diff --git a/.gitmodules b/.gitmodules
index de35e497e9770d1a60c763977fd8eb21cdc92177..4d8e22a41b30369fc849460bd35eaacaa98ef410 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -207,3 +207,6 @@
[submodule "dependencies/parsers/xps"]
path = dependencies/parsers/xps
url = https://github.com/nomad-coe/nomad-parser-xps.git
+[submodule "dependencies/parsers/aflow"]
+ path = dependencies/parsers/aflow
+ url = https://github.com/nomad-coe/nomad-parser-aflow.git
diff --git a/dependencies/parsers/aflow b/dependencies/parsers/aflow
new file mode 160000
index 0000000000000000000000000000000000000000..012e25e82f33c10dc8ea60ad28577477a8374535
--- /dev/null
+++ b/dependencies/parsers/aflow
@@ -0,0 +1 @@
+Subproject commit 012e25e82f33c10dc8ea60ad28577477a8374535
diff --git a/nomad/datamodel/metainfo/simulation/calculation.py b/nomad/datamodel/metainfo/simulation/calculation.py
index 6dd862df42c79c0d39bb3f0b7aaa14e16c14e76c..27b517e6aa0c7b011c14412d22971cf60ac2a406 100644
--- a/nomad/datamodel/metainfo/simulation/calculation.py
+++ b/nomad/datamodel/metainfo/simulation/calculation.py
@@ -1472,7 +1472,7 @@ class BaseCalculation(MSection):
categories=[FastAccess])
n_references = Quantity(
- type=np.dtype(np.float64),
+ type=np.dtype(np.int32),
shape=[],
description='''
Number of references to the current section calculation.
diff --git a/nomad/datamodel/metainfo/simulation/run.py b/nomad/datamodel/metainfo/simulation/run.py
index e00aa609bd50522f8056fd7e3b13f8c84782d53d..02f55447f2f5ace47d31600d484d2b6f007ad520 100644
--- a/nomad/datamodel/metainfo/simulation/run.py
+++ b/nomad/datamodel/metainfo/simulation/run.py
@@ -24,7 +24,7 @@ from nomad.metainfo import ( # pylint: disable=unused-import
from nomad.datamodel.metainfo.simulation.method import Method
from nomad.datamodel.metainfo.simulation.system import System
from nomad.datamodel.metainfo.simulation.calculation import Calculation
-
+from nomad.datamodel.metainfo.common import FastAccess
m_package = Package()
@@ -175,41 +175,6 @@ class MessageRun(MSection):
''')
-class RunReference(MSection):
- '''
- Section that describes the relationship between the current section to other run
- sections.
-
- The kind of relationship between the the current section and the referenced section
- run is described by kind. The referenced section is given by value (typically used for
- a run section in the same archive) or external_url.
- '''
-
- m_def = Section(validate=False)
-
- external_url = Quantity(
- type=str,
- shape=[],
- description='''
- URL used to reference an externally stored run section.
- ''')
-
- kind = Quantity(
- type=str,
- shape=[],
- description='''
- Defines the kind of relationship between the referenced section run with the
- present section.
- ''')
-
- value = Quantity(
- type=Reference(SectionProxy('Run')),
- shape=[],
- description='''
- Value of the referenced section run.
- ''')
-
-
class Run(MSection):
'''
Every section run represents a single call of a program.
@@ -240,6 +205,31 @@ class Run(MSection):
An optional calculation id, if one is found in the code input/output files.
''')
+ starting_run_ref = Quantity(
+ type=Reference(SectionProxy('Run')),
+ shape=[],
+ description='''
+ Links the current section run to a section run containing the calculations from
+ which the current section starts.
+ ''',
+ categories=[FastAccess])
+
+ n_references = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Number of references to the current section calculation.
+ ''')
+
+ runs_ref = Quantity(
+ type=Reference(SectionProxy('Run')),
+ shape=['n_references'],
+ description='''
+ Links the the current section to other run sections. Such a link is necessary for
+ example for workflows that may contain a series of runs.
+ ''',
+ categories=[FastAccess])
+
program = SubSection(sub_section=Program.m_def)
time_run = SubSection(sub_section=TimeRun.m_def)
@@ -252,7 +242,5 @@ class Run(MSection):
calculation = SubSection(sub_section=Calculation.m_def, repeats=True)
- run_ref = SubSection(sub_section=RunReference.m_def, repeats=True)
-
m_package.__init_metainfo__()
diff --git a/nomad/datamodel/metainfo/workflow.py b/nomad/datamodel/metainfo/workflow.py
index 8488afc2e57b78dfe75f696ca1b07e420e200575..f71e7f710d85f6013adcb3ec1486cb0d2e4d49da 100644
--- a/nomad/datamodel/metainfo/workflow.py
+++ b/nomad/datamodel/metainfo/workflow.py
@@ -6,7 +6,7 @@ from nomad.metainfo import ( # pylint: disable=unused-import
Reference, MEnum, derived)
from nomad.metainfo.search_extension import Search
from nomad.datamodel.metainfo.simulation.calculation import Calculation
-from nomad.datamodel.metainfo.simulation.run import RunReference
+from nomad.datamodel.metainfo.simulation.run import Run
from .common import FastAccess
@@ -1141,40 +1141,6 @@ class SinglePoint(MSection):
''')
-class WorkflowReference(MSection):
- '''
- Section that provides a link between a section to a section workflow. Such a link is
- necessary for example between an Debye model that uses a the poisson ratio calculated
- from an elastic workflow. The relationship should be described by kind and the
- referred section workflow is given by value. An external url can also be provided in
- place of value.
- '''
-
- m_def = Section(validate=False)
-
- kind = Quantity(
- type=str,
- shape=[],
- description='''
- Defines the relationship between the referenced section workflow and the present
- section.
- ''')
-
- external_url = Quantity(
- type=str,
- shape=[],
- description='''
- URL used to reference an externally stored section workflow.
