def plot_densities(self, ax=None, timesr2=False, **kwargs):
"""
Plot ae, ps and model densities on axis ax.
"""
ax, fig, plt = get_ax_fig_plt(ax)
lines, legends = [], []
for name, rho in self.densities.items():
d = rho.values if not timesr2 else rho.values * rho.rmesh**2
line, = ax.plot(rho.rmesh,
d,
linewidth=self.linewidth,
markersize=self.markersize)
lines.append(line)
legends.append(name)
ylabel = "$n(r)$" if not timesr2 else "$r^2 n(r)$"
decorate_ax(ax,
xlabel="r [Bohr]",
ylabel=ylabel,
title="Charge densities",
lines=lines,
legends=legends)
return fig
def plot_key(self, key, ax=None, **kwargs):
"""Plot a singol quantity specified by key."""
ax, fig, plt = get_ax_fig_plt(ax)
# key --> self.plot_key()
getattr(self, "plot_" + key)(ax=ax, **kwargs)
self._mplt.show()
def plot_stacked_hist(self, key="wall_time", nmax=5, ax=None, **kwargs):
"""
Plot stacked histogram of the different timers.
Args:
key: Keyword used to extract data from the timers. Only the first `nmax`
sections with largest value are show.
mmax: Maximum nuber of sections to show. Other entries are grouped together
in the `others` section.
ax: matplotlib :class:`Axes` or None if a new figure should be created.
Returns:
`matplotlib` figure
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
mpi_rank = "0"
timers = self.timers(mpi_rank=mpi_rank)
n = len(timers)
names, values = [], []
rest = np.zeros(n)
for idx, sname in enumerate(self.section_names(ordkey=key)):
sections = self.get_sections(sname)
svals = np.asarray([s.__dict__[key] for s in sections])
if idx < nmax:
names.append(sname)
values.append(svals)
else:
rest += svals
names.append("others (nmax=%d)" % nmax)
values.append(rest)
# The dataset is stored in values. Now create the stacked histogram.
ind = np.arange(n) # the locations for the groups
width = 0.35 # the width of the bars
colors = nmax * ['r', 'g', 'b', 'c', 'k', 'y', 'm']
bars = []
bottom = np.zeros(n)
for idx, vals in enumerate(values):
color = colors[idx]
bar = ax.bar(ind, vals, width, color=color, bottom=bottom)
bars.append(bar)
bottom += vals
ax.set_ylabel(key)
ax.set_title("Stacked histogram with the %d most important sections" % nmax)
ticks = ind + width / 2.0
labels = ["MPI=%d, OMP=%d" % (t.mpi_nprocs, t.omp_nthreads) for t in timers]
ax.set_xticks(ticks)
ax.set_xticklabels(labels, rotation=15)
# Add legend.
ax.legend([bar[0] for bar in bars], names, loc="best")
return fig
def plot_radial_wfs(self, ax=None, **kwargs):
"""
Plot ae and ps radial wavefunctions on axis ax.
lselect: List to select l channels.
"""
ax, fig, plt = get_ax_fig_plt(ax)
ae_wfs, ps_wfs = self.radial_wfs.ae, self.radial_wfs.ps
lselect = kwargs.get("lselect", [])
lines, legends = [], []
for nlk, ae_wf in ae_wfs.items():
ps_wf, l, k = ps_wfs[nlk], nlk.l, nlk.k
if l in lselect: continue
#print(nlk)
ae_line, = ax.plot(ae_wf.rmesh, ae_wf.values, **self._wf_pltopts(l, "ae"))
ps_line, = ax.plot(ps_wf.rmesh, ps_wf.values, **self._wf_pltopts(l, "ps"))
lines.extend([ae_line, ps_line])
if k is None:
legends.extend(["AE l=%s" % l, "PS l=%s" % l])
else:
legends.extend(["AE l=%s, k=%s" % (l, k), "PS l=%s, k=%s" % (l, k)])
decorate_ax(ax, xlabel="r [Bohr]", ylabel="$\phi(r)$", title="Wave Functions",
lines=lines, legends=legends)
return fig
def plot_der_densities(self, ax=None, order=1, **kwargs):
"""
Plot the derivatives of the densitiers on axis ax.
Used to analyze possible derivative discontinuities
"""
ax, fig, plt = get_ax_fig_plt(ax)
from scipy.interpolate import UnivariateSpline
lines, legends = [], []
for name, rho in self.densities.items():
if name != "rhoM": continue
# Need linear mesh for finite_difference --> Spline input densities on lin_rmesh
lin_rmesh, h = np.linspace(rho.rmesh[0], rho.rmesh[-1], num=len(rho.rmesh) * 4, retstep=True)
spline = UnivariateSpline(rho.rmesh, rho.values, s=0)
lin_values = spline(lin_rmesh)
vder = finite_diff(lin_values, h, order=order, acc=4)
line, = ax.plot(lin_rmesh, vder) #, **self._wf_pltopts(l, "ae"))
lines.append(line)
legends.append("%s-order derivative of %s" % (order, name))
decorate_ax(ax, xlabel="r [Bohr]", ylabel="$D^%s \n(r)$" % order, title="Derivative of the charge densities",
lines=lines, legends=legends)
return fig
def plot_xy_with_hue(data,
x,
y,
hue,
decimals=None,
ax=None,
xlims=None,
ylims=None,
fontsize=12,
**kwargs):
"""
Plot y = f(x) relation for different values of `hue`.
Useful for convergence tests done wrt to two parameters.
Args:
data: |pandas-DataFrame| containing columns `x`, `y`, and `hue`.
x: Name of the column used as x-value
y: Name of the column used as y-value
hue: Variable that define subsets of the data, which will be drawn on separate lines
decimals: Number of decimal places to round `hue` columns. Ignore if None
ax: |matplotlib-Axes| or None if a new figure should be created.
xlims ylims: Set the data limits for the x(y)-axis. Accept tuple e.g. `(left, right)`
or scalar e.g. `left`. If left (right) is None, default values are used
fontsize: Legend fontsize.
kwargs: Keywork arguments are passed to ax.plot method.
