Merge branch 'units' into 'v0.9.0'

Added a fixed Pint unit and constant file, added CLI command for creating unit conversion data for the GUI, added new React component for changing the units in the ArchiveBrowser.

See merge request !184

Dockerfile

@@ -70,6 +70,7 @@ RUN cp dist/nomad-lab-*.tar.gz dist/nomad-lab.tar.gz
 RUN python -m nomad.cli dev metainfo > gui/src/metainfo.json
 RUN python -m nomad.cli dev search-quantities > gui/src/searchQuantities.json
 RUN python -m nomad.cli dev toolkit-metadata > gui/src/toolkitMetadata.json
+RUN python -m nomad.cli dev units > gui/src/units.js
 WORKDIR /install/docs
 RUN make html
 RUN \
@@ -90,6 +91,7 @@ COPY --from=build /install/gui/src/metainfo.json /app/src/metainfo.json
 COPY --from=build /install/gui/src/searchQuantities.json /app/src/searchQuantities.json
 COPY --from=build /install/gui/src/parserMetadata.json /app/src/parserMetadata.json
 COPY --from=build /install/gui/src/toolkitMetadata.json /app/src/toolkitMetadata.json
+COPY --from=build /install/gui/src/units.js /app/src/units.js
 RUN yarn run build
 
 # Build the Encyclopedia GUI in the gui build image

gui/src/components/archive/ArchiveBrowser.js

-
 import React, { useMemo, useState, useCallback } from 'react'
 import PropTypes from 'prop-types'
 import { atom, useRecoilState, useRecoilValue } from 'recoil'
@@ -16,17 +15,36 @@ import { ErrorHandler, ErrorCard } from '../ErrorHandler'
 import DOS from '../visualization/DOS'
 import { StructureViewer, BrillouinZoneViewer } from '@lauri-codes/materia'
 import Markdown from '../Markdown'
-import { convert } from '../../utils'
+import { UnitSelector } from './UnitSelector'
+import { convertSI } from '../../utils'
+import { conversionMap } from '../../units'
 
 export const configState = atom({
   key: 'config',
   default: {
     'showMeta': false,
     'showCodeSpecific': false,
-    'showAllDefined': false
+    'showAllDefined': false,
+    'energyUnit': 'joule'
   }
 })
 
+let defaults = {}
+for (const dimension in conversionMap) {
+  const info = conversionMap[dimension]
+  defaults[dimension] = info.units[0]
+}
+const override = {
+  'length': 'angstrom',
+  'energy': 'electron_volt',
+  'system': 'custom'
+}
+defaults = {...defaults, ...override}
+export const unitsState = atom({
+  key: 'units',
+  default: defaults
+})
+
 // Shared instance of the StructureViewer
 const viewer = new StructureViewer()
 const bzViewer = new BrillouinZoneViewer()
@@ -50,6 +68,7 @@ ArchiveBrowser.propTypes = ({
 
 function ArchiveConfigForm({searchOptions}) {
   const [config, setConfig] = useRecoilState(configState)
+
   const handleConfigChange = event => {
     const changes = {[event.target.name]: event.target.checked}
     if (changes.showCodeSpecific) {
@@ -64,21 +83,23 @@ function ArchiveConfigForm({searchOptions}) {
   const { url } = useRouteMatch()
 
   return (
-    <Box marginTop={-6}>
-      <FormGroup row style={{alignItems: 'flex-end'}}>
-        <Autocomplete
-          options={searchOptions}
-          getOptionLabel={(option) => option.name}
-          style={{ width: 350 }}
-          onChange={(_, value) => {
-            if (value) {
-              history.push(url + value.path)
-            }
-          }}
-          renderInput={(params) => <TextField {...params} label="search" margin="normal" />}
-        />
+    <Box marginTop={-3} padding={0}>
+      <FormGroup row style={{alignItems: 'center'}}>
+        <Box style={{width: 350, height: 60}}>
+          <Autocomplete
+            options={searchOptions}
+            getOptionLabel={(option) => option.name}
+            style={{ width: 350, marginTop: -20 }}
+            onChange={(_, value) => {
+              if (value) {
+                history.push(url + value.path)
+              }
+            }}
+            renderInput={(params) => <TextField {...params} label="search" margin="normal" />}
+          />
+        </Box>
         <Box flexGrow={1} />
-        <Tooltip title="Enable to also show all code specfic data">
+        <Tooltip title="Enable to also show all code specific data">
           <FormControlLabel
             control={
               <Checkbox
@@ -113,6 +134,7 @@ function ArchiveConfigForm({searchOptions}) {
             label="definitions"
           />
         </Tooltip>
+        <UnitSelector unitsState={unitsState}></UnitSelector>
       </FormGroup>
     </Box>
   )
@@ -246,6 +268,7 @@ class QuantityAdaptor extends ArchiveAdaptor {
 }
 