- ''')
-
- value = Quantity(
- type=Reference(SectionProxy('Workflow')),
- shape=[],
- description='''
- Value of the referenced section wofklow.
- ''')
-
-
class Workflow(MSection):
'''
Section containing the results of a workflow.
@@ -1224,6 +1190,31 @@ class Workflow(MSection):
simulation.
''')
+ run_ref = Quantity(
+ type=Reference(Run.m_def),
+ shape=[],
+ description='''
+ Links the section workflow to the section run that contains the calculations.
+ ''',
+ categories=[FastAccess])
+
+ n_references = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Number of references to the current section workflow.
+ ''')
+
+ workflows_ref = Quantity(
+ type=Reference(SectionProxy('Workflow')),
+ shape=['n_references'],
+ description='''
+ Links the the current section to other workflow sections. Such a link is necessary
+ for example between an Debye model that uses a the poisson ratio calculated
+ from an elastic workflow.
+ ''',
+ categories=[FastAccess])
+
single_point = SubSection(
sub_section=SinglePoint.m_def,
# TODO determine if there is a need for this to be a repeating section
@@ -1280,9 +1271,3 @@ class Workflow(MSection):
thermodynamics = SubSection(
sub_section=Thermodynamics.m_def,
repeats=False)
-
- workflow_ref = SubSection(
- sub_section=WorkflowReference.m_def, repeats=True)
-
- run_ref = SubSection(
- sub_section=RunReference.m_def, repeats=True)
diff --git a/nomad/normalizing/workflow.py b/nomad/normalizing/workflow.py
index 14871fd1f376a5407a9b884fa8aa2668236ed634..09ebd0a88fe1911ddbaf31681fbcb4daa9eef8bc 100644
--- a/nomad/normalizing/workflow.py
+++ b/nomad/normalizing/workflow.py
@@ -383,7 +383,7 @@ class ThermodynamicsNormalizer(TaskNormalizer):
values.append(quantity.magnitude if hasattr(quantity, 'magnitude') else quantity)
except Exception:
pass
- unit = quantity.unit if hasattr(quantity, 'unit') else 1.0
+ unit = quantity.units if hasattr(quantity, 'units') else 1.0
setattr(self.section, name, np.array(values) * unit)
if not self.section.temperature:
diff --git a/nomad/parsing/parsers.py b/nomad/parsing/parsers.py
index 6b5d398c4f3684666ace0378db6fc2eccf1255b1..bdcf52134f86a206c93f97ddf0ae04d358e95189 100644
--- a/nomad/parsing/parsers.py
+++ b/nomad/parsing/parsers.py
@@ -72,6 +72,7 @@ from qboxparser import QboxParser
from openkimparser import OpenKIMParser
from xpsparser import XPSParser
from eelsdbparser import EELSDBParser
+from aflowparser import AFLOWParser
# TODO
# from mpesparser import MPESParser
# from aptfimparser import APTFIMParser
@@ -216,6 +217,7 @@ parsers = [
# APTFIMParser(),
EELSDBParser(),
XPSParser(),
+ AFLOWParser(),
ArchiveParser()
]
diff --git a/tests/data/parsers/aflow/aflow.agl.out b/tests/data/parsers/aflow/aflow.agl.out
new file mode 100644
index 0000000000000000000000000000000000000000..49b6bedabd703cf2360d55142c9d930509da5c7a
--- /dev/null
+++ b/tests/data/parsers/aflow/aflow.agl.out
@@ -0,0 +1,406 @@
+[AFLOW] **************************************************************************************************************************
+[AGL_RESULTS]START
+agl_thermal_conductivity_300K=2.95475 (W/m*K)
+agl_debye=374.916 (K)
+agl_acoustic_debye=187.5 (K)
+agl_gruneisen=2.22975
+agl_heat_capacity_Cv_300K=22.2739 (kB/cell)
+agl_heat_capacity_Cp_300K=23.0311 (kB/cell)
+agl_thermal_expansion_300K=5.04085e-05 (1/K)
+agl_bulk_modulus_static_300K=153.361 (GPa)
+agl_bulk_modulus_isothermal_300K=148.318 (GPa)
+agl_poisson_ratio_source=ael_poisson_ratio_0.364064
+agl_vibrational_free_energy_300K_cell=-54.2809 (meV/cell)
+agl_vibrational_free_energy_300K_atom=-6.78511 (meV/atom)
+agl_vibrational_entropy_300K_cell=2.40318 (meV/cell*K)
+agl_vibrational_entropy_300K_atom=0.300398 (meV/atom*K)
+[AGL_RESULTS]STOP
+[AFLOW] **************************************************************************************************************************
+[AGL_THERMAL_PROPERTIES_TEMPERATURE]START
+# T (K) Kappa (W/(m*K)) Debye temp. (K) Gruneisen Parameter Cv (kB/cell) Cp (kB/cell) Thermal Expan. (10^{-5}/K) B_static (Gpa) B_isothermal (GPa)
+ 0.00 0.000000 377.203016 2.222290 0.000000 0.000000 0.000000 157.205309 157.205309
+ 10.00 88.642556 377.202741 2.222291 0.034847 0.034847 0.007424 157.205708 157.205449
+ 20.00 44.321278 377.199501 2.222301 0.278776 0.278783 0.059389 157.210959 157.206809