Returns: |matplotlib-Figure|
"""
# Check here because pandas error messages are a bit criptic.
miss = [k for k in (x, y, hue) if k not in data]
if miss:
raise ValueError(
"Cannot find `%s` in dataframe.\nAvailable keys are: %s" %
(str(miss), str(data.keys())))
# Truncate values in hue column so that we can group.
if decimals is not None:
data = data.round({hue: decimals})
ax, fig, plt = get_ax_fig_plt(ax=ax)
for key, grp in data.groupby(hue):
#xvals, yvals = grp[x], grp[y]
# Sort xs and rearrange ys
xy = np.array(sorted(zip(grp[x], grp[y]), key=lambda t: t[0]))
xvals, yvals = xy[:, 0], xy[:, 1]
label = "{} = {}".format(hue, key)
if not kwargs:
ax.plot(xvals, yvals, 'o-', label=label)
else:
ax.plot(xvals, yvals, label=label, **kwargs)
ax.grid(True)
ax.set_xlabel(x)
ax.set_ylabel(y)
set_axlims(ax, xlims, "x")
set_axlims(ax, ylims, "y")
ax.legend(loc="best", fontsize=fontsize, shadow=True)
return fig
def plot(self,
ax=None,
components=('xx', ),
reim="reim",
vertical_lines=True,
**kwargs):
"""
Return an instance of the spectra and plot it using matplotlib
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
directions_map = {'x': 0, 'y': 1, 'z': 2}
functions_map = {'re': lambda x: x.real, 'im': lambda x: x.imag}
reim_label = {'re': 'Re', 'im': 'Im'}
for component in components:
i, j = [directions_map[direction] for direction in component]
for fstr in functions_map:
if fstr in reim:
f = functions_map[fstr]
label = "%s{$\epsilon_{%s}$}" % (reim_label[fstr],
component)
ax.plot(self.frequencies * 1000,
f(self.ir_spectra_tensor[:, i, j]),
label=label,
**kwargs)
if vertical_lines:
phfreqs = self.ir_spectra_generator.phfreqs[3:]
ax.scatter(phfreqs * 1000, np.zeros_like(phfreqs))
ax.set_xlabel('$\epsilon(\omega)$')
ax.set_xlabel('Frequency (meV)')
ax.legend()
return fig
def plot_atan_logders(self, ax=None, **kwargs):
"""Plot arctan of logder on axis ax."""
ae, ps = self.atan_logders.ae, self.atan_logders.ps
ax, fig, plt = get_ax_fig_plt(ax)
lines, legends = [], []
for l, ae_alog in ae.items():
ps_alog = ps[l]
# Add padd to avoid overlapping curves.
pad = (l + 1) * 1.0
ae_line, = ax.plot(ae_alog.energies, ae_alog.values + pad,
**self._wf_pltopts(l, "ae"))
ps_line, = ax.plot(ps_alog.energies, ps_alog.values + pad,
**self._wf_pltopts(l, "ps"))
lines.extend([ae_line, ps_line])
legends.extend(["AE l=%s" % str(l), "PS l=%s" % str(l)])
decorate_ax(ax,
xlabel="Energy [Ha]",
ylabel="ATAN(LogDer)",
title="ATAN(Log Derivative)",
lines=lines,
legends=legends)
return fig
def plot_errors_for_structure(self, struct_type, ax=None, **kwargs):
"""
Plot the errors for a given crystalline structure.
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
data = self[self["struct_type"] == struct_type].copy()
if not len(data):
print("No results available for struct_type:", struct_type)
return None
colnames = ["this", "gbrv_paw"]
for col in colnames:
data[col + "_rel_err"] = 100 * (data[col] - data["ae"]) / data["ae"]
#data[col + "_rel_err"] = abs(100 * (data[col] - data["ae"]) / data["ae"])
data.plot(x="formula", y=col + "_rel_err", ax=ax, style="o-", grid=True)
labels = data['formula'].values
ax.set_ylabel("relative error %% for %s" % struct_type)
ticks = list(range(len(data.index)))
ticks1 = range(min(ticks), max(ticks)+1, 2)
ticks2 = range(min(ticks)+1, max(ticks)+1, 2)
labels1 = [labels[i] for i in ticks1]
labels2 = [labels[i] for i in ticks2]
# ax.tick_params(which='both', direction='out')
#ax.set_ylim(-1, 1)
ax.set_xticks(ticks1)
ax.set_xticklabels(labels1, rotation=90)
ax2 = ax.twiny()
ax2.set_zorder(-1)
ax2.set_xticks(ticks2)
ax2.set_xticklabels(labels2, rotation=90)
ax2.set_xlim(ax.get_xlim())
return fig
def plot_hist(self, struct_type, ax=None, errtxt=True, **kwargs):
"""
Histogram plot.
"""
#if codes is None: codes = ["ae"]
ax, fig, plt = get_ax_fig_plt(ax)
import seaborn as sns
codes = ["this", "gbrv_paw"] #, "gbrv_uspp", "pslib", "vasp"]
new = self[self["struct_type"] == struct_type].copy()
ypos = 0.8
for i, code in enumerate(codes):
values = (100 * (new[code] - new["ae"]) / new["ae"]).dropna()
sns.distplot(values, ax=ax, rug=True, hist=False, label=code)
# Add text with Mean or (MARE/RMSRE)
if errtxt:
text = []
app = text.append
#app("%s MARE = %.2f" % (code, values.abs().mean()))
app("%s RMSRE = %.2f" % (code, np.sqrt((values**2).mean())))
ax.text(0.6, ypos, "\n".join(text), transform=ax.transAxes)
ypos -= 0.1
ax.grid(True)
ax.set_xlabel("relative error %")
ax.set_xlim(-0.8, 0.8)
return fig
def plot_eos(self, ax=None, accuracy="normal", **kwargs):
"""
Plot the equation of state.
Args:
ax: matplotlib :class:`Axes` or None if a new figure should be created.
Returns:
`matplotlib` figure.
"""
ax, fig, plt = get_ax_fig_plt(ax)
if not self.has_data(accuracy): return fig
d = self["accuracy"]
num_sites, volumes, etotals = d["num_sites"], np.array(
d["volumes"]), np.array(d["etotals"])
# Perform quadratic fit.
eos = EOS.Quadratic()
eos_fit = eos.fit(volumes / num_sites, etotals / num_sites)
label = "ecut %.1f" % d["ecut"]
eos_fit.plot(ax=ax, text=False, label=label,
show=False) # color=cmap(i/num_ecuts, alpha=1),
return fig
def plot_stacked_hist(self, key="wall_time", nmax=5, ax=None, **kwargs):
"""
Plot stacked histogram of the different timers.
Args:
key: Keyword used to extract data from the timers. Only the first `nmax`
sections with largest value are show.
mmax: Maximum nuber of sections to show. Other entries are grouped together
in the `others` section.
ax: matplotlib :class:`Axes` or None if a new figure should be created.
