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Fixed a compatibility issue in the plotting tool that could cause the…
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… plotting tool to fail with the error "AttributeError: 'module' object has no attribute '_cmapnames'" in some cases. Many thanks to Ryuichi Arafune (from MANA and NIMS) and C.H. Lee (from the National Cheng-Chi University, Taiwan), for having contacted me about this problem. Special thanks to Ryuichi Arafune, for suggesting a solution.
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Paulo V C Medeiros committed Jan 30, 2015
1 parent da7bde2 commit 112b16a
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2 changes: 1 addition & 1 deletion README
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ System requirements:
* Might work in other environments based on Unix
* Fortran 90 and C compilers
* Preferably Intel compilers (ifort and icc), version 12.1.4 (or higher)
* Python 2.7.x for the post-processing utilities
* Python 2.7 (or higher) for the post-processing utilities
* You will need to have the following packages installed
(you probably already have most of them):
* numpy
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2 changes: 1 addition & 1 deletion src/general_io_mod.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ module general_io
file_for_pc_reduced_to_prim_cell, file_for_SC_reduced_to_prim_cell

integer, parameter :: str_len=256
character(len=30), parameter :: package_version="2.5.0, 2015-01-28"
character(len=30), parameter :: package_version="2.5.1, 2015-01-30"
character(len=str_len), parameter :: file_header_BandUP="# File created by BandUP - &
Band Unfolding code for &
Plane-wave based calculations, &
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142 changes: 69 additions & 73 deletions utils/post_unfolding/plot/plot_unfolded_EBS_BandUP.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
#! /usr/bin/env python
# Copyright (C) 2013, 2014 Paulo V. C. Medeiros, Jonas Bjork
# Copyright (C) 2013-2015 Paulo V. C. Medeiros, Jonas Bjork
# This file is part of BandUP: Band Unfolding code for Plane-wave based calculations.
#
# BandUP is free software: you can redistribute it and/or modify
Expand All @@ -15,6 +15,7 @@
# You should have received a copy of the GNU General Public License
# along with BandUP. If not, see <http://www.gnu.org/licenses/>.
from __future__ import division
from __future__ import print_function
import argparse
from scipy.interpolate import griddata
import numpy as np
Expand Down Expand Up @@ -175,11 +176,7 @@ def __init__(self):


def get_available_cmaps(self):
colormap_names = []
for m in plt.cm._cmapnames:
colormap_names.append(m)
if(m + '_r' in dir(plt.cm)):
colormap_names.append(m + '_r')
colormap_names = sorted([m for m in plt.cm.datad], key=str.lower)
colormaps = dict([[cmap_name, plt.get_cmap(cmap_name)] for cmap_name in colormap_names])
# Custom colormaps - I'm still testing
try:
Expand Down Expand Up @@ -248,8 +245,8 @@ def __init__(self, plot_options):
if(not args.no_symm_lines or not args.no_symm_labels):
self.pos_high_symm_points, self.labels_high_symm_lines = self.get_pos_and_labels_high_symm_points()
if(not args.no_symm_lines):
print 'Vertical lines will be automatically drawn at: k = %s' \
% ', '.join(map("{:9.5f}".format, self.pos_high_symm_points))
print ('Vertical lines will be automatically drawn at: k = %s' \
% ', '.join(map("{:9.5f}".format, self.pos_high_symm_points)))

self.title = ''
self.x_axis_label = ''
Expand Down Expand Up @@ -310,7 +307,7 @@ def __init__(self, plot_options):
else:
self.fig_height_inches = self.fig_width_inches / args.aspect_ratio
if(not args.portrait and not args.running_from_GUI):
print 'Assuming portrait orientation for the output figure.'
print ('Assuming portrait orientation for the output figure.')

