diff --git a/dependencies/parsers/electronic b/dependencies/parsers/electronic
index 5c077f48adcda8e6ec2f5cfb2220adc04100c3e6..62a093b8d34752675e4203b53629a201caf57391 160000
--- a/dependencies/parsers/electronic
+++ b/dependencies/parsers/electronic
@@ -1 +1 @@
-Subproject commit 5c077f48adcda8e6ec2f5cfb2220adc04100c3e6
+Subproject commit 62a093b8d34752675e4203b53629a201caf57391
diff --git a/gui/src/components/entry/properties/ElectronicPropertiesCard.js b/gui/src/components/entry/properties/ElectronicPropertiesCard.js
index ca81caf2cb0d98bbd76061ab1984c2597203bc6f..5a3b94587064ee05f81e7d6eb5170ae4cf73f384 100644
--- a/gui/src/components/entry/properties/ElectronicPropertiesCard.js
+++ b/gui/src/components/entry/properties/ElectronicPropertiesCard.js
@@ -15,20 +15,33 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-import React from 'react'
+import React, { useMemo } from 'react'
import PropTypes from 'prop-types'
import { PropertyCard } from './PropertyCard'
-import { getLocation, resolveInternalRef } from '../../../utils'
+import { getLocation, resolveInternalRef, parseNomadUrl } from '../../../utils'
import ElectronicProperties from '../../visualization/ElectronicProperties'
import { refPath } from '../../archive/metainfo'
+import { useEntryStoreObj } from '../../DataStore'
+// import { useEntryPageContext } from '../EntryPageContext'
+// import { useApi } from '../../api'
const ElectronicPropertiesCard = React.memo(({index, properties, archive}) => {
const urlPrefix = `${getLocation()}/data`
+ // const {installationUrl} = useEntryPageContext()
+ // const api = useApi()
// Find out which properties are present
const hasDos = properties.has('dos_electronic')
const hasBs = properties.has('band_structure_electronic')
+ // const loadArchive = useMemo((url) => {
+ // const parsedUrl = parseNomadUrl(url)
+ // const entryStoreObj = useEntryStoreObj(parsedUrl.installationUrl, parsedUrl.entryId, false, '*')
+ // return entryStoreObj.archive
+ // })
+ console.log(useEntryStoreObj, useMemo, parseNomadUrl)
+ console.log(typeof archive)
+
// Do not show the card if none of the properties are available
if (!hasDos && !hasBs) {
return null
@@ -36,17 +49,38 @@ const ElectronicPropertiesCard = React.memo(({index, properties, archive}) => {
// Resolve DOS data
let dos = hasDos ? undefined : false
+ // const dos = []
const dosData = archive?.results?.properties?.electronic?.dos_electronic
if (dosData) {
- dos = {}
- dos.energies = resolveInternalRef(dosData.energies, archive)
- dos.densities = resolveInternalRef(dosData.total, archive).map(dos => dos.value)
- if (dosData.band_gap) {
- dos.energy_highest_occupied = Math.max(...dosData.band_gap.map(x => x.energy_highest_occupied))
- }
- dos.m_path = `${urlPrefix}/${refPath(dosData.energies.split('/').slice(0, -1).join('/'))}`
+ dos = []
+ const dosArchive = archive
+ dosData.forEach(source => {
+ const d = {}
+ if (!source.energies.startsWith('/')) {
+ console.log(source)
+ // dosArchive = loadArchive(source.energies)
+ } else {
+ d.energies = resolveInternalRef(source.energies, dosArchive)
+ d.densities = resolveInternalRef(source.total, dosArchive).map(dos => dos.value)
+ }
+ // if (source.energies.startswith('../entries')) {
+ // // resolve first external archive
+ // const uploadId = archive?.metadata?.upload_id
+ // const entryId = archive?.metadata?.entry_id
+ // const baseUrl = `${installationUrl}/uploads/${uploadId}/archive/${entryId}`
+ // const path = source.energies
+ // const url = resolveNomadUrl(source.energies, baseUrl)
+ // api.post(`/entries/${url.entryId}/archive/query`, {required: '*'})
+ // }
+ d.name = source.name
+ if (source.band_gap) {
+ d.energy_highest_occupied = Math.max(...source.band_gap.map(x => x.energy_highest_occupied))
+ }
+ d.m_path = `${urlPrefix}/${refPath(source.energies.split('/').slice(0, -1).join('/'))}`
+ if (d.energies && d.densities) dos.push(d)
+ })
+ dos = dos.length === 0 ? false : dos
}
-
// Resolve data for band structure, brillouin zone and band gaps.
let bs = hasBs ? undefined : false
let band_gap = hasBs ? undefined : false
diff --git a/gui/src/components/visualization/DOS.js b/gui/src/components/visualization/DOS.js
index 4a1e5235b1d356aaa341ea4b6f56376e4900807a..4ae3775a55dac2d321306d33715fd63332e7acc5 100644
--- a/gui/src/components/visualization/DOS.js
+++ b/gui/src/components/visualization/DOS.js
@@ -77,72 +77,80 @@ const DOS = React.memo(({
return
}
- // Determine the energy reference.