 function QuantityItemPreview({value, def}) {
+  const units = useRecoilState(unitsState)[0]
   if (def.type.type_kind === 'reference') {
     return <Box component="span" fontStyle="italic">
       <Typography component="span">reference ...</Typography>
@@ -280,9 +303,14 @@ function QuantityItemPreview({value, def}) {
       </Typography>
     </Box>
   } else {
+    let finalValue = value
+    let finalUnit = def.unit
+    if (def.unit) {
+      [finalValue, finalUnit] = convertSI(value, def.unit, units)
+    }
     return <Box component="span" whiteSpace="nowarp">
-      <Number component="span" variant="body1" value={value} exp={8} />
-      {def.unit && <Typography component="span">&nbsp;{def.unit}</Typography>}
+      <Number component="span" variant="body1" value={finalValue} exp={8} />
+      {finalUnit && <Typography component="span">&nbsp;{finalUnit}</Typography>}
     </Box>
   }
 }
@@ -292,10 +320,18 @@ QuantityItemPreview.propTypes = ({
 })
 
 function QuantityValue({value, def}) {
+  // Figure out the units
+  const units = useRecoilState(unitsState)[0]
+  let finalValue = value
+  let finalUnit = def.unit
+  if (def.unit) {
+    [finalValue, finalUnit] = convertSI(value, def.unit, units)
+  }
+
   return <Box
     marginTop={2} marginBottom={2} textAlign="center" fontWeight="bold"
   >
-    {def.shape.length > 0 ? <Matrix values={value} shape={def.shape} invert={def.shape.length === 1} /> : <Number value={value} exp={16} variant="body2" />}
+    {def.shape.length > 0 ? <Matrix values={finalValue} shape={def.shape} invert={def.shape.length === 1} /> : <Number value={finalValue} exp={16} variant="body2" />}
     {def.shape.length > 0 &&
       <Typography noWrap variant="caption">
         ({def.shape.map((dimension, index) => <span key={index}>
@@ -303,7 +339,7 @@ function QuantityValue({value, def}) {
         </span>)}&nbsp;)
       </Typography>
     }
-    {def.unit && <Typography noWrap>{def.unit}</Typography>}
+    {def.unit && <Typography noWrap>{finalUnit}</Typography>}
   </Box>
 }
 QuantityValue.propTypes = ({
@@ -371,14 +407,14 @@ function Overview({section, def}) {
     } else if (sectionPath === visualizedSystem.sectionPath && nAtoms === visualizedSystem.nAtoms) {
       positionsOnly = true
       system = {
-        positions: convert(section.atom_positions, 'm', 'angstrom')
+        positions: convertSI(section.atom_positions, 'meter', {length: 'angstrom'}, false)
       }
     // Completely new system
     } else {
       system = {
         'species': section.atom_species,
-        'cell': convert(section.lattice_vectors, 'm', 'angstrom'),
-        'positions': convert(section.atom_positions, 'm', 'angstrom'),
+        'cell': convertSI(section.lattice_vectors, 'meter', {length: 'angstrom'}, false),
+        'positions': convertSI(section.atom_positions, 'meter', {length: 'angstrom'}, false),
         'pbc': section.configuration_periodic_dimensions
       }
     }
@@ -409,6 +445,7 @@ function Overview({section, def}) {
               className={style.bands}
               data={section}
               aspectRatio={1}
+              unitsState={unitsState}
             ></BandStructure>
           </ErrorHandler>
         </Box>
@@ -453,6 +490,7 @@ function Overview({section, def}) {
         className={style.dos}
         data={section}
         aspectRatio={1 / 2}
+        unitsState={unitsState}
       ></DOS>
     </ErrorHandler>
   }

