From c5257df782709880f80b56b37cfecc1384147538 Mon Sep 17 00:00:00 2001 From: "Kieran B. Spooner" Date: Tue, 28 Mar 2023 09:30:00 +0100 Subject: [PATCH] fix uniform colour bug, update website --- docs/.doctrees/dos.doctree | Bin 8232 -> 9448 bytes docs/.doctrees/environment.pickle | Bin 443024 -> 445890 bytes docs/.doctrees/prophon.doctree | Bin 10708 -> 13109 bytes docs/.doctrees/tp.data.doctree | Bin 190554 -> 200265 bytes docs/.doctrees/tp.plot.doctree | Bin 723433 -> 725000 bytes docs/_modules/tp/data/load.html | 116 ++++++++++++++++++++++++----- docs/_modules/tp/plot/colour.html | 2 +- docs/_modules/tp/plot/phonons.html | 20 +++-- docs/_modules/tp/settings.html | 8 ++ docs/avg-rates.html | 5 +- docs/cumkappa.html | 1 + docs/dos.html | 51 +++++++++++++ docs/genindex.html | 10 ++- docs/objects.inv | Bin 1687 -> 1702 bytes docs/phonons.html | 1 + docs/prophon.html | 10 +++ docs/searchindex.js | 2 +- docs/tp.data.html | 43 +++++++++++ docs/tp.plot.html | 5 +- docs/waterfalls.html | 5 +- tp/plot/colour.py | 2 +- 21 files changed, 245 insertions(+), 36 deletions(-) diff 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--- a/docs/_modules/tp/data/load.html +++ b/docs/_modules/tp/data/load.html @@ -759,33 +759,25 @@

Source code for tp.data.load

 
     x = [d['distance'] for d in data['phonon']]
     qp = [q['q-position'] for q in data['phonon']]
-    d2, ticks = get_path(data)
-    eigs = [[b['frequency'] for b in p['band']] for p in data['phonon']]
-
-    # scale data to other path
+    tickpos, ticks = get_path(data)
+    f = [[b['frequency'] for b in p['band']] for p in data['phonon']]
 
     if xdata is not None:
-        d1 = xdata['tick_position']
-        n = 0
-        for i, d0 in enumerate(x):
-            while n <= len(d2) and not (d0 >= d2[n] and d0 <= d2[n+1]):
-                n += 1
-            x[i] = d1[n] + ((d0 - d2[n]) * (d1[n+1] - d1[n]) / \
-                                           (d2[n+1] - d2[n]))
-    else:
-        d1 = d2
+        # scale data to other path
+        x = scale_to_path(x, tickpos, xdata['tick_position'])
+        tickpos = xdata['tick_position']
 
     units = tp.settings.units()
     dimensions = settings.dimensions()
     data2 = {'x':             x,
              'qpoint':        qp,
-             'frequency':     eigs,
-             'tick_position': d1,
+             'frequency':     f,
+             'tick_position': tickpos,
              'tick_label':    ticks,
              'meta':
                  {'phonon_dispersion_source': 'phonopy',
-                     'units':      {'frequency': units['frequency']},
-                     'dimensions': {'frequency': dimensions['frequency']}}}
+                  'units':      {'frequency': units['frequency']},
+                  'dimensions': {'frequency': dimensions['frequency']}}}
 
     for c in pconversions:
         if c in data2:
@@ -879,6 +871,61 @@ 
Source code for tp.data.load
 
     return data2

 
+
[docs]def phonopy_gruneisen(filename):
+    """Loads phonopy gruneisen data.
+
+    Does not load path data, but can load from files with a q-point
+    path, which will often be preferable if projecting onto a phonon
+    dispersion.
+
+    Arguments
+    ---------
+
+        filename : str
+            phonopy gruneisen.yaml filepath.
+
+    Returns
+    -------
+
+        dict
+            gruneisen data.
+    """
+
+    import yaml
+
+    pconversions = settings.phonopy_conversions()
+    conversions = settings.conversions()
+
+    # load data
+
+    with open(filename, 'r') as f:
+        data = yaml.safe_load(f)
+    
+    x = np.ravel([[q['distance'] for q in path['phonon']] for path in data['path']])
+    qp = np.ravel([[q['q-position'] for q in path['phonon']] for path in data['path']])
+    g = [[[band['gruneisen'] for band in q['band']] for q in path['phonon']] for path in data['path']]
+    g = np.reshape(g, (-1, np.shape(g)[-1]))
+
+    units = tp.settings.units()
+    dimensions = settings.dimensions()
+    data2 = {'x':             x,
+             'qpoint':        qp,
+             'gruneisen':     g,
+             'meta':
+                 {'gruneisen_source': 'phonopy',
+                  'units':      {'gruneisen': units['gruneisen']},
+                  'dimensions': {'gruneisen': dimensions['gruneisen']}}}
+
+    for c in pconversions:
+        if c in data2:
+            data2[c] = np.multiply(data2[c], float(pconversions[c]))
+
+    for c in conversions:
+        if c in data2:
+            data2[c] = np.multiply(data2[c], float(conversions[c]))
+
+    return data2

+
 
[docs]def get_path(yamldata):
     """Extracts the path from a phonopy yaml.
 