Returns:
`matplotlib` figure
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
mpi_rank = "0"
timers = self.timers(mpi_rank=mpi_rank)
n = len(timers)
names, values = [], []
rest = np.zeros(n)
for idx, sname in enumerate(self.section_names(ordkey=key)):
sections = self.get_sections(sname)
svals = np.asarray([s.__dict__[key] for s in sections])
if idx < nmax:
names.append(sname)
values.append(svals)
else:
rest += svals
names.append("others (nmax=%d)" % nmax)
values.append(rest)
# The dataset is stored in values. Now create the stacked histogram.
ind = np.arange(n) # the locations for the groups
width = 0.35 # the width of the bars
colors = nmax * ['r', 'g', 'b', 'c', 'k', 'y', 'm']
bars = []
bottom = np.zeros(n)
for idx, vals in enumerate(values):
color = colors[idx]
bar = ax.bar(ind, vals, width, color=color, bottom=bottom)
bars.append(bar)
bottom += vals
ax.set_ylabel(key)
ax.set_title("Stacked histogram with the %d most important sections" % nmax)
ticks = ind + width / 2.0
labels = ["MPI=%d, OMP=%d" % (t.mpi_nprocs, t.omp_nthreads) for t in timers]
ax.set_xticks(ticks)
ax.set_xticklabels(labels, rotation=15)
# Add legend.
ax.legend([bar[0] for bar in bars], names, loc="best")
return fig
def plot_der_potentials(self, ax=None, order=1, **kwargs):
"""
Plot the derivatives of vl and vloc potentials on axis ax.
Used to analyze the derivative discontinuity introduced by the RRKJ method at rc.
"""
ax, fig, plt = get_ax_fig_plt(ax)
from abipy.tools.derivatives import finite_diff
from scipy.interpolate import UnivariateSpline
lines, legends = [], []
for l, pot in self.potentials.items():
# Need linear mesh for finite_difference --> Spline input potentials on lin_rmesh
lin_rmesh, h = np.linspace(pot.rmesh[0], pot.rmesh[-1], num=len(pot.rmesh) * 4, retstep=True)
spline = UnivariateSpline(pot.rmesh, pot.values, s=0)
lin_values = spline(lin_rmesh)
vder = finite_diff(lin_values, h, order=order, acc=4)
line, = ax.plot(lin_rmesh, vder, **self._wf_pltopts(l, "ae"))
lines.append(line)
if l == -1:
legends.append("%s-order derivative Vloc" % order)
else:
legends.append("$s-order derivative PS l=%s" % str(l))
decorate_ax(ax, xlabel="r [Bohr]", ylabel="$D^%s \phi(r)$" % order,
title="Derivative of the ion Pseudopotentials",
lines=lines, legends=legends)
return fig
def cpuwall_histogram(self, ax=None, **kwargs):
ax, fig, plt = get_ax_fig_plt(ax=ax)
nk = len(self.sections)
ind = np.arange(nk) # the x locations for the groups
width = 0.35 # the width of the bars
cpu_times = self.get_values("cpu_time")
rects1 = plt.bar(ind, cpu_times, width, color='r')
wall_times = self.get_values("wall_time")
rects2 = plt.bar(ind + width, wall_times, width, color='y')
# Add ylable and title
ax.set_ylabel('Time (s)')
#if title:
# plt.title(title)
#else:
# plt.title('CPU-time and Wall-time for the different sections of the code')
ticks = self.get_values("name")
ax.set_xticks(ind + width, ticks)
ax.legend((rects1[0], rects2[0]), ('CPU', 'Wall'), loc="best")
return fig
def cpuwall_histogram(self, ax=None, **kwargs):
ax, fig, plt = get_ax_fig_plt(ax=ax)
nk = len(self.sections)
ind = np.arange(nk) # the x locations for the groups
width = 0.35 # the width of the bars
cpu_times = self.get_values("cpu_time")
rects1 = plt.bar(ind, cpu_times, width, color='r')
wall_times = self.get_values("wall_time")
rects2 = plt.bar(ind + width, wall_times, width, color='y')
# Add ylable and title
ax.set_ylabel('Time (s)')
#if title:
# plt.title(title)
#else:
# plt.title('CPU-time and Wall-time for the different sections of the code')
ticks = self.get_values("name")
ax.set_xticks(ind + width, ticks)
ax.legend((rects1[0], rects2[0]), ('CPU', 'Wall'), loc="best")
return fig
def plot_den_formfact(self, ecut=60, ax=None, **kwargs):
"""
Plot the density form factor as function of ecut (Ha units). Return matplotlib Figure.
"""
ax, fig, plt = get_ax_fig_plt(ax)
lines, legends = [], []
for name, rho in self.densities.items():
if name == "rhoC": continue
form = rho.get_intr2j0(ecut=ecut) / (4 * np.pi)
line, = ax.plot(form.mesh, form.values, linewidth=self.linewidth, markersize=self.markersize)
lines.append(line); legends.append(name)
intg = rho.r2f_integral()[-1]
print("r2 f integral: ", intg)
print("form_factor(0): ", name, form.values[0])
# Plot vloc(q)
#for l, pot in self.potentials.items():
# if l != -1: continue
# form = pot.get_intr2j0(ecut=ecut)
# mask = np.where(np.abs(form.values) > 20); form.values[mask] = 20
# line, = ax.plot(form.mesh, form.values, linewidth=self.linewidth, markersize=self.markersize)
# lines.append(line); legends.append("Vloc(q)")
decorate_ax(ax, xlabel="Ecut [Ha]", ylabel="$n(q)$", title="Form factor, l=0 ", lines=lines, legends=legends)
return fig
def cpuwall_histogram(self, ax=None, **kwargs):
"""
Plot histogram with cpu- and wall-time on axis `ax`.
Args:
ax: matplotlib :class:`Axes` or None if a new figure should be created.
Returns: `matplotlib` figure
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
nk = len(self.sections)
ind = np.arange(nk) # the x locations for the groups
width = 0.35 # the width of the bars
cpu_times = self.get_values("cpu_time")
rects1 = plt.bar(ind, cpu_times, width, color='r')
wall_times = self.get_values("wall_time")
rects2 = plt.bar(ind + width, wall_times, width, color='y')
# Add ylable and title
ax.set_ylabel('Time (s)')
# plt.title('CPU-time and Wall-time for the different sections of the code')
ticks = self.get_values("name")
ax.set_xticks(ind + width, ticks)
ax.legend((rects1[0], rects2[0]), ('CPU', 'Wall'), loc="best")
return fig
def plot_projectors(self, ax=None, **kwargs):
"""
Plot oncvpsp projectors on axis ax.
lselect: List to select l channels
"""
ax, fig, plt = get_ax_fig_plt(ax)
lselect = kwargs.get("lselect", [])
linestyle = {1: "solid", 2: "dashed"}
lines, legends = [], []
for nlk, proj in self.projectors.items():
#print(nlk)
if nlk.l in lselect: continue
line, = ax.plot(proj.rmesh,
proj.values,
color=self.color_l.get(nlk.l, 'black'),
linestyle=linestyle[nlk.n],
linewidth=self.linewidth,
markersize=self.markersize)
lines.append(line)
legends.append("Proj %s" % str(nlk))
decorate_ax(ax,
xlabel="r [Bohr]",
ylabel="$p(r)$",
title="Projector Wave Functions",
lines=lines,
legends=legends)
return fig
def plot_hist(self, struct_type, ax=None, errtxt=True, **kwargs):
"""
Histogram plot.
