Using org-entries like a database

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I recently added an org export to jasp which provides an org-mode representation of a Vasp calculation. It is still a work in progress, but the main ideas are developed. The idea is to represent a calculation as an org-mode headline with tabular data, properties and tags. This will make the representation human readable, but machine accessible. Here I examine how we could use it.

1 Generating the entries

We will loop over a set of calculations that define the equation of state for two different Al-Ni alloy structures. For each calculation this code generates a level 3 headline with some tags derived from the calculation directory. I chose level 3 so they would all be nested in this level 2 headline. We write out two sets of data because later we will selectively get portions of the data.

from jasp import *
from jasp.utils import get_jasp_dirs

for d in get_jasp_dirs('10'):
    with jasp(d) as calc:
        print calc.org(level=3)

for d in get_jasp_dirs('11'):
    with jasp(d) as calc:
        print calc.org(level=3)

1.1 10/eos-exp/f+0   10 eos_dash_exp f_plus_0

  x y z
A0 -1.98408 0.0 -1.98408
A1 0.0 -1.98408 1.98408
A2 -3.53625 3.53625 3.53625
species x y z fx fy fz free x free y free z
Al -3.77549 1.79141 1.79141 0.000773 -0.000773 -0.000773 T T T
Al -1.74484 -0.23924 1.74484 -0.000773 0.000773 0.000773 T T T
Ni 0.0 0.0 0.0 0.0 0.0 0.0 T T T
Parameter Value
nbands 25
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Ni potpawPBE/Ni/POTCAR 6c814bc7144b98435771aded093fb4ebe527acd9
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2

1.2 10/eos-exp/f+10   10 eos_dash_exp f_plus_10

  x y z
A0 -2.04813 0.0 -2.04813
A1 0.0 -2.04813 2.04813
A2 -3.6504 3.6504 3.6504
species x y z fx fy fz free x free y free z
Al -3.85098179507 1.84576178527 1.83645153581 -0.012598 0.014577 -0.007395 T T T
Al -1.7283215185 -0.279882546245 1.73598892646 0.000817 0.006771 0.025221 T T T
Ni -5.63955668642 1.58856076097 3.61420953773 0.011781 -0.021349 -0.017826 T T T
Parameter Value
nbands 25
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Ni potpawPBE/Ni/POTCAR 6c814bc7144b98435771aded093fb4ebe527acd9
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2

1.3 10/eos-exp/f+12   10 eos_dash_exp f_plus_12

  x y z
A0 -2.06046 0.0 -2.06046
A1 0.0 -2.06046 2.06046
A2 -3.67239 3.67239 3.67239
species x y z fx fy fz free x free y free z
Al -3.86530078437 1.85683453967 1.84560971979 -0.017615 0.018377 -0.00588 T T T
Al -1.72555029376 -0.287469117251 1.73429429921 0.009139 -0.000441 0.020494 T T T
Ni -5.66232892187 1.59473457758 3.628735981 0.008476 -0.017936 -0.014613 T T T
Parameter Value
nbands 25
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Ni potpawPBE/Ni/POTCAR 6c814bc7144b98435771aded093fb4ebe527acd9
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2

1.4 10/eos-exp/f+15   10 eos_dash_exp f_plus_15

  x y z
A0 -2.0787 0.0 -2.0787
A1 0.0 -2.0787 2.0787
A2 -3.70489 3.70489 3.70489
species x y z fx fy fz free x free y free z
Al -3.88717652995 1.87379242704 1.86009271779 -0.022309 0.021755 -0.006413 T T T
Al -1.72325929808 -0.297739728075 1.73317610987 0.033819 -0.022553 -0.000329 T T T
Ni -5.69348417197 1.60230730103 3.64787117234 -0.01151 0.000799 0.006742 T T T
Parameter Value
nbands 25
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Ni potpawPBE/Ni/POTCAR 6c814bc7144b98435771aded093fb4ebe527acd9
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2

1.5 10/eos-exp/f+2   10 eos_dash_exp f_plus_2

  x y z
A0 -1.99722 0.0 -1.99722
A1 0.0 -1.99722 1.99722
A2 -3.55967 3.55967 3.55967
species x y z fx fy fz free x free y free z
Al -3.78897262915 1.80298810692 1.80238679997 -0.00052 -0.01106 -0.017256 T T T
Al -1.74283113391 -0.243416998758 1.743431885 0.011316 -0.021883 -0.005492 T T T
Ni -5.54541623693 1.55504889184 3.55010131503 -0.010796 0.032943 0.022747 T T T
Parameter Value
nbands 25
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Ni potpawPBE/Ni/POTCAR 6c814bc7144b98435771aded093fb4ebe527acd9
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2