+ 30.00 29.547519 377.189907 2.222332 0.936564 0.936689 0.199533 157.219347 157.198435
+ 40.00 22.160639 377.164257 2.222415 2.144133 2.145004 0.456929 157.219756 157.155920
+ 50.00 17.728511 377.110694 2.222589 3.839306 3.842799 0.818707 157.200191 157.057296
+ 60.00 14.773759 377.023892 2.222870 5.802300 5.811885 1.238585 157.157478 156.898293
+ 70.00 12.663222 376.900808 2.223269 7.808703 7.828989 1.669219 157.090632 156.683602
+ 80.00 11.080319 376.742554 2.223782 9.708118 9.744020 2.078726 157.006332 156.427845
+ 90.00 9.849173 376.551941 2.224402 11.425732 11.481799 2.451114 156.907899 156.141707
+ 100.00 8.864256 376.332871 2.225114 12.938111 13.018179 2.781231 156.796755 155.832377
+ 110.00 8.058414 376.088863 2.225910 14.250271 14.357387 3.069971 156.672833 155.503937
+ 120.00 7.386880 375.822650 2.226779 15.380380 15.516868 3.321010 156.537312 155.160390
+ 130.00 6.818658 375.536923 2.227714 16.351028 16.518610 3.538999 156.390752 154.804158
+ 140.00 6.331611 375.234051 2.228707 17.184829 17.384756 3.728603 156.234435 154.437714
+ 150.00 5.909504 374.916157 2.229752 17.902451 18.135618 3.894091 156.069802 154.063238
+ 160.00 5.540160 374.584892 2.230843 18.521945 18.788981 4.039200 155.898134 153.682446
+ 170.00 5.214268 374.241783 2.231976 19.058678 19.360024 4.167105 155.720828 153.296974
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+ 210.00 4.221074 372.780237 2.236835 20.605983 21.046793 4.554123 154.967400 151.721719
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+ 1040.00 0.852332 332.411062 2.398150 23.877553 28.177036 7.219659 133.524494 113.150233
+ 1050.00 0.844215 331.833803 2.400943 23.880275 28.249994 7.258436 133.213582 112.608057
+ 1060.00 0.836251 331.253839 2.403766 23.882917 28.323894 7.297817 132.900717 112.062870
+ 1070.00 0.828435 330.671076 2.406621 23.885484 28.398775 7.337834 132.585684 111.514429
+ 1080.00 0.820764 330.085486 2.409508 23.887978 28.474665 7.378493 132.268603 110.962832
+ 1090.00 0.813234 329.497014 2.412427 23.890401 28.551599 7.419821 131.949346 110.407925
+ 1100.00 0.805841 328.905585 2.415380 23.892757 28.629628 7.461862 131.627536 109.849303
+ 1110.00 0.798582 328.311235 2.418366 23.895047 28.708749 7.504577 131.304018 109.287789
+ 1120.00 0.791451 327.713824 2.421388 23.897274 28.789039 7.548050 130.977836 108.722395
+ 1130.00 0.784447 327.113335 2.424446 23.899441 28.870530 7.592293 130.649118 108.153222
+ 1140.00 0.777566 326.509666 2.427540 23.901549 28.953232 7.637283 130.318501 107.580874
+ 1150.00 0.770805 325.902684 2.430672 23.903601 29.037259 7.683153 129.984428 107.003759
+ 1160.00 0.764160 325.292717 2.433840 23.905598 29.122569 7.729808 129.648499 106.423472
+ 1170.00 0.757629 324.679194 2.437050 23.907543 29.209288 7.777385 129.309218 105.838449
+ 1180.00 0.751208 324.062277 2.440299 23.909437 29.297428 7.825867 128.967162 105.249249
+ 1190.00 0.744895 323.441937 2.443589 23.911283 29.387033 7.875274 128.622385 104.655892
+ 1200.00 0.738688 322.818102 2.446921 23.913081 29.478161 7.925647 128.274715 104.058172
+ 1210.00 0.732583 322.675694 2.447685 23.914578 29.538971 7.940942 128.308664 103.877942
+ 1220.00 0.726578 321.992292 2.451369 23.916317 29.636082 7.996785 127.913153 103.225909
+ 1230.00 0.720671 321.307575 2.455088 23.918012 29.734894 8.053654 127.516056 102.570756
+ 1240.00 0.714859 320.621566 2.458844 23.919663 29.835423 8.111530 127.117979 101.913060
+ 1250.00 0.709140 319.934424 2.462636 23.921272 29.937731 8.170457 126.718687 101.252571
+ 1260.00 0.703512 319.245895 2.466466 23.922840 30.041915 8.230520 126.317578 100.588636
+ 1270.00 0.697973 318.556096 2.470334 23.924369 30.147997 8.291702 125.915213 99.921795
+ 1280.00 0.692520 317.865039 2.474241 23.925859 30.256050 8.354053 125.511389 99.251816
+ 1290.00 0.687152 317.172571 2.478187 23.927313 30.366169 8.417651 125.105638 98.578185
+ 1300.00 0.681866 316.478819 2.482173 23.928731 30.478388 8.482492 124.698406 97.901326
+ 1310.00 0.676661 315.783882 2.486199 23.930114 30.592756 8.548590 124.289930 97.221453
+ 1320.00 0.671535 315.087587 2.490266 23.931463 30.709404 8.616062 123.879384 96.537690
+ 1330.00 0.666485 314.389933 2.494375 23.932780 30.828386 8.684920 123.467078 95.850312
+ 1340.00 0.661512 313.690853 2.498527 23.934066 30.949787 8.755217 123.052945 95.159210
