def test_velocity_traj():
# Test Trajectory.get_velocity() against velocities output from CP2K. The
# agreement is very good. Works only for fixed-cell MDs, however!
dr = 'files/cp2k/md/nvt_print_low'
base = os.path.dirname(dr)
fn = '%s/cp2k.out' %dr
print common.backtick('tar -C {0} -xzf {1}.tgz'.format(base,dr))
tr = io.read_cp2k_md(fn)
# read from data file
v1 = tr.velocity.copy()
# If tr.velocity != None, then get_velocity() doesn't calculate it. Then,
# it simply returns tr.velocity, which is what we of course usually want.
tr.velocity = None
# calculate from coords + time step, b/c of central diffs, only steps 1:-1
# are the same
v2 = tr.get_velocity()
print ">>>> np.abs(v1).max()", np.abs(v1).max()
print ">>>> np.abs(v1).min()", np.abs(v1).min()
print ">>>> np.abs(v2).max()", np.abs(v2).max()
print ">>>> np.abs(v2).min()", np.abs(v2).min()
print ">>>> np.abs(v1-v2).max()", np.abs(v1-v2).max()
print ">>>> np.abs(v1-v2).min()", np.abs(v1-v2).min()
assert np.allclose(v1[1:-1,...], v2[1:-1,...], atol=1e-4)
##from pwtools import mpl
##fig,ax = mpl.fig_ax()
##ax.plot(v1[1:-1,:,0], 'b')
##ax.plot(v2[1:-1,:,0], 'r')
##mpl.plt.show()
shape = (100,10,3)
arr = np.random.rand(*shape)
assert crys.velocity_traj(arr, axis=0).shape == shape
assert crys.velocity_traj(arr, axis=0, endpoints=False).shape == (98,10,3)
def omp_num_threads(action='check', num=1, omp_dct=OMP_DCT, err=False):
key = 'OMP_NUM_THREADS'
has_key = os.environ.has_key(key)
if action == 'check':
if has_key:
print "[omp_num_threads] os.environ['%s']: %s" %(key, os.environ[key])
print "[omp_num_threads] shell$ echo %s" %(key)
print backtick('echo $%s' %key)
if err and os.environ[key] != '3':
return 'err'
else:
print "[omp_num_threads] no os.environ['%s']" %key
if err:
return 'err'
elif action == 'backup':
if has_key:
print "[omp_num_threads] backup os.environ['%s'] = '%s'" %(key, os.environ[key])
omp_dct['num_threads'] = os.environ[key]
else:
omp_dct['num_threads'] = None
elif action == 'restore':
if has_key:
print "[omp_num_threads] restoring os.environ['%s'] = '%s'" \
%(key, omp_dct['num_threads'])
os.environ[key] = omp_dct['num_threads']
elif action == 'set':
print "[omp_num_threads] setting os.environ['%s'] = '%s'" %(key, str(num))
os.environ[key] = str(num)
def test_cp2k_scf():
attr_lst = parse.Cp2kSCFOutputFile().attr_lst
for base in ['cp2k.scf.out.print_low', 'cp2k.scf.out.print_medium']:
fn = 'files/cp2k/scf/%s' %base
print "testing: %s" %fn
print common.backtick("gunzip %s.gz" %fn)
st = io.read_cp2k_scf(fn)
assert_attrs_not_none(st, attr_lst=attr_lst)
def test_cp2k_md():
attr_lst = parse.Cp2kMDOutputFile().attr_lst
# This parser and others have get_econst(), but not all, so ATM it's not
# part of the Trajectory API
attr_lst.pop(attr_lst.index('econst'))
for dr in ['files/cp2k/md/npt_f_print_low', 'files/cp2k/md/nvt_print_low']:
base = os.path.dirname(dr)
fn = '%s/cp2k.out' %dr
print "testing: %s" %fn
print common.backtick('tar -C {0} -xzf {1}.tgz'.format(base,dr))
tr = io.read_cp2k_md(fn)
assert_attrs_not_none(tr, attr_lst=attr_lst)
pp = parse.Cp2kMDOutputFile(fn)
forces_outfile = pp._get_forces_from_outfile()*Ha/Bohr/eV*Ang
assert np.allclose(forces_outfile, tr.forces, rtol=1e-3)
def _fit(self):
# volume[Bohr^3] etot[Ha] for eos.x
volume = self.volume * (Ang**3.0 / Bohr**3.0)
energy = self.energy * (eV / Ha)
data = np.array([volume, energy]).T
infn_txt =\
"""
%s
%i
%i
%f, %f, %i
%i
%s
"""%(self.name,
self.natoms,
self.etype,
volume[0], volume[-1], self.npoints,
len(volume),
common.str_arr(data))
common.file_write(self.infn, infn_txt)
out = common.backtick('cd %s && %s' % (self.dir, self.app_basename))
if self.verbose:
print(out)
print((open(os.path.join(self.dir, 'PARAM.OUT')).read()))
# Remove normalization on natoms. See .../eos/output.f90:
# fitev: [volume [Bohr^3] / natoms, energy [Ha] / natoms]
# fitpv: [volume [Bohr^3] / natoms, pressure [GPa]]
fitev = np.loadtxt(os.path.join(self.dir, 'EVPAI.OUT')) * self.natoms
# convert energy back to [Ang^3, eV]
fitev[:, 0] *= (Bohr**3 / Ang**3)
fitev[:, 1] *= (Ha / eV)
self.ev = fitev
fitpv = np.loadtxt(os.path.join(self.dir, 'PVPAI.OUT'))
fitpv[:, 0] *= (self.natoms * Bohr**3 / Ang**3)
self.pv = fitpv
def _fit(self):
# volume[Bohr^3] etot[Ha] for eos.x
volume = self.volume*(Ang**3.0 / Bohr**3.0)
energy = self.energy*(eV / Ha)
data = np.array([volume, energy]).T
infn_txt =\
"""
%s
%i
%i
%f, %f, %i
%i
%s
"""%(self.name,
self.natoms,
self.etype,
volume[0], volume[-1], self.npoints,
len(volume),
common.str_arr(data))
common.file_write(self.infn, infn_txt)
out = common.backtick('cd %s && %s' %(self.dir, self.app_basename))
if self.verbose:
print out
print(open(os.path.join(self.dir,'PARAM.OUT')).read())
# Remove normalization on natoms. See .../eos/output.f90:
# fitev: [volume [Bohr^3] / natoms, energy [Ha] / natoms]
# fitpv: [volume [Bohr^3] / natoms, pressure [GPa]]
fitev = np.loadtxt(os.path.join(self.dir,'EVPAI.OUT')) * self.natoms
# convert energy back to [Ang^3, eV]
fitev[:,0] *= (Bohr**3 / Ang**3)
fitev[:,1] *= (Ha / eV)
self.ev = fitev
fitpv = np.loadtxt(os.path.join(self.dir,'PVPAI.OUT'))
fitpv[:,0] *= (self.natoms * Bohr**3 / Ang**3)
self.pv = fitpv
def test_velocity_traj():
# Test Trajectory.get_velocity() against velocities output from CP2K. The
# agreement is very good. Works only for fixed-cell MDs, however!
dr = 'files/cp2k/md/nvt_print_low'
base = os.path.dirname(dr)
fn = '%s/cp2k.out' %dr
print(common.backtick('tar -C {0} -xzf {1}.tgz'.format(base,dr)))
tr = io.read_cp2k_md(fn)
# read from data file
v1 = tr.velocity.copy()
# If tr.velocity != None, then get_velocity() doesn't calculate it. Then,
# it simply returns tr.velocity, which is what we of course usually want.
tr.velocity = None
# calculate from coords + time step, b/c of central diffs, only steps 1:-1
# are the same
v2 = tr.get_velocity()
print(">>>> np.abs(v1).max()", np.abs(v1).max())
print(">>>> np.abs(v1).min()", np.abs(v1).min())
print(">>>> np.abs(v2).max()", np.abs(v2).max())
print(">>>> np.abs(v2).min()", np.abs(v2).min())
print(">>>> np.abs(v1-v2).max()", np.abs(v1-v2).max())
print(">>>> np.abs(v1-v2).min()", np.abs(v1-v2).min())
assert np.allclose(v1[1:-1,...], v2[1:-1,...], atol=1e-4)
##from pwtools import mpl
##fig,ax = mpl.fig_ax()
##ax.plot(v1[1:-1,:,0], 'b')
##ax.plot(v2[1:-1,:,0], 'r')
##mpl.plt.show()
shape = (100,10,3)
arr = np.random.rand(*shape)
assert crys.velocity_traj(arr, axis=0).shape == shape
assert crys.velocity_traj(arr, axis=0, endpoints=False).shape == (98,10,3)
def omp_num_threads(action='check', num=1, omp_dct=OMP_DCT, err=False):
key = 'OMP_NUM_THREADS'
has_key = key in os.environ
if action == 'check':
if has_key:
print("[omp_num_threads] os.environ['%s']: %s" %
(key, os.environ[key]))
print("[omp_num_threads] shell$ echo %s" % (key))
print(backtick('echo $%s' % key))
if err and os.environ[key] != '3':
return 'err'
else:
print("[omp_num_threads] no os.environ['%s']" % key)
if err:
return 'err'
elif action == 'backup':
if has_key:
print("[omp_num_threads] backup os.environ['%s'] = '%s'" %
(key, os.environ[key]))
omp_dct['num_threads'] = os.environ[key]
else:
omp_dct['num_threads'] = None
elif action == 'restore':
if has_key:
print("[omp_num_threads] restoring os.environ['%s'] = '%s'" \
%(key, omp_dct['num_threads']))
os.environ[key] = omp_dct['num_threads']
elif action == 'set':
print("[omp_num_threads] setting os.environ['%s'] = '%s'" %
(key, str(num)))
os.environ[key] = str(num)
def read_dynmat(path='.', natoms=None, filename='dynmat.out', axsf='dynmat.axsf'):
"""Read ``dynmat.x`` output.