1.6 10/eos-exp/f+4   10 eos_dash_exp f_plus_4

  x y z
A0 -2.01019 0.0 -2.01019
A1 0.0 -2.01019 2.01019
A2 -3.58278 3.58278 3.58278
species x y z fx fy fz free x free y free z
Al -3.80137127251 1.81395280614 1.81276515721 -0.021611 -0.002318 -0.01379 T T T
Al -1.73979870776 -0.248609560277 1.74098667865 0.017491 -0.038446 -0.007248 T T T
Ni -5.57213001973 1.55941675414 3.56527816415 0.004121 0.040764 0.021038 T T T
Parameter Value
nbands 25
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Ni potpawPBE/Ni/POTCAR 6c814bc7144b98435771aded093fb4ebe527acd9
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2

1.7 10/eos-exp/f+6   10 eos_dash_exp f_plus_6

  x y z
A0 -2.02299 0.0 -2.02299
A1 0.0 -2.02299 2.02299
A2 -3.60561 3.60561 3.60561
species x y z fx fy fz free x free y free z
Al -3.81674368134 1.82268911017 1.81846628092 -0.03365 0.021418 0.006392 T T T
Al -1.73592646487 -0.259496276667 1.73977985143 0.007575 -0.01713 0.007756 T T T
Ni -5.5962598538 1.5715971665 3.58361386765 0.026075 -0.004288 -0.014148 T T T
Parameter Value
nbands 25
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Ni potpawPBE/Ni/POTCAR 6c814bc7144b98435771aded093fb4ebe527acd9
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2

1.8 10/eos-exp/f+8   10 eos_dash_exp f_plus_8

  x y z
A0 -2.03564 0.0 -2.03564
A1 0.0 -2.03564 2.03564
A2 -3.62814 3.62814 3.62814
species x y z fx fy fz free x free y free z
Al -3.83039067392 1.83353256518 1.82788023062 -0.042201 0.025424 0.00725 T T T
Al -1.73261729052 -0.266893248067 1.73758502884 0.008197 -0.020125 0.010395 T T T
Ni -5.62110203556 1.57803068288 3.59892474053 0.034004 -0.005299 -0.017645 T T T
Parameter Value
nbands 25
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Ni potpawPBE/Ni/POTCAR 6c814bc7144b98435771aded093fb4ebe527acd9
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2

1.9 10/eos-exp/f-10   10 eos_dash_exp f_dash_10

  x y z
A0 -1.91561 0.0 -1.91561
A1 0.0 -1.91561 1.91561
A2 -3.41421 3.41421 3.41421
species x y z fx fy fz free x free y free z
Al -3.69513184604 1.73676514888 1.75200457401 -0.00015 -0.016008 0.015593 T T T
Al -1.76033286748 -0.198966401698 1.74405584289 0.003022 -0.015555 -0.029074 T T T
Ni -0.0648652864789 0.0143712528207 0.040189583095 -0.002872 0.031562 0.013481 T T T
Parameter Value
nbands 25
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Ni potpawPBE/Ni/POTCAR 6c814bc7144b98435771aded093fb4ebe527acd9
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2

1.10 10/eos-exp/f-12   10 eos_dash_exp f_dash_12

  x y z
A0 -1.90131 0.0 -1.90131
A1 0.0 -1.90131 1.90131
A2 -3.38873 3.38873 3.38873
species x y z fx fy fz free x free y free z
Al -3.67627852264 1.72365573425 1.74704265204 -0.021096 -0.003148 0.019104 T T T
Al -1.76353019483 -0.189393782717 1.73913926696 -0.006667 -0.016634 -0.009534 T T T
Ni -0.0805212825263 0.0179080484715 0.050068081002 0.027763 0.019782 -0.00957 T T T
Parameter Value
nbands 25
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Ni potpawPBE/Ni/POTCAR 6c814bc7144b98435771aded093fb4ebe527acd9
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2