gui/src/components/archive/UnitSelector.js

+import React, { useCallback, useState } from 'react'
+import { useRecoilState } from 'recoil'
+import { makeStyles } from '@material-ui/core/styles'
+import {
+  Box,
+  Button,
+  Menu,
+  MenuItem,
+  FormControl,
+  InputLabel,
+  Select,
+  FormLabel,
+  FormControlLabel,
+  RadioGroup,
+  Radio,
+  Tooltip
+} from '@material-ui/core'
+import PropTypes from 'prop-types'
+import clsx from 'clsx'
+import { conversionMap, unitMap, unitSystems } from '../../units'
+
+/**
+ * Component that wraps it's children in a container that can be 'floated',
+ * i.e. displayed on an html element that is positioned relative to the
+ * viewport and is above all other elements.
+ */
+export function UnitSelector({className, classes, unitsState, onUnitChange, onSystemChange}) {
+  // States
+  const [canSelect, setCanSelect] = useState(true)
+  const [anchorEl, setAnchorEl] = React.useState(null)
+  const open = Boolean(anchorEl)
+  const [units, setUnits] = useRecoilState(unitsState)
+
+  // Styles
+  const useStyles = makeStyles((theme) => {
+    return {
+      menuItem: {
+        width: '10rem'
+      },
+      systems: {
+        margin: theme.spacing(2),
+        marginTop: theme.spacing(1)
+      }
+    }
+  })
+  const style = useStyles(classes)
+
+  // Callbacks
+  const openMenu = useCallback((event) => {
+    setAnchorEl(event.currentTarget)
+  }, [])
+  const closeMenu = useCallback(() => {
+    setAnchorEl(null)
+  }, [])
+  const handleSystemChange = useCallback((event) => {
+    const systemName = event.target.value
+    let changes = {system: systemName}
+    if (systemName === 'custom') {
+      setCanSelect(true)
+    } else {
+      setCanSelect(false)
+      const system = unitSystems[systemName]
+      changes = {...changes, ...system.units}
+    }
+    setUnits({...units, ...changes})
+    if (onSystemChange) {
+      onSystemChange(event)
+    }
+  // eslint-disable-next-line react-hooks/exhaustive-deps
+  }, [])
+  const handleUnitChange = useCallback(event => {
+    const changes = {[event.target.name]: event.target.value}
+    if (onUnitChange) {
+      onUnitChange(event)
+    }
+    console.log(changes)
+    setUnits({...units, ...changes})
+  // eslint-disable-next-line react-hooks/exhaustive-deps
+  }, [])
+
+  // Ordered list of controllable units. It may be smaller than the full list of
+  // units.
+  const unitNames = ['energy', 'length', 'force', 'mass', 'time', 'temperature']
+  const systemNames = ['SI', 'AU']
+
+  return (
+    <Box className={clsx(style.root, className)}>
+      <Button
+        aria-controls="customized-menu"
+        aria-haspopup="true"
+        variant="outlined"
+        color="primary"
+        onClick={openMenu}
+      >
+        Select units
+      </Button>
+      <Menu
+        id="select-unit"
+        anchorEl={anchorEl}
+        getContentAnchorEl={null}
+        anchorOrigin={{ vertical: 'bottom', horizontal: 'right' }}
+        transformOrigin={{ vertical: 'top', horizontal: 'right' }}
+        keepMounted
+        open={open}
+        onClose={closeMenu}
+      >
+        <FormControl
+          component="fieldset"
+          classes={{root: style.systems}}
+        >
+          <FormLabel component="legend">Unit system</FormLabel>
+          <RadioGroup aria-label="gender" name="gender1" value={units.system} onChange={handleSystemChange}>
+            <Tooltip title="Custom units">
+              <FormControlLabel value="custom" control={<Radio />} label="Custom" />
+            </Tooltip>
+            {systemNames.map((systemName) => {
+              const system = unitSystems[systemName]
+              return <Tooltip key={systemName} title={system.description}>
+                <FormControlLabel value={systemName} control={<Radio />} label={system.label} />
+              </Tooltip>
+            })}
+          </RadioGroup>
+        </FormControl>
+        {unitNames.map((dimension) => {
+          const unitList = conversionMap[dimension].units
+          return <MenuItem
+            key={dimension}
+          >
+            <FormControl disabled={!canSelect}>
+              <InputLabel id="demo-simple-select-label">{dimension}</InputLabel>
+              <Select
+                classes={{root: style.menuItem}}
+                labelId="demo-simple-select-label"
+                id="demo-simple-select"
+                name={dimension}
+                value={units[dimension]}
+                onChange={handleUnitChange}
+              >
+                {unitList.map((unit) => {
+                  const unitLabel = unitMap[unit].label
+                  return <MenuItem key={unit} value={unit}>{unitLabel}</MenuItem>
+                })}
+              </Select>
+            </FormControl>
+          </MenuItem>
+        })}
+      </Menu>
+    </Box>
+  )
+}
+
+UnitSelector.propTypes = {
+  /**
+   * CSS class for the root element.
+   */
+  className: PropTypes.string,
+  /**
+   * CSS classes for this component.
+   */
+  classes: PropTypes.object,
+  /**
+   * Recoil atom containing the unit configuration that this component will
+   * attach to.
+   */
+  unitsState: PropTypes.object,
+  /**
+   * Callback for unit selection.
+   */
+  onUnitChange: PropTypes.func,
+  /**
+   * Callback for unit system selection.
+   */
+  onSystemChange: PropTypes.func
+}
+UnitSelector.defaultProps = {
+  float: false
+}