`freqs` are parsed from `filename` and `vecs` from `axsf`. `qpoints` is
alawys Gamma, i.e. [0,0,0].
Output format is the same as in :func:`read_dyn`.
Parameters
----------
path : str
path where output files are
natoms : int
filename : str
Text output from dynmat.x, where the frequencies are printed, relative
to `path`.
axsf : str
AXSF file (``filxsf`` in input) with mode vectors as forces.
Returns
-------
qpoints, freqs, vecs
qpoints : 1d array (3,)
The qpoint, which is Gamma, i.e. [0,0,0]
freqs : 1d array, (nmodes,) where nmodes = 3*natoms
3*natoms phonon frequencies in [cm^-1] at the q-point.
vecs : 3d real array (nmodes, natoms, 3)
Real parts (???) if the eigenvectors of the dynamical matrix for the
q-point.
Notes
-----
We assume the output to be generated with ``dynmat.x < dynmat.in >
dynmat.out``.
"""
assert natoms is not None, ("natoms is None")
nmodes = 3*natoms
out_fn = pj(path, filename)
axsf_fn = pj(path, axsf)
cmd = "grep -A{0} PRIMCO {1} | sed -re '/PRIMCO.*/{{N;d;}}' | \
awk '{{print $5\" \"$6\" \"$7}}'".format(natoms+1, axsf_fn)
qpoints = np.zeros((3,))
vecs = np.fromstring(common.backtick(cmd), sep=' ').reshape(nmodes,natoms,3)
cmd = "grep -A{0} 'mode.*cm-1' {1} | grep -v mode | \
awk '{{print $2}}'".format(nmodes, out_fn)
freqs = np.fromstring(common.backtick(cmd), sep=' ')
return qpoints,freqs,vecs
def unpack_compressed(src, prefix='tmp', testdir=testdir, ext=None):
"""Convenience function to uncompress files/some_file.out.gz into a random
location. Return the filename "path/to/random_location/some_file.out"
without ".gz", which can be used in subsequent commands.
Supported file types: gz, tgz, tar.gz
gunzip path/to/random_location/some_file.out.gz
tar -C path/to/random_location -xzf path/to/random_location/some_file.out.tgz
Other compress formats may be implemented as needed.
Can also be used for slightly more complex unpack business, see for
example test_cpmd_md.py.
Parameters
----------
src : str
path to the compressed file, i.e. files/some_file.out.gz
prefix : str, optional
prefix for mkdtemp(), usually __file__ of the test script
to identify which test script created the random dir
testdir : str, optional
'path/to' in the example above, usually
``pwtools.test.testenv.testdir``
ext : str, optional
file extension of compressed file ('gz', 'tgz', 'tar.gz'), if None then
it will be guessed from `src`
"""
# 'path/to/random_location'
workdir = tempfile.mkdtemp(dir=testdir, prefix=prefix)
# 'gz'
ext = src.split('.')[-1] if ext is None else ext
# 'some_file.out'
base = os.path.basename(src).replace('.'+ext, '')
# path/to/random_location/some_file.out
filename = '{workdir}/{base}'.format(workdir=workdir, base=base)
cmd = "mkdir -p {workdir}; cp {src} {workdir}/; "
if ext == 'gz':
cmd += "gunzip {filename}.{ext};"
elif ext in ['tgz', 'tar.gz']:
cmd += "tar -C {workdir} -xzf {filename}.{ext};"
else:
raise StandardError("unsuported file format of file: {}".format(src))
cmd = cmd.format(workdir=workdir, src=src, filename=filename, ext=ext)
print common.backtick(cmd)
assert os.path.exists(filename), "unpack failed: '%s' not found" %filename
return filename
def read_dynmat(path='.', natoms=None, filename='dynmat.out', axsf='dynmat.axsf'):
"""Read ``dynmat.x`` output.
`freqs` are parsed from `filename` and `vecs` from `axsf`. `qpoints` is
alawys Gamma, i.e. [0,0,0].
Output format is the same as in :func:`read_dyn`.
Parameters
----------
path : str
path where output files are
natoms : int
filename : str
Text output from dynmat.x, where the frequencies are printed, relative
to `path`.
axsf : str
AXSF file (``filxsf`` in input) with mode vectors as forces.
Returns
-------
qpoints, freqs, vecs
qpoints : 1d array (3,)
The qpoint, which is Gamma, i.e. [0,0,0]
freqs : 1d array, (nmodes,) where nmodes = 3*natoms
3*natoms phonon frequencies in [cm^-1] at the q-point.
vecs : 3d real array (nmodes, natoms, 3)
Real parts (???) if the eigenvectors of the dynamical matrix for the
q-point.
Notes
-----
We assume the output to be generated with ``dynmat.x < dynmat.in >
dynmat.out``.
"""
assert natoms is not None, ("natoms is None")
nmodes = 3*natoms
out_fn = pj(path, filename)
axsf_fn = pj(path, axsf)
cmd = "grep -A{0} PRIMCO {1} | sed -re '/PRIMCO.*/{{N;d;}}' | \
awk '{{print $5\" \"$6\" \"$7}}'".format(natoms+1, axsf_fn)
qpoints = np.zeros((3,))
vecs = np.fromstring(common.backtick(cmd), sep=' ').reshape(nmodes,natoms,3)
cmd = "grep -A{0} 'mode.*cm-1' {1} | grep -v mode | \
awk '{{print $2}}'".format(nmodes, out_fn)
freqs = np.fromstring(common.backtick(cmd), sep=' ')
return qpoints,freqs,vecs
def test_cp2k_scf():
attr_lst = parse.Cp2kSCFOutputFile().attr_lst
for base in ['cp2k.scf.out.print_low', 'cp2k.scf.out.print_medium']:
fn = 'files/cp2k/scf/%s' % base
print("testing: %s" % fn)
print(common.backtick("gunzip %s.gz" % fn))
st = io.read_cp2k_scf(fn)
assert_attrs_not_none(st, attr_lst=attr_lst)
def read_dynmat_ir_raman(filename='dynmat.out', natoms=None,
cols={1: 'freqs', 3:'ir', 4: 'raman', 5: 'depol'}):
"""Read ``dynmat.x`` text output file and extract IR and Raman
intensities.
Parameters
----------
filename : str
dynmat.x text output file (e.g. from ``dynmat.x < dynmat.in >
dynmat.out``)
natoms : int
number of atoms in the cell
cols : dict
column numbers of the text block
Returns
-------
cols = None
Return the parsed array as found in the file
cols = dict
Return dict with keys from `cols` and 1d arrays ``{'freqs': <array>,
'ir': <array>, 'raman': <array>, 'depol': <array>}``. If a column is
not present, the array is None.
Notes
-----
The parsed textblock looks like this::
# mode [cm-1] [THz] IR Raman depol.fact
1 0.00 0.0000 0.0000 0.0005 0.7414
2 0.00 0.0000 0.0000 0.0005 0.7465
3 0.00 0.0000 0.0000 0.0018 0.2647
4 252.27 7.5627 0.0000 0.0073 0.7500
5 252.27 7.5627 0.0000 0.0073 0.7500
6 548.44 16.4419 0.0000 0.0000 0.7434
7 603.32 18.0872 35.9045 18.9075 0.7366
8 656.82 19.6910 0.0000 7.9317 0.7500
9 656.82 19.6910 0.0000 7.9317 0.7500
10 669.67 20.0762 31.5712 5.0265 0.7500
11 738.22 22.1311 0.0000 0.0000 0.7306
12 922.64 27.6600 31.5712 5.0265 0.7500
Some columns (e.g. IR, Raman) may be missing.
"""
assert natoms is not None, ("natoms is None")
cmd = "grep -A{0} 'mode.*cm-1' {1} | grep -v mode".format(3*natoms, filename)
arr = parse.arr2d_from_txt(common.backtick(cmd))
if cols is None:
return arr
else:
dct = {}
for ii,name in cols.items():
if arr.shape[1] >= (ii+1):
dct[name] = arr[:,ii]
else:
dct[name] = None
return dct
def read_dynmat_ir_raman(filename='dynmat.out', natoms=None,
cols={1: 'freqs', 3:'ir', 4: 'raman', 5: 'depol'}):
"""Read ``dynmat.x`` text output file and extract IR and Raman
intensities.
Parameters
----------
filename : str
dynmat.x text output file (e.g. from ``dynmat.x < dynmat.in >
dynmat.out``)
natoms : int
number of atoms in the cell
cols : dict
column numbers of the text block
Returns
-------
cols = None
Return the parsed array as found in the file
cols = dict
Return dict with keys from `cols` and 1d arrays ``{'freqs': <array>,
'ir': <array>, 'raman': <array>, 'depol': <array>}``. If a column is
not present, the array is None.
Notes
-----
The parsed textblock looks like this::
# mode [cm-1] [THz] IR Raman depol.fact
1 0.00 0.0000 0.0000 0.0005 0.7414
2 0.00 0.0000 0.0000 0.0005 0.7465
3 0.00 0.0000 0.0000 0.0018 0.2647
4 252.27 7.5627 0.0000 0.0073 0.7500
5 252.27 7.5627 0.0000 0.0073 0.7500
6 548.44 16.4419 0.0000 0.0000 0.7434
7 603.32 18.0872 35.9045 18.9075 0.7366
8 656.82 19.6910 0.0000 7.9317 0.7500
9 656.82 19.6910 0.0000 7.9317 0.7500
10 669.67 20.0762 31.5712 5.0265 0.7500
11 738.22 22.1311 0.0000 0.0000 0.7306
12 922.64 27.6600 31.5712 5.0265 0.7500
Some columns (e.g. IR, Raman) may be missing.