@@ -912,6 +959,41 @@ 
Source code for tp.data.load
              '$\mathregular{{{}}}$'.format(i.strip('$')) for i in ticks]
 
     return tickpos, ticks

+
+
[docs]def scale_to_path(x, tickpos, scalepos):
+    """Scales data to a path.
+
+    Useful to make different phonopy runs fit together or to map
+    gruneisen data on a phonon dispersion.
+
+    Arguments
+    ---------
+
+        x : list
+            wavevector ordinates.
+        tickpos : list
+            tick wavevectors for scaling.
+        scalepos : list
+            scale tick wavevectors.
+
+    Returns
+    -------
+
+        list
+            wavevector ordinates.
+    """
+
+    n = 0
+    # for each x, while within data and between two high-symmetry
+    # points, interpolate onto scale data
+    for i in range(len(x)):
+        while n <= len(tickpos) and \
+              not (x[i] >= tickpos[n] and x[i] <= tickpos[n+1]):
+            n += 1
+        x[i] = scalepos[n] + ((x[i] - tickpos[n]) * (scalepos[n+1] - scalepos[n]) / \
+                             (tickpos[n+1] - tickpos[n]))
+
+    return x
diff --git a/docs/_modules/tp/plot/colour.html b/docs/_modules/tp/plot/colour.html index 6fc504f..c84d14d 100644 --- a/docs/_modules/tp/plot/colour.html +++ b/docs/_modules/tp/plot/colour.html @@ -164,7 +164,7 @@

Source code for tp.plot.colour

     cmid = np.array(to_rgba(cmid, alpha))
     cnorm = (cmid[:3] - cmin[:3]) / (cmax[:3] - cmin[:3])
     # pythagoras
-    midpoint = np.sqrt((cnorm[0]**2 + cnorm[1]**2 + cnorm[2]**2)/3)
+    midpoint = np.sqrt(cnorm[0]**2 + cnorm[1]**2 + cnorm[2]**2)/3
     x = [0, midpoint, 1]
     y = [cmin, cmid, cmax]
     x2 = np.linspace(0, 1, density)
diff --git a/docs/_modules/tp/plot/phonons.html b/docs/_modules/tp/plot/phonons.html
index 4990b7b..9c38de6 100644
--- a/docs/_modules/tp/plot/phonons.html
+++ b/docs/_modules/tp/plot/phonons.html
@@ -432,8 +432,8 @@ 
Source code for tp.plot.phonons
 
[docs]@tp.docstring_replace(workers=str(workers))
 def add_alt_dispersion(ax, data, pdata, quantity, bandmin=None, bandmax=None,
                        temperature=300, direction='avg', label=['Longitudinal',
-                       'Transverse_1', 'Transverse_2', 'Optic'],
-                       poscar='POSCAR', main=True, log=False,
+                       'Transverse$_1$', 'Transverse$_2$', 'Optic'],
+                       poscar='POSCAR', scatter=False, main=True, log=False,
                        interpolate=10000, smoothing=5, colour=['#44ffff',
                        '#ff8044', '#ff4444', '#00000010'], linestyle='-',
                        marker=None, workers=workers, xmarkkwargs={}, verbose=False,
@@ -487,8 +487,10 @@ 
Source code for tp.plot.phonons
             labels per line. A single dataset could have a single label,
             or the default labels the lines by type. You'll want to
             change this if a minimum band index is set.
-            Default: ['Longitudinal', 'Transverse_1', 'Transverse_2',
+            Default: ['Longitudinal', 'Transverse$_1$', 'Transverse$_2$',
             'Optic'].
+        scatter : bool, optional
+            plot scatter rather than line graph. Default: False.
 
         poscar : str, optional
             VASP POSCAR filepath. Default: POSCAR.
@@ -625,8 +627,8 @@ 
Source code for tp.plot.phonons
     y2 = np.abs(yinterp(x2))
     ysort = np.ravel(y2)
     ysort = ysort[ysort.argsort()]
-    ymin = ysort[int(round(len(ysort)/100, 0))]
-    ymax = ysort[-1]
+    ymin = ysort[int(round(len(ysort)/100 - 1, 0))]
+    ymax = ysort[int(round(len(ysort)*99.9/100 - 1, 0))]
 
     # line appearance
 
@@ -641,8 +643,12 @@ 
Source code for tp.plot.phonons
     # plotting
 
     for n in range(len(y2[0])):
-        ax.plot(x2, y2[:,n], color=colour[n], linestyle=linestyle[n],
-                label=label[n], marker=marker[n], **kwargs)
+        if scatter:
+            ax.scatter(x2, y2[:,n], color=colour[n], linestyle=linestyle[n],
+                       label=label[n], marker=marker[n], **kwargs)
+        else:
+            ax.plot(x2, y2[:,n], color=colour[n], linestyle=linestyle[n],
+                    label=label[n], marker=marker[n], **kwargs)
 