- let energyHighestOccupied
+ // Create the final data that will be plotted.
+ const plotData = []
let normalized
- if (type === 'vibrational') {
- energyHighestOccupied = 0
- normalized = true
- } else {
- if (data.energy_highest_occupied === undefined) {
+ const mins = []
+ const maxes = []
+ data.forEach((d, n) => {
+ console.log(d)
+ // Determine the energy reference.
+ let energyHighestOccupied
+ if (type === 'vibrational') {
energyHighestOccupied = 0
- normalized = false
- } else {
- energyHighestOccupied = new Quantity(data.energy_highest_occupied, energyUnit).toSystem(units).value()
normalized = true
+ } else {
+ if (d.energy_highest_occupied === undefined) {
+ energyHighestOccupied = 0
+ normalized = false
+ } else {
+ energyHighestOccupied = new Quantity(d.energy_highest_occupied, energyUnit).toSystem(units).value()
+ normalized = true
+ }
}
- }
- // Convert units and determine range
- const mins = []
- const maxes = []
- const nChannels = data.densities.length
- let energies = new Quantity(data.energies, energyUnit).toSystem(units).value()
- const values1 = new Quantity(data.densities[0], valueUnit).toSystem(units).value()
- let values2
- mins.push(Math.min(...values1))
- maxes.push(Math.max(...values1))
- if (nChannels === 2) {
- values2 = new Quantity(data.densities[1], valueUnit).toSystem(units).value()
- mins.push(Math.min(...values2))
- maxes.push(Math.max(...values2))
- }
- const range = [Math.min(...mins), Math.max(...maxes)]
- if (energyHighestOccupied !== 0) {
- energies = add(energies, -energyHighestOccupied)
- }
+ // Convert units and determine range
+ const nChannels = d.densities.length
+ let energies = new Quantity(d.energies, energyUnit).toSystem(units).value()
+ const values1 = new Quantity(d.densities[0], valueUnit).toSystem(units).value()
+ let values2
+ mins.push(Math.min(...values1))
+ maxes.push(Math.max(...values1))
+ if (nChannels === 2) {
+ values2 = new Quantity(d.densities[1], valueUnit).toSystem(units).value()
+ mins.push(Math.min(...values2))
+ maxes.push(Math.max(...values2))
+ }
+ if (energyHighestOccupied !== 0) {
+ energies = add(energies, -energyHighestOccupied)
+ }
- // Create the final data that will be plotted.
- const plotData = []
- if (nChannels === 2) {
+ const dash = (d.name !== undefined && n === 1) ? 'dot' : undefined
+ if (nChannels === 2) {
+ plotData.push(
+ {
+ x: values2,
+ y: energies,
+ type: 'scatter',
+ mode: 'lines',
+ showlegend: false,
+ line: {
+ color: theme.palette.secondary.main,
+ width: 2,
+ dash: dash
+ }
+ }
+ )
+ }
plotData.push(
{
- x: values2,
+ x: values1,
y: energies,
+ name: d.name,
type: 'scatter',
mode: 'lines',
- showlegend: false,
+ showlegend: d.name !== undefined,
line: {
- color: theme.palette.secondary.main,
- width: 2
+ color: theme.palette.primary.main,
+ width: 2,
+ dash: dash
}
}
)
- }
- plotData.push(
- {
- x: values1,
- y: energies,
- type: 'scatter',
- mode: 'lines',
- showlegend: false,
- line: {
- color: theme.palette.primary.main,
- width: 2
- }
- }
- )
+ })
+ const range = [Math.min(...mins), Math.max(...maxes)]
+ console.log(range)
// Normalization line
if (type !== 'vibrational' && normalizedToHOE) {
plotData.push({
@@ -197,12 +205,13 @@ const DOS = React.memo(({
DOS.propTypes = {
data: PropTypes.oneOfType([
PropTypes.bool, // Set to False to show NoData component
- PropTypes.shape({
+ PropTypes.arrayOf(PropTypes.shape({
energies: PropTypes.array.isRequired, // DOS energies array
densities: PropTypes.array.isRequired, // DOS values array
energy_highest_occupied: PropTypes.number, // Highest occupied energy.