"""
assert natoms is not None, ("natoms is None")
cmd = "grep -A{0} 'mode.*cm-1' {1} | grep -v mode".format(3*natoms, filename)
arr = parse.arr2d_from_txt(common.backtick(cmd))
if cols is None:
return arr
else:
dct = {}
for ii,name in cols.iteritems():
if arr.shape[1] >= (ii+1):
dct[name] = arr[:,ii]
else:
dct[name] = None
return dct
def test_pwscf_calculator():
if not have_ase():
skip("no ASE found, skipping test")
elif not have_pwx():
skip("no pw.x found, skipping test")
else:
pseudo_dir = pj(testdir, prefix, 'pseudo')
print common.backtick("mkdir -pv {p}; cp files/qe_pseudos/*.gz {p}/; \
gunzip {p}/*".format(p=pseudo_dir))
at = get_atoms_with_calc_pwscf(pseudo_dir)
print "scf"
# trigger calculation here
forces = at.get_forces()
etot = at.get_potential_energy()
stress = at.get_stress(voigt=False) # 3x3
st = io.read_pw_scf(at.calc.label + '.out')
assert np.allclose(forces, st.forces)
assert np.allclose(etot, st.etot)
assert np.allclose(st.stress, -stress * constants.eV_by_Ang3_to_GPa)
# files/ase/pw.scf.out.start is a norm-conserving LDA struct,
# calculated with pz-vbc.UPF, so the PBE vc-relax will make the cell
# a bit bigger
print "vc-relax"
from ase.optimize import BFGS
from ase.constraints import UnitCellFilter
opt = BFGS(UnitCellFilter(at))
cell = parse.arr2d_from_txt("""
-1.97281509 0. 1.97281509
0. 1.97281509 1.97281509
-1.97281509 1.97281509 0.""")
assert np.allclose(cell, at.get_cell())
opt.run(fmax=0.05) # run only 2 steps
cell = parse.arr2d_from_txt("""
-2.01837531 0. 2.01837531
0. 2.01837531 2.01837531
-2.01837531 2.01837531 0""")
assert np.allclose(cell, at.get_cell())
# at least 1 backup files must exist: pw.*.0 is the SCF run, backed up
# in the first iter of the vc-relax
assert os.path.exists(at.calc.infile + '.0')
def read_dyn(filename, natoms=None):
"""Read one dynamical matrix file (for 1 qpoint) produced by ``ph.x`` and
extract the same as :func:`read_matdyn_modes` for this qpoint only.
All arrays have one dim less compared to :func:`read_matdyn_modes`.
Parameters
----------
filename : str
Name of dyn file. Example: "ph.dyn3" for qpoint 3.
natoms : int
number of atoms in the cell (used for nmodes=3*natoms only)
Returns
-------
qpoints, freqs, vecs
qpoints : 1d array (3,)
The qpoint of the dyn file.
freqs : 1d array, (nmodes,) where nmodes = 3*natoms
3*natoms phonon frequencies in [cm^-1] at the q-point.
vecs : 3d complex array (nmodes, natoms, 3)
Complex eigenvectors of the dynamical matrix for the q-point.
"""
assert natoms is not None
cmd = r"egrep 'q.*=.*\(' %s | tail -n1 | sed -re 's/.*q\s*=.*\((.*)\)/\1/'" %filename
qpoints = np.fromstring(common.backtick(cmd), sep=' ')
assert qpoints.shape == (3,)
nmodes = 3*natoms
cmd = r"grep -v 'q.*=' %s | grep '^[ ]*(' | sed -re 's/^\s*\((.*)\)/\1/g'" %filename
# vecs_file_flat: (nmodes * natoms, 6)
# this line is the bottleneck
vecs_file_flat = parse.arr2d_from_txt(common.backtick(cmd))
vecs_flat = np.empty((vecs_file_flat.shape[0], 3), dtype=complex)
vecs_flat[:,0] = vecs_file_flat[:,0] + 1j*vecs_file_flat[:,1]
vecs_flat[:,1] = vecs_file_flat[:,2] + 1j*vecs_file_flat[:,3]
vecs_flat[:,2] = vecs_file_flat[:,4] + 1j*vecs_file_flat[:,5]
vecs = vecs_flat.flatten().reshape(nmodes, natoms, 3)
cmd = r"grep omega %s | sed -re \
's/.*omega.*=.*\[.*=(.*)\s*\[.*/\1/g'" %filename
freqs = np.fromstring(common.backtick(cmd), sep=' ')
return qpoints, freqs, vecs
def read_dyn(filename, natoms=None):
"""Read one dynamical matrix file (for 1 qpoint) produced by ``ph.x`` and
extract the same as :func:`read_matdyn_modes` for this qpoint only.
All arrays have one dim less compared to :func:`read_matdyn_modes`.
Parameters
----------
filename : str
Name of dyn file. Example: "ph.dyn3" for qpoint 3.
natoms : int
number of atoms in the cell (used for nmodes=3*natoms only)
Returns
-------
qpoints, freqs, vecs
qpoints : 1d array (3,)
The qpoint of the dyn file.
freqs : 1d array, (nmodes,) where nmodes = 3*natoms
3*natoms phonon frequencies in [cm^-1] at the q-point.
vecs : 3d complex array (nmodes, natoms, 3)
Complex eigenvectors of the dynamical matrix for the q-point.
"""
assert natoms is not None
cmd = r"egrep 'q.*=.*\(' %s | tail -n1 | sed -re 's/.*q\s*=.*\((.*)\)/\1/'" %filename
qpoints = np.fromstring(common.backtick(cmd), sep=' ')
assert qpoints.shape == (3,)
nmodes = 3*natoms
cmd = r"grep -v 'q.*=' %s | grep '^[ ]*(' | sed -re 's/^\s*\((.*)\)/\1/g'" %filename
# vecs_file_flat: (nmodes * natoms, 6)
# this line is the bottleneck
vecs_file_flat = parse.arr2d_from_txt(common.backtick(cmd))
vecs_flat = np.empty((vecs_file_flat.shape[0], 3), dtype=complex)
vecs_flat[:,0] = vecs_file_flat[:,0] + 1j*vecs_file_flat[:,1]
vecs_flat[:,1] = vecs_file_flat[:,2] + 1j*vecs_file_flat[:,3]
vecs_flat[:,2] = vecs_file_flat[:,4] + 1j*vecs_file_flat[:,5]
vecs = vecs_flat.flatten().reshape(nmodes, natoms, 3)
cmd = r"grep omega %s | sed -re \
's/.*omega.*=.*\[.*=(.*)\s*\[.*/\1/g'" %filename
freqs = np.fromstring(common.backtick(cmd), sep=' ')
return qpoints, freqs, vecs
def test_lammps_calculator():
if not have_ase():
skip("no ASE found, skipping test")
elif not have_lmp():
skip("no lammps found, skipping test")
else:
at = get_atoms_with_calc_lammps()
at.rattle(stdev=0.001, seed=int(time.time()))
common.makedirs(at.calc.directory)
print common.backtick("cp -v utils/lammps/AlN.tersoff {p}/".format(
p=at.calc.directory))
print "scf"
forces = at.get_forces()
etot = at.get_potential_energy()
stress = at.get_stress(voigt=False) # 3x3
st = io.read_lammps_md_txt(at.calc.label + '.out')[0]
assert np.allclose(forces, st.forces)
assert np.allclose(etot, st.etot)
assert np.allclose(st.stress, -stress * constants.eV_by_Ang3_to_GPa,
atol=1e-10)
print "relax"
from ase.optimize import BFGS
opt = BFGS(at, maxstep=0.04)
opt.run(fmax=0.001, steps=10)
coords_frac = parse.arr2d_from_txt("""
3.3333341909920072e-01 6.6666683819841532e-01 4.4325467247779138e-03
6.6666681184103216e-01 3.3333362368205072e-01 5.0443254824788963e-01
3.3333341909918301e-01 6.6666683819838046e-01 3.8356759709402671e-01
6.6666681184101539e-01 3.3333362368201563e-01 8.8356759861713752e-01
""")
assert np.allclose(coords_frac, at.get_scaled_positions(), atol=1e-2)
# at least 1 backup files must exist
assert os.path.exists(at.calc.infile + '.0')
assert os.path.exists(at.calc.outfile + '.0')
assert os.path.exists(at.calc.dumpfile + '.0')
assert os.path.exists(at.calc.structfile + '.0')
def test_cp2k_cell_opt():
attr_lst = parse.Cp2kRelaxOutputFile().attr_lst
attr_lst.pop(attr_lst.index('econst'))