     # axes formatting
 
diff --git a/docs/_modules/tp/settings.html b/docs/_modules/tp/settings.html
index 80d3d1e..12e5311 100644
--- a/docs/_modules/tp/settings.html
+++ b/docs/_modules/tp/settings.html
@@ -374,6 +374,7 @@ 
Source code for tp.settings
              'frequency':                       'THz',
              'gamma':                           'THz',
              'group_velocity':                  'm s-1',
+             'gruneisen':                       '',
              'gv_by_gv':                        'm2 s-2',
              'hall_carrier_concentration':      'cm-3',
              'heat_capacity':                   'J K-1',
@@ -423,6 +424,7 @@ 
Source code for tp.settings
             'frequency':                       ['qpoint', 'band'],
             'gamma':                           ['temperature', 'qpoint', 'band'],
             'group_velocity':                  ['qpoint', 'band', 3],
+            'gruneisen':                       ['qpoint', 'band'],
             'gv_by_gv':                        ['qpoint', 'band', 6],
             'hall_carrier_concentration':      [],
             'heat_capacity':                   ['temperature', 'qpoint', 'band'],
@@ -545,6 +547,8 @@ 
Source code for tp.settings
                   'Imaginary Self Energy (THz)',
               'group_velocity':
                   'Group Velocity (m s$\mathregular{^{-1}}$)',
+              'gruneisen':
+                  'Gruneisen Parameter',
               'gv_by_gv':
                   'Group Velocity Outer Product (m$\mathregular{^2\ s^{-2}}$)',
               'heat_capacity':
@@ -623,6 +627,8 @@ 
Source code for tp.settings
                   'Imaginary Self Energy (THz)',
               'group_velocity':
                   'Group Velocity (m s$\mathregular{^{-1}}$)',
+              'gruneisen':
+                  'Gruneisen Parameter',
               'gv_by_gv':
                   'Group Vel. Outer Prod. (m$\mathregular{^2\ s^{-2}}$)',
               'heat_capacity':
@@ -701,6 +707,8 @@ 
Source code for tp.settings
                   '$\mathregular{\Gamma}$ (THz)',
               'group_velocity':
                   '$\mathregular{g_v\ (m\ s^{-1})}$',
+              'gruneisen':
+                  '$\gamma$',
               'gv_by_gv':
                   '$\mathregular{g_v \otimes g_v\ (m^2\ s^{-2})}$',
               'heat_capacity':
diff --git a/docs/avg-rates.html b/docs/avg-rates.html
index 3bd006a..78f9d06 100644
--- a/docs/avg-rates.html
+++ b/docs/avg-rates.html
@@ -17,7 +17,7 @@
     
     
     
-     
+     
 
 
  
@@ -42,6 +42,7 @@
 
  • Density of States (DoS)
    • 
 
  • Cumulative Kappa
    • 
 
  • Waterfalls
    • 
+
  • Projected Phonons
    • 
 
  • Average Scattering Rates
    • 
 
  • Reference
    • 
 
@@ -205,7 +206,7 @@ 
    Average Rates
-        
+        
         
     
    
 
diff --git a/docs/cumkappa.html b/docs/cumkappa.html
index 9c808f7..b239ce7 100644
--- a/docs/cumkappa.html
+++ b/docs/cumkappa.html
@@ -42,6 +42,7 @@
 
  • Density of States (DoS)
    • 
 
  • Cumulative Kappa
    • 
 
  • Waterfalls
    • 
+
  • Projected Phonons
    • 
 
  • Average Scattering Rates
    • 
 
  • Reference
    • 
 
diff --git a/docs/dos.html b/docs/dos.html
index e2c7e49..482df84 100644
--- a/docs/dos.html
+++ b/docs/dos.html
@@ -98,6 +98,57 @@ 
    Density of States (DoS)
    
 
    
 
    Or the whole thing in python with:
    
+
     1
+ 2
+ 3
+ 4
+ 5
+ 6
+ 7
+ 8
+ 9
+10
+11
+12
+13
+14
+15
+16
+17
+18
+19
+20
+21
+22
+23
+24
+25
    #!/usr/bin/env python3
+
+import tp
+
+dosfile = '../data/basno3/projected_dos.dat'
+poscar = '../data/basno3/POSCAR'
+
+colours = {'Ba':  '#ff00ff',
+           'Sn':  '#00ffff',
+           'O':   '#ff0000',
+           'O_2': '#ff8000'}
+
+fig, ax, add_legend = tp.axes.small.two_h()
+
+# Unsmeared, read from POSCAR with total
+dos1 = tp.data.load.phonopy_dos(dosfile, poscar=poscar)
+tp.plot.frequency.add_dos(ax[0], dos1, total=True, colour=colours)
+
+# Smeared (sigma=0.2), custom atoms with no total
+dos2 = tp.data.load.phonopy_dos(dosfile, atoms='Ba Sn O O_2 2')
+tp.plot.frequency.add_dos(ax[1], dos2, sigma=0.2, colour=colours)
+
+add_legend(title='$BaSnO_3$', location=2, ncol=1)
+
+fig.savefig('dos.png')
+
    