- m_path: PropTypes.string // Path of the section containing the data in the Archive
- })
+ m_path: PropTypes.string, // Path of the section containing the data in the Archive
+ name: PropTypes.string
+ }))
]),
layout: PropTypes.object,
className: PropTypes.string,
diff --git a/nomad/datamodel/metainfo/workflow.py b/nomad/datamodel/metainfo/workflow.py
index 907e4b87e7fa46773fd68c4c041e573b06e35c7e..e91c4726668c2fddeab40051338fd5e6a90b3704 100644
--- a/nomad/datamodel/metainfo/workflow.py
+++ b/nomad/datamodel/metainfo/workflow.py
@@ -4,7 +4,7 @@ from nptyping import NDArray
from nomad.metainfo import ( # pylint: disable=unused-import
MSection, MEnum, Quantity, Section, SubSection, SectionProxy,
Reference, derived)
-from nomad.datamodel.metainfo.simulation.calculation import Calculation
+from nomad.datamodel.metainfo.simulation.calculation import Calculation, Dos
from nomad.datamodel.metainfo.simulation.run import Run
from nomad.datamodel.metainfo.simulation.system import System, Atoms, AtomsGroup
from .common import FastAccess
@@ -1988,6 +1988,40 @@ class MeanSquaredDisplacement(CorrelationFunction):
mean_squared_displacement_values = SubSection(sub_section=MeanSquaredDisplacementValues.m_def, repeats=True)
+class GW(MSection):
+ '''
+ Section containing results of a GW workflow
+ '''
+
+ m_def = Section(validate=False)
+
+ # TODO external referencing is a bit tricky for the gui
+ dos_dft = Quantity(
+ type=Reference(Dos),
+ description='''
+ DFT density of states
+ ''')
+
+ dos_gw = Quantity(
+ type=Reference(Dos),
+ description='''
+ GW density of states
+ ''')
+
+ # dos_dft = Quantity(
+ # type=Dos,
+ # shape=['*']
+ # )
+ # dos_gw = Quantity(
+ # type=Dos,
+ # shape=['*']
+ # )
+
+ # dos_dft = SubSection(sub_section=Dos.m_def, repeats=False)
+
+ # dos_gw = SubSection(sub_section=Dos.m_def, repeats=False)
+
+
class SinglePoint(MSection):
'''
Section containing results of a single point workflow.
@@ -2120,6 +2154,7 @@ class Workflow(MSection):
type = Quantity(
type=MEnum([
+ "gw",
"single_point",
"geometry_optimization",
"phonon",
@@ -2208,8 +2243,11 @@ class Workflow(MSection):
single_point = SubSection(
sub_section=SinglePoint.m_def,
- # TODO determine if there is a need for this to be a repeating section
- # such as in the context of fhi-vibes single_point
+ repeats=False,
+ categories=[FastAccess])
+
+ gw = SubSection(
+ sub_section=GW.m_def,
repeats=False,
categories=[FastAccess])
diff --git a/nomad/datamodel/results.py b/nomad/datamodel/results.py
index a166e4a45434de38d1978d78086f500f51e54460..f12faacf8f1d223b07383f41060f8c653aa0176c 100644
--- a/nomad/datamodel/results.py
+++ b/nomad/datamodel/results.py
@@ -1519,6 +1519,12 @@ class DOSElectronic(DOS):
Contains the total electronic density of states.
''',
)
+ name = Quantity(
+ type=str,
+ description='''
+ Label to identify the DOS data, e.g. the method employed.
+ ''')
+
spin_polarized = Quantity(
type=bool,
description='''
@@ -1824,7 +1830,7 @@ class ElectronicProperties(MSection):
''',
)
band_structure_electronic = SubSection(sub_section=BandStructureElectronic.m_def, repeats=False)
- dos_electronic = SubSection(sub_section=DOSElectronic.m_def, repeats=False)
+ dos_electronic = SubSection(sub_section=DOSElectronic.m_def, repeats=True)
class QuantityDynamic(MSection):
diff --git a/nomad/normalizing/results.py b/nomad/normalizing/results.py
index 765919918959cd1f830fb785e8aab51d35ae362b..f2d6a25a8e6cc993fecf0d9808b705f1674b600d 100644
--- a/nomad/normalizing/results.py
+++ b/nomad/normalizing/results.py
@@ -278,7 +278,7 @@ class ResultsNormalizer(Normalizer):
return None
- def dos_electronic(self) -> Union[DOSElectronic, None]:
+ def dos_electronic(self) -> List[Union[DOSElectronic, None]]:
"""Returns a reference to the section containing an electronic dos. In
the case of multiple valid DOSes, only the latest one is reported.
@@ -286,25 +286,40 @@ class ResultsNormalizer(Normalizer):
- There is a non-empty array of dos_values_normalized.
- There is a non-empty array of dos_energies.