+ 1350.00 0.656612 312.990522 2.502722 23.935320 31.073680 8.826992 122.637003 94.464383
+ 1360.00 0.651783 312.288786 2.506961 23.936546 31.200200 8.900353 122.218661 93.765187
+ 1370.00 0.647026 311.585734 2.511244 23.937742 31.329357 8.975253 121.798905 93.062579
+ 1380.00 0.642337 310.880890 2.515575 23.938910 31.461374 9.051893 121.376306 92.355042
+ 1390.00 0.637716 310.171438 2.519972 23.940053 31.596621 9.130584 120.948944 91.640309
+ 1400.00 0.633161 309.456201 2.524444 23.941171 31.735342 9.211510 120.516033 90.917404
+ 1410.00 0.628671 308.734858 2.528994 23.942265 31.877741 9.294818 120.077073 90.185722
+ 1420.00 0.624243 308.007441 2.533624 23.943336 32.023982 9.380608 119.631997 89.445126
+ 1430.00 0.619878 307.273611 2.538337 23.944384 32.174279 9.469028 119.180470 88.695162
+ 1440.00 0.615573 306.533219 2.543136 23.945411 32.328859 9.560231 118.722111 87.935355
+ 1450.00 0.611328 305.786001 2.548024 23.946416 32.487938 9.654353 118.256833 87.165497
+ 1460.00 0.607141 305.031969 2.553004 23.947401 32.651735 9.751530 117.784555 86.385422
+ 1470.00 0.603011 304.270478 2.558082 23.948365 32.820570 9.851988 117.304646 85.594325
+ 1480.00 0.598936 303.501498 2.563259 23.949311 32.994712 9.955899 116.816915 84.791910
+ 1490.00 0.594916 302.724935 2.568540 23.950238 33.174416 10.063413 116.321483 83.978183
+ 1500.00 0.590950 301.940113 2.573929 23.951147 33.360131 10.174863 115.817196 83.151791
+ 1510.00 0.587037 301.146951 2.579432 23.952038 33.552159 10.290424 115.304201 82.312754
+ 1520.00 0.583175 300.345167 2.585051 23.952912 33.750932 10.410396 114.781838 81.460247
+ 1530.00 0.579363 300.285737 2.585470 23.953539 33.836938 10.430514 114.862200 81.312208
+ 1540.00 0.575601 299.360977 2.592029 23.954415 34.063343 10.572043 114.236032 80.334373
+ 1550.00 0.571887 298.432445 2.598695 23.955273 34.297910 10.718725 113.604318 79.346598
+ 1560.00 0.568222 297.500191 2.605469 23.956113 34.541161 10.870911 112.966517 78.348226
+ 1570.00 0.564602 296.564095 2.612355 23.956936 34.793646 11.028954 112.322289 77.338775
+ 1580.00 0.561029 295.624104 2.619355 23.957742 35.055911 11.193194 111.671597 76.318065
+ 1590.00 0.557500 294.680114 2.626473 23.958531 35.328583 11.364025 111.014200 75.285704
+ 1600.00 0.554016 293.732193 2.633711 23.959305 35.612308 11.541854 110.349956 74.241417
+ 1610.00 0.550575 292.780262 2.641072 23.960062 35.907864 11.727190 109.678334 73.184517
+ 1620.00 0.547176 291.824382 2.648559 23.960804 36.215950 11.920446 108.999619 72.115146
+ 1630.00 0.543819 290.864415 2.656175 23.961531 36.537489 12.122223 108.313236 71.032550
+ 1640.00 0.540503 289.900263 2.663924 23.962244 36.873418 12.333110 107.619002 69.936365
+ 1650.00 0.537228 288.931939 2.671809 23.962943 37.224710 12.553705 106.916941 68.826447
+ 1660.00 0.533991 287.956341 2.679859 23.963628 37.593468 12.785513 106.203535 67.698518
+ 1670.00 0.530794 286.963185 2.688165 23.964304 37.983843 13.031565 105.470739 66.542315
+ 1680.00 0.527634 285.951194 2.696745 23.964970 38.398384 13.293612 104.716186 65.354839
+ 1690.00 0.524512 284.918403 2.705626 23.965626 38.839828 13.573453 103.938615 64.134012
+ 1700.00 0.521427 283.863780 2.714827 23.966274 39.311403 13.873274 103.135847 62.876971
+ 1710.00 0.518378 282.785767 2.724372 23.966914 39.816760 14.195493 102.306237 61.581222
+ 1720.00 0.515364 281.682197 2.734292 23.967545 40.360215 14.542957 101.448081 60.244017
+ 1730.00 0.512385 280.551176 2.744620 23.968170 40.947165 14.919311 100.558231 58.861140
+ 1740.00 0.509440 279.390364 2.755392 23.968788 41.583914 15.328761 99.633915 57.428557
+ 1750.00 0.506529 280.016499 2.749560 23.969003 41.455610 15.161926 100.288431 57.985246
+ 1760.00 0.503651 278.442875 2.764316 23.969691 42.315126 15.731324 98.989462 56.073253
+ 1770.00 0.500805 276.852131 2.779570 23.970366 43.261328 16.357929 97.661291 54.112461
+ 1780.00 0.497992 275.243968 2.795347 23.971030 44.308397 17.051098 96.301930 52.099752
+ 1790.00 0.495210 273.618179 2.811669 23.971683 45.473153 17.821831 94.910639 50.033209
+ 1800.00 0.492459 271.973892 2.828571 23.972325 46.776907 18.684108 93.485844 47.909816
+ 1810.00 0.489738 270.311160 2.846076 23.972956 48.246434 19.655558 92.025308 45.726046