# There is no PROJECT-frc-1.xyz file, but the input file has
# &force_eval
# &print
# &forces
# &end forces
# &end print
# &end force_eval
# therefore we can parse forces from the outfile.
none_attrs = ['ekin',
'temperature',
'timestep',
'velocity',
]
for dr in ['files/cp2k/cell_opt/cell_opt']:
base = os.path.dirname(dr)
fn = '%s/cp2k.out' %dr
print "testing: %s" %fn
print common.backtick('tar -C {0} -xzf {1}.tgz'.format(base,dr))
tr = io.read_cp2k_relax(fn)
assert_attrs_not_none(tr, attr_lst=attr_lst, none_attrs=none_attrs)
def test_cp2k_md():
attr_lst = parse.Cp2kMDOutputFile().attr_lst
# This parser and others have get_econst(), but not all, so ATM it's not
# part of the Trajectory API
attr_lst.pop(attr_lst.index('econst'))
for dr in ['files/cp2k/md/npt_f_print_low', 'files/cp2k/md/nvt_print_low']:
base = os.path.dirname(dr)
fn = '%s/cp2k.out' % dr
print("testing: %s" % fn)
print(common.backtick('tar -C {0} -xzf {1}.tgz'.format(base, dr)))
tr = io.read_cp2k_md(fn)
assert_attrs_not_none(tr, attr_lst=attr_lst)
pp = parse.Cp2kMDOutputFile(fn)
forces_outfile = pp._get_forces_from_outfile() * Ha / Bohr / eV * Ang
assert np.allclose(forces_outfile, tr.forces, rtol=1e-3)
def test_write_lammps():
st = crys.Structure(coords_frac=rand(20, 3),
cell=rand(3, 3),
symbols=['Al'] * 10 + ['N'] * 10)
# align cell to lammps standard [[x,0,0],...]
st.coords = None
st.cell = None
st.set_all()
st_fn = common.pj(testdir, 'lmp.struct')
io.write_lammps(st_fn, st)
symbols = common.file_read(st_fn + '.symbols').split()
assert st.symbols == symbols
cmd = r"grep -A22 Atoms %s | grep '^[0-9]'" % st_fn
arr = parse.arr2d_from_txt(common.backtick(cmd))
assert arr.shape == (20, 5)
assert np.allclose(st.coords, arr[:, 2:])
def test_write_lammps():
st = crys.Structure(coords_frac=rand(20,3),
cell=rand(3,3),
symbols=['Al']*10+['N']*10)
# align cell to lammps standard [[x,0,0],...]
st.coords = None
st.cell = None
st.set_all()
st_fn = common.pj(testdir, 'lmp.struct')
io.write_lammps(st_fn, st)
symbols = common.file_read(st_fn + '.symbols').split()
assert st.symbols == symbols
cmd = r"grep -A22 Atoms %s | grep '^[0-9]'" %st_fn
arr = parse.arr2d_from_txt(common.backtick(cmd))
assert arr.shape == (20,5)
assert np.allclose(st.coords, arr[:,2:])
def unpack_compressed(src, prefix='tmp', testdir=testdir, ext=None):
"""Convenience function to uncompress files/some_file.out.gz into a random
location. Return the filename "path/to/random_location/some_file.out"
without ".gz", which can be used in subsequent commands.
Supported file types: gz, tgz, tar.gz
gunzip path/to/random_location/some_file.out.gz
tar -C path/to/random_location -xzf path/to/random_location/some_file.out.tgz
Other compress formats may be implemented as needed.
Can also be used for slightly more complex unpack business, see for
example test_cpmd_md.py.
Parameters
----------
src : str
path to the compressed file, i.e. files/some_file.out.gz
prefix : str, optional
prefix for mkdtemp(), usually __file__ of the test script
to identify which test script created the random dir
testdir : str, optional
'path/to' in the example above, usually
``pwtools.test.testenv.testdir``
ext : str, optional
file extension of compressed file ('gz', 'tgz', 'tar.gz'), if None then
it will be guessed from `src`
"""
# 'path/to/random_location'
workdir = tempfile.mkdtemp(dir=testdir, prefix=prefix)
# 'gz'
ext = src.split('.')[-1] if ext is None else ext
# 'some_file.out'
base = os.path.basename(src).replace('.' + ext, '')
# path/to/random_location/some_file.out
filename = '{workdir}/{base}'.format(workdir=workdir, base=base)
cmd = "mkdir -p {workdir}; cp {src} {workdir}/; "
if ext == 'gz':
cmd += "gunzip {filename}.{ext};"
elif ext in ['tgz', 'tar.gz']:
cmd += "tar -C {workdir} -xzf {filename}.{ext};"
else:
raise Exception("unsuported file format of file: {}".format(src))
cmd = cmd.format(workdir=workdir, src=src, filename=filename, ext=ext)
print(common.backtick(cmd))
assert os.path.exists(filename), "unpack failed: '%s' not found" % filename
return filename
def test_pwscf_calculator():
if not have_ase():
skip("no ASE found, skipping test")
elif not have_pwx():
skip("no pw.x found, skipping test")
else:
pseudo_dir = pj(testdir, prefix, 'pseudo')
print(common.backtick("mkdir -pv {p}; cp files/qe_pseudos/*.gz {p}/; \
gunzip {p}/*".format(p=pseudo_dir)))
at = get_atoms_with_calc_pwscf(pseudo_dir)
print("scf")
# trigger calculation here
forces = at.get_forces()
etot = at.get_potential_energy()
stress = at.get_stress(voigt=False) # 3x3
st = io.read_pw_scf(at.calc.label + '.out')
assert np.allclose(forces, st.forces)
assert np.allclose(etot, st.etot)
assert np.allclose(st.stress, -stress * constants.eV_by_Ang3_to_GPa)
# files/ase/pw.scf.out.start is a norm-conserving LDA struct,
# calculated with pz-vbc.UPF, so the PBE vc-relax will make the cell
# a bit bigger
print("vc-relax")
from ase.optimize import BFGS
from ase.constraints import UnitCellFilter
opt = BFGS(UnitCellFilter(at))
cell = parse.arr2d_from_txt("""
-1.97281509 0. 1.97281509
0. 1.97281509 1.97281509
-1.97281509 1.97281509 0.""")
assert np.allclose(cell, at.get_cell())
opt.run(fmax=0.05) # run only 2 steps
cell = parse.arr2d_from_txt("""
-2.01837531 0. 2.01837531
0. 2.01837531 2.01837531
-2.01837531 2.01837531 0""")
assert np.allclose(cell, at.get_cell())
# at least 1 backup files must exist: pw.*.0 is the SCF run, backed up
# in the first iter of the vc-relax
assert os.path.exists(at.calc.infile + '.0')
def test_lammps_calculator():
if not have_ase():
skip("no ASE found, skipping test")
elif not have_lmp():
skip("no lammps found, skipping test")
else:
at = get_atoms_with_calc_lammps()
at.rattle(stdev=0.001, seed=int(time.time()))
common.makedirs(at.calc.directory)
print(common.backtick("cp -v utils/lammps/AlN.tersoff {p}/".format(
p=at.calc.directory)))
print("scf")
forces = at.get_forces()
etot = at.get_potential_energy()
stress = at.get_stress(voigt=False) # 3x3
st = io.read_lammps_md_txt(at.calc.label + '.out')[0]
assert np.allclose(forces, st.forces)
assert np.allclose(etot, st.etot)
assert np.allclose(st.stress, -stress * constants.eV_by_Ang3_to_GPa,
atol=1e-10)
print("relax")
from ase.optimize import BFGS
opt = BFGS(at, maxstep=0.04)
opt.run(fmax=0.001, steps=10)
coords_frac = parse.arr2d_from_txt("""
3.3333341909920072e-01 6.6666683819841532e-01 4.4325467247779138e-03
6.6666681184103216e-01 3.3333362368205072e-01 5.0443254824788963e-01
3.3333341909918301e-01 6.6666683819838046e-01 3.8356759709402671e-01
6.6666681184101539e-01 3.3333362368201563e-01 8.8356759861713752e-01
""")
assert np.allclose(coords_frac, at.get_scaled_positions(), atol=1e-2)
# at least 1 backup files must exist
assert os.path.exists(at.calc.infile + '.0')
assert os.path.exists(at.calc.outfile + '.0')
assert os.path.exists(at.calc.dumpfile + '.0')
assert os.path.exists(at.calc.structfile + '.0')
def test_cp2k_cell_opt():
attr_lst = parse.Cp2kRelaxOutputFile().attr_lst
attr_lst.pop(attr_lst.index('econst'))
# There is no PROJECT-frc-1.xyz file, but the input file has
# &force_eval
# &print
# &forces
# &end forces
# &end print
# &end force_eval
# therefore we can parse forces from the outfile.
none_attrs = [
'ekin',
'temperature',
'timestep',
'velocity',
]
for dr in ['files/cp2k/cell_opt/cell_opt']:
base = os.path.dirname(dr)
fn = '%s/cp2k.out' % dr
print("testing: %s" % fn)
print(common.backtick('tar -C {0} -xzf {1}.tgz'.format(base, dr)))
tr = io.read_cp2k_relax(fn)
assert_attrs_not_none(tr, attr_lst=attr_lst, none_attrs=none_attrs)
#!/usr/bin/python2
# Use inside a hg repo to plot a gragh showing the number of changesets vs.
# tags.
#
# usage:
# cd /path/to/repo
# ./<this_script>.py
from cStringIO import StringIO
from matplotlib import pyplot as plt
import numpy as np
from pwtools import common, mpl
st = common.backtick("hg tags | sed -re 's/^(.*)\s+([0-9]+):.*$/\\1 \\2/'")
data = np.loadtxt(StringIO(st), dtype=str)
tags = data[:,0][::-1]
commits = data[:,1].astype(int)[::-1]
fig, ax = mpl.fig_ax()
xx = range(len(tags))
ax.plot(xx, commits, '.-')
ax.set_xticks(xx)
ax.set_xticklabels(tags, rotation='vertical')
plt.show()
def test_absolute_signal():
# std lib signal
from pwtools.common import signal
assert not hasattr(signal, 'fftsample')
from pwtools import common
print(common.backtick('ls'))
def test_write_mol():
units={'forces': Ha / eV}
nstep = 2
cell2d = np.random.rand(3,3)
cell3d = np.random.rand(nstep,3,3)
# fractional
coords2d_frac = np.array([[0.5, 0.5, 0.5],
[1,1,1]])
# fractional, 2 time steps: (2,2,3) = (nstep, natoms, 3)
coords3d_frac = np.array([coords2d_frac, coords2d_frac[...,None]*0.8])
# cartesian = coords3d_frac + cell2d (fixed cell). For varialbe cell cases
# below, cell3d is used!
coords3d_cart = crys.coord_trans(coords3d_frac,
old=cell2d,
new=np.identity(3),
axis=-1)
coords2d_cart = coords3d_cart[0,...]