"""
- path = ["run", "calculation", "dos_electronic"]
- for dos in self.traverse_reversed(path):
- energies = dos.energies
- values = np.array([d.value.magnitude for d in dos.total])
- if valid_array(energies) and valid_array(values):
- dos_new = DOSElectronic()
- dos_new.energies = dos
- dos_new.total = dos.total
- n_channels = values.shape[0]
- dos_new.spin_polarized = n_channels > 1
- dos_new.energy_fermi = dos.energy_fermi
- for info in dos.band_gap:
- info_new = dos_new.m_create(BandGap)
- info_new.index = info.index
- info_new.energy_highest_occupied = info.energy_highest_occupied
- info_new.energy_lowest_unoccupied = info.energy_lowest_unoccupied
- return dos_new
- return None
+ def resolve_dos(path):
+ for dos in self.traverse_reversed(path):
+ energies = dos.energies
+ values = np.array([d.value.magnitude for d in dos.total])
+ if valid_array(energies) and valid_array(values):
+ dos_new = DOSElectronic()
+ dos_new.energies = dos
+ dos_new.total = dos.total
+ n_channels = values.shape[0]
+ dos_new.spin_polarized = n_channels > 1
+ dos_new.energy_fermi = dos.energy_fermi
+ for info in dos.band_gap:
+ info_new = dos_new.m_create(BandGap)
+ info_new.index = info.index
+ info_new.energy_highest_occupied = info.energy_highest_occupied
+ info_new.energy_lowest_unoccupied = info.energy_lowest_unoccupied
+ return dos_new
+
+ try:
+ workflow_type = self.entry_archive.workflow[-1].type
+ except Exception:
+ workflow_type = None
+
+ if workflow_type == 'gw':
+ dos_dft = resolve_dos(["workflow", "gw", "dos_dft"])
+ dos_dft.name = 'DFT'
+ dos_gw = resolve_dos(["workflow", "gw", "dos_gw"])
+ dos_gw.name = 'GW'
+ return [dos_dft, dos_gw] if dos_dft and dos_gw else []
+ elif workflow_type == 'single_point':
+ return [resolve_dos(["run", "calculation", "dos_electronic"])]
+ else:
+ return []
def band_structure_phonon(self) -> Union[BandStructurePhonon, None]:
"""Returns a new section containing a phonon band structure. In
diff --git a/nomad/normalizing/workflow.py b/nomad/normalizing/workflow.py
index e5a1a5adbdc105c0794ac2ca2dfb41322296f83a..770420e458685690818b5aadfe60d89e37331d46 100644
--- a/nomad/normalizing/workflow.py
+++ b/nomad/normalizing/workflow.py
@@ -507,7 +507,9 @@ class WorkflowNormalizer(Normalizer):
if not self.entry_archive.run:
return
+ created = False
if not self.entry_archive.workflow:
+ created = True
self.entry_archive.m_create(Workflow)
for n, sec_workflow in enumerate(self.entry_archive.workflow):
@@ -547,5 +549,5 @@ class WorkflowNormalizer(Normalizer):
ThermodynamicsNormalizer(self.entry_archive, n).normalize()
# remove the section workflow again, if the parser/normalizer could not produce a result
- if sec_workflow.calculation_result_ref is None:
+ if sec_workflow.calculation_result_ref is None and created:
self.entry_archive.m_remove_sub_section(EntryArchive.workflow, n)
diff --git a/nomad/parsing/parser.py b/nomad/parsing/parser.py
index e488a22d94a807d179430c7c5f02c1f86fdf3aff..26cdd0984ab499bd59ead0fe71b0210578eb7fba 100644
--- a/nomad/parsing/parser.py
+++ b/nomad/parsing/parser.py
@@ -347,6 +347,9 @@ class MatchingParserInterface(MatchingParser):
return self._mainfile_parser
def parse(self, mainfile: str, archive: EntryArchive, logger=None, child_archives=None):
+ # TODO include child_archives in parse
+ if child_archives:
+ self.mainfile_parser._child_archives = child_archives
self.mainfile_parser.parse(mainfile, archive, logger)
def import_parser_class(self):
@@ -361,6 +364,22 @@ class MatchingParserInterface(MatchingParser):
return parser
+ def is_mainfile(
+ self, filename: str, mime: str, buffer: bytes, decoded_buffer: str,
+ compression: str = None) -> Union[bool, Iterable[str]]:
+ is_mainfile = super().is_mainfile(
+ filename=filename, mime=mime, buffer=buffer,
+ decoded_buffer=decoded_buffer, compression=compression)
+ if is_mainfile:
+ try:
+ self.creates_children = True
+ # try to resolve mainfile keys from parser
+ mainfile_keys = self.mainfile_parser.get_mainfile_keys(filename)
+ return mainfile_keys
+ except Exception:
+ return is_mainfile
+ return is_mainfile
+
class ArchiveParser(MatchingParser):
def __init__(self):