+ 1820.00 0.487047 268.629337 2.864217 23.973577 49.914986 20.757899 90.528463 43.479749
+ 1830.00 0.484386 266.927909 2.883030 23.974187 51.826978 22.020371 88.992147 41.166097
+ 1840.00 0.481753 265.178978 2.902863 23.974793 54.071684 23.502949 87.389369 38.747490
+ 1850.00 0.479149 263.304877 2.924693 23.975408 56.852501 25.344016 85.640997 36.115875
+ 1860.00 0.476573 261.269242 2.949101 23.976038 60.429803 27.718027 83.706316 33.211193
+ 1870.00 0.474024 259.018636 2.976965 23.976692 65.281145 30.945127 81.523120 29.942102
+ 1880.00 0.471503 222.364240 3.597724 23.982919 -30.669231 -33.691438 40.566752 -31.722645
+ 1890.00 0.469008 222.364240 3.597724 23.983096 -34.534883 -35.883471 42.889445 -29.785006
+[AGL_THERMAL_PROPERTIES_TEMPERATURE]STOP
+[AFLOW] **************************************************************************************************************************
+[AGL_ENERGIES_TEMPERATURE]START
+# T (K) G (eV/cell) Fvib (meV/cell) Uvib (meV/cell) Svib (meV/cell*K) G (eV/atom) Fvib (meV/atom) Uvib (meV/atom) Svib (meV/atom*K)
+ 0.00 -34.587552 292.543868 292.543868 0.000000 -4.323444 36.567984 36.567984 0.000000
+ 10.00 -34.587555 292.541152 292.551162 0.001001 -4.323444 36.567644 36.568895 0.000125
+ 20.00 -34.587607 292.501102 292.661263 0.008008 -4.323451 36.562638 36.582658 0.001001
+ 30.00 -34.587795 292.331041 293.141037 0.027000 -4.323474 36.541380 36.642630 0.003375
+ 40.00 -34.588254 291.875592 294.408515 0.063323 -4.323532 36.484449 36.801064 0.007915
+ 50.00 -34.589168 290.935442 296.918210 0.119655 -4.323646 36.366930 37.114776 0.014957
+ 60.00 -34.590730 289.308560 300.998645 0.194835 -4.323841 36.163570 37.624831 0.024354
+ 70.00 -34.593112 286.820213 306.780064 0.285141 -4.324139 35.852527 38.347508 0.035643
+ 80.00 -34.596455 283.340502 314.232414 0.386149 -4.324557 35.417563 39.279052 0.048269
+ 90.00 -34.600849 278.783273 323.230953 0.493863 -4.325106 34.847909 40.403869 0.061733
+ 100.00 -34.606344 273.099116 333.610669 0.605116 -4.325793 34.137389 41.701334 0.075639
+ 110.00 -34.612959 266.265755 345.199145 0.717576 -4.326620 33.283219 43.149893 0.089697
+ 120.00 -34.620697 258.280012 357.833784 0.829615 -4.327587 32.285001 44.729223 0.103702
+ 130.00 -34.629547 249.152359 371.369527 0.940132 -4.328693 31.144045 46.421191 0.117517
+ 140.00 -34.639490 238.902130 385.680474 1.048417 -4.329936 29.862766 48.210059 0.131052
+ 150.00 -34.650502 227.554302 400.659051 1.154032 -4.331313 28.444288 50.082381 0.144254
+ 160.00 -34.662556 215.136946 416.213966 1.256731 -4.332820 26.892118 52.026746 0.157091
+ 170.00 -34.675623 201.679961 432.268112 1.356401 -4.334453 25.209995 54.033514 0.169550
+ 180.00 -34.689672 187.214393 448.756517 1.453012 -4.336209 23.401799 56.094565 0.181626
+ 190.00 -34.704672 171.770989 465.624121 1.546595 -4.338084 21.471374 58.203015 0.193324
+ 200.00 -34.720593 155.379822 482.824179 1.637222 -4.340074 19.422478 60.353022 0.204653
+ 210.00 -34.737407 138.070096 500.316906 1.724985 -4.342176 17.258762 62.539613 0.215623
+ 220.00 -34.755084 119.869774 518.068273 1.809993 -4.344385 14.983722 64.758534 0.226249
+ 230.00 -34.773596 100.805716 536.049113 1.892363 -4.346700 12.600714 67.006139 0.236545
+ 240.00 -34.792919 80.903522 554.234307 1.972212 -4.349115 10.112940 69.279288 0.246526
+ 250.00 -34.813028 60.187573 572.602145 2.049658 -4.351628 7.523447 71.575268 0.256207
+ 260.00 -34.833899 38.681138 591.133802 2.124818 -4.354237 4.835142 73.891725 0.265602
+ 270.00 -34.855504 17.013740 609.913189 2.195924 -4.356938 2.126717 76.239149 0.274490
+ 280.00 -34.877839 -6.029217 628.715734 2.266946 -4.359730 -0.753652 78.589467 0.283368
+ 290.00 -34.900873 -29.800481 647.639606 2.336000 -4.362609 -3.725060 80.954951 0.292000
+ 300.00 -34.924588 -54.280851 666.673676 2.403182 -4.365574 -6.785106 83.334210 0.300398
+ 310.00 -34.948966 -79.452129 685.808097 2.468581 -4.368621 -9.931516 85.726012 0.308573
+ 320.00 -34.973987 -105.297048 705.034133 2.532285 -4.371748 -13.162131 88.129267 0.316536
+ 330.00 -34.999636 -131.799087 724.344028 2.594373 -4.374955 -16.474886 90.543004 0.324297
+ 340.00 -35.025897 -158.942747 743.730836 2.654922 -4.378237 -19.867843 92.966355 0.331865
+ 350.00 -35.052756 -186.713193 763.188354 2.714004 -4.381594 -23.339149 95.398544 0.339251
