In [1]:

    

%matplotlib notebook
from __future__ import print_function
import pytest
import os, sys
import numpy as np
sys.path.insert(0, os.path.abspath('../../..'))
import hublib.rappture as rappture


    

In [2]:

    

io = rappture.RapXML('dftmatprop_run.xml')


    

In [3]:

    

io


    

    
Out[3]:




INPUTS
Path
Label
Description
input.group(tabs).group(basicInput).drawing()
input.group(tabs).group(basicInput).choice(materialType)
Material Type:
input.group(tabs).group(geomInput).string(atomStruct)
Atomic Structure:
Fractional coordinates
input.group(tabs).group(geomInput).string(cellVect)
Cell Vectors (A):
Primitive cell
input.group(tabs).group(geomInput).boolean(eos_enable)
Equation of State Calculations:
input.group(tabs).group(geomInput).group(eos_options).number(volMin)
Minimum Volume:
input.group(tabs).group(geomInput).group(eos_options).number(volMax)
Maximum Volume:
input.group(tabs).group(geomInput).group(eos_options).integer(volSteps)
Steps:
input.group(tabs).group(EnEx).choice(approx)
Exchange and Correlation functional
Determines the exchange-correlation func
input.group(tabs).group(EnEx).choice(relax)
Relax
Determines whether to relax system
input.group(tabs).group(EnEx).group(relax_options).choice(ion_dynam)
Ionic Dynamics
Select ionic dynamics
input.group(tabs).group(EnEx).group(relax_options).choice(cell_dynam)
Cell Dynamics
Select cell dynamics
input.group(tabs).group(EnEx).group(kgrid).integer(x_size)
X direction
Specifies the number of k points in reci
input.group(tabs).group(EnEx).group(kgrid).integer(y_size)
Y direction
Specifies the number of k points in reci
input.group(tabs).group(EnEx).group(kgrid).integer(z_size)
Z direction
Specifies the number of k points in reci
input.group(tabs).group(EnEx).number(ke_cutoff)
Wavefunction Kinetic Energy cutoff (Ry)
kinetic energy cutoff (Ry) for wavefunct
input.group(tabs).group(EnEx).number(ke_cutoff_potential)
Charge Density Kinetic Energy cutoff (Ry)
kinetic energy cutoff (Ry) for charge de
input.group(tabs).group(EnEx).number(convergence)
SCF Convergence Criterion (Ry)
Self consistent field convergence criter
input.group(tabs).group(EnEx).integer(scf_maxstep)
SCF maximum steps
Maximum number of Self consistent field 
input.group(tabs).group(EnEx).boolean(occupation_enable)
Enable occupation options
Enable occupation options
input.group(tabs).group(EnEx).group(occupation_options).choice(occupations)
Occupation
Select smearing for gaussian smearing fo
input.group(tabs).group(EnEx).group(occupation_options).choice(smearing)
Smearing
Select a smearing option
input.group(tabs).group(EnEx).group(occupation_options).number(degauss)
Gaussian Spreading (Ry)
Value of the Gaussian spreading
input.group(tabs).group(EnEx).boolean(mixing_enable)
Enable mixing options
Enable mixing options
input.group(tabs).group(EnEx).group(mixing_options).choice(mixing_mode)
Mixing Mode
input.group(tabs).group(EnEx).group(mixing_options).number(mixing_beta)
Mixing factor
mixing factor for self-consistency
input.group(tabs).group(bandstructure).boolean(bandstructure_enable)
Band Structure Calculations
Do you want to do band structure calcula
input.group(tabs).group(bandstructure).group(bandstructure_options).string(k_path)
Path
List of high symmetry points describing 
input.group(tabs).group(bandstructure).group(bandstructure_options).integer(k_num)
Number of Points
Number of Points to display on Band Stru
input.group(tabs).group(bandstructure).boolean(dos_enable)
Density of States Options
Do you want to do DoS calculations?
input.group(tabs).group(bandstructure).group(dos_options).number(dos_min_E)
minimum Energy (eV)
minimum energy for DOS plot
input.group(tabs).group(bandstructure).group(dos_options).number(dos_max_E)
maximum Energy (eV)
maximum energy for DOS plot
input.group(tabs).group(bandstructure).group(dos_options).number(dos_delta_E)
energy grid step (eV)
energy increments on DOS plot
input.group(tabs).group(dielec).boolean(dielec_enable)
Dielectric Calculations
input.group(tabs).group(dielec).group(dielec_options).number(dielec_smearing)
Smearing:
input.group(tabs).group(dielec).group(dielec_options).number(dielec_min_E)
Min E:
input.group(tabs).group(dielec).group(dielec_options).number(dielec_max_E)
Max E:
input.group(tabs).group(dielec).group(dielec_options).integer(dielec_pts)
Number of Points:
input.boolean(advanced)
Advanced Options:

