def writetxt(fn, arr, axis=-1, maxdim=TXT_MAXDIM, header=True):
"""Write 1d, 2d or 3d arrays to txt file.
If 3d, write as 2d chunks. Take the 2d chunks along `axis`. Write a
commented out ini-style header in the file with infos needed by readtxt()
to restore the right shape.
Parameters
----------
fn : filename
arr : nd array
axis : axis along which 2d chunks are written
maxdim : highest number of dims that `arr` is allowed to have
header : bool
Write ini style header. Can be used by readtxt().
"""
verbose("[writetxt] writing: %s" %fn)
common.assert_cond(arr.ndim <= maxdim, 'no rank > %i arrays supported' %maxdim)
fh = open(fn, 'wb+')
if header:
c = ConfigParser()
sec = 'array'
c.add_section(sec)
c.set(sec, 'shape', common.seq2str(arr.shape))
c.set(sec, 'axis', str(axis))
_write_header_config(fh, c)
# 1d and 2d case
if arr.ndim < maxdim:
np.savetxt(fh, arr)
# 3d
else:
# TODO get rid of loop?
# write 2d arrays, one by one
sl = [slice(None)]*arr.ndim
for ind in range(arr.shape[axis]):
sl[axis] = ind
np.savetxt(fh, arr[sl])
fh.close()
def writetxt(fn, arr, axis=-1, maxdim=TXT_MAXDIM, header=True):
"""Write 1d, 2d or 3d arrays to txt file.
If 3d, write as 2d chunks. Take the 2d chunks along `axis`. Write a
commented out ini-style header in the file with infos needed by readtxt()
to restore the right shape.
Parameters
----------
fn : filename
arr : nd array
axis : axis along which 2d chunks are written
maxdim : highest number of dims that `arr` is allowed to have
header : bool
Write ini style header. Can be used by readtxt().
"""
verbose("[writetxt] writing: %s" %fn)
common.assert_cond(arr.ndim <= maxdim, 'no rank > %i arrays supported' %maxdim)
fh = open(fn, 'w+')
if header:
c = PydosConfigParser()
sec = 'array'
c.add_section(sec)
c.set(sec, 'shape', common.seq2str(arr.shape))
c.set(sec, 'axis', axis)
_write_header_config(fh, c)
# 1d and 2d case
if arr.ndim < maxdim:
np.savetxt(fh, arr)
# 3d
else:
# TODO get rid of loop?
# write 2d arrays, one by one
sl = [slice(None)]*arr.ndim
for ind in range(arr.shape[axis]):
sl[axis] = ind
np.savetxt(fh, arr[sl])
fh.close()
def plot_dis(path_norm,
freqs,
special_points_path=None,
show_coords=None,
dos=None,
ax=None,
ylim=None,
**kwargs):
"""Plot dispersion.
See ``bin/plot_dispersion.py`` for a usage example. This lives here (and not in
:mod:`~pwtools.pwscf`) b/c it is not PWscf-specific. It can be used for any
dispersion data (band structure).
See :func:`~pwtools.pwscf.read_matdyn_freq` for how to get `freqs` in the
case of phonon dispersions.
This function is a convenience function, which can even plot the DOS as
well. We do not expose many matplotlib parameters here. If you want to tweak
your plot much, then operate on the returned `fig`, `ax` (dispersion) and
`axdos` (dos), or copy and hack the function, which might be actually the easiest
way.
Parameters
----------
path_norm : array (nks,)
x-axis with cumulative norms of points along the k-path, see
:func:`get_path_norm`
freqs : array (nks, nbnd)
`nbnd` frequencies for each band at each k-point
special_points_path : optional, :class:`SpecialPointsPath` instance
used for pretty-printing the x-axis (set special point labels)
show_coords : 'cart', 'frac', None
Show the cartesian or fractional coordinates of special points in the
x-axis label, on neither if None.