def __color_E_f_and_high_symm_lines(self, image, args_linecolor):
# Defining the colors of the vertical and horizontal lines.
Expand All @@ -332,7 +329,7 @@ def color_high_symm_lines(self, image):


def read_BandUP_output(self):
print 'Reading input file "%s"' % self.args.input_file
print ('Reading input file "%s"' % self.args.input_file)

spin_projections = None
spin_projections_read = False
Expand All @@ -359,26 +356,26 @@ def read_BandUP_output(self):
if(not spin_projections_read):
KptsCoords, energies, delta_Ns = np.loadtxt(self.args.input_file, usecols=(0,1,2),unpack=True)
if(failed_reading_spin_projections):
print self.indent + 'WARNING: Could not read spin info.'
print (self.indent + 'WARNING: Could not read spin info.')


print self.indent + '* Max. delta_N: ' + "{:7.3f}".format(np.max(delta_Ns))
print self.indent + '* Min. non-zero delta_N: ' + "{:7.3f}".format(min([value for value in delta_Ns if abs(value) > 0.95E-3]))
print (self.indent + '* Max. delta_N: ' + "{:7.3f}".format(np.max(delta_Ns)))
print (self.indent + '* Min. non-zero delta_N: ' + "{:7.3f}".format(min([value for value in delta_Ns if abs(value) > 0.95E-3])))
if(spin_projections is not None):
print self.indent + 'Plotting also spin info (projections of the expectation values of Pauli matrices, still under test!).'
print 2 * self.indent + '* Maxval of the projections: ' + \
"{:7.3f}".format(np.max(spin_projections))
print (self.indent + 'Plotting also spin info (projections of the expectation values of Pauli matrices).')
print (2 * self.indent + '* Maxval of the projections: ' + \
"{:7.3f}".format(np.max(spin_projections)))
try:
min_proj = min([value for value in spin_projections if abs(value) > 0.95E-3])
except ValueError:
min_proj = 0.0
print 2 * self.indent + '* Minval of the projections:' + \
"{:7.3f}".format(min_proj)
print (2 * self.indent + '* Minval of the projections:' + \
"{:7.3f}".format(min_proj))
if(abs(min_proj) > 0.95E-3 or abs(np.max(spin_projections)) > 0.95E-3):
print 2 * self.indent + '* Positive projection values will be shown in blue.'
print 2 * self.indent + '* Negative projection values will be shown in red.'
print (2 * self.indent + '* Positive projection values will be shown in blue.')
print (2 * self.indent + '* Negative projection values will be shown in red.')

print 'Eliminating duplicated points...'
print ('Eliminating duplicated points...')
sorted_index_data = np.lexsort((energies, KptsCoords))
KptsCoords = KptsCoords[sorted_index_data] + self.args.shift_kpts_coords
energies = energies[sorted_index_data] + self.args.shift_energy
Expand Down Expand Up @@ -424,7 +421,7 @@ def read_BandUP_output(self):
spin_projections = np.array(new_spin_projections)
else:
spin_projections = None
print self.indent + '* Done with eliminating duplicated points.'
print (self.indent + '* Done with eliminating duplicated points.')

return KptsCoords, energies, delta_Ns, spin_projections

Expand All @@ -433,7 +430,7 @@ def reduced_read_data(self):
size_of_old_data = float(len(self.KptsCoords))
if(self.kmin>self.KptsCoords.min() or self.kmax<self.KptsCoords.max() or
self.emin>self.energies.min() or self.emax<self.energies.max()):
print 'Trying to reduce data such that only the needed part of it is parsed.'
print ('Trying to reduce data such that only the needed part of it is parsed.')
new_KptsCoords = []
new_energies = []
new_delta_Ns = []
Expand All @@ -452,9 +449,8 @@ def reduced_read_data(self):
if(new_spin_projections):
spin_projections = np.array(new_spin_projections)
size_of_new_data = float(len(KptsCoords))
print self.indent + '* Done. Working with %.2f' % (100.0*size_of_new_data/size_of_old_data), \
'% of the data read in.'

print (self.indent + '* Done. Working with %.2f' % (100.0*size_of_new_data/size_of_old_data), \
'% of the data read in.')
return KptsCoords, energies, delta_Ns, spin_projections