"""
#if codes is None: codes = ["ae"]
ax, fig, plt = get_ax_fig_plt(ax)
import seaborn as sns
codes = ["this", "gbrv_paw"] #, "gbrv_uspp", "pslib", "vasp"]
new = self[self["struct_type"] == struct_type].copy()
ypos = 0.8
for i, code in enumerate(codes):
values = (100 * (new[code] - new["ae"]) / new["ae"]).dropna()
sns.distplot(values, ax=ax, rug=True, hist=False, label=code)
# Add text with Mean or (MARE/RMSRE)
if errtxt:
text = []; app = text.append
#app("%s MARE = %.2f" % (code, values.abs().mean()))
app("%s RMSRE = %.2f" % (code, np.sqrt((values**2).mean())))
ax.text(0.6, ypos, "\n".join(text), transform=ax.transAxes)
ypos -= 0.1
ax.grid(True)
ax.set_xlabel("relative error %")
ax.set_xlim(-0.8, 0.8)
return fig
def plot_stacked_hist(self, key="wall_time", nmax=5, ax=None, **kwargs):
"""Stacked histogram of the different timers."""
ax, fig, plt = get_ax_fig_plt(ax=ax)
mpi_rank = "0"
timers = self.timers(mpi_rank=mpi_rank)
n = len(timers)
names, values = [], []
rest = np.zeros(n)
for idx, sname in enumerate(self.section_names(ordkey=key)):
sections = self.get_sections(sname)
svals = np.asarray([s.__dict__[key] for s in sections])
if idx < nmax:
names.append(sname)
values.append(svals)
else:
rest += svals
names.append("others (nmax = %d)" % nmax)
values.append(rest)
#for (n, vals) in zip(names, values): print(n, vals)
# The dataset is stored in values.
# Now create the stacked histogram.
ind = np.arange(n) # the locations for the groups
width = 0.35 # the width of the bars
# this does not work with matplotlib < 1.0
#plt.rcParams['axes.color_cycle'] = ['r', 'g', 'b', 'c']
colors = nmax * ['r', 'g', 'b', 'c', 'k', 'y', 'm']
bars = []
bottom = np.zeros(n)
for idx, vals in enumerate(values):
color = colors[idx]
bar = plt.bar(ind, vals, width, color=color, bottom=bottom)
bars.append(bar)
bottom += vals
ax.set_ylabel(key)
#ax.title("Stacked histogram for the %d most important sections" % nmax)
labels = [
"MPI = %d, OMP = %d" % (t.mpi_nprocs, t.omp_nthreads)
for t in timers
]
plt.xticks(ind + width / 2.0, labels, rotation=15)
#plt.yticks(np.arange(0,81,10))
ax.legend([bar[0] for bar in bars], names, loc="best")
return fig
def scatter_hist(self, ax=None, **kwargs):
"""
Scatter plot + histogram.
Args:
ax: matplotlib :class:`Axes` or None if a new figure should be created.
Returns: `matplotlib` figure
"""
from mpl_toolkits.axes_grid1 import make_axes_locatable
ax, fig, plt = get_ax_fig_plt(ax=ax)
x = np.asarray(self.get_values("cpu_time"))
y = np.asarray(self.get_values("wall_time"))
# the scatter plot:
axScatter = plt.subplot(1, 1, 1)
axScatter.scatter(x, y)
axScatter.set_aspect("auto")
# create new axes on the right and on the top of the current axes
# The first argument of the new_vertical(new_horizontal) method is
# the height (width) of the axes to be created in inches.
divider = make_axes_locatable(axScatter)
axHistx = divider.append_axes("top", 1.2, pad=0.1, sharex=axScatter)
axHisty = divider.append_axes("right", 1.2, pad=0.1, sharey=axScatter)
# make some labels invisible
plt.setp(axHistx.get_xticklabels() + axHisty.get_yticklabels(),
visible=False)
# now determine nice limits by hand:
binwidth = 0.25
xymax = np.max([np.max(np.fabs(x)), np.max(np.fabs(y))])
lim = (int(xymax / binwidth) + 1) * binwidth
bins = np.arange(-lim, lim + binwidth, binwidth)
axHistx.hist(x, bins=bins)
axHisty.hist(y, bins=bins, orientation="horizontal")
# the xaxis of axHistx and yaxis of axHisty are shared with axScatter,
# thus there is no need to manually adjust the xlim and ylim of these axis.
# axHistx.axis["bottom"].major_ticklabels.set_visible(False)
for tl in axHistx.get_xticklabels():
tl.set_visible(False)
axHistx.set_yticks([0, 50, 100])
# axHisty.axis["left"].major_ticklabels.set_visible(False)
for tl in axHisty.get_yticklabels():
tl.set_visible(False)
axHisty.set_xticks([0, 50, 100])
# plt.draw()
return fig
def plot(self, ax=None, **kwargs):
"""
Plot the histogram with matplotlib, returns `matplotlib` figure.
"""
ax, fig, plt = get_ax_fig_plt(ax)
yy = [len(v) for v in self.values]
ax.plot(self.binvals, yy, **kwargs)
return fig
def plot(self, ax=None, **kwargs):
"""
Plot the histogram with matplotlib, returns `matplotlib` figure.
"""
ax, fig, plt = get_ax_fig_plt(ax)
yy = [len(v) for v in self.values]
ax.plot(self.binvals, yy, **kwargs)
return fig
def plot_ax(self, ax=None, fontsize=12, **kwargs):
"""
Plot the equation of state on axis `ax`
Args:
ax: matplotlib :class:`Axes` or None if a new figure should be created.
fontsize: Legend fontsize.
color (str): plot color.
label (str): Plot label
text (str): Legend text (options)
Returns:
Matplotlib figure object.
"""
# pylint: disable=E1307
ax, fig, plt = get_ax_fig_plt(ax=ax)
color = kwargs.get("color", "r")
label = kwargs.get("label", f"{self.__class__.__name__} fit")
lines = [
"Equation of State: %s" % self.__class__.__name__,
"Minimum energy = %1.2f eV" % self.e0,
"Minimum or reference volume = %1.2f Ang^3" % self.v0,
f"Bulk modulus = {self.b0:1.2f} eV/Ang^3 = {self.b0_GPa:1.2f} GPa",
"Derivative of bulk modulus wrt pressure = %1.2f" % self.b1,
]
text = "\n".join(lines)
text = kwargs.get("text", text)
# Plot input data.
ax.plot(self.volumes, self.energies, linestyle="None", marker="o", color=color)
# Plot eos fit.
vmin, vmax = min(self.volumes), max(self.volumes)
vmin, vmax = (vmin - 0.01 * abs(vmin), vmax + 0.01 * abs(vmax))
vfit = np.linspace(vmin, vmax, 100)
ax.plot(vfit, self.func(vfit), linestyle="dashed", color=color, label=label)
ax.grid(True)
ax.set_xlabel("Volume $\\AA^3$")
ax.set_ylabel("Energy (eV)")
ax.legend(loc="best", shadow=True)
# Add text with fit parameters.
ax.text(
0.5,
0.5,
text,
fontsize=fontsize,
horizontalalignment="center",
verticalalignment="center",
transform=ax.transAxes,
)
return fig
def plot_errors_for_elements(self, ax=None, **kwargs):
"""
Plot the relative errors associated to the chemical elements.