1.11 10/eos-exp/f-15   10 eos_dash_exp f_dash_15

  x y z
A0 -1.87946 0.0 -1.87946
A1 0.0 -1.87946 1.87946
A2 -3.34978 3.34978 3.34978
species x y z fx fy fz free x free y free z
Al -3.65183912264 1.70528638812 1.73537994296 -0.037051 0.019573 0.044452 T T T
Al -1.76884279383 -0.178373914577 1.73770842538 0.010475 -0.025221 -0.029082 T T T
Ni -0.0996480835307 0.0252575264549 0.0631616316537 0.026577 0.005648 -0.01537 T T T
Parameter Value
nbands 25
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Ni potpawPBE/Ni/POTCAR 6c814bc7144b98435771aded093fb4ebe527acd9
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2

1.12 10/eos-exp/f-2   10 eos_dash_exp f_dash_2

  x y z
A0 -1.97076 0.0 -1.97076
A1 0.0 -1.97076 1.97076
A2 -3.51252 3.51252 3.51252
species x y z fx fy fz free x free y free z
Al -3.76146938751 1.7792636125 1.77972964831 0.002765 0.010416 0.018609 T T T
Al -1.74832410416 -0.234109027383 1.74785846541 -0.002339 0.016333 -0.006172 T T T
Ni -0.0105365083339 0.00701541488599 0.00866188628634 -0.000426 -0.026749 -0.012437 T T T
Parameter Value
nbands 25
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Ni potpawPBE/Ni/POTCAR 6c814bc7144b98435771aded093fb4ebe527acd9
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2

1.13 10/eos-exp/f-4   10 eos_dash_exp f_dash_4

  x y z
A0 -1.95726 0.0 -1.95726
A1 0.0 -1.95726 1.95726
A2 -3.48846 3.48846 3.48846
species x y z fx fy fz free x free y free z
Al -3.74916407088 1.76890327148 1.76974035279 0.025717 0.002077 0.019316 T T T
Al -1.75040151275 -0.230732012577 1.74956509347 -0.018564 0.049532 8.6e-05 T T T
Ni -0.0207644163691 0.0139987410966 0.0169445537375 -0.007153 -0.051609 -0.019402 T T T
Parameter Value
nbands 25
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Ni potpawPBE/Ni/POTCAR 6c814bc7144b98435771aded093fb4ebe527acd9
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2

1.14 10/eos-exp/f-6   10 eos_dash_exp f_dash_6

  x y z
A0 -1.94358 0.0 -1.94358
A1 0.0 -1.94358 1.94358
A2 -3.46406 3.46406 3.46406
species x y z fx fy fz free x free y free z
Al -3.73031485721 1.75693465653 1.76095910776 -0.000377 0.017266 0.043872 T T T
Al -1.75673108966 -0.217813140979 1.75241474358 0.034718 -0.014395 -0.060867 T T T
Ni -0.0332840531202 0.0130484844485 0.0228761486573 -0.034341 -0.002871 0.016995 T T T
Parameter Value
nbands 25
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Ni potpawPBE/Ni/POTCAR 6c814bc7144b98435771aded093fb4ebe527acd9
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2

1.15 10/eos-exp/f-8   10 eos_dash_exp f_dash_8

  x y z
A0 -1.92969 0.0 -1.92969
A1 0.0 -1.92969 1.92969
A2 -3.43932 3.43932 3.43932
species x y z fx fy fz free x free y free z
Al -3.71109103713 1.74742547037 1.75920312374 -0.003371 -0.008528 0.015983 T T T
Al -1.75760409593 -0.206692341706 1.74515790595 0.004847 -0.014457 -0.026033 T T T
Ni -0.0516348669472 0.011436871336 0.0318889703136 -0.001476 0.022985 0.01005 T T T
Parameter Value
nbands 25
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Ni potpawPBE/Ni/POTCAR 6c814bc7144b98435771aded093fb4ebe527acd9
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2

1.16 11/eos-exp/f+0   11 eos_dash_exp f_plus_0

  x y z
A0 -1.83341 0.0 -1.83341
A1 0.0 -1.83341 1.83341
A2 -3.44161 3.44161 3.44161
species x y z fx fy fz free x free y free z
Al -1.75834 -0.07507 1.75834 0.0 0.0 0.0 T T T
Fe -3.39510205563 3.39510205563 3.39510205563 0.065417 -0.065417 -0.065417 T T T
Fe -3.56318794437 1.72977794437 1.72977794437 -0.065417 0.065417 0.065417 T T T
Parameter Value
nbands 21
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2
Fe potpawPBE/Fe/POTCAR 201d71adcb39575fc20d69f0abd331ae9c01ed2e