Expand Down Expand Up @@ -500,10 +496,10 @@ def define_plot_boundaries(self):
kmin, kmax = kmax, kmin
if(kmin < self.KptsCoords.min()):
kmin = self.KptsCoords.min()
print 'WARNING: Resetting k_min to %s.' % "{:9.5f}".format(kmin)
print ('WARNING: Resetting k_min to %s.' % "{:9.5f}".format(kmin))
if(kmax > self.KptsCoords.max()):
kmax = self.KptsCoords.max()
print 'WARNING: Resetting k_max to %s.' % "{:9.5f}".format(kmax)
print ('WARNING: Resetting k_max to %s.' % "{:9.5f}".format(kmax))
if emin > emax:
emin, emax = emax, emin
# Setting emin and emax to the nearest values in the energy grid
Expand Down Expand Up @@ -613,20 +609,20 @@ def get_pos_and_labels_high_symm_points(self):
for idir in range(ndirections):
if(coords_type[0].upper() == 'C'):
if(not a0_informed_in_kpts_file):
print 'ERROR: You have selected cartesian coordinates in your input k-points file, ' \
'but you have not passed a scaling parameter "a0".'
print ' The actuall coordiates of the k-points are given by: '\
'ki[actual] = two_pi*ki[passed in file]/a0.'
print ' Please write the value of a0 after your tag "' + \
coords_type + '", and run the code again.'
print 'Stopping now.'
print ('ERROR: You have selected cartesian coordinates in your input k-points file, ' \
'but you have not passed a scaling parameter "a0".')
print (' The actuall coordiates of the k-points are given by: '\
'ki[actual] = two_pi*ki[passed in file]/a0.')
print (' Please write the value of a0 after your tag "' + \
coords_type + '", and run the code again.')
print ('Stopping now.')
sys.exit(0)
k_start[idir] = (2.0*np.pi)*read_k_start[idir]/latt_param_kpts_file
k_end[idir] = (2.0*np.pi)*read_k_end[idir]/latt_param_kpts_file
else:
if((coords_type[0].upper() != 'R') and (idir==0)):
print 'WARNING: Assuming that the pc-kpts have been informed in '\
'fractional (reciprocal) coordinates.'
print ('WARNING: Assuming that the pc-kpts have been informed in '\
'fractional (reciprocal) coordinates.')
for i in range(3):
k_start[idir] += read_k_start[idir,i]*b_matrix_pc[i]
k_end[idir] += read_k_end[idir,i]*b_matrix_pc[i]
Expand Down Expand Up @@ -692,20 +688,20 @@ def make_plot(plot):
indent = plot.plot_options.indent
args = plot.plot_options.args
# Creating the plot
print 'Generating the plot...'
print ('Generating the plot...')
fig = plt.figure(figsize=(plot.fig_width_inches,plot.fig_height_inches))
ax = fig.add_subplot(111)
# Defining the color schemes.
print indent + '>>> Using the "' + plot.cmap_name + '" colormap.'
print (indent + '>>> Using the "' + plot.cmap_name + '" colormap.')
if(plot.plot_options.using_default_cmap and not args.running_from_GUI):
print 2 * indent + 'Tip: You can try different colormaps by either:'
print 2 * indent + ' * Running the plot tool with the option -icmap n, ' \
'with n in the range from 0 to', len(plot.plot_options.cmaps) - 1
print 2 * indent + ' * Running the plot tool with the option "-cmap cmap_name".'
print 2 * indent + '> Take a look at'
print 4 * indent + '<http://matplotlib.org/examples/color/colormaps_reference.html>'
print 2 * indent + ' for a list of colormaps, or run'
print 4 * indent + '"./plot_unfolded_EBS_BandUP.py --help".'
print (2 * indent + 'Tip: You can try different colormaps by either:')
print (2 * indent + ' * Running the plot tool with the option -icmap n, ' \
'with n in the range from 0 to', len(plot.plot_options.cmaps) - 1)
print (2 * indent + ' * Running the plot tool with the option "-cmap cmap_name".')
print (2 * indent + '> Take a look at')
print (4 * indent + '<http://matplotlib.org/examples/color/colormaps_reference.html>')
print (2 * indent + ' for a list of colormaps, or run')
print (4 * indent + '"./plot_unfolded_EBS_BandUP.py --help".')