dos : array (N,2) or None
array with phonon dos to plot: ``dos[:,0]=freq``, ``dos[:,1]=phdos``
ax : matplotlib AxesSubplot (e.g. from ``fig,ax=pwtools.mpl.fig_ax()``)
automatically created if None
ylim : tuple (2,)
frequency axis limits
**kwargs : keywords
passed to plot()
Returns
-------
fig, ax, axdos
fig : matplotlib Figure to ax
ax : matplotlib AxesSubplot with dispersion
axdos : matplotlib AxesSubplot with dos, or None if `dos=None`
Examples
--------
>>> spp = kpath.SpecialPointsPath(ks=np.array([[0,0,0], [1.5,0,0], [2.3,0,0]]),
symbols=['A', 'B', 'C'])
>>> path_norm = np.linspace(0,2.5,100)
>>> freqs = np.random.rand(100,5)*500
>>> # create fig,ax inside, returned axdos=None
>>> fig,ax,axdos = kpath.plot_dis(path_norm, freqs, spp)
>>> # pass ax from outside, returns fig,ax but we don't use that b/c ax
>>> # is in-place modified
>>> fig,ax = mpl.fig_ax()
>>> kpath.plot_dis(path_norm, freqs, spp, ax=ax)
>>> # plot also DOS
>>> dos = np.empty((30,2)); dos[:,0]=np.linspace(0,500,30); dos[:,1]=rand(30)
>>> fig,ax,axdos = kpath.plot_dis(path_norm, freqs, spp, dos=dos)
See Also
--------
:func:`get_path_norm`
:func:`pwtools.pwscf.read_matdyn_freq`
:ref:`dispersion_example`
"""
if ax is None:
fig, ax = mpl.fig_ax()
else:
fig = ax.get_figure()
# Plot columns of `freq` against q points (path_norm)
ax.plot(path_norm, freqs, **kwargs)
if special_points_path is not None:
ylim = ax.get_ylim() if ylim is None else ylim
ks, ks_frac, nrm, symbols = \
special_points_path.ks, \
special_points_path.ks_frac, \
special_points_path.path_norm, \
special_points_path.symbols
ax.vlines(nrm, ylim[0], ylim[1])
fmtfunc = lambda x: "%.2g" % x
if show_coords is None:
labels = symbols
else:
if show_coords == 'cart':
ks_plot = ks
elif show_coords == 'frac':
ks_plot = ks_frac
else:
raise Exception("show_coords = 'cart', 'frac' or "
"None needed")
labels = ['%s\n[%s]' %(sym, common.seq2str(kk, func=fmtfunc,sep=','))\
for sym,kk in zip(symbols, ks_plot)]
ax.set_xticks(nrm)
ax.set_xticklabels(labels)
ax.set_xlim(path_norm[0], path_norm[-1])
ax.set_ylabel("frequency (cm$^{-1}$)")
if dos is not None:
# http://matplotlib.org/examples/axes_grid/scatter_hist.html
from mpl_toolkits.axes_grid1 import make_axes_locatable
divider = make_axes_locatable(ax)
axdos = divider.append_axes("right", 1.2, pad=0.1, sharey=ax)
axdos.plot(dos[:, 1], dos[:, 0], 'b')
mpl.plt.setp(axdos.get_yticklabels(), visible=False)
mpl.plt.setp(axdos.get_xticklabels(), visible=False)
axdos.xaxis.set_tick_params(size=0)
else:
axdos = None
return fig, ax, axdos
}
for ii, cd in enumerate(celldm):
rules['cd%i' %(ii+1,)] = cd
print out.format(**rules)
#-------------------------------------------------------------------------------
# ABINIT
#-------------------------------------------------------------------------------
print "\n"
print bar
print "ABINIT"
print bar
print "natom %i" %struct.natoms
print "ntypat %i" %struct.ntypat
print "typat %s" %seq2str(struct.typat)
print "znucl %s" %seq2str(struct.znucl)
print "acell %s" %str_arr(struct.cryst_const[:3])
print "angdeg %s" %str_arr(struct.cryst_const[3:])
print "xred\n%s" %str_arr(struct.coords_frac)
print "pseudopotential order:\n%s" %"\n".join(["%s %i" %(sym, zz) for sym,zz in
zip(struct.symbols_unique,
struct.znucl)])
#-------------------------------------------------------------------------------
# CPMD
#-------------------------------------------------------------------------------
print "\n"
print bar
print "CPMD"
print bar
}
for ii, cd in enumerate(celldm):
rules['cd%i' % (ii + 1, )] = cd
print(out.format(**rules))
#-------------------------------------------------------------------------------
# ABINIT
#-------------------------------------------------------------------------------
print("\n")
print(bar)
print("ABINIT")
print(bar)
print("natom %i" % struct.natoms)
print("ntypat %i" % struct.ntypat)
print("typat %s" % seq2str(struct.typat))
print("znucl %s" % seq2str(struct.znucl))
print("acell %s" % str_arr(struct.cryst_const[:3]))
print("angdeg %s" % str_arr(struct.cryst_const[3:]))
print("xred\n%s" % str_arr(struct.coords_frac))
print("pseudopotential order:\n%s" % "\n".join([
"%s %i" % (sym, zz) for sym, zz in zip(struct.symbols_unique, struct.znucl)
]))
#-------------------------------------------------------------------------------
# CPMD
#-------------------------------------------------------------------------------
print("\n")
print(bar)
print("CPMD")
print(bar)
def plot_dis(path_norm, freqs, special_points_path=None, show_coords=None, dos=None, ax=None, ylim=None, **kwargs):
"""Plot dispersion.