1.17 11/eos-exp/f+10   11 eos_dash_exp f_plus_10

  x y z
A0 -1.89259 0.0 -1.89259
A1 0.0 -1.89259 1.89259
A2 -3.55271 3.55271 3.55271
species x y z fx fy fz free x free y free z
Al -1.71768562473 -0.12420477333 1.72897811362 -0.027763 -0.002052 0.049582 T T T
Fe -5.29679962665 1.54076691889 3.42444208823 0.067989 -0.02176 -0.05605 T T T
Fe -3.59473474862 1.74065785444 1.72979979816 -0.040226 0.023812 0.006467 T T T
Parameter Value
nbands 21
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2
Fe potpawPBE/Fe/POTCAR 201d71adcb39575fc20d69f0abd331ae9c01ed2e

1.18 11/eos-exp/f+12   11 eos_dash_exp f_plus_12

  x y z
A0 -1.90399 0.0 -1.90399
A1 0.0 -1.90399 1.90399
A2 -3.57411 3.57411 3.57411
species x y z fx fy fz free x free y free z
Al -1.71395551429 -0.137649234072 1.73446168186 0.003858 -0.016816 0.003362 T T T
Fe -5.30314000606 1.54316547516 3.42737702355 0.034226 -0.051683 -0.060287 T T T
Fe -3.60352447965 1.74030375892 1.7213812946 -0.038084 0.068499 0.056924 T T T
Parameter Value
nbands 21
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2
Fe potpawPBE/Fe/POTCAR 201d71adcb39575fc20d69f0abd331ae9c01ed2e

1.19 11/eos-exp/f+15   11 eos_dash_exp f_plus_15

  x y z
A0 -1.92084 0.0 -1.92084
A1 0.0 -1.92084 1.92084
A2 -3.60574 3.60574 3.60574
species x y z fx fy fz free x free y free z
Al -1.70274811209 -0.152372217551 1.72799358203 -0.001016 -0.015145 0.009612 T T T
Fe -5.31888643404 1.53641622409 3.43283036647 0.011105 -0.02964 -0.037354 T T T
Fe -3.61583545387 1.74492599346 1.7223960515 -0.010088 0.044785 0.027742 T T T
Parameter Value
nbands 21
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2
Fe potpawPBE/Fe/POTCAR 201d71adcb39575fc20d69f0abd331ae9c01ed2e

1.20 11/eos-exp/f+2   11 eos_dash_exp f_plus_2

  x y z
A0 -1.84555 0.0 -1.84555
A1 0.0 -1.84555 1.84555
A2 -3.4644 3.4644 3.4644
species x y z fx fy fz free x free y free z
Al -1.75029374339 -0.0841326953171 1.75144674035 -0.006952 -0.003547 0.01682 T T T
Fe -5.24418323089 1.55674197758 3.40127583308 0.081175 -0.052085 -0.064081 T T T
Fe -3.56770302572 1.73165071774 1.73049742657 -0.074224 0.055633 0.047261 T T T
Parameter Value
nbands 21
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2
Fe potpawPBE/Fe/POTCAR 201d71adcb39575fc20d69f0abd331ae9c01ed2e

1.21 11/eos-exp/f+4   11 eos_dash_exp f_plus_4

  x y z
A0 -1.85754 0.0 -1.85754
A1 0.0 -1.85754 1.85754
A2 -3.4869 3.4869 3.4869
species x y z fx fy fz free x free y free z
Al -1.74219271636 -0.0933112216124 1.74481701196 -0.01609 -0.003222 0.033588 T T T
Fe -5.26036201118 1.55320104576 3.40867525476 0.120223 -0.071335 -0.093285 T T T
Fe -3.57161527246 1.73238017585 1.72972773328 -0.104133 0.074557 0.059697 T T T
Parameter Value
nbands 21
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2
Fe potpawPBE/Fe/POTCAR 201d71adcb39575fc20d69f0abd331ae9c01ed2e