# Building the countour plot from the read data
# Defining the (ki,Ej) grid.
Expand Down Expand Up @@ -738,24 +734,24 @@ def make_plot(plot):
if(manually_normalize_colorbar_min_and_maxval or not args.disable_auto_round_vmin_and_vmax):
modified_vmin_or_vmax = False
if not args.disable_auto_round_vmin_and_vmax and not args.running_from_GUI:
print plot.indent + '* Automatically renormalizing color scale '\
'(you can disable this with the option --disable_auto_round_vmin_and_vmax):'
print (plot.indent + '* Automatically renormalizing color scale '\
'(you can disable this with the option --disable_auto_round_vmin_and_vmax):')
if manually_normalize_colorbar_min_and_maxval:
print plot.indent + '* Manually renormalizing color scale'
print (plot.indent + '* Manually renormalizing color scale')
if(minval_for_colorbar is not None):
previous_vmin = np.min(grid_freq)
if(abs(previous_vmin - minval_for_colorbar) >= 0.1):
modified_vmin_or_vmax = True
print 2 * indent + 'Previous vmin = %.1f, new vmin = %.1f' % (previous_vmin,
minval_for_colorbar)
print (2 * indent + 'Previous vmin = %.1f, new vmin = %.1f' % (previous_vmin,
minval_for_colorbar))
else:
minval_for_colorbar = np.min(grid_freq)
if(maxval_for_colorbar is not None):
previous_vmax = np.max(grid_freq)
if(abs(previous_vmax - maxval_for_colorbar) >= 0.1):
modified_vmin_or_vmax = True
print 2 * indent + 'Previous vmax = %.1f, new vmax = %.1f' % (previous_vmax,
maxval_for_colorbar)
print (2 * indent + 'Previous vmax = %.1f, new vmax = %.1f' % (previous_vmax,
maxval_for_colorbar))
else:
maxval_for_colorbar = np.max(grid_freq)
if(modified_vmin_or_vmax):
Expand All @@ -767,13 +763,13 @@ def make_plot(plot):
v = np.linspace(minval_for_colorbar, maxval_for_colorbar, args.n_levels, endpoint=True)
else:
v = np.linspace(np.min(grid_freq), np.max(grid_freq), args.n_levels, endpoint=True)
print indent + '* Drawing contour plot...'
print 2 * indent + '> Using %i color levels. Use the option "--n_levels" to choose a different number.' %args.n_levels
print (indent + '* Drawing contour plot...')
print (2 * indent + '> Using %i color levels. Use the option "--n_levels" to choose a different number.' %args.n_levels)
image = ax.contourf(ki, Ei, grid_freq, levels=v, cmap=plot.cmap)

plot_spin_proj_requested = args.plot_spin_perp or args.plot_spin_para or args.plot_sigma_x or args.plot_sigma_y or args.plot_sigma_z
if(plot_spin_proj_requested and plot.spin_projections is not None):
print indent + '* Drawing spin projection info (still under test!)'
print (indent + '* Drawing spin projection info')
cmap_for_spin_plot = [plt.cm.bwr, plt.cm.RdBu, plt.cm.seismic_r][0]

if(args.clip_spin is None):
Expand All @@ -782,8 +778,8 @@ def make_plot(plot):
else:
vmax_spin = abs(args.clip_spin)
vmin_spin = -1.0 * abs(args.clip_spin)
print 2 * indent + '* New maxval for spin: %.2f' % vmax_spin
print 2 * indent + '* New minval for spin: %.2f' % vmin_spin
print (2 * indent + '* New maxval for spin: %.2f' % vmax_spin)
print (2 * indent + '* New minval for spin: %.2f' % vmin_spin)