+ 360.00 -35.080197 -215.096098 782.711036 2.771686 -4.385025 -26.887012 97.838880 0.346461
+ 370.00 -35.108205 -244.077589 802.293914 2.828031 -4.388526 -30.509699 100.286739 0.353504
+ 380.00 -35.136770 -273.644596 821.932486 2.883098 -4.392096 -34.205575 102.741561 0.360387
+ 390.00 -35.165876 -303.784877 841.622665 2.936942 -4.395735 -37.973110 105.202833 0.367118
+ 400.00 -35.195514 -334.486545 861.360764 2.989618 -4.399439 -41.810818 107.670095 0.373702
+ 410.00 -35.225671 -365.738683 881.143399 3.041176 -4.403209 -45.717335 110.142925 0.380147
+ 420.00 -35.256337 -397.530019 900.967557 3.091661 -4.407042 -49.691252 112.620945 0.386458
+ 430.00 -35.287500 -429.850396 920.830441 3.141118 -4.410938 -53.731300 115.103805 0.392640
+ 440.00 -35.319152 -462.689964 940.729507 3.189590 -4.414894 -57.836245 117.591188 0.398699
+ 450.00 -35.351283 -496.039095 960.662436 3.237115 -4.418910 -62.004887 120.082804 0.404639
+ 460.00 -35.383884 -529.888852 980.627085 3.283730 -4.422985 -66.236106 122.578386 0.410466
+ 470.00 -35.416945 -564.230457 1000.621499 3.329472 -4.427118 -70.528807 125.077687 0.416184
+ 480.00 -35.450459 -599.055227 1020.643890 3.374373 -4.431307 -74.881903 127.580486 0.421797
+ 490.00 -35.484417 -634.355137 1040.692594 3.418465 -4.435552 -79.294392 130.086574 0.427308
+ 500.00 -35.518811 -670.122379 1060.766080 3.461777 -4.439851 -83.765297 132.595760 0.432722
+ 510.00 -35.553635 -706.349457 1080.862931 3.504338 -4.444204 -88.293682 135.107866 0.438042
+ 520.00 -35.588880 -743.029184 1100.981833 3.546175 -4.448610 -92.878648 137.622729 0.443272
+ 530.00 -35.624540 -780.154415 1121.121580 3.587313 -4.453067 -97.519302 140.140198 0.448414
+ 540.00 -35.660609 -817.718577 1141.281036 3.627777 -4.457576 -102.214822 142.660130 0.453472
+ 550.00 -35.697078 -855.715480 1161.459141 3.667590 -4.462135 -106.964435 145.182393 0.458449
+ 560.00 -35.733943 -894.141328 1181.654824 3.706779 -4.466743 -111.767666 147.706853 0.463347
+ 570.00 -35.771195 -932.990983 1201.867151 3.745365 -4.471399 -116.623873 150.233394 0.468171
+ 580.00 -35.808829 -972.259108 1222.095271 3.783370 -4.476104 -121.532389 152.761909 0.472921
+ 590.00 -35.846841 -1011.939915 1242.338411 3.820811 -4.480855 -126.492489 155.292301 0.477601
+ 600.00 -35.885225 -1052.028617 1262.595821 3.857707 -4.485653 -131.503577 157.824478 0.482213
+ 610.00 -35.923975 -1092.520334 1282.866807 3.894077 -4.490497 -136.565042 160.358351 0.486760
+ 620.00 -35.963087 -1133.409612 1303.150745 3.929936 -4.495386 -141.676202 162.893843 0.491242
+ 630.00 -36.002556 -1174.692257 1323.447013 3.965300 -4.500319 -146.836532 165.430877 0.495663
+ 640.00 -36.042376 -1216.363446 1343.755053 4.000185 -4.505297 -152.045431 167.969382 0.500023
+ 650.00 -36.082543 -1258.418964 1364.074325 4.034605 -4.510318 -157.302370 170.509291 0.504326
+ 660.00 -36.123053 -1300.854431 1384.404332 4.068574 -4.515382 -162.606804 173.050542 0.508572
+ 670.00 -36.163900 -1343.666046 1404.744593 4.102105 -4.520488 -167.958256 175.593074 0.512763
+ 680.00 -36.205082 -1386.849665 1425.094668 4.135212 -4.525635 -173.356208 178.136833 0.516902
+ 690.00 -36.246592 -1430.401415 1445.454137 4.167907 -4.530824 -178.800177 180.681767 0.520988
+ 700.00 -36.288428 -1474.317641 1465.822604 4.200200 -4.536054 -184.289705 183.227825 0.525025
+ 710.00 -36.330586 -1518.594760 1486.199692 4.232105 -4.541323 -189.824345 185.774962 0.529013
+ 720.00 -36.373061 -1563.229624 1506.585041 4.263631 -4.546633 -195.403703 188.323130 0.532954
+ 730.00 -36.415850 -1608.218569 1526.978322 4.294790 -4.551981 -201.027321 190.872290 0.536849
+ 740.00 -36.458949 -1653.558555 1547.379215 4.325592 -4.557369 -206.694819 193.422402 0.540699
+ 750.00 -36.502355 -1699.246692 1567.787412 4.356045 -4.562794 -212.405836 195.973426 0.544506
+ 760.00 -36.546063 -1745.279027 1588.202649 4.386160 -4.568258 -218.159878 198.525331 0.548270
+ 770.00 -36.590072 -1791.653644 1608.624633 4.415946 -4.573759 -223.956705 201.078079 0.551993
+ 780.00 -36.634378 -1838.367446 1629.053113 4.445411 -4.579297 -229.795931 203.631639 0.555676
+ 790.00 -36.678966 -1883.441691 1649.525276 4.472110 -4.584871 -235.430211 206.190659 0.559014
+ 800.00 -36.723857 -1930.967676 1669.962384 4.501163 -4.590482 -241.370959 208.745298 0.562645