gui/src/components/visualization/BandStructure.js

 import React, {useState, useEffect, useMemo} from 'react'
+import { useRecoilValue } from 'recoil'
 import PropTypes from 'prop-types'
 import { makeStyles, useTheme } from '@material-ui/core/styles'
 import clsx from 'clsx'
@@ -6,11 +7,12 @@ import {
   Box
 } from '@material-ui/core'
 import Plot from '../visualization/Plot'
-import { convert, distance, mergeObjects } from '../../utils'
+import { convertSI, distance, mergeObjects } from '../../utils'
 
-export default function BandStructure({data, layout, aspectRatio, className, classes, onRelayout, onAfterPlot, onRedraw, onRelayouting}) {
+export default function BandStructure({data, layout, aspectRatio, className, classes, onRelayout, onAfterPlot, onRedraw, onRelayouting, unitsState}) {
   const [finalData, setFinalData] = useState(undefined)
   const [pathSegments, setPathSegments] = useState(undefined)
+  const units = useRecoilValue(unitsState)
 
   // Styles
   const useStyles = makeStyles(
@@ -89,7 +91,7 @@ export default function BandStructure({data, layout, aspectRatio, className, cla
 
       // Create plot data entry for each band
       for (let band of bands) {
-        band = convert(band, 'joule', 'eV')
+        band = convertSI(band, 'joule', units, false)
         plotData.push(
           {
             x: path,
@@ -122,7 +124,7 @@ export default function BandStructure({data, layout, aspectRatio, className, cla
 
     // Create plot data entry for each band
     for (let band of bands) {
-      band = convert(band, 'joule', 'eV')
+      band = convertSI(band, 'joule', units, false)
       plotData.push(
         {
           x: path,
@@ -138,7 +140,7 @@ export default function BandStructure({data, layout, aspectRatio, className, cla
     }
 
     setFinalData(plotData)
-  }, [data, theme.palette.primary.main, theme.palette.secondary.main])
+  }, [data, theme.palette.primary.main, theme.palette.secondary.main, units])
 
   // Merge custom layout with default layout
   const tmpLayout = useMemo(() => {
@@ -241,5 +243,6 @@ BandStructure.propTypes = {
   onAfterPlot: PropTypes.func,
   onRedraw: PropTypes.func,
   onRelayout: PropTypes.func,
-  onRelayouting: PropTypes.func
+  onRelayouting: PropTypes.func,
+  unitsState: PropTypes.object // Recoil atom containing the unit configuration
 }

gui/src/components/visualization/DOS.js

 import React, {useState, useEffect, useMemo} from 'react'
+import { useRecoilValue } from 'recoil'
 import PropTypes from 'prop-types'
 import { makeStyles, useTheme } from '@material-ui/core/styles'
 import clsx from 'clsx'
@@ -6,22 +7,23 @@ import {
   Box
 } from '@material-ui/core'
 import Plot from '../visualization/Plot'
-import { convert, mergeObjects } from '../../utils'
+import { convertSI, convertSILabel, mergeObjects } from '../../utils'
 
-export default function DOS({data, layout, aspectRatio, className, classes, onRelayout, onAfterPlot, onRedraw, onRelayouting}) {
+export default function DOS({data, layout, aspectRatio, className, classes, onRelayout, onAfterPlot, onRedraw, onRelayouting, unitsState}) {
   const [finalData, setFinalData] = useState(undefined)
+  const units = useRecoilValue(unitsState)
 