1.22 11/eos-exp/f+6   11 eos_dash_exp f_plus_6

  x y z
A0 -1.86937 0.0 -1.86937
A1 0.0 -1.86937 1.86937
A2 -3.50911 3.50911 3.50911
species x y z fx fy fz free x free y free z
Al -1.73452887124 -0.101697405678 1.73856189969 -0.015386 -0.012456 0.039644 T T T
Fe -5.27502082144 1.54772132046 3.4142939235 0.127115 -0.055701 -0.087484 T T T
Fe -3.57645030732 1.73441608522 1.73036417681 -0.111729 0.068157 0.04784 T T T
Parameter Value
nbands 21
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2
Fe potpawPBE/Fe/POTCAR 201d71adcb39575fc20d69f0abd331ae9c01ed2e

1.23 11/eos-exp/f+8   11 eos_dash_exp f_plus_8

  x y z
A0 -1.88105 0.0 -1.88105
A1 0.0 -1.88105 1.88105
A2 -3.53104 3.53104 3.53104
species x y z fx fy fz free x free y free z
Al -1.72649034784 -0.11573354282 1.73674863604 -0.016594 -0.002774 0.032443 T T T
Fe -5.28013390733 1.54597101428 3.41783536417 0.029827 -0.01744 -0.039596 T T T
Fe -3.59105574483 1.73852252854 1.7286359998 -0.013233 0.020213 0.007153 T T T
Parameter Value
nbands 21
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2
Fe potpawPBE/Fe/POTCAR 201d71adcb39575fc20d69f0abd331ae9c01ed2e

1.24 11/eos-exp/f-10   11 eos_dash_exp f_dash_10

  x y z
A0 -1.77014 0.0 -1.77014
A1 0.0 -1.77014 1.77014
A2 -3.32284 3.32284 3.32284
species x y z fx fy fz free x free y free z
Al -1.7975784663 -0.01829295971 1.78049380651 -0.007299 0.023676 -0.013472 T T T
Fe -0.0656240800248 0.0224466618076 0.0395349460384 0.084793 -0.065991 -0.04627 T T T
Fe -3.53058745368 1.7228162979 1.74035124745 -0.077494 0.042315 0.059741 T T T
Parameter Value
nbands 21
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2
Fe potpawPBE/Fe/POTCAR 201d71adcb39575fc20d69f0abd331ae9c01ed2e

1.25 11/eos-exp/f-12   11 eos_dash_exp f_dash_12

  x y z
A0 -1.75693 0.0 -1.75693
A1 0.0 -1.75693 1.75693
A2 -3.29804 3.29804 3.29804
species x y z fx fy fz free x free y free z
Al -1.80588201814 -0.00576933899531 1.78487378934 -0.004797 0.023557 -0.019673 T T T
Fe -0.0889524804644 0.0361683086543 0.057258635695 0.086292 -0.05927 -0.035757 T T T
Fe -3.52375550139 1.72137103034 1.74304757497 -0.081495 0.035713 0.05543 T T T
Parameter Value
nbands 21
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2
Fe potpawPBE/Fe/POTCAR 201d71adcb39575fc20d69f0abd331ae9c01ed2e

1.26 11/eos-exp/f-15   11 eos_dash_exp f_dash_15

  x y z
A0 -1.73673 0.0 -1.73673
A1 0.0 -1.73673 1.73673
A2 -3.26013 3.26013 3.26013
species x y z fx fy fz free x free y free z
Al -1.81850401219 0.0184814979188 1.7846748897 -0.013651 0.006945 0.022302 T T T
Fe -0.121256908412 0.0564193466513 0.0901670119937 0.073536 -0.071854 -0.082079 T T T
Fe -3.5167390794 1.71477915543 1.7482480983 -0.059885 0.064909 0.059777 T T T
Parameter Value
nbands 21
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2
Fe potpawPBE/Fe/POTCAR 201d71adcb39575fc20d69f0abd331ae9c01ed2e

1.27 11/eos-exp/f-2   11 eos_dash_exp f_dash_2

  x y z
A0 -1.8211 0.0 -1.8211
A1 0.0 -1.8211 1.8211
A2 -3.41851 3.41851 3.41851
species x y z fx fy fz free x free y free z
Al -1.76538350661 -0.067067453209 1.76453861606 -0.008756 0.02094 -0.003441 T T T
Fe -3.39061275864 3.3875708672 3.38853117003 0.024749 -0.062564 -0.052235 T T T
Fe -3.56063373475 1.72930658601 1.73015021391 -0.015993 0.041624 0.055675 T T T
Parameter Value
nbands 21
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2
Fe potpawPBE/Fe/POTCAR 201d71adcb39575fc20d69f0abd331ae9c01ed2e

