq.gp")
>>> kpoints,freqs = pwscf.read_matdyn_freq("matdyn.freq")
>>> allclose(d[:,0], kpath.get_path_norm(kpoints))
>>> allclose(d[:,1:], freqs)
Parameters
----------
filename : file with k-points and phonon frequencies
Returns
-------
kpoints : array (nks, 3)
Array with `nks` k-points. AFAIK the unit is always ``2*pi/alat`` with
``alat = celldm(1)``.
freqs : array (nks, nbnd)
Array with `nbnd` energies/frequencies at each of the `nks` k-points.
For phonon DOS, nbnd == 3*natoms.
Notes
-----
`matdyn.in`::
&input
asr='simple',
amass(1)=26.981538,
amass(2)=14.00674,
flfrc='fc',
flfrq='matdyn.freq.disp'
/
101 | nks
0.000000 0.000000 0.000000 |
0.037500 0.037500 0.000000 | List of nks = 101 k-points
.... |
`filename` has the form::
<header>
<k-point, (3,)>
<frequencies,(nbnd,)
<k-point, (3,)>
<frequencies,(nbnd,)
...
for example::
&plot nbnd= 6, nks= 101 /
0.000000 0.000000 0.000000
0.0000 0.0000 0.0000 456.2385 456.2385 871.5931
0.037500 0.037500 0.000000
23.8811 37.3033 54.3776 455.7569 457.2338 869.8832
.....
See Also
--------
bin/plot_dispersion.py, :func:`pwtools.kpath.plot_dis`,
:func:`pwtools.kpath.get_path_norm`
"""
lines = file_readlines(filename)
# Read number of bands (nbnd) and k-points (nks). OK, Fortran's namelists
# win here :)
# nbnd: number of bands = number of frequencies per k-point = 3*natoms for
# phonons
# nks: number of k-points
pat = r'.*\s+nbnd\s*=\s*([0-9]+)\s*,\s*nks\s*=\s*([0-9]+)\s*/'
match = re.match(pat, lines[0])
assert (match is not None), "match is None"
nbnd = int(match.group(1))
nks = int(match.group(2))
kpoints = np.empty((nks, 3), dtype=float)
freqs = np.empty((nks, nbnd), dtype=float)
step = 3 + nbnd
# nasty trick: join all lines containing data into one 1d array: " ".join()
# does "1 2\n3 4" -> "1 2\n 3 4" and split() splits at \n + whitespace.
items = np.array(' '.join(lines[1:]).split(), dtype=float)
for ii in range(len(items) // step):
kpoints[ii,:] = items[ii*step:(ii*step+3)]
freqs[ii,:] = items[(ii*step+3):(ii*step+step)]
return kpoints, freqs