+ 810.00 -36.769035 -1978.822727 1690.405511 4.529911 -4.596129 -247.352841 211.300689 0.566239
+ 820.00 -36.814497 -2027.004119 1710.854437 4.558364 -4.601812 -253.375515 213.856805 0.569796
+ 830.00 -36.860240 -2075.509126 1731.308956 4.586528 -4.607530 -259.438641 216.413620 0.573316
+ 840.00 -36.906262 -2124.335304 1751.768867 4.614410 -4.613283 -265.541913 218.971108 0.576801
+ 850.00 -36.952560 -2173.480152 1772.233981 4.642017 -4.619070 -271.685019 221.529248 0.580252
+ 860.00 -36.999131 -2222.940592 1792.704127 4.669354 -4.624891 -277.867574 224.088016 0.583669
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+[AGL_ENERGIES_TEMPERATURE]STOP
+[AFLOW] **************************************************************************************************************************
diff --git a/tests/data/parsers/aflow/aflowlib.json b/tests/data/parsers/aflow/aflowlib.json
new file mode 100644
index 0000000000000000000000000000000000000000..e4d523dd8b5af65719266d7e3a70c01deff5952f
--- /dev/null
+++ b/tests/data/parsers/aflow/aflowlib.json
@@ -0,0 +1 @@
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GL_edos_gap_pressure.json","AGL_edos_gap_pressure.out","AGL_energies_temperature.out","AGL_energy.json","AGL_energy_structures.json","AGL_energy_volume.out","AGL_gibbs_energy_pT.out","AGL_thermal_properties_temperature.out","ARUN.AEL_0_SF_N_1_0.99","ARUN.AEL_10_SF_N_3_1.005","ARUN.AEL_11_SF_N_3_1.01","ARUN.AEL_12_SF_S_1_0.99","ARUN.AEL_13_SF_S_1_0.995","ARUN.AEL_14_SF_S_1_1.005","ARUN.AEL_15_SF_S_1_1.01","ARUN.AEL_16_SF_S_2_0.99","ARUN.AEL_17_SF_S_2_0.995","ARUN.AEL_18_SF_S_2_1.005","ARUN.AEL_19_SF_S_2_1.01","ARUN.AEL_1_SF_N_1_0.995","ARUN.AEL_20_SF_S_3_0.99","ARUN.AEL_21_SF_S_3_0.995","ARUN.AEL_22_SF_S_3_1.005","ARUN.AEL_23_SF_S_3_1.01","ARUN.AEL_2_SF_N_1_1.005","ARUN.AEL_3_SF_N_1_1.01","ARUN.AEL_4_SF_N_2_0.99","ARUN.AEL_5_SF_N_2_0.995","ARUN.AEL_6_SF_N_2_1.005","ARUN.AEL_7_SF_N_2_1.01","ARUN.AEL_8_SF_N_3_0.99","ARUN.AEL_9_SF_N_3_0.995","ARUN.AGL_0_SF_0.86","ARUN.AGL_10_SF_0.96","ARUN.AGL_11_SF_0.97","ARUN.AGL_12_SF_0.98","ARUN.AGL_13_SF_0.99","ARUN.AGL_14_SF_1","ARUN.AGL_15_SF_1.01","ARUN.AGL_16_SF_1.02","ARUN.AGL_17_SF_1.03","ARUN.AGL_18_SF_1.04","ARUN.AGL_19_SF_1.05","ARUN.AGL_1_SF_0.87","ARUN.AGL_20_SF_1.06","ARUN.AGL_21_SF_1.07","ARUN.AGL_22_SF_1.08","ARUN.AGL_23_SF_1.09","ARUN.AGL_24_SF_1.1","ARUN.AGL_25_SF_1.11","ARUN.AGL_26_SF_1.12","ARUN.AGL_27_SF_1.13","ARUN.AGL_2_SF_0.88","ARUN.AGL_3_SF_0.89","ARUN.AGL_4_SF_0.9","ARUN.AGL_5_SF_0.91","ARUN.AGL_6_SF_0.92","ARUN.AGL_7_SF_0.93","ARUN.AGL_8_SF_0.94","ARUN.AGL_9_SF_0.95","Ag1Co1O2_ICSD_246157.cif","Ag1Co1O2_ICSD_246157_Bader_10_Ag.jvxl","Ag1Co1O2_ICSD_246157_Bader_10_Co.jvxl","Ag1Co1O2_ICSD_246157_Bader_10_O.jvxl","Ag1Co1O2_ICSD_246157_Bader_20_Ag.jvxl","Ag1Co1O2_ICSD_246157_Bader_20_Co.jvxl","Ag1Co1O2_ICSD_246157_Bader_20_O.jvxl","Ag1Co1O2_ICSD_246157_Bader_25_Ag.jvxl","Ag1Co1O2_ICSD_246157_Bader_25_Co.jvxl","Ag1Co1O2_ICSD_246157_Bader_25_O.jvxl","Ag1Co1O2_ICSD_246157_Bader_30_Ag.jvxl","Ag1Co1O2_ICSD_246157_Bader_30_Co.jvxl","Ag1Co1O2_ICSD_246157_Bader_30_O.jvxl","Ag1Co1O2_ICSD_246157_Bader_33_Ag.jvxl","Ag1Co1O2_ICSD_246157_Bader_33_Co.jvxl","Ag1Co1O2_ICSD_246157_Bader_33_O.jvxl","Ag1Co1O2_ICSD_246157_Bader_40_Ag.jvxl","Ag1Co1O2_ICSD_246157_Bader_40_Co.jvxl","Ag1Co1O2_ICSD_246157_Bader_40_O.jvxl","Ag1Co1O2_ICSD_246157_Bader_50_Ag.jvxl","Ag1Co1O2_ICSD_246157_Bader_50_Co.jvxl","Ag1Co1O2_ICSD_246157_Bader_50_O.jvxl","Ag1Co1O2_ICSD_246157_Bader_60_Ag.jvxl","Ag1Co1O2_ICSD_246157_Bader_60_Co.jvxl","Ag1Co1O2_ICSD_246157_Bader_60_O.jvxl","Ag1Co1O2_ICSD_246157_Bader_67_Ag.jvxl","Ag1Co1O2_ICSD_246157_Bader_67_Co.jvxl","Ag1Co1O2_ICSD_246157_Bader_67_O.jvxl","Ag1Co1O2_ICSD_246157_Bader_75_Ag.jvxl","Ag1Co1O2_ICSD_246157_Bader_75_Co.jvxl","Ag1Co1O2_ICSD_246157_Bader_75_O.jvxl","Ag1Co1O2_ICSD_246157_Bader_80_Ag.jvxl","Ag1Co1O2_ICSD_246157_Bader_80_Co.jvxl","Ag1Co1O2_ICSD_246157_Bader_80_O.jvxl","Ag1Co1O2_ICSD_246157_Bader_90_Ag.jvxl","Ag1Co1O2_ICSD_246157_Bader_90_Co.jvxl","Ag1Co1O2_ICSD_246157_Bader_90_O.jvxl","Ag1Co1O2_ICSD_246157_abader.out","Ag1Co1O2_ICSD_246157_banddos.png","Ag1Co1O2_ICSD_246157_bandsdata.json.xz","Ag1Co1O2_ICSD_246157_corner.cif","Ag1Co1O2_ICSD_246157_dos.png","Ag1Co1O2_ICSD_246157_dos_Ag_1.png","Ag1Co1O2_ICSD_246157_dos_Co_3.png","Ag1Co1O2_ICSD_246157_dos_O_5.