1.28 11/eos-exp/f-4   11 eos_dash_exp f_dash_4

  x y z
A0 -1.80863 0.0 -1.80863
A1 0.0 -1.80863 1.80863
A2 -3.3951 3.3951 3.3951
species x y z fx fy fz free x free y free z
Al -1.77477734473 -0.0548385641908 1.77147863672 0.018222 -8.4e-05 -0.038433 T T T
Fe -3.38991272702 3.37906159113 3.38279256816 0.054526 -0.094194 -0.078195 T T T
Fe -3.55193992824 1.72558697306 1.72894879512 -0.072747 0.094278 0.116628 T T T
Parameter Value
nbands 21
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2
Fe potpawPBE/Fe/POTCAR 201d71adcb39575fc20d69f0abd331ae9c01ed2e

1.29 11/eos-exp/f-6   11 eos_dash_exp f_dash_6

  x y z
A0 -1.79598 0.0 -1.79598
A1 0.0 -1.79598 1.79598
A2 -3.37135 3.37135 3.37135
species x y z fx fy fz free x free y free z
Al -1.78297699606 -0.0446680285269 1.77821103953 0.028987 -0.000194 -0.062433 T T T
Fe -0.0156774252598 -0.000431572871362 0.00517398273374 0.050099 -0.112472 -0.086264 T T T
Fe -3.54662557868 1.7235596014 1.72848497774 -0.079085 0.112666 0.148697 T T T
Parameter Value
nbands 21
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2
Fe potpawPBE/Fe/POTCAR 201d71adcb39575fc20d69f0abd331ae9c01ed2e

1.30 11/eos-exp/f-8   11 eos_dash_exp f_dash_8

  x y z
A0 -1.78315 0.0 -1.78315
A1 0.0 -1.78315 1.78315
A2 -3.34727 3.34727 3.34727
species x y z fx fy fz free x free y free z
Al -1.78874833405 -0.029531043967 1.77374404304 -0.022672 0.030355 0.013661 T T T
Fe -0.0461476403345 0.00738880489013 0.0220586228803 0.121535 -0.072896 -0.06196 T T T
Fe -3.53446402561 1.72468223908 1.74014733408 -0.098863 0.042541 0.048299 T T T
Parameter Value
nbands 21
encut 375.0
sigma 0.1
prec Normal
kpts [12, 12, 5]
xc PBE
txt -
gamma True
Al potpawPBE/Al/POTCAR c8d9ecb0b6ebec0256c5f5072cee4de6a046dac2
Fe potpawPBE/Fe/POTCAR 201d71adcb39575fc20d69f0abd331ae9c01ed2e

2 Tabulating the results in column mode

We can use column view to see the results in a tabular like form. For example, here we capture the VOLUME and TOTALENERGY properties.