spin_projections = np.clip(plot.spin_projections, vmin_spin, vmax_spin)
grid_freq_spin = griddata((plot.KptsCoords, plot.energies), spin_projections, (ki[None,:], Ei[:,None]),
Expand All @@ -810,7 +806,7 @@ def make_plot(plot):
linewidth=[100.0 * plot.dE_for_hist2d * (item ** 2) for item in spin_projections_for_scatter],
c=spin_projections_for_scatter, cmap=cmap_for_spin_plot)
else:
print 2 * indent + '* The abs values of the spin projections were all < 1E-3.'
print (2 * indent + '* The abs values of the spin projections were all < 1E-3.')

#Preparing the plot
ax.set_xlim(plot.kmin, plot.kmax)
Expand All @@ -833,10 +829,10 @@ def make_plot(plot):
plot.pos_high_symm_points[i] in x_tiks_positions]
x_tiks_labels = [xlabel for xlabel in x_tiks_labels if xlabel]
if x_tiks_labels:
print indent + '* K-point labels read from the "' + args.kpoints_file + '" file:'
print (indent + '* K-point labels read from the "' + args.kpoints_file + '" file:')
for ilabel in range(len(x_tiks_labels)):
print 2 * indent + "k = {:9.5f}".format(x_tiks_positions[ilabel]) + ', label =',\
x_tiks_labels[ilabel]
print(2 * indent + "k = {:9.5f}".format(x_tiks_positions[ilabel]) + ', label =',\
x_tiks_labels[ilabel])
plt.xticks(x_tiks_positions, x_tiks_labels, fontsize=plot.tick_marks_size)
else:
plot.x_axis_label = '$k \hspace{0.25} (\AA^{-1})$'
Expand Down Expand Up @@ -900,24 +896,24 @@ def make_plot(plot):
if(args.output_file is None):
args.output_file = abspath(default_out_basename + '.' + args.file_format)

print 'Savig figure to file "%s" ...' % args.output_file
print ('Savig figure to file "%s" ...' % args.output_file)
if(args.fig_resolution[0].upper() == 'H'):
print indent + '* High-resolution figure (600 dpi).'
print (indent + '* High-resolution figure (600 dpi).')
fig_resolution_in_dpi = 600
elif (args.fig_resolution[0].upper() == 'M'):
print indent + '* Medium-resolution figure (300 dpi).'
print (indent + '* Medium-resolution figure (300 dpi).')
fig_resolution_in_dpi = 300
elif (args.fig_resolution[0].upper() == 'L'):
print indent + '* Low-resolution figure (100 dpi).'
print (indent + '* Low-resolution figure (100 dpi).')
fig_resolution_in_dpi = 100
else:
print indent + 'Assuming medium-resolution (300 dpi) for the figure.'
print (indent + 'Assuming medium-resolution (300 dpi) for the figure.')
fig_resolution_in_dpi = 300
plt.savefig(args.output_file, dpi=fig_resolution_in_dpi, bbox_inches='tight')
print indent + '* Done saving figure (%s).' % args.output_file
print (indent + '* Done saving figure (%s).' % args.output_file)

if args.saveshow:
print 'Opening saved figure (%s)...' % default_out_basename
print ('Opening saved figure (%s)...' % default_out_basename)
# 'xdg-open' might fail to find the defualt program in some systems
# For such cases, one can try to use other alternatives (just add more to the list below)
image_viewer_list = ['xdg-open', 'eog']
Expand All @@ -928,12 +924,12 @@ def make_plot(plot):
if(success_opening_file):
break
if(not success_opening_file):
print indent + '* Failed (%s): no image viewer detected.' % default_out_basename
print (indent + '* Failed (%s): no image viewer detected.' % default_out_basename)

if args.show:
print 'Showing figure (%s)...' % default_out_basename
print ('Showing figure (%s)...' % default_out_basename)
plt.show()
print indent + '* Done showing figure (%s).' % default_out_basename
print (indent + '* Done showing figure (%s).' % default_out_basename)


if __name__ == '__main__':
Expand Down

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