+
    
 
    The most foolproof way of specifying colours is through a dictionary
 (lines 8-11), but colours, linestyles etc. as well as atoms can also be
 specified in POSCAR order.
    
diff --git a/docs/genindex.html b/docs/genindex.html
index 783ee63..b6bd5f3 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -451,11 +451,13 @@ 
    P
    
 
       
  • phonopy_conversions() (in module tp.settings)
 
    • 
-  
-  
+  
      
       
    • phonopy_dos() (in module tp.data.load)
+
      • 
+      
    • phonopy_gruneisen() (in module tp.data.load)
 
      • 
       
    • plot_io_function() (in module tp.cli.options)
 
      • 
@@ -481,10 +483,12 @@ 
      S
      
   
   
        
+      
      • set_locators() (in module tp.plot.utilities)
+
        • 
       
      • short_labels() (in module tp.settings)
 
        • 
       
      • skelton() (in module tp.plot.colour)
diff --git a/docs/objects.inv b/docs/objects.inv
index 109241c34bed9d541d803fb5eebb953c1ed58ce5..2762a1bdb188d193050bf858e868402e02729b5c 100644
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diff --git a/docs/phonons.html b/docs/phonons.html
index c1c2d59..2de3b75 100644
--- a/docs/phonons.html
+++ b/docs/phonons.html
@@ -42,6 +42,7 @@
 
      • Density of States (DoS)
        • 
 
      • Cumulative Kappa
        • 
 
      • Waterfalls
        • 
+
      • Projected Phonons
        • 
 
      • Average Scattering Rates
        • 
 
      • Reference
        • 
 
      
diff --git a/docs/prophon.html b/docs/prophon.html
index 1a32337..3d9f9ce 100644
--- a/docs/prophon.html
+++ b/docs/prophon.html
@@ -225,6 +225,16 @@ 
      Projected Phononsfig.savefig('prophon.png')
 
    
 
    
+
    Another similar function is tp.plot.phonons.add_alt_dispersion,
+which plots other phonon properties onto the y-axis along the high-
+symmetry path provided by Phonopy. This will work with Phono3py
+data, but also Gruneisen data from Phonopy
+(tp.data.load.phonopy_gruneisen). Some useful tags for making the
+Gruneisen data clearer include scatter=True (to clean up the bits
+around &Gamma;), bandmax=3 (only acoustic phonons) and manually
+setting the y-limit (some outliers are automatically hidden, but
+especially if only the acoustic modes are shown, it can be useful to
+cut some of the data off the top).
    
 
    
 
 