ITEM VOLUME TOTALENERGY
* Using org-entries like a database    
** Generating the entries    
* 10/eos-exp/f+0 :10:eosdashexp:fplus0: 41.7621235495 -13.997605
* 10/eos-exp/f+10 :10:eosdashexp:fplus10: 45.9384934449 -13.874719
* 10/eos-exp/f+12 :10:eosdashexp:fplus12: 46.7733446838 -13.826981
* 10/eos-exp/f+15 :10:eosdashexp:fplus15: 48.0264189364 -13.744565
* 10/eos-exp/f+2 :10:eosdashexp:fplus2: 42.5973719405 -13.991505
* 10/eos-exp/f+4 :10:eosdashexp:fplus4: 43.4325784041 -13.97507
* 10/eos-exp/f+6 :10:eosdashexp:fplus6: 44.2677528152 -13.949606
* 10/eos-exp/f+8 :10:eosdashexp:fplus8: 45.10318841 -13.915655
* 10/eos-exp/f-10 :10:eosdashexp:fdash10: 37.5859624695 -13.819891
* 10/eos-exp/f-12 :10:eosdashexp:fdash12: 36.75057064 -13.730761
* 10/eos-exp/f-15 :10:eosdashexp:fdash15: 35.4979860465 -13.553386
* 10/eos-exp/f-2 :10:eosdashexp:fdash2: 40.9267763602 -13.991485
* 10/eos-exp/f-4 :10:eosdashexp:fdash4: 40.0914758244 -13.971902
* 10/eos-exp/f-6 :10:eosdashexp:fdash6: 39.2564933754 -13.938219
* 10/eos-exp/f-8 :10:eosdashexp:fdash8: 38.4210237246 -13.888471
* 11/eos-exp/f+0 :11:eosdashexp:fplus0: 34.7058033185 -20.281953
* 11/eos-exp/f+10 :11:eosdashexp:fplus10: 38.1763228931 -20.095119
* 11/eos-exp/f+12 :11:eosdashexp:fplus12: 38.870353968 -20.024412
* 11/eos-exp/f+15 :11:eosdashexp:fplus15: 39.9114994655 -19.90227
* 11/eos-exp/f+2 :11:eosdashexp:fplus2: 35.3998087733 -20.271762
* 11/eos-exp/f+4 :11:eosdashexp:fplus4: 36.0941730661 -20.24583
* 11/eos-exp/f+6 :11:eosdashexp:fplus6: 36.7882199604 -20.206804
* 11/eos-exp/f+8 :11:eosdashexp:fplus8: 37.4821566447 -20.157092
* 11/eos-exp/f-10 :11:eosdashexp:fdash10: 31.2353169019 -20.038179
* 11/eos-exp/f-12 :11:eosdashexp:fdash12: 30.5411995447 -19.912894
* 11/eos-exp/f-15 :11:eosdashexp:fdash15: 29.4999164187 -19.662755
* 11/eos-exp/f-2 :11:eosdashexp:fdash2: 34.0114931233 -20.275411
* 11/eos-exp/f-4 :11:eosdashexp:fdash4: 33.31756747 -20.249632
* 11/eos-exp/f-6 :11:eosdashexp:fdash6: 32.6233149155 -20.202731
* 11/eos-exp/f-8 :11:eosdashexp:fdash8: 31.9291793012 -20.133749
** Tabulating the results in column mode    
** org-map-entries to get the data    
** Getting specific data from a calculation    
** Summary    

That is more or less what we want, but we cannot use that table as a data source very directly. While you can use it as a data source, you just get a string of the whole table, e.g.

print data.__class__
<type 'str'>

You could parse that string, or try converting it to a table, but we skip that for now. In the next section we consider another approach that more directly gets at the data.

3 org-map-entries to get the data

Let us try a different approach. Here we map over headlines that match a criteria, and get specific data. We add a header of labels and horizontal line to the beginning of the table. Here we find the results tagged with 11, and that match fdash* (we actually use a regular expression).

(cons '(label volume energy) 
      (cons 'hline
            (org-map-entries
             (lambda ()
               (list (nth 4 (org-heading-components))
                     (org-entry-get (point) "VOLUME")
                     (org-entry-get (point) "TOTAL_ENERGY"))) 
             ;; this next line specifies headlines tagged with 11
             ;; and that match the regular expression in {}
             "+11+{f_dash_.*}")))
label volume energy
11/eos-exp/f-10 31.2353169019 -20.038179
11/eos-exp/f-12 30.5411995447 -19.912894
11/eos-exp/f-15 29.4999164187 -19.662755
11/eos-exp/f-2 34.0114931233 -20.275411
11/eos-exp/f-4 33.31756747 -20.249632
11/eos-exp/f-6 32.6233149155 -20.202731
11/eos-exp/f-8 31.9291793012 -20.133749

Now, since there are strings in the table (or in the results from the named code-block), we will have to cast the results to floats using a numpy array. Note it appears that we actually run the code block to get the results, they do not come from the table. The table is just helpful to know what data you are using.

import matplotlib.pyplot as plt
import numpy as np

print E

plt.plot(np.array(V), np.array(E), 'ko')
plt.xlabel('Volume $\AA^3$')
plt.ylabel('Energy (eV)')
plt.savefig('11-eos.png')
['-20.038179', '-19.912894', '-19.662755', '-20.275411', '-20.249632', '-20.202731', '-20.133749']

And here you have the figure. We extracted some data into an org-file in human readable form. Then, we extracted the data from those entries to a table, and finally plotted it.