See ``bin/plot_dispersion.py`` for a usage example. This lives here (and not in
:mod:`~pwtools.pwscf`) b/c it is not PWscf-specific. It can be used for any
dispersion data (band structure).
See :func:`~pwtools.pwscf.read_matdyn_freq` for how to get `freqs` in the
case of phonon dispersions.
This function is a convenience function, which can even plot the DOS as
well. We do not expose many matplotlib parameters here. If you want to tweak
your plot much, then operate on the returned `fig`, `ax` (dispersion) and
`axdos` (dos), or copy and hack the function, which might be actually the easiest
way.
Parameters
----------
path_norm : array (nks,)
x-axis with cumulative norms of points along the k-path, see
:func:`get_path_norm`
freqs : array (nks, nbnd)
`nbnd` frequencies for each band at each k-point
special_points_path : optional, :class:`SpecialPointsPath` instance
used for pretty-printing the x-axis (set special point labels)
show_coords : 'cart', 'frac', None
Show the cartesian or fractional coordinates of special points in the
x-axis label, on neither if None.
dos : array (N,2) or None
array with phonon dos to plot: ``dos[:,0]=freq``, ``dos[:,1]=phdos``
ax : matplotlib AxesSubplot (e.g. from ``fig,ax=pwtools.mpl.fig_ax()``)
automatically created if None
ylim : tuple (2,)
frequency axis limits
**kwargs : keywords
passed to plot()
Returns
-------
fig, ax, axdos
fig : matplotlib Figure to ax
ax : matplotlib AxesSubplot with dispersion
axdos : matplotlib AxesSubplot with dos, or None if `dos=None`
Examples
--------
>>> spp = kpath.SpecialPointsPath(ks=np.array([[0,0,0], [1.5,0,0], [2.3,0,0]]),
symbols=['A', 'B', 'C'])
>>> path_norm = np.linspace(0,2.5,100)
>>> freqs = np.random.rand(100,5)*500
>>> # create fig,ax inside, returned axdos=None
>>> fig,ax,axdos = kpath.plot_dis(path_norm, freqs, spp)
>>> # pass ax from outside, returns fig,ax but we don't use that b/c ax
>>> # is in-place modified
>>> fig,ax = mpl.fig_ax()
>>> kpath.plot_dis(path_norm, freqs, spp, ax=ax)
>>> # plot also DOS
>>> dos = np.empty((30,2)); dos[:,0]=np.linspace(0,500,30); dos[:,1]=rand(30)
>>> fig,ax,axdos = kpath.plot_dis(path_norm, freqs, spp, dos=dos)
See Also
--------
:func:`get_path_norm`
:func:`pwtools.pwscf.read_matdyn_freq`
:ref:`dispersion_example`
"""
if ax is None:
fig, ax = mpl.fig_ax()
else:
fig = ax.get_figure()
# Plot columns of `freq` against q points (path_norm)
ax.plot(path_norm, freqs, **kwargs)
if special_points_path is not None:
ylim = ax.get_ylim() if ylim is None else ylim
ks, ks_frac, nrm, symbols = (
special_points_path.ks,
special_points_path.ks_frac,
special_points_path.path_norm,
special_points_path.symbols,
)
ax.vlines(nrm, ylim[0], ylim[1])
fmtfunc = lambda x: "%.2g" % x
if show_coords is None:
labels = symbols
else:
if show_coords == "cart":
ks_plot = ks
elif show_coords == "frac":
ks_plot = ks_frac
else:
raise StandardError("show_coords = 'cart', 'frac' or " "None needed")
labels = [
"%s\n[%s]" % (sym, common.seq2str(kk, func=fmtfunc, sep=",")) for sym, kk in zip(symbols, ks_plot)
]
ax.set_xticks(nrm)
ax.set_xticklabels(labels)
ax.set_xlim(path_norm[0], path_norm[-1])
ax.set_ylabel("frequency (cm$^{-1}$)")
if dos is not None:
# http://matplotlib.org/examples/axes_grid/scatter_hist.html
from mpl_toolkits.axes_grid1 import make_axes_locatable
divider = make_axes_locatable(ax)
axdos = divider.append_axes("right", 1.2, pad=0.1, sharey=ax)
axdos.plot(dos[:, 1], dos[:, 0], "b")
mpl.plt.setp(axdos.get_yticklabels(), visible=False)
mpl.plt.setp(axdos.get_xticklabels(), visible=False)
axdos.xaxis.set_tick_params(size=0)
else:
axdos = None
return fig, ax, axdos