diff --git a/docs/searchindex.js b/docs/searchindex.js
index b8ce1bd..913b045 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
-Search.setIndex({docnames:["avg-rates","contents","cumkappa","dos","gallery","heatmaps","index","modules","phonons","prophon","tp","tp.axes","tp.cli","tp.data","tp.plot","tp.setup","tutorial-00","tutorial-01","tutorial-02","tutorial-03","tutorial-04","tutorial-05","tutorial-06","tutorial-0X","tutorials","waterfalls"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":3,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":2,"sphinx.domains.rst":2,"sphinx.domains.std":1,"sphinx.ext.intersphinx":1,"sphinx.ext.viewcode":1,sphinx:56},filenames:["avg-rates.rst","contents.rst","cumkappa.rst","dos.rst","gallery.rst","heatmaps.rst","index.rst","modules.rst","phonons.rst","prophon.rst","tp.rst","tp.axes.rst","tp.cli.rst","tp.data.rst","tp.plot.rst","tp.setup.rst","tutorial-00.rst","tutorial-01.rst","tutorial-02.rst","tutorial-03.rst","tutorial-04.rst","tutorial-05.rst","tutorial-06.rst","tutorial-0X.rst","tutorials.rst","waterfalls.rst"],objects:{"":{tp:[10,0,0,"-"]},"tp.axes":{large:[11,0,0,"-"],legend:[11,0,0,"-"],small:[11,0,0,"-"]},"tp.axes.large":{four_square:[11,1,1,""],four_square_colourbars:[11,1,1,""],one:[11,1,1,""],one_colourbar:[11,1,1,""],one_dos:[11,1,1,""],one_dos_colourbar:[11,1,1,""],three_h:[11,1,1,""],three_h_colourbars:[11,1,1,""],three_square:[11,1,1,""],three_square_colourbars:[11,1,1,""],two_h:[11,1,1,""],two_h_colourbars:[11,1,1,""],two_v:[11,1,1,""],two_v_colourbars:[11,1,1,""]},"tp.axes.legend":{add_add_legend:[11,1,1,""],alphabetise:[11,1,1,""],consolidate:[11,1,1,""]},"tp.axes.small":{four_square:[11,1,1,""],four_square_colourbars:[11,1,1,""],one:[11,1,1,""],one_colourbar:[11,1,1,""],one_dos:[11,1,1,""],one_dos_colourbar:[11,1,1,""],three_h:[11,1,1,""],three_h_colourbars:[11,1,1,""],three_square:[11,1,1,""],three_square_colourbars:[11,1,1,""],two_h:[11,1,1,""],two_h_colourbars:[11,1,1,""],two_v:[11,1,1,""],two_v_colourbars:[11,1,1,""]},"tp.calculate":{be_occupation:[10,1,1,""],cumulate:[10,1,1,""],dfdde:[10,1,1,""],from_tp:[10,1,1,""],gaussian:[10,1,1,""],interpolate:[10,1,1,""],kl:[10,1,1,""],kl_fromdict:[10,1,1,""],lifetime:[10,1,1,""],lorentzian:[10,1,1,""],mfp:[10,1,1,""],power_factor:[10,1,1,""],power_factor_fromdict:[10,1,1,""],thermal_conductivity:[10,1,1,""],to_tp:[10,1,1,""],zt:[10,1,1,""],zt_fromdict:[10,1,1,""]},"tp.cli":{cli:[12,0,0,"-"],options:[12,0,0,"-"]},"tp.cli.options":{c_limit_options:[12,1,1,""],direction_option:[12,1,1,""],directions_option:[12,1,1,""],doping_option:[12,1,1,""],doping_type_option:[12,1,1,""],dopings_option:[12,1,1,""],dos_function:[12,1,1,""],fill_options:[12,1,1,""],inputs_function:[12,1,1,""],interpolate_options:[12,1,1,""],kpoints_options:[12,1,1,""],legend_function:[12,1,1,""],line_options:[12,1,1,""],plot_io_function:[12,1,1,""],temperature_option:[12,1,1,""],verbose_option:[12,1,1,""],xy_limit_options:[12,1,1,""]},"tp.data":{load:[13,0,0,"-"],run:[13,0,0,"-"],save:[13,0,0,"-"],utilities:[13,0,0,"-"]},"tp.data.load":{amset:[13,1,1,""],amset_mesh:[13,1,1,""],boltztrap:[13,1,1,""],get_path:[13,1,1,""],phono3py:[13,1,1,""],phonopy_dispersion:[13,1,1,""],phonopy_dos:[13,1,1,""]},"tp.data.run":{boltztrap:[13,1,1,""]},"tp.data.save":{cumkappa:[13,1,1,""],hdf5:[13,1,1,""],kappa_target:[13,1,1,""],phono3py:[13,1,1,""],prompt:[13,1,1,""],zt:[13,1,1,""]},"tp.data.utilities":{merge:[13,1,1,""],resolve:[13,1,1,""]},"tp.plot":{colour:[14,0,0,"-"],frequency:[14,0,0,"-"],heatmap:[14,0,0,"-"],mfp:[14,0,0,"-"],phonons:[14,0,0,"-"],utilities:[14,0,0,"-"]},"tp.plot.colour":{elbow:[14,1,1,""],highlight:[14,1,1,""],hsb2rgb:[14,1,1,""],linear:[14,1,1,""],skelton:[14,1,1,""],uniform:[14,1,1,""]},"tp.plot.frequency":{add_cum_kappa:[14,1,1,""],add_density:[14,1,1,""],add_dos:[14,1,1,""],add_projected_waterfall:[14,1,1,""],add_waterfall:[14,1,1,""],format_waterfall:[14,1,1,""]},"tp.plot.heatmap":{add_heatmap:[14,1,1,""],add_kappa_target:[