"""
dict_list = []
for idx, row in self.iterrows():
rerr = 100 * (row["this"] - row["ae"]) / row["ae"]
for symbol in set(species_from_formula(row.formula)):
dict_list.append(dict(
element=symbol,
rerr=rerr,
formula=row.formula,
struct_type=row.struct_type,
))
frame = DataFrame(dict_list)
order = sort_symbols_by_Z(set(frame["element"]))
#print_frame(frame)
import seaborn as sns
ax, fig, plt = get_ax_fig_plt(ax=ax)
# Draw violinplot
#sns.violinplot(x="element", y="rerr", order=order, data=frame, ax=ax, orient="v")
# Box plot
ax = sns.boxplot(x="element", y="rerr", data=frame, ax=ax, order=order, whis=np.inf, color="c")
# Add in points to show each observation
sns.stripplot(x="element", y="rerr", data=frame, ax=ax, order=order, hue='struct_type',
# jitter=True, size=5, color=".3", linewidth=0)
jitter=0, size=4, color=".3", linewidth=0, palette=sns.color_palette("muted"))
sns.despine(left=True)
ax.set_ylabel("Relative error %")
labels = ax.get_xticklabels()
ticks = ax.get_xticks()
ticks1 = range(min(ticks), max(ticks)+1, 2)
ticks2 = range(min(ticks) + 1, max(ticks)+1, 2)
labels1 = [labels[i].get_text() for i in ticks1]
labels2 = [labels[i].get_text() for i in ticks2]
# ax.tick_params(which='both', direction='out')
#ax.set_ylim(-1, 1)
ax.set_xticks(ticks1)
ax.set_xticklabels(labels1, rotation=90)
ax2 = ax.twiny()
ax2.set_zorder(-1)
ax2.set_xticks(ticks2)
ax2.set_xticklabels(labels2, rotation=90)
ax2.set_xlim(ax.get_xlim())
ax.grid(True)
return fig
def plot_hints(self, with_soc=False, **kwargs):
# Build pandas dataframe with results.
rows = []
for p in self:
if not p.has_dojo_report:
cprint("Cannot find dojo_report in %s" % p.basename, "magenta")
continue
report = p.dojo_report
row = {att: getattr(p, att) for att in ("basename", "symbol", "Z", "Z_val", "l_max")}
# Get deltafactor data with/without SOC
df_dict = report.get_last_df_results(with_soc=with_soc)
row.update(df_dict)
for struct_type in ["fcc", "bcc"]:
gbrv_dict = report.get_last_gbrv_results(struct_type, with_soc=with_soc)
row.update(gbrv_dict)
# Get the hints
hint = p.hint_for_accuracy(accuracy="normal")
row.update(dict(ecut=hint.ecut, pawecutdg=hint.pawecutdg))
rows.append(row)
import pandas as pd
frame = pd.DataFrame(rows)
def print_frame(x):
import pandas as pd
with pd.option_context('display.max_rows', len(x),
'display.max_columns', len(list(x.keys()))):
print(x)
print_frame(frame)
# Create axes
#import matplotlib.pyplot as plt
import seaborn as sns
ax, fig, plt = get_ax_fig_plt(ax=None)
#order = sort_symbols_by_Z(set(frame["element"]))
# Box plot
ax = sns.boxplot(x="symbol", y="ecut", data=frame, ax=ax, #order=order,
whis=np.inf, color="c")
# Add in points to show each observation
sns.stripplot(x="symbol", y="ecut", data=frame, ax=ax, #order=order,
jitter=True, size=5, color=".3", linewidth=0)
sns.despine(left=True)
ax.set_ylabel("Relative error %")
ax.grid(True)
return fig
def plot_xy_with_hue(data, x, y, hue, decimals=None, ax=None,
xlims=None, ylims=None, fontsize=12, **kwargs):
"""
Plot y = f(x) relation for different values of `hue`.
Useful for convergence tests done wrt to two parameters.
Args:
data: |pandas-DataFrame| containing columns `x`, `y`, and `hue`.
x: Name of the column used as x-value
y: Name of the column used as y-value
hue: Variable that define subsets of the data, which will be drawn on separate lines
decimals: Number of decimal places to round `hue` columns. Ignore if None
ax: |matplotlib-Axes| or None if a new figure should be created.
xlims ylims: Set the data limits for the x(y)-axis. Accept tuple e.g. `(left, right)`
or scalar e.g. `left`. If left (right) is None, default values are used
fontsize: Legend fontsize.
kwargs: Keywork arguments are passed to ax.plot method.
Returns: |matplotlib-Figure|
"""
# Check here because pandas error messages are a bit criptic.
miss = [k for k in (x, y, hue) if k not in data]
if miss:
raise ValueError("Cannot find `%s` in dataframe.\nAvailable keys are: %s" % (str(miss), str(data.keys())))
# Truncate values in hue column so that we can group.
if decimals is not None:
data = data.round({hue: decimals})
ax, fig, plt = get_ax_fig_plt(ax=ax)
for key, grp in data.groupby(hue):
# Sort xs and rearrange ys
xy = np.array(sorted(zip(grp[x], grp[y]), key=lambda t: t[0]))
xvals, yvals = xy[:, 0], xy[:, 1]
label = "{} = {}".format(hue, key)
if not kwargs:
ax.plot(xvals, yvals, 'o-', label=label)
else:
ax.plot(xvals, yvals, label=label, **kwargs)
ax.grid(True)
ax.set_xlabel(x)
ax.set_ylabel(y)
set_axlims(ax, xlims, "x")
set_axlims(ax, ylims, "y")
ax.legend(loc="best", fontsize=fontsize, shadow=True)
return fig
def plot_ene_vs_ecut(self, ax=None, **kwargs):
"""Plot the converge of ene wrt ecut on axis ax."""
ax, fig, plt = get_ax_fig_plt(ax)
lines, legends = [], []
for l, data in self.ene_vs_ecut.items():
line, = ax.plot(data.energies, data.values, **self._wf_pltopts(l, "ae"))
lines.append(line)
legends.append("Conv l=%s" % str(l))
decorate_ax(ax, xlabel="Ecut [Ha]", ylabel="$\Delta E$", title="Energy error per electron [Ha]",
lines=lines, legends=legends)
ax.set_yscale("log")
return fig
def _plot_thermo(self,
func,
temperatures,
factor=1,
ax=None,
ylabel=None,
label=None,
ylim=None,
**kwargs):
"""
Plots a thermodynamic property for a generic function from a PhononDos instance.