4 Getting specific data from a calculation

Say you want the stress from some calculation. Each heading is identified by a CUSTOMID, so we can temporarily go to that headline, and get the property. Easy!

(save-excursion
  (org-open-link-from-string "[[#10/eos-exp/f+0]]")
  (org-entry-get (point) "STRESS"))
[-0.003191325893994518, -0.003191325893994518, -0.003191325893994518, -0.00042576435655845916, 0.00042576435655845916, 0.00042576435655845916]

Note, however, that the value returned is a string, so we need to convert it to numbers if we want to do anything with it, e.g. find the maximum component. Here, we eval the string in Python to make it a list, and then find the maximum value.

import numpy as np
print np.abs(np.array(eval(stress))).max()
0.00319132589399

Next, we get the unit cell from that calculation, so we can calculate the volume using python. The unit cell is stored in a table and we extract the unit cell vectors from it in the code block header.

import numpy as np

print('cell = {}'.format(np.array(data)))
print('Volume = {}'.format(np.linalg.det(np.array(data))))
cell = [[-1.98408  0.      -1.98408]
 [ 0.      -1.98408  1.98408]
 [-3.53625  3.53625  3.53625]]
Volume = 41.7621235495

Compare that to the volume we computed when the entry was generated, and you can see they are the same.

(save-excursion
  (org-open-link-from-string "[[#10/eos-exp/f+0]]")
  (org-entry-get (point) "VOLUME"))
41.7621235495

The last example is getting the formula for the calculation. The atoms positions are stored in a table in the entry, and the species for each atom is stored in the first column. We extract the species into a variable, then then get counts for each species, and finally construct a string representation of the formula.

(let* ((unique-species '())
      (counts))
  ;; first get unique species
  (mapcar (lambda (s) (add-to-list 'unique-species s)) species)

  ;; now get counts
  (setq counts
        (mapcar (lambda (s)
                  (--count (string= it s) species)) unique-species))

  ;; Now put them together
  (mapconcat 'identity (cl-mapcar (lambda (s n)
                  (format "%s%s" s n)) unique-species counts) ""))
Ni1Al2

Suppose we want to sort the elements alphabetically. We can make a list of cons cells of element and count, sort the list by element, and then put them back together. We do this in lisp.

(let* ((unique-species '())
      (counts))
  ;; first get unique species
  (mapcar (lambda (s) (add-to-list 'unique-species s)) species)

  ;; now get counts
  (setq counts
        (mapcar (lambda (s)
                  (--count (string= it s) species)) unique-species))

  (mapconcat (lambda (x)
               (format "%s%s" (car x) (cdr x)))
             (cl-sort
              (cl-mapcar (lambda (a b) (cons a b)) unique-species counts)
              'string-lessp :key 'car)
             ""))
Al2Ni1

That is not too bad. It is a little verbose, some of that could be put into a library to be reused. For example, here is the same code in Python for the unsorted formula

from collections import Counter
counts = Counter(species)
print ''.join(['{0}{1}'.format(x, counts[x]) for x in counts])
Ni1Al2

and for the sorted formula.

from collections import Counter
counts = Counter(species)
print ''.join(['{0}{1}'.format(x, counts[x]) for x in sorted(counts.keys())])
Al2Ni1

Obviously a lot must be happening behind the scenes in those short, dense python blocks. For example, the list comprehension syntax in Python is functionally similar to the mapcar code, and the join function is similar to the mapconcat code in lisp.

5 Summary

This has some potential. It is a hybrid approach to human and machine readable data, that enables inline analysis. You can mix programming languages, which is great if one language has unique capabilities or is just more convenient. There are some limitations, mostly that org-properties are read as strings, and they have to be converted to the right data type, e.g. numbers or lists or arrays, etc… But, these can be saved as forms that can be directly evaled in some languages. On the other hand, it is possible to do analysis on another machine where the original data does not exist.

This is a very different mental model of data than I am used to. We typically have thought about data in files, and paths to get to that data. Here, data is in headings, and we use links to get to the data. We also use different syntax to link data to code blocks. That means in some cases the code blocks cannot be run independently of this file.

Copyright (C) 2014 by John Kitchin. See the License for information about copying.

org-mode source

Org-mode version = 8.2.7c

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