14,1,1,""],add_pfdiff:[14,1,1,""],add_pfmap:[14,1,1,""],add_ztdiff:[14,1,1,""],add_ztmap:[14,1,1,""]},"tp.plot.mfp":{add_cum_kappa:[14,1,1,""],add_markers:[14,1,1,""]},"tp.plot.phonons":{add_alt_dispersion:[14,1,1,""],add_alt_projected_dispersion:[14,1,1,""],add_dispersion:[14,1,1,""],add_multi:[14,1,1,""],add_projected_dispersion:[14,1,1,""],add_wideband:[14,1,1,""],formatting:[14,1,1,""],get_equivalent_qpoint:[14,1,1,""],tile_properties:[14,1,1,""]},"tp.plot.utilities":{colour_scale:[14,1,1,""],parse_colours:[14,1,1,""],scale_to_axis:[14,1,1,""],set_locators:[14,1,1,""]},"tp.settings":{amset_conversions:[10,1,1,""],boltztrap_conversions:[10,1,1,""],inverted_labels:[10,1,1,""],labels:[10,1,1,""],locator:[10,1,1,""],long_labels:[10,1,1,""],phono3py_conversions:[10,1,1,""],phonopy_conversions:[10,1,1,""],short_labels:[10,1,1,""],to_amset:[10,1,1,""],to_boltztrap:[10,1,1,""],to_phono3py:[10,1,1,""],to_tp:[10,1,1,""],units:[10,1,1,""]},"tp.setup":{vasp:[15,0,0,"-"]},"tp.setup.vasp":{gen_ibz:[15,1,1,""],get_kpar:[15,1,1,""],get_kpoin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:[5,9,13,16],simpl:[0,8],simplest:[4,16],simpli:[16,17,25],simplic:4,simplifi:6,singh:13,singl:[5,6,9,11,13,14,18,19,25],singular:12,six:22,size:[4,8,10,11,17,20,22],skelton:14,slash:16,slightli:[4,10],slower:11,small:[2,3,5,7,9,10,17,19,20,21,22,25],smallest:10,smear:[3,4],smooth:14,smtg:6,snyder:13,soc:13,solid:14,solv:20,some:[4,9,11,17,18,20,21,23,24],someth:[14,16,20],sometim:14,somewhat:11,sort:[0,10,14],sourc:[6,10,11,12,13,14,15,17,21],space:[8,11,18,19,20],specialis:24,specialist:6,specif:[4,6,12,13,14],specifi:[0,2,3,5,13,14,18,19,21,22,23],sphinx:6,spin:13,split:[6,8,20],spooner:6,squar:[11,16],src:6,stage:[6,17],stand:[18,20],standard:[10,13,18,19,22],standardis:13,start:[3,11,14,16,20],state:[2,6,8,13,14,25],stdout:13,step:[6,13,17,18],still:[6,14],stitch:15,stop:[18,20],str:[10,11,13,14,15],straightforward:[0,6],streamlin:[4,12,19],string:[13,14,18,19],strong:20,structur:[2,6,13,14,16,24],stuff:[10,18],style:[6,8,9,10,11,18,20,21,22,24],stylelib:18,stype:[0,13],sub:[5,20],subdictionari:[13,21],subfig:17,submit:6,submodul:[1,7],subpackag:[1,7],subplot:6,subplots_adjust:21,subsequ:11,subset:14,substitut:[6,16],suffix:[11,21],suggest:[12,15,23],suit:[6,9,11],suitabl:[9,23],sum:13,sumo:13,sup:5,supercel:[4,8,20],supplement:6,suppli:[2,5,9,15],support:[2,6,20],sure:[5,14,21],swap:[6,13],symmetri:[6,9,14,15],symmop:14,symop:14,symprec:15,tab10:14,tag:[0,2,9,16,25],take:[6,11,13,14,16,17,18,19,21],taken:[14,17],target:[4,5,6,10,12,13,14],tdata:0,tell:18,temperatur:[0,2,4,5,6,9,10,12,13,14,18,20,21,25],temperature_opt:12,templat:[5,22],test:1,text:[11,13,16],than:[3,8,9,11,13,14,18,19,20,22,25],thank:6,thats:4,thei:[0,6,8,13,14,17,19,20],them:[0,4,8,17,18,19,20],themselv:16,therebi:0,therefor:20,thermal:[4,5,6,10,12,13,14,25],thermal_conduct:10,thermoelectr:6,thermoplott:[0,4,5,6,10,16,17,18,19,21,24],thi:[0,2,3,4,5,6,8,9,10,13,14,15,16,17,18,19,20,21,24,25],thing:[3,4,11,14,16,17,21],third:[4,23],those:[5,6,14,22],three:[4,5,11,13,16,17],three_h:11,three_h_colourbar:11,three_squar:11,three_square_colourbar:11,through:[3,21],throughout:17,thrown:[5,17],thz:10,tick:[0,8,10,13,14,20,22],tick_label:14,tick_posit:14,ticklabel:14,tickpo:13,tidi:18,tidier:5,tile:14,tile_properti:14,time:[13,21,23],tinterp:13,titl:[0,2,3,4,8,19,21],tmax:13,tmin:[13,21],to_amset:10,to_boltztrap:10,to_phono3pi:10,to_tp:10,to_xxx:22,togeth:[13,15,19],toggl:[12,16],tol:14,toler:14,too:[14,17,22,23],tool:[4,5,6,10,13,14,15,23],toolkit:6,top:[5,9,11,16,18,19,21,22,25],total:[0,3,10,13,14,16],totalcolour:14,totallabel:14,tprc:[6,10,14,24],tracker:6,tradit:14,translat:10,transpar:18,transport:[4,6,12,13,21],transport_75x75x75:21,transvers:14,transverse_1:[],transverse_2:[],treat:14,trivial:17,trnasport:[],tstep:13,tupl:14,turn:[13,14,20],tutori:[0,1,4,6],twice:14,two:[2,3,5,6,8,9,11,14,15,17,18,21,23],two_h:[0,2,3,11,20],two_h_colourbar:11,two_v:[11,20],two_