png","Ag1Co1O2_ICSD_246157_dosdata.json.xz","Ag1Co1O2_ICSD_246157_sconv.cif","Ag1Co1O2_ICSD_246157_sconv_corner.cif","Ag1Co1O2_ICSD_246157_sprim.cif","Ag1Co1O2_ICSD_246157_sprim_corner.cif","Ag1Co1O2_ICSD_246157_structure_relax.json","Ag1Co1O2_ICSD_246157_structure_relax1.json","CHGCAR.static.xz","CONTCAR.relax","CONTCAR.relax.abinit","CONTCAR.relax.aims","CONTCAR.relax.qe","CONTCAR.relax.vasp","CONTCAR.relax1","DOSCAR.static.xz","EIGENVAL.bands.xz","INCAR.bands","KPOINTS.bands","KPOINTS.relax","KPOINTS.static","OUTCAR.static.xz","POSCAR.bands","aflow.ael.out","aflow.agl.out","aflow.agroup.bands.json.xz","aflow.agroup.bands.out.xz","aflow.agroup.orig.json.xz","aflow.agroup.orig.out.xz","aflow.agroup.relax.json.xz","aflow.agroup.relax.out.xz","aflow.fgroup.bands.json.xz","aflow.fgroup.bands.out.xz","aflow.fgroup.orig.json.xz","aflow.fgroup.orig.out.xz","aflow.fgroup.relax.json.xz","aflow.fgroup.relax.out.xz","aflow.iatoms.bands.json.xz","aflow.iatoms.bands.out.xz","aflow.iatoms.orig.json.xz","aflow.iatoms.orig.out.xz","aflow.iatoms.relax.json.xz","aflow.iatoms.relax.out.xz","aflow.pgroup.bands.json.xz","aflow.pgroup.bands.out.xz","aflow.pgroup.orig.json.xz","aflow.pgroup.orig.out.xz","aflow.pgroup.relax.json.xz","aflow.pgroup.relax.out.xz","aflow.pgroup_xtal.bands.json.xz","aflow.pgroup_xtal.bands.out.xz","aflow.pgroup_xtal.orig.json.xz","aflow.pgroup_xtal.orig.out.xz","aflow.pgroup_xtal.relax.json.xz","aflow.pgroup_xtal.relax.out.xz","aflow.pgroupk.bands.json.xz","aflow.pgroupk.bands.out.xz","aflow.pgroupk.orig.json.xz","aflow.pgroupk.orig.out.xz","aflow.pgroupk.relax.json.xz","aflow.pgroupk.relax.out.xz","aflow.pgroupk_xtal.bands.json.xz","aflow.pgroupk_xtal.bands.out.xz","aflow.pgroupk_xtal.orig.json.xz","aflow.pgroupk_xtal.orig.out.xz","aflow.pgroupk_xtal.relax.json.xz","aflow.pgroup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diff --git a/tests/normalizing/test_system.py b/tests/normalizing/test_system.py
index 92e43f8c4b14c8799ccf6b7f858a436d96cae62a..49dde1d4bab6e3741605eebcb3d24ff2ee842b75 100644
--- a/tests/normalizing/test_system.py
+++ b/tests/normalizing/test_system.py
@@ -74,7 +74,8 @@ parser_exceptions = {
'parsers/cpmd': ['formula', 'dft.basis_set', 'dft.xc_functional', 'dft.system'],
'parser/onetep': ['formula', 'atoms', 'dft.basis_set', 'dft.xc_functional', 'dft.system'],
'parsers/siesta': ['dft.basis_set', 'dft.xc_functional', 'dft.system'],
- 'parsers/xps': ['formula', 'atoms']
+ 'parsers/xps': ['formula', 'atoms'],
+ 'parsers/aflow': ['dft.basis_set', 'dft.xc_functional']
}
'''
Keys that the normalizer for certain parsers might not produce. In an ideal world this
diff --git a/tests/parsing/test_parsing.py b/tests/parsing/test_parsing.py
index c08fc74a7433a33852374655caea1ec013df1cef..f413059d0431f113dc122cfae48e115080e3c0c9 100644
--- a/tests/parsing/test_parsing.py
+++ b/tests/parsing/test_parsing.py
@@ -40,7 +40,7 @@ parser_examples = [
('parsers/fhi-aims', 'tests/data/parsers/fhi-aims/aims.out'),
('parsers/fhi-vibes', 'tests/data/parsers/fhi-vibes/molecular_dynamics.nc'),
('parsers/cp2k', 'tests/data/parsers/cp2k/si_bulk8.out'),
- # ('parsers/crystal', 'tests/data/parsers/crystal/si.out'),
+ ('parsers/crystal', 'tests/data/parsers/crystal/si.out'),
('parsers/cpmd', 'tests/data/parsers/cpmd/geo_output.out'),
('parsers/nwchem', 'tests/data/parsers/nwchem/single_point/output.out'),
('parsers/bigdft', 'tests/data/parsers/bigdft/n2_output.out'),
@@ -71,9 +71,10 @@ parser_examples = [
('parser/onetep', 'tests/data/parsers/onetep/fluor/12-difluoroethane.out'),
('parsers/eels', 'tests/data/parsers/eels.json'),
('parsers/xps', 'tests/data/parsers/xps/multiple_channels.xy'),
+ ('parsers/aflow', 'tests/data/parsers/aflow/aflow_agl.out'),
# ('parsers/aptfim', 'tests/data/parsers/aptfim.aptfim'),
# ('parsers/mpes', 'tests/data/parsers/mpes.meta'),
- ('parsers/archive', 'tests/data/parsers/archive.json')
+ ('parsers/archive', 'tests/data/parsers/archive.json'),
]
# We need to remove some cases with external mainfiles, which might not exist
@@ -84,7 +85,7 @@ for parser, mainfile in parser_examples:
fixed_parser_examples.append((parser, mainfile))
parser_examples = fixed_parser_examples
-correct_num_output_files = 116
+correct_num_output_files = 117
def create_reference(data, pretty):