OUTPUTS
Path
Label
Description
output.curve(eos)
Energy vs Volume
output.curve(fit)
Quadratic Fit
0.00679594531122*x^2 + -0.556558429626*x + -202.988912765
output.curve(murn)
Murnaghan Fit
output.number(eqVol)
(Murnaghan) Equilibrium Volume (A^3)
output.number(bulkMod)
(Murnaghan) Bulk Modulus (GPa)
output.sequence(bandSeq).element(0).curve(band1)
Band 1
output.sequence(bandSeq).element(0).curve(band2)
Band 2
output.sequence(bandSeq).element(0).curve(band3)
Band 3
output.sequence(bandSeq).element(0).curve(band4)
Band 4
output.sequence(bandSeq).element(0).curve(band5)
Band 5
output.sequence(bandSeq).element(0).curve(band6)
Band 6
output.sequence(bandSeq).element(0).curve(band7)
Band 7
output.sequence(bandSeq).element(0).curve(band8)
Band 8
output.sequence(bandSeq).element(1).curve(band1)
Band 1
output.sequence(bandSeq).element(1).curve(band2)
Band 2
output.sequence(bandSeq).element(1).curve(band3)
Band 3
output.sequence(bandSeq).element(1).curve(band4)
Band 4
output.sequence(bandSeq).element(1).curve(band5)
Band 5
output.sequence(bandSeq).element(1).curve(band6)
Band 6
output.sequence(bandSeq).element(1).curve(band7)
Band 7
output.sequence(bandSeq).element(1).curve(band8)
Band 8
output.sequence(bandSeq).element(2).curve(band1)
Band 1
output.sequence(bandSeq).element(2).curve(band2)
Band 2
output.sequence(bandSeq).element(2).curve(band3)
Band 3
output.sequence(bandSeq).element(2).curve(band4)
Band 4
output.sequence(bandSeq).element(2).curve(band5)
Band 5
output.sequence(bandSeq).element(2).curve(band6)
Band 6
output.sequence(bandSeq).element(2).curve(band7)
Band 7
output.sequence(bandSeq).element(2).curve(band8)
Band 8
output.sequence(bandSeq).element(3).curve(band1)
Band 1
output.sequence(bandSeq).element(3).curve(band2)
Band 2
output.sequence(bandSeq).element(3).curve(band3)
Band 3
output.sequence(bandSeq).element(3).curve(band4)
Band 4
output.sequence(bandSeq).element(3).curve(band5)
Band 5
output.sequence(bandSeq).element(3).curve(band6)
Band 6
output.sequence(bandSeq).element(3).curve(band7)
Band 7
output.sequence(bandSeq).element(3).curve(band8)
Band 8
output.sequence(bandSeq).element(4).curve(band1)
Band 1
output.sequence(bandSeq).element(4).curve(band2)
Band 2
output.sequence(bandSeq).element(4).curve(band3)
Band 3
output.sequence(bandSeq).element(4).curve(band4)
Band 4
output.sequence(bandSeq).element(4).curve(band5)
Band 5
output.sequence(bandSeq).element(4).curve(band6)
Band 6
output.sequence(bandSeq).element(4).curve(band7)
Band 7
output.sequence(bandSeq).element(4).curve(band8)
Band 8
output.sequence(bandSeq).element(5).curve(band1)
Band 1
output.sequence(bandSeq).element(5).curve(band2)
Band 2
output.sequence(bandSeq).element(5).curve(band3)
Band 3
output.sequence(bandSeq).element(5).curve(band4)
Band 4
output.sequence(bandSeq).element(5).curve(band5)
Band 5
output.sequence(bandSeq).element(5).curve(band6)
Band 6
output.sequence(bandSeq).element(5).curve(band7)
Band 7
output.sequence(bandSeq).element(5).curve(band8)
Band 8
output.sequence(bandSeq).element(6).curve(band1)
Band 1
output.sequence(bandSeq).element(6).curve(band2)
Band 2
output.sequence(bandSeq).element(6).curve(band3)
Band 3
output.sequence(bandSeq).element(6).curve(band4)
Band 4
output.sequence(bandSeq).element(6).curve(band5)
Band 5
output.sequence(bandSeq).element(6).curve(band6)
Band 6
output.sequence(bandSeq).element(6).curve(band7)
Band 7
output.sequence(bandSeq).element(6).curve(band8)
Band 8
output.sequence(bandSeq).element(7).curve(band1)
Band 1
output.sequence(bandSeq).element(7).curve(band2)
Band 2
output.sequence(bandSeq).element(7).curve(band3)
Band 3
output.sequence(bandSeq).element(7).curve(band4)
Band 4
output.sequence(bandSeq).element(7).curve(band5)
Band 5
output.sequence(bandSeq).element(7).curve(band6)
Band 6
output.sequence(bandSeq).element(7).curve(band7)
Band 7
output.sequence(bandSeq).element(7).curve(band8)
Band 8
output.sequence(dosSeq).element(0).curve(dos)
Density of States
output.sequence(dosSeq).element(1).curve(dos)
Density of States
output.sequence(dosSeq).element(2).curve(dos)
Density of States
output.sequence(dosSeq).element(3).curve(dos)
Density of States
output.sequence(dosSeq).element(4).curve(dos)
Density of States
output.sequence(dosSeq).element(5).curve(dos)
Density of States
output.sequence(dosSeq).element(6).curve(dos)
Density of States
output.sequence(dosSeq).element(7).curve(dos)
Density of States
output.string(scf)
SCF Input File