v_colourbar:11,type:[4,8,10,11,12,13,14,15,16,17,18,24],typic:16,ucl:6,unalik:19,under:[5,6,8,14],undercolour:14,underli:[17,22],uniform:[5,14,18],unit:[6,10,13,17,21,22,24],unittest:6,unless:14,unoccupi:14,unsmear:3,unweight:23,unweighted_kpoint:23,updat:[10,22],usag:[1,2,16],use:[0,2,4,5,6,9,10,16,17,18,20,21,22,24,25],use_tprc:10,used:[0,2,3,4,5,6,8,9,10,11,14,16,17,18,19,20,21,24,25],useful:[4,6,8,9,11,14,19,21],user:[6,18,22,24],uses:[5,6,11,19,23],using:[0,5,6,10,13,14,17,19,21],usr:[0,2,3,5,8,9,17,18,19,20,21,25],usual:[8,16,19],util:[0,4,7,10,20,21,23],valu:[3,10,13,14,16,21,23],valuabl:5,vari:13,variabl:[10,13,14,21],variable_nam:21,variat:21,variou:[6,8,14],vasp:[7,10,13,14,24],vasprun:13,veloc:10,verbos:[12,14],verbose_opt:12,veri:[0,23],version:[2,9,13,17,18,19,20],vertic:[11,20],via:[0,9,16,21],viridi:[9,14,20,25],viridis_r:14,visibl:[14,20],volum:4,wai:[3,4,5,6,14,16,17,18,19],want:[0,2,5,6,9,14,18,19,22,23],warda:6,waterfal:[2,6,12,14,20],wavevector:13,weight:[0,4,12,13,15],weighted_kpoint:23,weighted_mfp:0,weighted_r:[0,13],welcom:[6,22],well:[3,4,10,14,20,24,25],wether:5,what:[15,18,21,23],when:[0,6,10,21,23,24],where:[4,5,6,11,14,17,18,20,21,25],wherea:14,whether:6,which:[0,2,3,4,5,6,8,9,11,13,14,15,16,17,18,19,20,21,22,23,24,25],whilst:11,white:[5,9,14],who:6,whole:[3,13,14,17],wide:[6,18],wideband:[4,9,12,18],widen:4,widest:9,width:[10,11,14],wiedemann:13,willi:6,wink:[],winter_r:[14,20],within:[5,14,17],without:[5,13,15,20,22,23],work:[9,11,13,14,20,21],worker:[10,14],workflow:4,worri:22,worth:[13,20],would:[13,14,15,20,22,23],wrap:5,wrapper:[6,10,13,14],write:[13,14,15,22],written:[16,18],wrt:[10,13],x_tick:14,xdata:13,xinterp:14,xmarker:[2,14],xmarkkwarg:14,xmax:14,xmin:14,xml:13,xquantiti:14,xscale:14,xxx:4,xxx_name:22,xy_limit_opt:12,y_tick:14,yaml:[4,6,8,9,10,13,14,17,18,19,20,24],yamldata:13,year:4,yet:[2,20],yinterp:14,ymarker:[2,14],ymax:14,ymin:14,you:[0,2,4,5,6,9,11,13,14,15,16,17,18,19,20,21,22,23,24,25],your:[5,6,11,17,18,19,22],your_hdf5_path:6,yourself:14,yourstyl:22,yquantiti:14,yscale:14,yyi:4,zdiff:4,zero:[5,12,13,14,15],zero_weight:15,zhu:6,zno:[2,5,8,9,17,18,19],zt_fromdict:10,ztdiff:[4,5,12,16],ztmap:[4,5,12]},titles:["Average Rates","ThermoPlotter","Cumulative Lattice Thermal Conductivity","Density of States (DoS)","Gallery","Heatmaps","Installation","tp","Phonons","Projected Phonons","tp package","tp.axes package","tp.cli package","tp.data package","tp.plot package","tp.setup package","Tutorial-00: CLI Fundamentals","Tutorial-01: Python Foundations","Tutorial-02: Individual Customisation","Tutorial-03: Compound Axes","Tutorial-04: Layered Plots","Tutorial-05: Helper Functions","Tutorial-06: Package Customisation","Tutorial-0X: VASP Assists","Tutorials","Waterfall"],titleterms:{"function":[10,11,12,13,14,15,21],Axes:[17,18,19,20,21],DoS:3,assist:23,averag:0,axes:11,calcul:10,cli:[12,16],colour:14,colourmap:18,command:6,compound:19,conducit:23,conduct:2,content:[10,11,12,13,14,15],contribut:6,contributor:6,cumul:2,customis:[18,22],data:13,densiti:3,extend:22,format:20,foundat:17,frequenc:14,fundament:16,galleri:4,heatmap:[5,14],help:17,helper:21,indic:1,individu:18,instal:6,label:21,larg:11,lattic:[2,23],layer:20,legend:[11,19,21],licens:6,line:[6,17,18,19,20,21],load:[13,17,18,20],locat:21,mac:6,merg:23,mfp:14,modul:[10,11,12,13,14,15],more:17,option:12,packag:[10,11,12,13,14,15,22],phonon:[8,9,14],plot:[14,17,18,19,20],point:23,project:9,python:[6,17],rate:0,refer:4,requir:6,resolv:21,run:13,save:[13,17],set:10,setup:15,small:11,state:3,submodul:[10,11,12,13,14,15],subpackag:10,tabl:1,target:23,test:6,thermal:[2,23],thermoplott:[1,22],tick:21,tprc:22,tutori:[16,17,18,19,20,21,22,23,24],usag:6,util:[13,14],variabl:18,vasp:[15,23],waterfal:25,weight:23,yaml:22,zero:23}})
\ No newline at end of file
diff --git a/docs/tp.data.html b/docs/tp.data.html
index 1713b52..9835d32 100644
--- a/docs/tp.data.html
+++ b/docs/tp.data.html
@@ -330,6 +330,49 @@ 
    Functions
+
    