Args:
func: the thermodynamic function to be used to calculate the property
temperatures: a list of temperatures
factor: a multiplicative factor applied to the thermodynamic property calculated. Used to change
the units.
ax: matplotlib :class:`Axes` or None if a new figure should be created.
ylabel: label for the y axis
label: label of the plot
ylim: tuple specifying the y-axis limits.
kwargs: kwargs passed to the matplotlib function 'plot'.
Returns:
matplotlib figure
"""
ax, fig, plt = get_ax_fig_plt(ax)
values = []
for t in temperatures:
values.append(func(t, structure=self.structure) * factor)
ax.plot(temperatures, values, label=label, **kwargs)
if ylim:
ax.set_ylim(ylim)
ax.set_xlim((np.min(temperatures), np.max(temperatures)))
ylim = plt.ylim()
if ylim[0] < 0 < ylim[1]:
plt.plot(plt.xlim(), [0, 0], "k-", linewidth=1)
ax.set_xlabel(r"$T$ (K)")
if ylabel:
ax.set_ylabel(ylabel)
return fig
def scatter_hist(self, ax=None, **kwargs):
from mpl_toolkits.axes_grid1 import make_axes_locatable
ax, fig, plt = get_ax_fig_plt(ax=ax)
x = np.asarray(self.get_values("cpu_time"))
y = np.asarray(self.get_values("wall_time"))
# the scatter plot:
axScatter = plt.subplot(1, 1, 1)
axScatter.scatter(x, y)
axScatter.set_aspect("auto")
# create new axes on the right and on the top of the current axes
# The first argument of the new_vertical(new_horizontal) method is
# the height (width) of the axes to be created in inches.
divider = make_axes_locatable(axScatter)
axHistx = divider.append_axes("top", 1.2, pad=0.1, sharex=axScatter)
axHisty = divider.append_axes("right", 1.2, pad=0.1, sharey=axScatter)
# make some labels invisible
plt.setp(axHistx.get_xticklabels() + axHisty.get_yticklabels(), visible=False)
# now determine nice limits by hand:
binwidth = 0.25
xymax = np.max([np.max(np.fabs(x)), np.max(np.fabs(y))])
lim = (int(xymax / binwidth) + 1) * binwidth
bins = np.arange(-lim, lim + binwidth, binwidth)
axHistx.hist(x, bins=bins)
axHisty.hist(y, bins=bins, orientation='horizontal')
# the xaxis of axHistx and yaxis of axHisty are shared with axScatter,
# thus there is no need to manually adjust the xlim and ylim of these axis.
#axHistx.axis["bottom"].major_ticklabels.set_visible(False)
for tl in axHistx.get_xticklabels():
tl.set_visible(False)
axHistx.set_yticks([0, 50, 100])
#axHisty.axis["left"].major_ticklabels.set_visible(False)
for tl in axHisty.get_yticklabels():
tl.set_visible(False)
axHisty.set_xticks([0, 50, 100])
#plt.draw()
return fig
def plot_potentials(self, ax=None, **kwargs):
"""Plot vl and vloc potentials on axis ax"""
ax, fig, plt = get_ax_fig_plt(ax)
lines, legends = [], []
for l, pot in self.potentials.items():
line, = ax.plot(pot.rmesh, pot.values, **self._wf_pltopts(l, "ae"))
lines.append(line)
if l == -1:
legends.append("Vloc")
else:
legends.append("PS l=%s" % str(l))
decorate_ax(ax, xlabel="r [Bohr]", ylabel="$v_l(r)$", title="Ion Pseudopotentials",
lines=lines, legends=legends)
return fig
def plot_ax(self, ax=None, fontsize=12, **kwargs):
"""
Plot the equation of state on axis `ax`
Args:
ax: matplotlib :class:`Axes` or None if a new figure should be created.
fontsize: Legend fontsize.
color (str): plot color.
label (str): Plot label
text (str): Legend text (options)
Returns:
Matplotlib figure object.
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
color = kwargs.get("color", "r")
label = kwargs.get("label", "{} fit".format(self.__class__.__name__))
lines = ["Equation of State: %s" % self.__class__.__name__,
"Minimum energy = %1.2f eV" % self.e0,
"Minimum or reference volume = %1.2f Ang^3" % self.v0,
"Bulk modulus = %1.2f eV/Ang^3 = %1.2f GPa" %
(self.b0, self.b0_GPa),
"Derivative of bulk modulus wrt pressure = %1.2f" % self.b1]
text = "\n".join(lines)
text = kwargs.get("text", text)
# Plot input data.
ax.plot(self.volumes, self.energies, linestyle="None", marker="o", color=color)
# Plot eos fit.
vmin, vmax = min(self.volumes), max(self.volumes)
vmin, vmax = (vmin - 0.01 * abs(vmin), vmax + 0.01 * abs(vmax))
vfit = np.linspace(vmin, vmax, 100)
ax.plot(vfit, self.func(vfit), linestyle="dashed", color=color, label=label)
ax.grid(True)
ax.set_xlabel("Volume $\\AA^3$")
ax.set_ylabel("Energy (eV)")
ax.legend(loc="best", shadow=True)
# Add text with fit parameters.
ax.text(0.5, 0.5, text, fontsize=fontsize, horizontalalignment='center',
verticalalignment='center', transform=ax.transAxes)
return fig
def pie(self, key="wall_time", minfract=0.05, ax=None, **kwargs):
"""
Plot pie chart for this timer.
Args:
key: Keyword used to extract data from the timer.
minfract: Don't show sections whose relative weight is less that minfract.
ax: matplotlib :class:`Axes` or None if a new figure should be created.
Returns: `matplotlib` figure
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
# Set aspect ratio to be equal so that pie is drawn as a circle.
ax.axis("equal")
# Don't show section whose value is less that minfract
labels, vals = self.names_and_values(key, minfract=minfract)
ax.pie(vals, explode=None, labels=labels, autopct="%1.1f%%", shadow=True)
return fig
def plot_pie(self, key="wall_time", minfract=0.05, ax=None, **kwargs):
"""Pie charts of the different timers."""
ax, fig, plt = get_ax_fig_plt(ax=ax)
timers = self.timers()
n = len(timers)
# Make square figures and axes
the_grid = plt.GridSpec(n, 1)
fig = plt.figure(1, figsize=(6, 6))
for idx, timer in enumerate(timers):
plt.subplot(the_grid[idx, 0])
plt.title(str(timer))
timer.pie(key=key, minfract=minfract)
return fig
def plot(self, ax=None, **kwargs):
"""
Plot the evolution of the energies.