symbols = ['H']*2
forces2d = np.random.random(coords2d_frac.shape)
forces3d = np.random.random(coords3d_frac.shape)
# --- AXSF ---------------------------------------------------------------
# fixed cell, forces=0
axsf_fn = pj(testdir, 'foo.axsf')
io.write_axsf(axsf_fn,
Trajectory(units=units,coords_frac=coords3d_frac,
cell=cell2d,
symbols=symbols),
)
arr = np.loadtxt(StringIO(
common.backtick("grep -A3 PRIMVEC %s | egrep -v -e '--|PRIMVEC'" %axsf_fn)))
np.testing.assert_array_almost_equal(arr, np.concatenate((cell2d, cell2d), axis=0))
arr = np.loadtxt(StringIO(
common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" %axsf_fn)))
arr2 = np.vstack((coords3d_cart[0,...],coords3d_cart[1,...]))
np.testing.assert_array_almost_equal(arr, arr2)
# fixed cell, forces3d, coords_frac
axsf_fn = pj(testdir, 'foo3.axsf')
io.write_axsf(axsf_fn,
Trajectory(units=units,coords_frac=coords3d_frac,
cell=cell2d,
symbols=symbols,
forces=forces3d),
)
arr = np.loadtxt(StringIO(
common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" %axsf_fn)))
t0 = np.concatenate((coords3d_cart[0,...], forces3d[0,...]), axis=-1)
t1 = np.concatenate((coords3d_cart[1,...], forces3d[1,...]), axis=-1)
arr2 = np.vstack((t0,t1))
print arr
print arr2
print "----------------"
np.testing.assert_array_almost_equal(arr, arr2)
# variable cell, forces3d, coords_frac
axsf_fn = pj(testdir, 'foo4.axsf')
io.write_axsf(axsf_fn,
Trajectory(units=units,coords_frac=coords3d_frac,
cell=cell3d,
symbols=symbols,
forces=forces3d))
arr = np.loadtxt(StringIO(
common.backtick("grep -A3 PRIMVEC %s | grep -v -e '--' -e 'PRIMVEC'" %axsf_fn)))
arr2 = np.vstack((cell3d[0,...], cell3d[1,...]))
print arr
print arr2
print "----------------"
np.testing.assert_array_almost_equal(arr, arr2)
arr = np.loadtxt(StringIO(
common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" %axsf_fn)))
t0 = np.concatenate((np.dot(coords3d_frac[0,...], cell3d[0,...]),
forces3d[0,...]), axis=-1)
t1 = np.concatenate((np.dot(coords3d_frac[1,...], cell3d[1,...]),
forces3d[1,...]), axis=-1)
arr2 = np.vstack((t0,t1))
print arr
print arr2
print "----------------"
np.testing.assert_array_almost_equal(arr, arr2)
# single struct, coords_cart
axsf_fn = pj(testdir, 'foo6.axsf')
io.write_axsf(axsf_fn,
Structure(units=units,coords=coords2d_cart,
cell=cell2d,
symbols=symbols,
forces=forces2d))
arr = np.loadtxt(StringIO(
common.backtick("grep -A3 PRIMVEC %s | grep -v -e '--' -e 'PRIMVEC'" %axsf_fn)))
arr2 = cell2d
print arr
print arr2
print "----------------"
np.testing.assert_array_almost_equal(arr, arr2)
arr = np.loadtxt(StringIO(
common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" %axsf_fn)))
arr2 = np.concatenate((coords2d_cart, forces2d), axis=1)
print arr
print arr2
print "----------------"
np.testing.assert_array_almost_equal(arr, arr2)
# --- XYZ ----------------------------------------------------------------
# Use cell, coords, etc from above
# input: coords_frac
xyz_fn = pj(testdir, 'foo_frac_input.xyz')
io.write_xyz(xyz_fn,
Trajectory(units=units,coords_frac=coords3d_frac,
cell=cell2d,
symbols=symbols),
name='foo')
arr = np.loadtxt(StringIO(
common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" %xyz_fn)))
arr2 = np.concatenate([coords3d_cart[0,...], coords3d_cart[1,...]], axis=0)
np.testing.assert_array_almost_equal(arr, arr2)
# input: coords_cart, cell=None
xyz_fn = pj(testdir, 'foo_cart_input.xyz')
io.write_xyz(xyz_fn,
Trajectory(units=units,coords=coords3d_cart,
symbols=symbols),
name='foo')
arr = np.loadtxt(StringIO(
common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" %xyz_fn)))
arr2 = np.concatenate((coords3d_cart[0,...], coords3d_cart[1,...]), axis=0)
np.testing.assert_array_almost_equal(arr, arr2)
# input: coords2d_frac, cell=cell2d
xyz_fn = pj(testdir, 'foo_cart_input.xyz')
io.write_xyz(xyz_fn,
Structure(units=units,coords_frac=coords2d_frac,
cell=cell2d,
symbols=symbols),
name='foo')
arr = np.loadtxt(StringIO(
common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" %xyz_fn)))
arr2 = coords2d_cart
np.testing.assert_array_almost_equal(arr, arr2)
def test_write_mol():
units = {'forces': Ha / eV}
nstep = 2
cell2d = np.random.rand(3, 3)
cell3d = np.random.rand(nstep, 3, 3)
# fractional
coords2d_frac = np.array([[0.5, 0.5, 0.5], [1, 1, 1]])
# fractional, 2 time steps: (2,2,3) = (nstep, natoms, 3)
coords3d_frac = np.array([coords2d_frac, coords2d_frac * 0.8])
# cartesian = coords3d_frac + cell2d (fixed cell). For varialbe cell cases
# below, cell3d is used!
coords3d_cart = crys.coord_trans(coords3d_frac,
old=cell2d,
new=np.identity(3),
axis=-1)
coords2d_cart = coords3d_cart[0, ...]
symbols = ['H'] * 2
forces2d = np.random.random(coords2d_frac.shape)
forces3d = np.random.random(coords3d_frac.shape)
# --- AXSF ---------------------------------------------------------------
# fixed cell, forces=0
axsf_fn = pj(testdir, 'foo.axsf')
io.write_axsf(
axsf_fn,
Trajectory(units=units,
coords_frac=coords3d_frac,
cell=cell2d,
symbols=symbols),
)
arr = np.loadtxt(
StringIO(
common.backtick("grep -A3 PRIMVEC %s | grep -vE -e '--|PRIMVEC'" %
axsf_fn)))
np.testing.assert_array_almost_equal(
arr, np.concatenate((cell2d, cell2d), axis=0))
arr = np.loadtxt(
StringIO(common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" % axsf_fn)))
arr2 = np.vstack((coords3d_cart[0, ...], coords3d_cart[1, ...]))
np.testing.assert_array_almost_equal(arr, arr2)
# fixed cell, forces3d, coords_frac
axsf_fn = pj(testdir, 'foo3.axsf')
io.write_axsf(
axsf_fn,
Trajectory(units=units,
coords_frac=coords3d_frac,
cell=cell2d,
symbols=symbols,
forces=forces3d),
)
arr = np.loadtxt(
StringIO(common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" % axsf_fn)))
t0 = np.concatenate((coords3d_cart[0, ...], forces3d[0, ...]), axis=-1)
t1 = np.concatenate((coords3d_cart[1, ...], forces3d[1, ...]), axis=-1)
arr2 = np.vstack((t0, t1))
print(arr)
print(arr2)
print("----------------")
np.testing.assert_array_almost_equal(arr, arr2)
# variable cell, forces3d, coords_frac
axsf_fn = pj(testdir, 'foo4.axsf')
io.write_axsf(
axsf_fn,
Trajectory(units=units,
coords_frac=coords3d_frac,
cell=cell3d,
symbols=symbols,
forces=forces3d))
arr = np.loadtxt(
StringIO(
common.backtick(
"grep -A3 PRIMVEC %s | grep -v -e '--' -e 'PRIMVEC'" %
axsf_fn)))
arr2 = np.vstack((cell3d[0, ...], cell3d[1, ...]))