+tp.data.load.phonopy_gruneisen(filename)[source]
    
+
    Loads phonopy gruneisen data.
    
+
    Does not load path data, but can load from files with a q-point
+path, which will often be preferable if projecting onto a phonon
+dispersion.
    
+
    
+
    Parameters
    
+
    filename (str) – phonopy gruneisen.yaml filepath.
    
+
    
+
    Returns
    
+
    gruneisen data.
    
+
    
+
    Return type
    
+
    dict
    
+
    
+
    
+
    
+
+
    
+
    
+tp.data.load.scale_to_path(x, tickpos, scalepos)[source]
    
+
    Scales data to a path.
    
+
    Useful to make different phonopy runs fit together or to map
+gruneisen data on a phonon dispersion.
    
+
    
+
    Parameters
    
+
      
+
    • x (list) – wavevector ordinates.
      • 
+
    • tickpos (list) – tick wavevectors for scaling.
      • 
+
    • scalepos (list) – scale tick wavevectors.
      • 
+
    
+
    
+
    Returns
    
+
    wavevector ordinates.
    
+
    
+
    Return type
    
+
    list
    
+
    
+
    
+
    
+
 
    
 
    
 
    
diff --git a/docs/tp.plot.html b/docs/tp.plot.html
index 9fc2a60..b5aa5da 100644
--- a/docs/tp.plot.html
+++ b/docs/tp.plot.html
@@ -1123,7 +1123,7 @@ 
    Functions
 
    
-tp.plot.phonons.add_alt_dispersion(ax, data, pdata, quantity, bandmin=None, bandmax=None, temperature=300, direction='avg', label=['Longitudinal', 'Transverse_1', 'Transverse_2', 'Optic'], poscar='POSCAR', main=True, log=False, interpolate=10000, smoothing=5, colour=['#44ffff', '#ff8044', '#ff4444', '#00000010'], linestyle='-', marker=None, workers=8, xmarkkwargs={}, verbose=False, **kwargs)[source]
    
+tp.plot.phonons.add_alt_dispersion(ax, data, pdata, quantity, bandmin=None, bandmax=None, temperature=300, direction='avg', label=['Longitudinal', 'Transverse$_1$', 'Transverse$_2$', 'Optic'], poscar='POSCAR', scatter=False, main=True, log=False, interpolate=10000, smoothing=5, colour=['#44ffff', '#ff8044', '#ff4444', '#00000010'], linestyle='-', marker=None, workers=8, xmarkkwargs={}, verbose=False, **kwargs)[source]
 
    Plots a phono3py quantity on a high-symmetry path.
    
 
    Labels, colours and linestyles can be given one for the whole
 dispersion, or one for each band, with the last entry filling all
@@ -1167,8 +1167,9 @@ 
    Functions
     
     
-    
+    
      
 
 
@@ -42,6 +42,7 @@
 
  • Density of States (DoS)
    • 
 
  • Cumulative Kappa
    • 
 
  • Waterfalls
    • 
+
  • Projected Phonons
    • 
 
  • Average Scattering Rates
    • 
 
  • Reference
    • 
 
@@ -282,7 +283,7 @@ 
    Waterfall
         
-        
+        
     
    
 
   
    
diff --git a/tp/plot/colour.py b/tp/plot/colour.py
index 4d219e7..09fd848 100644
--- a/tp/plot/colour.py
+++ b/tp/plot/colour.py
@@ -89,7 +89,7 @@ def uniform(cmid, cmin='white', cmax='#333333', alpha=1.,
     cmid = np.array(to_rgba(cmid, alpha))
     cnorm = (cmid[:3] - cmin[:3]) / (cmax[:3] - cmin[:3])
     # pythagoras
-    midpoint = np.sqrt((cnorm[0]**2 + cnorm[1]**2 + cnorm[2]**2)/3)
+    midpoint = np.sqrt(cnorm[0]**2 + cnorm[1]**2 + cnorm[2]**2)/3
     x = [0, midpoint, 1]
     y = [cmin, cmid, cmax]
     x2 = np.linspace(0, 1, density)