Args:
ax (Axes): a matplotlib Axes or None if a new figure should be created.
kwargs: arguments passed to matplotlib plot function.
Returns:
A matplotlib Figure
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
ax.plot(range(self.n_steps), self.total, **kwargs)
ax.set_xlabel("Steps")
ax.set_ylabel("Energy")
return fig
def pie(self, key="wall_time", minfract=0.05, ax=None, **kwargs):
"""
Plot pie chart for this timer.
Args:
key: Keyword used to extract data from the timer.
minfract: Don't show sections whose relative weight is less that minfract.
ax: matplotlib :class:`Axes` or None if a new figure should be created.
Returns:
`matplotlib` figure
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
# Set aspect ratio to be equal so that pie is drawn as a circle.
ax.axis("equal")
# Don't show section whose value is less that minfract
labels, vals = self.names_and_values(key, minfract=minfract)
ax.pie(vals, explode=None, labels=labels, autopct='%1.1f%%', shadow=True)
return fig
def _plot_thermo(self, func, temperatures, factor=1, ax=None, ylabel=None, label=None, ylim=None, **kwargs):
"""
Plots a thermodynamic property for a generic function from a PhononDos instance.
Args:
func: the thermodynamic function to be used to calculate the property
temperatures: a list of temperatures
factor: a multiplicative factor applied to the thermodynamic property calculated. Used to change
the units.
ax: matplotlib :class:`Axes` or None if a new figure should be created.
ylabel: label for the y axis
label: label of the plot
ylim: tuple specifying the y-axis limits.
kwargs: kwargs passed to the matplotlib function 'plot'.
Returns:
matplotlib figure
"""
ax, fig, plt = get_ax_fig_plt(ax)
values = []
for t in temperatures:
values.append(func(t, structure=self.structure) * factor)
ax.plot(temperatures, values, label=label, **kwargs)
if ylim:
ax.set_ylim(ylim)
ax.set_xlim((np.min(temperatures), np.max(temperatures)))
ylim = plt.ylim()
if ylim[0] < 0 < ylim[1]:
plt.plot(plt.xlim(), [0, 0], 'k-', linewidth=1)
ax.set_xlabel(r"$T$ (K)")
if ylabel:
ax.set_ylabel(ylabel)
return fig
def plot_errors_for_structure(self, struct_type, ax=None, **kwargs):
"""
Plot the errors for a given crystalline structure.
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
data = self[self["struct_type"] == struct_type].copy()
if not len(data):
print("No results available for struct_type:", struct_type)
return None
colnames = ["this", "gbrv_paw"]
for col in colnames:
data[col +
"_rel_err"] = 100 * (data[col] - data["ae"]) / data["ae"]
#data[col + "_rel_err"] = abs(100 * (data[col] - data["ae"]) / data["ae"])
data.plot(x="formula",
y=col + "_rel_err",
ax=ax,
style="o-",
grid=True)
labels = data['formula'].values
ax.set_ylabel("relative error %% for %s" % struct_type)
ticks = list(range(len(data.index)))
ticks1 = range(min(ticks), max(ticks) + 1, 2)
ticks2 = range(min(ticks) + 1, max(ticks) + 1, 2)
labels1 = [labels[i] for i in ticks1]
labels2 = [labels[i] for i in ticks2]
# ax.tick_params(which='both', direction='out')
#ax.set_ylim(-1, 1)
ax.set_xticks(ticks1)
ax.set_xticklabels(labels1, rotation=90)
ax2 = ax.twiny()
ax2.set_zorder(-1)
ax2.set_xticks(ticks2)
ax2.set_xticklabels(labels2, rotation=90)
ax2.set_xlim(ax.get_xlim())
return fig
def plot_eos(self, ax=None, accuracy="normal", **kwargs):
"""
Plot the equation of state.
Args:
ax: matplotlib :class:`Axes` or None if a new figure should be created.
Returns:
`matplotlib` figure.
"""
ax, fig, plt = get_ax_fig_plt(ax)
if not self.has_data(accuracy): return fig
d = self["accuracy"]
num_sites, volumes, etotals = d["num_sites"], np.array(d["volumes"]), np.array(d["etotals"])
# Perform quadratic fit.
eos = EOS.Quadratic()
eos_fit = eos.fit(volumes/num_sites, etotals/num_sites)
label = "ecut %.1f" % d["ecut"]
eos_fit.plot(ax=ax, text=False, label=label, show=False) # color=cmap(i/num_ecuts, alpha=1),
return fig
def plot_errors_for_elements(self, ax=None, **kwargs):
"""
Plot the relative errors associated to the chemical elements.
"""
dict_list = []
for idx, row in self.iterrows():
rerr = 100 * (row["this"] - row["ae"]) / row["ae"]
for symbol in set(species_from_formula(row.formula)):
dict_list.append(
dict(
element=symbol,
rerr=rerr,
formula=row.formula,
struct_type=row.struct_type,
))
frame = DataFrame(dict_list)
order = sort_symbols_by_Z(set(frame["element"]))
#print_frame(frame)
import seaborn as sns
ax, fig, plt = get_ax_fig_plt(ax=ax)
# Draw violinplot
#sns.violinplot(x="element", y="rerr", order=order, data=frame, ax=ax, orient="v")
# Box plot
ax = sns.boxplot(x="element",
y="rerr",
data=frame,
ax=ax,
order=order,
whis=np.inf,
color="c")
# Add in points to show each observation
sns.stripplot(
x="element",
y="rerr",
data=frame,
ax=ax,
order=order,
hue='struct_type',
# jitter=True, size=5, color=".3", linewidth=0)
jitter=0,
size=4,
color=".3",
linewidth=0,
palette=sns.color_palette("muted"))
sns.despine(left=True)
ax.set_ylabel("Relative error %")
labels = ax.get_xticklabels()
ticks = ax.get_xticks()
ticks1 = range(min(ticks), max(ticks) + 1, 2)
ticks2 = range(min(ticks) + 1, max(ticks) + 1, 2)
labels1 = [labels[i].get_text() for i in ticks1]
labels2 = [labels[i].get_text() for i in ticks2]
# ax.tick_params(which='both', direction='out')
#ax.set_ylim(-1, 1)
ax.set_xticks(ticks1)
ax.set_xticklabels(labels1, rotation=90)
ax2 = ax.twiny()
ax2.set_zorder(-1)
ax2.set_xticks(ticks2)
ax2.set_xticklabels(labels2, rotation=90)
ax2.set_xlim(ax.get_xlim())
ax.grid(True)
return fig
def plot_efficiency(self, key="wall_time", what="good+bad", nmax=5, ax=None, **kwargs):
"""
Plot the parallel efficiency
Args:
key: Parallel efficiency is computed using the wall_time.
what: Specifies what to plot: `good` for sections with good parallel efficiency.