print(arr)
print(arr2)
print("----------------")
np.testing.assert_array_almost_equal(arr, arr2)
arr = np.loadtxt(
StringIO(common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" % axsf_fn)))
t0 = np.concatenate(
(np.dot(coords3d_frac[0, ...], cell3d[0, ...]), forces3d[0, ...]),
axis=-1)
t1 = np.concatenate(
(np.dot(coords3d_frac[1, ...], cell3d[1, ...]), forces3d[1, ...]),
axis=-1)
arr2 = np.vstack((t0, t1))
print(arr)
print(arr2)
print("----------------")
np.testing.assert_array_almost_equal(arr, arr2)
# single struct, coords_cart
axsf_fn = pj(testdir, 'foo6.axsf')
io.write_axsf(
axsf_fn,
Structure(units=units,
coords=coords2d_cart,
cell=cell2d,
symbols=symbols,
forces=forces2d))
arr = np.loadtxt(
StringIO(
common.backtick(
"grep -A3 PRIMVEC %s | grep -v -e '--' -e 'PRIMVEC'" %
axsf_fn)))
arr2 = cell2d
print(arr)
print(arr2)
print("----------------")
np.testing.assert_array_almost_equal(arr, arr2)
arr = np.loadtxt(
StringIO(common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" % axsf_fn)))
arr2 = np.concatenate((coords2d_cart, forces2d), axis=1)
print(arr)
print(arr2)
print("----------------")
np.testing.assert_array_almost_equal(arr, arr2)
# --- XYZ ----------------------------------------------------------------
# Use cell, coords, etc from above
# input: coords_frac
xyz_fn = pj(testdir, 'foo_frac_input.xyz')
io.write_xyz(xyz_fn,
Trajectory(units=units,
coords_frac=coords3d_frac,
cell=cell2d,
symbols=symbols),
name='foo')
arr = np.loadtxt(
StringIO(common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" % xyz_fn)))
arr2 = np.concatenate([coords3d_cart[0, ...], coords3d_cart[1, ...]],
axis=0)
np.testing.assert_array_almost_equal(arr, arr2)
# input: coords_cart, cell=None
xyz_fn = pj(testdir, 'foo_cart_input.xyz')
io.write_xyz(xyz_fn,
Trajectory(units=units, coords=coords3d_cart,
symbols=symbols),
name='foo')
arr = np.loadtxt(
StringIO(common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" % xyz_fn)))
arr2 = np.concatenate((coords3d_cart[0, ...], coords3d_cart[1, ...]),
axis=0)
np.testing.assert_array_almost_equal(arr, arr2)
# input: coords2d_frac, cell=cell2d
xyz_fn = pj(testdir, 'foo_cart_input.xyz')
io.write_xyz(xyz_fn,
Structure(units=units,
coords_frac=coords2d_frac,
cell=cell2d,
symbols=symbols),
name='foo')
arr = np.loadtxt(
StringIO(common.backtick("sed -nre 's/^H(.*)/\\1/gp' %s" % xyz_fn)))
arr2 = coords2d_cart
np.testing.assert_array_almost_equal(arr, arr2)
def test_eos():
# load reference fitted with ElkEOSFit, data points [Bohr^3, Ha] -> [Ang^3, eV]
# EV input data [Bohr^3, Ry] -> [Ang^3, eV]
data = np.loadtxt("files/ev/evdata.txt")
volume = data[:,0] * Bohr3_to_Ang3
energy = data[:,1] * (Ry / eV)
ref_ev = np.loadtxt("files/ev/EVPAI.OUT.gz")
ref_ev[:,0] *= Bohr3_to_Ang3
ref_ev[:,1] *= (Ha / eV)
ref_pv = np.loadtxt("files/ev/PVPAI.OUT.gz")
ref_pv[:,0] *= Bohr3_to_Ang3
ref_min = np.loadtxt("files/ev/min.txt")
ref_min[0] *= Bohr3_to_Ang3 # v0
ref_min[1] *= (Ry / eV) # e0
assert ref_ev.shape[0] == ref_pv.shape[0], ("reference data lengths "
"inconsistent")
ref = {}
ref['ev'] = ref_ev
ref['pv'] = ref_pv
ref['v0'], ref['e0'], ref['p0'], ref['b0'] = ref_min
# test new EosFit class, default func=Vinet()
eos = EosFit(volume=volume,
energy=energy)
assert np.allclose(eos.params['v0'], eos.spl.get_min())
assert np.allclose(eos.params['v0'], eos.get_min())
assert np.allclose(eos.params['e0'], eos(eos.params['v0']))
assert np.allclose(eos.params['b0']*eV_by_Ang3_to_GPa, eos.bulkmod(eos.params['v0']))
now = {}
now['v0'] = eos.params['v0']
now['e0'] = eos.params['e0']
now['b0'] = eos.params['b0'] * eV_by_Ang3_to_GPa
now['p0'] = eos.pressure(eos.params['v0'])
for key,val in now.items():
msg = "EosFit: key=%s, ref=%e, val=%e" %(key, ref[key], val)
assert np.allclose(val, ref[key], atol=1e-7), msg
# Test legacy ElkEOSFit / ExternEOS.
# 'exe' must be on your $PATH.
exe = 'eos.x'
app = common.backtick("which %s" %exe).strip()
if app == '':
tools.skip("cannot find '%s' on PATH, skipping test" %exe)
else:
eos_store = {}
type_arr = type(np.array([1.0,2.0]))
for bv_method in ['ev', 'pv']:
print("bv_method: %s" %bv_method)
# natoms = 1, no normalization
eos = ElkEOSFit(energy=energy,
volume=volume,
natoms=1,
etype=1,
npoints=300,
dir=testdir,
bv_method=bv_method)
eos.fit()
now = {}
now['ev'] = eos.ev
now['pv'] = eos.pv
now.update(eos.get_min())
# compare to reference
for key, val in ref.items():
print("ElkEOSFit: testing:", key)
if type(val) == type_arr:
np.testing.assert_array_almost_equal(now[key], ref[key])
else:
np.testing.assert_almost_equal(now[key], ref[key],
decimal=3)
eos_store[bv_method] = eos
# internal check: are the splines correct?
for name in ['ev', 'pv', 'bv']:
# API
getter = getattr(eos, 'get_spl_' + name)
assert getattr(eos, 'spl_' + name) == getter()
# (N,2) arrays self.{ev,pv,bv}
data = getattr(eos, name)
vv = data[:,0]
yy = data[:,1]
# self.spl_{ev,pv,bv}
spl = getattr(eos, 'spl_' + name)
np.testing.assert_array_almost_equal(yy, spl(vv))
# Other attrs for which we do not have external ref data. Test only
# among the two bv_methods 'ev' and 'pv'.
print("bv")
np.testing.assert_array_almost_equal(eos_store['ev'].bv,
eos_store['pv'].bv,
decimal=2)
def read_matdyn_modes(filename, natoms=None):
"""Parse modes file produced by QE's matdyn.x.
Parameters
----------
filename : str
File to parse (usually "matdyn.modes")
natoms : int
Number of atoms.
Returns
-------
qpoints, freqs, vecs
qpoints : 2d array (nqpoints, 3)
All qpoints on the grid.
freqs : 2d array, (nqpoints, nmodes) where nmodes = 3*natoms
Each row: 3*natoms phonon frequencies in [cm^-1] at each q-point.
vecs : 4d complex array (nqpoints, nmodes, natoms, 3)
Complex eigenvectors of the dynamical matrix for each q-point.
Examples
--------
>>> qpoints,freqs,vecs=read_matdyn_modes('matdyn.modes',natoms=27)
# how many q-points? -> 8
>>> qpoints.shape
(8,3)
# 1st q-point in file, mode #3 (out of 3*27) -> vectors on all 27 atoms
>>> vecs[0,2,...].shape
(27,3)
# 1st q-point in file, mode #3, vector on atom #15
>>> vecs[0,2,14,:].real
array([-0.010832, 0.026063, -0.089511])
>>> vecs[0,2,14,:].imag
array([ 0., 0., 0.])
Notes
-----
The file to be parsed looks like this::
diagonalizing the dynamical matrix ...
q = 0.0000 0.0000 0.0000
**************************************************************************
omega( 1) = -26.663631 [THz] = -889.402992 [cm-1]
( -0.218314 0.000000 -0.025643 0.000000 -0.116601 0.000000 )
( -0.086633 0.000000 0.108966 0.000000 -0.066513 0.000000 )
[... natoms lines: x_real x_imag y_real y_imag z_real z_imag ... until
next omega ...]
omega( 2) = -16.330246 [THz] = -544.718372 [cm-1]
( 0.172149 0.000000 0.008336 0.000000 -0.121991 0.000000 )
( -0.061497 0.000000 0.003782 0.000000 -0.018304 0.000000 )
[... until omega(3*natoms) ...]
**************************************************************************
diagonalizing the dynamical matrix ...
[... until next q-point ...]
q = 0.0000 0.0000 -0.5000
**************************************************************************
omega( 1) = -24.881828 [THz] = -829.968443 [cm-1]
( -0.225020 0.000464 -0.031584 0.000061 -0.130217 0.000202 )
( -0.085499 0.000180 0.107383 -0.000238 -0.086854 0.000096 )
[...]