CURVE GROUPS
Electronic Band Structure
output.sequence(bandSeq).element(0).curve(band1)
output.sequence(bandSeq).element(0).curve(band2)
output.sequence(bandSeq).element(0).curve(band3)
output.sequence(bandSeq).element(0).curve(band4)
output.sequence(bandSeq).element(0).curve(band5)
output.sequence(bandSeq).element(0).curve(band6)
output.sequence(bandSeq).element(0).curve(band7)
output.sequence(bandSeq).element(0).curve(band8)
output.sequence(bandSeq).element(0).curve(band1)
output.sequence(bandSeq).element(0).curve(band2)
output.sequence(bandSeq).element(0).curve(band3)
output.sequence(bandSeq).element(0).curve(band4)
output.sequence(bandSeq).element(0).curve(band5)
output.sequence(bandSeq).element(0).curve(band6)
output.sequence(bandSeq).element(0).curve(band7)
output.sequence(bandSeq).element(0).curve(band8)
output.sequence(bandSeq).element(0).curve(band1)
output.sequence(bandSeq).element(0).curve(band2)
output.sequence(bandSeq).element(0).curve(band3)
output.sequence(bandSeq).element(0).curve(band4)
output.sequence(bandSeq).element(0).curve(band5)
output.sequence(bandSeq).element(0).curve(band6)
output.sequence(bandSeq).element(0).curve(band7)
output.sequence(bandSeq).element(0).curve(band8)
output.sequence(bandSeq).element(0).curve(band1)
output.sequence(bandSeq).element(0).curve(band2)
output.sequence(bandSeq).element(0).curve(band3)
output.sequence(bandSeq).element(0).curve(band4)
output.sequence(bandSeq).element(0).curve(band5)
output.sequence(bandSeq).element(0).curve(band6)
output.sequence(bandSeq).element(0).curve(band7)
output.sequence(bandSeq).element(0).curve(band8)
output.sequence(bandSeq).element(0).curve(band1)
output.sequence(bandSeq).element(0).curve(band2)
output.sequence(bandSeq).element(0).curve(band3)
output.sequence(bandSeq).element(0).curve(band4)
output.sequence(bandSeq).element(0).curve(band5)
output.sequence(bandSeq).element(0).curve(band6)
output.sequence(bandSeq).element(0).curve(band7)
output.sequence(bandSeq).element(0).curve(band8)
output.sequence(bandSeq).element(0).curve(band1)
output.sequence(bandSeq).element(0).curve(band2)
output.sequence(bandSeq).element(0).curve(band3)
output.sequence(bandSeq).element(0).curve(band4)
output.sequence(bandSeq).element(0).curve(band5)
output.sequence(bandSeq).element(0).curve(band6)
output.sequence(bandSeq).element(0).curve(band7)
output.sequence(bandSeq).element(0).curve(band8)
output.sequence(bandSeq).element(0).curve(band1)
output.sequence(bandSeq).element(0).curve(band2)
output.sequence(bandSeq).element(0).curve(band3)
output.sequence(bandSeq).element(0).curve(band4)
output.sequence(bandSeq).element(0).curve(band5)
output.sequence(bandSeq).element(0).curve(band6)
output.sequence(bandSeq).element(0).curve(band7)
output.sequence(bandSeq).element(0).curve(band8)
output.sequence(bandSeq).element(0).curve(band1)
output.sequence(bandSeq).element(0).curve(band2)
output.sequence(bandSeq).element(0).curve(band3)
output.sequence(bandSeq).element(0).curve(band4)
output.sequence(bandSeq).element(0).curve(band5)
output.sequence(bandSeq).element(0).curve(band6)
output.sequence(bandSeq).element(0).curve(band7)
output.sequence(bandSeq).element(0).curve(band8)