`bad` for sections with bad efficiency. Options can be concatenated with `+`.
nmax: Maximum number of entries in plot
ax: matplotlib :class:`Axes` or None if a new figure should be created.
================ ====================================================
kwargs Meaning
================ ====================================================
linewidth matplotlib linewidth. Default: 2.0
markersize matplotlib markersize. Default: 10
================ ====================================================
Returns:
`matplotlib` figure
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
lw = kwargs.pop("linewidth", 2.0)
msize = kwargs.pop("markersize", 10)
what = what.split("+")
timers = self.timers()
peff = self.pefficiency()
n = len(timers)
xx = np.arange(n)
#ax.set_color_cycle(['g', 'b', 'c', 'm', 'y', 'k'])
ax.set_prop_cycle(color=['g', 'b', 'c', 'm', 'y', 'k'])
lines, legend_entries = [], []
# Plot sections with good efficiency.
if "good" in what:
good = peff.good_sections(key=key, nmax=nmax)
for g in good:
#print(g, peff[g])
yy = peff[g][key]
line, = ax.plot(xx, yy, "-->", linewidth=lw, markersize=msize)
lines.append(line)
legend_entries.append(g)
# Plot sections with bad efficiency.
if "bad" in what:
bad = peff.bad_sections(key=key, nmax=nmax)
for b in bad:
#print(b, peff[b])
yy = peff[b][key]
line, = ax.plot(xx, yy, "-.<", linewidth=lw, markersize=msize)
lines.append(line)
legend_entries.append(b)
# Add total if not already done
if "total" not in legend_entries:
yy = peff["total"][key]
total_line, = ax.plot(xx, yy, "r", linewidth=lw, markersize=msize)
lines.append(total_line)
legend_entries.append("total")
ax.legend(lines, legend_entries, loc="best", shadow=True)
#ax.set_title(title)
ax.set_xlabel('Total_NCPUs')
ax.set_ylabel('Efficiency')
ax.grid(True)
# Set xticks and labels.
labels = ["MPI=%d, OMP=%d" % (t.mpi_nprocs, t.omp_nthreads) for t in timers]
ax.set_xticks(xx)
ax.set_xticklabels(labels, fontdict=None, minor=False, rotation=15)
return fig
def plot_efficiency(self,
key="wall_time",
what="good+bad",
nmax=5,
ax=None,
**kwargs):
"""
Plot the parallel efficiency
Args:
key: Parallel efficiency is computed using the wall_time.
what: Specifies what to plot: `good` for sections with good parallel efficiency.
`bad` for sections with bad efficiency. Options can be concatenated with `+`.
nmax: Maximum number of entries in plot
ax: matplotlib :class:`Axes` or None if a new figure should be created.
================ ====================================================
kwargs Meaning
================ ====================================================
linewidth matplotlib linewidth. Default: 2.0
markersize matplotlib markersize. Default: 10
================ ====================================================
Returns:
`matplotlib` figure
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
lw = kwargs.pop("linewidth", 2.0)
msize = kwargs.pop("markersize", 10)
what = what.split("+")
timers = self.timers()
peff = self.pefficiency()
n = len(timers)
xx = np.arange(n)
# ax.set_color_cycle(['g', 'b', 'c', 'm', 'y', 'k'])
ax.set_prop_cycle(color=['g', 'b', 'c', 'm', 'y', 'k'])
lines, legend_entries = [], []
# Plot sections with good efficiency.
if "good" in what:
good = peff.good_sections(key=key, nmax=nmax)
for g in good:
# print(g, peff[g])
yy = peff[g][key]
line, = ax.plot(xx, yy, "-->", linewidth=lw, markersize=msize)
lines.append(line)
legend_entries.append(g)
# Plot sections with bad efficiency.
if "bad" in what:
bad = peff.bad_sections(key=key, nmax=nmax)
for b in bad:
# print(b, peff[b])
yy = peff[b][key]
line, = ax.plot(xx, yy, "-.<", linewidth=lw, markersize=msize)
lines.append(line)
legend_entries.append(b)
# Add total if not already done
if "total" not in legend_entries:
yy = peff["total"][key]
total_line, = ax.plot(xx, yy, "r", linewidth=lw, markersize=msize)
lines.append(total_line)
legend_entries.append("total")
ax.legend(lines, legend_entries, loc="best", shadow=True)
# ax.set_title(title)
ax.set_xlabel('Total_NCPUs')
ax.set_ylabel('Efficiency')
ax.grid(True)
# Set xticks and labels.
labels = [
"MPI=%d, OMP=%d" % (t.mpi_nprocs, t.omp_nthreads) for t in timers
]
ax.set_xticks(xx)
ax.set_xticklabels(labels, fontdict=None, minor=False, rotation=15)
return fig
def plot(self, ax=None, **kwargs):
"""
Uses Matplotlib to plot the energy curve.
Args:
ax: :class:`Axes` object. If ax is None, a new figure is produced.
================ ==============================================================
kwargs Meaning
================ ==============================================================
style
color
text
label
================ ==============================================================
Returns:
Matplotlib figure.
"""
ax, fig, plt = get_ax_fig_plt(ax)
vmin, vmax = self.volumes.min(), self.volumes.max()
emin, emax = self.energies.min(), self.energies.max()
vmin, vmax = (vmin - 0.01 * abs(vmin), vmax + 0.01 * abs(vmax))
emin, emax = (emin - 0.01 * abs(emin), emax + 0.01 * abs(emax))
color = kwargs.pop("color", "r")
label = kwargs.pop("label", None)
# Plot input data.
ax.plot(self.volumes,
self.energies,
linestyle="None",
marker="o",
color=color) #, label="Input Data")
# Plot EOS.
vfit = np.linspace(vmin, vmax, 100)
if label is None:
label = self.name + ' fit'
if self.eos_name == "deltafactor":
xx = vfit**(-2. / 3.)
ax.plot(vfit,
np.polyval(self.eos_params, xx),
linestyle="dashed",
color=color,
label=label)
else:
ax.plot(vfit,
self.func(vfit, *self.eos_params),
linestyle="dashed",
color=color,
label=label)
# Set xticks and labels.
ax.grid(True)
ax.set_xlabel("Volume $\AA^3$")
ax.set_ylabel("Energy (eV)")
ax.legend(loc="best", shadow=True)
# Add text with fit parameters.
if kwargs.pop("text", True):
text = []
app = text.append
app("Min Volume = %1.2f $\AA^3$" % self.v0)
app("Bulk modulus = %1.2f eV/$\AA^3$ = %1.2f GPa" %
(self.b0, self.b0_GPa))
app("B1 = %1.2f" % self.b1)
fig.text(0.4, 0.5, "\n".join(text), transform=ax.transAxes)
return fig