**************************************************************************
"""
assert natoms is not None
cmd = r"grep 'q.*=' %s | sed -re 's/.*q\s*=(.*)/\1/'" %filename
qpoints = parse.arr2d_from_txt(common.backtick(cmd))
nqpoints = qpoints.shape[0]
nmodes = 3*natoms
cmd = r"grep '^[ ]*(' %s | sed -re 's/^\s*\((.*)\)/\1/g'" %filename
# vecs_file_flat: (nqpoints * nmodes * natoms, 6)
# this line is the bottleneck
vecs_file_flat = parse.arr2d_from_txt(common.backtick(cmd))
vecs_flat = np.empty((vecs_file_flat.shape[0], 3), dtype=complex)
vecs_flat[:,0] = vecs_file_flat[:,0] + 1j*vecs_file_flat[:,1]
vecs_flat[:,1] = vecs_file_flat[:,2] + 1j*vecs_file_flat[:,3]
vecs_flat[:,2] = vecs_file_flat[:,4] + 1j*vecs_file_flat[:,5]
vecs = vecs_flat.flatten().reshape(nqpoints, nmodes, natoms, 3)
cmd = r"grep omega %s | sed -re \
's/.*omega.*=.*\[.*=(.*)\s*\[.*/\1/g'" %filename
freqs = np.fromstring(common.backtick(cmd), sep=' ').reshape((nqpoints, nmodes))
return qpoints, freqs, vecs
def test_absolute_signal():
# std lib signal
from pwtools.common import signal
assert not hasattr(signal, 'fftsample')
from pwtools import common
print common.backtick('ls')
def test_eos():
# load reference fitted with ElkEOSFit, data points [Bohr^3, Ha] -> [Ang^3, eV]
# EV input data [Bohr^3, Ry] -> [Ang^3, eV]
data = np.loadtxt("files/ev/evdata.txt")
volume = data[:,0] * Bohr3_to_Ang3
energy = data[:,1] * (Ry / eV)
ref_ev = np.loadtxt("files/ev/EVPAI.OUT.gz")
ref_ev[:,0] *= Bohr3_to_Ang3
ref_ev[:,1] *= (Ha / eV)
ref_pv = np.loadtxt("files/ev/PVPAI.OUT.gz")
ref_pv[:,0] *= Bohr3_to_Ang3
ref_min = np.loadtxt("files/ev/min.txt")
ref_min[0] *= Bohr3_to_Ang3 # v0
ref_min[1] *= (Ry / eV) # e0
assert ref_ev.shape[0] == ref_pv.shape[0], ("reference data lengths "
"inconsistent")
ref = {}
ref['ev'] = ref_ev
ref['pv'] = ref_pv
ref['v0'], ref['e0'], ref['p0'], ref['b0'] = ref_min
# test new EosFit class, default func=Vinet()
eos = EosFit(volume=volume,
energy=energy)
assert np.allclose(eos.params['v0'], eos.spl.get_min())
assert np.allclose(eos.params['v0'], eos.get_min())
assert np.allclose(eos.params['e0'], eos(eos.params['v0']))
assert np.allclose(eos.params['b0']*eV_by_Ang3_to_GPa, eos.bulkmod(eos.params['v0']))
now = {}
now['v0'] = eos.params['v0']
now['e0'] = eos.params['e0']
now['b0'] = eos.params['b0'] * eV_by_Ang3_to_GPa
now['p0'] = eos.pressure(eos.params['v0'])
for key,val in now.iteritems():
msg = "EosFit: key=%s, ref=%e, val=%e" %(key, ref[key], val)
assert np.allclose(val, ref[key], atol=1e-7), msg
# Test legacy ElkEOSFit / ExternEOS.
# 'exe' must be on your $PATH.
exe = 'eos.x'
app = common.backtick("which %s" %exe).strip()
if app == '':
tools.skip("cannot find '%s' on PATH, skipping test" %exe)
else:
eos_store = {}
type_arr = type(np.array([1.0,2.0]))
for bv_method in ['ev', 'pv']:
print "bv_method: %s" %bv_method
# natoms = 1, no normalization
eos = ElkEOSFit(energy=energy,
volume=volume,
natoms=1,
etype=1,
npoints=300,
dir=testdir,
bv_method=bv_method)
eos.fit()
now = {}
now['ev'] = eos.ev
now['pv'] = eos.pv
now.update(eos.get_min())
# compare to reference
for key, val in ref.iteritems():
print "ElkEOSFit: testing:", key
if type(val) == type_arr:
np.testing.assert_array_almost_equal(now[key], ref[key])
else:
np.testing.assert_almost_equal(now[key], ref[key],
decimal=3)
eos_store[bv_method] = eos
# internal check: are the splines correct?
for name in ['ev', 'pv', 'bv']:
# API
getter = getattr(eos, 'get_spl_' + name)
assert getattr(eos, 'spl_' + name) == getter()
# (N,2) arrays self.{ev,pv,bv}
data = getattr(eos, name)
vv = data[:,0]
yy = data[:,1]
# self.spl_{ev,pv,bv}
spl = getattr(eos, 'spl_' + name)
np.testing.assert_array_almost_equal(yy, spl(vv))
# Other attrs for which we do not have external ref data. Test only
# among the two bv_methods 'ev' and 'pv'.
print "bv"
np.testing.assert_array_almost_equal(eos_store['ev'].bv,
eos_store['pv'].bv,
decimal=2)
def read_matdyn_modes(filename, natoms=None):
"""Parse modes file produced by QE's matdyn.x.
Parameters
----------
filename : str
File to parse (usually "matdyn.modes")
natoms : int
Number of atoms.
Returns
-------
qpoints, freqs, vecs
qpoints : 2d array (nqpoints, 3)
All qpoints on the grid.
freqs : 2d array, (nqpoints, nmodes) where nmodes = 3*natoms
Each row: 3*natoms phonon frequencies in [cm^-1] at each q-point.
vecs : 4d complex array (nqpoints, nmodes, natoms, 3)
Complex eigenvectors of the dynamical matrix for each q-point.
Examples
--------
>>> qpoints,freqs,vecs=read_matdyn_modes('matdyn.modes',natoms=27)
# how many q-points? -> 8
>>> qpoints.shape
(8,3)
# 1st q-point in file, mode #3 (out of 3*27) -> vectors on all 27 atoms
>>> vecs[0,2,...].shape
(27,3)
# 1st q-point in file, mode #3, vector on atom #15
>>> vecs[0,2,14,:].real
array([-0.010832, 0.026063, -0.089511])
>>> vecs[0,2,14,:].imag
array([ 0., 0., 0.])
Notes
-----
The file to be parsed looks like this::
diagonalizing the dynamical matrix ...
q = 0.0000 0.0000 0.0000
**************************************************************************
omega( 1) = -26.663631 [THz] = -889.402992 [cm-1]
( -0.218314 0.000000 -0.025643 0.000000 -0.116601 0.000000 )
( -0.086633 0.000000 0.108966 0.000000 -0.066513 0.000000 )
[... natoms lines: x_real x_imag y_real y_imag z_real z_imag ... until
next omega ...]
omega( 2) = -16.330246 [THz] = -544.718372 [cm-1]
( 0.172149 0.000000 0.008336 0.000000 -0.121991 0.000000 )
( -0.061497 0.000000 0.003782 0.000000 -0.018304 0.000000 )
[... until omega(3*natoms) ...]
**************************************************************************
diagonalizing the dynamical matrix ...
[... until next q-point ...]
q = 0.0000 0.0000 -0.5000
**************************************************************************
omega( 1) = -24.881828 [THz] = -829.968443 [cm-1]
( -0.225020 0.000464 -0.031584 0.000061 -0.130217 0.000202 )
( -0.085499 0.000180 0.107383 -0.000238 -0.086854 0.000096 )
[...]
**************************************************************************
"""
assert natoms is not None
cmd = r"grep 'q.*=' %s | sed -re 's/.*q\s*=(.*)/\1/'" %filename
qpoints = parse.arr2d_from_txt(common.backtick(cmd))
nqpoints = qpoints.shape[0]
nmodes = 3*natoms
cmd = r"grep '^[ ]*(' %s | sed -re 's/^\s*\((.*)\)/\1/g'" %filename
# vecs_file_flat: (nqpoints * nmodes * natoms, 6)
# this line is the bottleneck
vecs_file_flat = parse.arr2d_from_txt(common.backtick(cmd))
vecs_flat = np.empty((vecs_file_flat.shape[0], 3), dtype=complex)
vecs_flat[:,0] = vecs_file_flat[:,0] + 1j*vecs_file_flat[:,1]
vecs_flat[:,1] = vecs_file_flat[:,2] + 1j*vecs_file_flat[:,3]
vecs_flat[:,2] = vecs_file_flat[:,4] + 1j*vecs_file_flat[:,5]
vecs = vecs_flat.flatten().reshape(nqpoints, nmodes, natoms, 3)
cmd = r"grep omega %s | sed -re \
's/.*omega.*=.*\[.*=(.*)\s*\[.*/\1/g'" %filename
freqs = np.fromstring(common.backtick(cmd), sep=' ').reshape((nqpoints, nmodes))
return qpoints, freqs, vecs
def test_sql():