Equation of State
output.curve(eos)
output.curve(fit)
output.curve(murn)

In [13]:

    

print(io['input.group(tabs).group(basicInput).drawing'].xml())


    

    




<drawing>
                    <substitutions>                        <variable>
                            <name>ek</name>
                            <path>input.group(tabs).group(basicInput).loader(task)</path>
                            <map>
                                <from>
                                </from>
                                <to>ek_selected.png</to>
                            </map>
                            <map>
                                <from>E-K Diagrams</from>
                                <to>blue</to>
                            </map>
                            <map>
                                <from>Dielectric Constant and Optical Properties</from>
                                <to>
                                </to>
                            </map>
                            <map>
                                <from>Equation of State</from>
                                <to>
                                </to>
                            </map>
                        </variable>
                        <variable>
                            <name>dielec</name>
                            <path>input.group(tabs).group(basicInput).loader(task)</path>
                            <map>
                                <from>E-K Diagrams</from>
                                <to>
                                </to>
                            </map>
                            <map>
                                <from>Dielectric Constant and Optical Properties</from>
                                <to>blue</to>
                            </map>
                            <map>
                                <from>Equation of State</from>
                                <to>
                                </to>
                            </map>
                        </variable>
                        <variable>
                            <name>eos</name>
                            <path>input.group(tabs).group(basicInput).loader(task)</path>
                            <map>
                                <from>E-K Diagrams</from>
                                <to>
                                </to>
                            </map>
                            <map>
                                <from>Dielectric Constant and Optical Properties</from>
                                <to>
                                </to>
                            </map>
                            <map>
                                <from>Equation of State</from>
                                <to>blue</to>
                            </map>
                        </variable>
<!--
						<variable>
							<name>ek</name>
							<path>input.group(tabs).group(basicInput).boolean(ek)</path>
							<map><from>yes</from><to>ek_selected.png</to></map>
							<map><from>no</from><to>ek_notselected.png</to></map>
						</variable>
						<variable>
							<name>dielec</name>
							<path>input.group(tabs).group(basicInput).boolean(dielec)</path>
							<map><from>yes</from><to>blue</to></map>
							<map><from>no</from><to>black</to></map>
						</variable>
						<variable>
							<name>eos</name>
							<path>input.group(tabs).group(basicInput).boolean(eos)</path>
							<map><from>yes</from><to>blue</to></map>
							<map><from>no</from><to>black</to></map>
						</variable>
						--></substitutions>
                    <background>
                        <width>800</width>
                        <height>300</height>
                        <color>white</color>
                    </background>
                    <components>
                        <picture>
                            <coords>.86 .9   0.99 0.98</coords>
                            <contents>file://click.png</contents>
                        </picture>
                        <picture>
                            <coords>.0625 .1667   .9375 .8333</coords>
                            <contents>file://options.png</contents>
                        </picture>
                        <rectangle>
                            <coords>.0500 .1333   .3250 .8667</coords>
                            <linewidth>5</linewidth>
                            <fill>
                            </fill>
                            <outline>${ek}</outline>
                        </rectangle>
                        <rectangle>
                            <coords>.3625 .1333   .6375 .8667</coords>
                            <linewidth>5</linewidth>
                            <fill>
                            </fill>
                            <outline>${dielec}</outline>
                        </rectangle>
                        <rectangle>
                            <coords>.6750 .1333   .9500 .8667</coords>
                            <linewidth>5</linewidth>
                            <fill>
                            </fill>
                            <outline>${eos}</outline>
                        </rectangle>
                    </components>
                    <current>
                    </current>
                </drawing>
                

In [5]:

    

io['output.curve(eos)'].plot()


    

In [6]:

    

io['output.curve(fit)'].plot()


    

In [7]:

    

io['output.curve(murn)'].plot()