# Check for sqlite3 command line tool. In Python 3.3, we can use
# shutil.which().
have_sqlite3 = False
for pp in sys.path:
exe = pj(pp, 'sqlite3')
if os.path.isfile(exe):
print "found:", exe
have_sqlite3 = True
break
# --- SQLiteDB ----------------------------------------------------
dbfn = pj(testdir, 'test.db')
if os.path.exists(dbfn):
os.remove(dbfn)
header = [('idx', 'INTEGER'), ('foo', 'REAL'), ('bar', 'TEXT')]
db = SQLiteDB(dbfn, table='calc')
db.execute("CREATE TABLE calc (%s)" %','.join("%s %s" %(x[0], x[1]) \
for x in header))
vals = [[0, 1.1, 'a'],
[1, 2.2, 'b'],
[2, 3.3, 'c']]
for lst in vals:
db.execute("INSERT INTO calc (idx, foo, bar) VALUES (?,?,?)", tuple(lst))
db.commit()
# get_max_rowid
assert db.get_max_rowid() == 3
# has_table
assert db.has_table('calc')
assert not db.has_table('foo')
# has_column
assert db.has_column('idx')
assert not db.has_column('grrr')
# get_single
assert float(db.get_single("select foo from calc where idx==0")) == 1.1
assert header == db.get_header()
if have_sqlite3:
# call sqlite3, the cmd line interface
assert common.backtick("sqlite3 %s 'select * from calc'" %dbfn) \
== '0|1.1|a\n1|2.2|b\n2|3.3|c\n'
# ret =
# [(0, 1.1000000000000001, u'a'),
# (1, 2.2000000000000002, u'b'),
# (2, 3.2999999999999998, u'c')]
ret = db.execute("select * from calc").fetchall()
for idx, lst in enumerate(vals):
assert list(ret[idx]) == lst
# generator object, yields
# tup = (0, 1.1000000000000001, u'a')
# tup = (1, 2.2000000000000002, u'b')
# tup = (2, 3.2999999999999998, u'c')
itr = db.execute("select * from calc")
for idx, tup in enumerate(itr):
assert list(tup) == vals[idx]
# [(0, 1.1000000000000001, u'a')]
assert db.execute("select * from calc where idx==0").fetchall() == \
[tuple(vals[0])]
# (0, 1.1000000000000001, u'a')
assert db.execute("select * from calc where idx==0").fetchone() == \
tuple(vals[0])
assert db.execute("select bar from calc where idx==0").fetchone()[0] == \
'a'
# get_list1d(), get_array1d(), get_array()
assert db.get_list1d("select idx from calc") == [0,1,2]
np.testing.assert_array_equal(db.get_array1d("select idx from calc"),
np.array([0,1,2]))
np.testing.assert_array_equal(db.get_array("select idx from calc"),
np.array([0,1,2])[:,None])
np.testing.assert_array_equal(db.get_array("select idx,foo from calc"),
np.array(vals, dtype='S3')[:,:2].astype(float))
# add_column(), fill with values
db.add_column('baz', 'TEXT')
add_header = [('baz', 'TEXT')]
header += add_header
assert db.get_header() == header
db.execute("UPDATE %s SET baz='xx' where idx==0" %db.table)
db.execute("UPDATE %s SET baz='yy' where idx==1" %db.table)
db.execute("UPDATE %s SET baz=? where idx==2" %db.table, ('zz',))
db.commit()
if have_sqlite3:
print common.backtick("sqlite3 %s 'select * from calc'" %dbfn)
print db.execute("select baz from calc").fetchall()
assert db.execute("select baz from calc").fetchall() == \
[(u'xx',), (u'yy',), (u'zz',)]
# add even more cols with add_columns()
add_header = [('bob', 'TEXT'), ('alice', 'BLOB')]
header += add_header
db.add_columns(add_header)
assert db.get_header() == header
# create_table()
dbfn2 = pj(testdir, 'test2.db')
header2 = [('a', 'REAL'), ('b', 'TEXT')]
db2 = SQLiteDB(dbfn2, table='foo')
db2.create_table(header2)
assert db2.get_header() == header2
# get_dict()
dct = db.get_dict("select foo,bar from calc")
cols = [x[0] for x in db.get_header()]
for key in ['foo', 'bar']:
assert key in cols
foo = db.get_list1d("select foo from calc")
bar = db.get_list1d("select bar from calc")
assert foo == dct['foo']
assert bar == dct['bar']
# step 6
# ------
#
# Now, we extend the study. This time we write input for both machines. Since
# for one machine, input is already there, a backup will be made
# (calc_host0.0). Observe the changes to calc.db: revision=1, column "hostname"
# mentions both machines. calc_*/run.sh refers only to the new calculations. A
# file "excl_push" is written, which lists all old calculation indices. Can be
# used with ``rsync --exclude-from=excl_push``.
#
params_lst = []
for ecutwfc in np.array([70, 80.0]):
for pseudo in ["Si.paw"]:
params_lst.append([sql.SQLEntry(key="ecutwfc", sqlval=ecutwfc), sql.SQLEntry(key="pseudo", sqlval=pseudo)])
calc = batch.ParameterStudy(machines=[host0, host1], templates=templates, params_lst=params_lst, study_name=study_name)
calc.write_input(sleep=0, backup=True, mode="a")
# Load written sqlite DB and print table.
print common.backtick(
"sqlite3 -column -header calc.db \
'select * from calc'"
)
# Some example db query using Python.
db = sql.SQLiteDB("calc.db", table="calc")
print db.get_dict("select idx,ecutwfc,pseudo from calc where ecutwfc <= 60")
def test_sql():
# Check for sqlite3 command line tool. In Python 3.3, we can use
# shutil.which().
have_sqlite3 = False
for pp in sys.path:
exe = pj(pp, 'sqlite3')
if os.path.isfile(exe):
print("found:", exe)
have_sqlite3 = True
break
# --- SQLiteDB ----------------------------------------------------
dbfn = pj(testdir, 'test.db')
if os.path.exists(dbfn):
os.remove(dbfn)
header = [('idx', 'INTEGER'), ('foo', 'REAL'), ('bar', 'TEXT')]
db = SQLiteDB(dbfn, table='calc')
db.execute("CREATE TABLE calc (%s)" %','.join("%s %s" %(x[0], x[1]) \
for x in header))
vals = [[0, 1.1, 'a'], [1, 2.2, 'b'], [2, 3.3, 'c']]
for lst in vals:
db.execute("INSERT INTO calc (idx, foo, bar) VALUES (?,?,?)",
tuple(lst))
db.commit()
# get_max_rowid
assert db.get_max_rowid() == 3
# has_table
assert db.has_table('calc')
assert not db.has_table('foo')
# has_column
assert db.has_column('idx')
assert not db.has_column('grrr')
# get_single
assert float(db.get_single("select foo from calc where idx==0")) == 1.1
assert header == db.get_header()
if have_sqlite3:
# call sqlite3, the cmd line interface
assert common.backtick("sqlite3 %s 'select * from calc'" %dbfn) \
== '0|1.1|a\n1|2.2|b\n2|3.3|c\n'
# ret =
# [(0, 1.1000000000000001, u'a'),
# (1, 2.2000000000000002, u'b'),
# (2, 3.2999999999999998, u'c')]
ret = db.execute("select * from calc").fetchall()
for idx, lst in enumerate(vals):
assert list(ret[idx]) == lst
# generator object, yields
# tup = (0, 1.1000000000000001, u'a')
# tup = (1, 2.2000000000000002, u'b')
# tup = (2, 3.2999999999999998, u'c')
itr = db.execute("select * from calc")
for idx, tup in enumerate(itr):
assert list(tup) == vals[idx]
# [(0, 1.1000000000000001, u'a')]
assert db.execute("select * from calc where idx==0").fetchall() == \
[tuple(vals[0])]
# (0, 1.1000000000000001, u'a')
assert db.execute("select * from calc where idx==0").fetchone() == \
tuple(vals[0])
assert db.execute("select bar from calc where idx==0").fetchone()[0] == \
'a'
# get_list1d(), get_array1d(), get_array()
assert db.get_list1d("select idx from calc") == [0, 1, 2]
np.testing.assert_array_equal(db.get_array1d("select idx from calc"),
np.array([0, 1, 2]))
np.testing.assert_array_equal(db.get_array("select idx from calc"),
np.array([0, 1, 2])[:, None])
np.testing.assert_array_equal(
db.get_array("select idx,foo from calc"),
np.array(vals, dtype='S3')[:, :2].astype(float))
# add_column(), fill with values
db.add_column('baz', 'TEXT')
add_header = [('baz', 'TEXT')]
header += add_header
assert db.get_header() == header
db.execute("UPDATE %s SET baz='xx' where idx==0" % db.table)
db.execute("UPDATE %s SET baz='yy' where idx==1" % db.table)
db.execute("UPDATE %s SET baz=? where idx==2" % db.table, ('zz', ))
db.commit()
if have_sqlite3:
print(common.backtick("sqlite3 %s 'select * from calc'" % dbfn))
print(db.execute("select baz from calc").fetchall())
assert db.execute("select baz from calc").fetchall() == \
[('xx',), ('yy',), ('zz',)]
# add even more cols with add_columns()
add_header = [('bob', 'TEXT'), ('alice', 'BLOB')]
header += add_header
db.add_columns(add_header)
assert db.get_header() == header
# create_table()
dbfn2 = pj(testdir, 'test2.db')
header2 = [('a', 'REAL'), ('b', 'TEXT')]
db2 = SQLiteDB(dbfn2, table='foo')
db2.create_table(header2)
assert db2.get_header() == header2
# get_dict()
dct = db.get_dict("select foo,bar from calc")
cols = [x[0] for x in db.get_header()]
for key in ['foo', 'bar']:
assert key in cols
foo = db.get_list1d("select foo from calc")
bar = db.get_list1d("select bar from calc")
assert foo == dct['foo']
assert bar == dct['bar']
def test_cif2sgroup():
print common.backtick("../bin/cif2sgroup.py files/cif_struct.cif")
# for one machine, input is already there, a backup will be made
# (calc_host0.0). Observe the changes to calc.db: revision=1, column "hostname"
# mentions both machines. calc_*/run.sh refers only to the new calculations. A
# file "excl_push" is written, which lists all old calculation indices. Can be
# used with ``rsync --exclude-from=excl_push``.
#
params_lst = []
for ecutwfc in np.array([70, 80.0]):
for pseudo in ['Si.paw']:
params_lst.append([
sql.SQLEntry(key='ecutwfc', sqlval=ecutwfc),
sql.SQLEntry(key='pseudo', sqlval=pseudo)
])
calc = batch.ParameterStudy(
machines=[host0, host1],
templates=templates,
params_lst=params_lst,
study_name=study_name,
)
calc.write_input(sleep=0, backup=True, mode='a')
# Load written sqlite DB and print table.
print(
common.backtick("sqlite3 -column -header calc.db \
'select * from calc'"))
# Some example db query using Python.
db = sql.SQLiteDB('calc.db', table='calc')
print(db.get_dict("select idx,ecutwfc,pseudo from calc where ecutwfc <= 60"))
def test_cif2any():
print common.backtick("../bin/cif2any.py files/cif_struct.cif")