   // Merge custom layout with default layout
   const tmpLayout = useMemo(() => {
     let defaultLayout = {
       yaxis: {
         title: {
-          text: 'Energy (eV)'
+          text: `Energy (${convertSILabel('joule', units)})`
         }
       }
     }
     return mergeObjects(layout, defaultLayout)
-  }, [layout])
+  }, [layout, units])
 
   // Styles
   const useStyles = makeStyles(
@@ -45,7 +47,7 @@ export default function DOS({data, layout, aspectRatio, className, classes, onRe
     const plotData = []
     if (data !== undefined) {
       let nChannels = data[valueName].length
-      let energies = convert(data[energyName], 'joule', 'eV')
+      let energies = convertSI(data[energyName], 'joule', units, false)
       if (nChannels === 2) {
         plotData.push(
           {
@@ -74,7 +76,7 @@ export default function DOS({data, layout, aspectRatio, className, classes, onRe
       )
     }
     setFinalData(plotData)
-  }, [data, theme.palette.primary.main, theme.palette.secondary.main])
+  }, [data, theme.palette.primary.main, theme.palette.secondary.main, units])
 
   // Compute layout that depends on data.
   const computedLayout = useMemo(() => {
@@ -85,12 +87,12 @@ export default function DOS({data, layout, aspectRatio, className, classes, onRe
     let defaultLayout = {
       xaxis: {
         title: {
-          text: norm ? 'states/eV/m<sup>3</sup>/atom' : 'states/eV/cell'
+          text: norm ? convertSILabel('states/joule/m^3/atom', units) : convertSILabel('states/joule/cell', units)
         }
       }
     }
     return defaultLayout
-  }, [data])
+  }, [data, units])
 
   // Merge the given layout and layout computed from data
   const finalLayout = useMemo(() => {
@@ -123,5 +125,6 @@ DOS.propTypes = {
   onAfterPlot: PropTypes.func,
   onRedraw: PropTypes.func,
   onRelayout: PropTypes.func,
-  onRelayouting: PropTypes.func
+  onRelayouting: PropTypes.func,
+  unitsState: PropTypes.object // Recoil atom containing the unit configuration
 }

gui/src/units.js

+// Generated by NOMAD CLI. Do not edit manually.
+export const unitMap = {
+  second: {
+    dimension: 'time',
+    label: 'Second',
+    abbreviation: 's'
+  },
+  atomic_unit_of_time: {
+    dimension: 'time',
+    label: 'Atomic unit of time',
+    abbreviation: 'atomic_unit_of_time'
+  },
+  meter: {
+    dimension: 'length',
+    label: 'Meter',
+    abbreviation: 'm'
+  },
+  bohr: {
+    dimension: 'length',
+    label: 'Bohr',
+    abbreviation: 'bohr'
+  },
+  angstrom: {
+    dimension: 'length',
+    label: '\u00c5ngstrom',
+    abbreviation: '\u00c5'
+  },
+  kilogram: {
+    dimension: 'mass',
+    label: 'Kilogram',
+    abbreviation: 'kg'
+  },
+  electron_mass: {
+    dimension: 'mass',
+    label: 'Electron mass',
+    abbreviation: 'm\u2091'
+  },
+  unified_atomic_mass_unit: {
+    dimension: 'mass',
+    label: 'Unified atomic mass unit',
+    abbreviation: 'u'
+  },
+  ampere: {
+    dimension: 'current',
+    label: 'Ampere',
+    abbreviation: 'A'
+  },
+  atomic_unit_of_current: {
+    dimension: 'current',
+    label: 'Atomic unit of current',
+    abbreviation: 'atomic_unit_of_current'
+  },
+  mole: {
+    dimension: 'substance',
+    label: 'Mole',
+    abbreviation: 'mole'
+  },
+  candela: {
+    dimension: 'luminosity',
+    label: 'Candela',
+    abbreviation: 'cd'
+  },
+  kelvin: {
+    dimension: 'temperature',
+    label: 'Kelvin',
+    abbreviation: 'K'
+  },
+  celsius: {
+    dimension: 'temperature',
+    label: 'Celsius',
+    abbreviation: '\u00b0C'
+  },
+  fahrenheit: {
+    dimension: 'temperature',
+    label: 'Fahrenheit',
+    abbreviation: '\u00b0F'
+  },
+  atomic_unit_of_temperature: {
+    dimension: 'temperature',
+    label: 'Atomic unit of temperature',
+    abbreviation: 'atomic_unit_of_temperature'
+  },
+  newton: {
+    dimension: 'force',
+    label: 'Newton',
+    abbreviation: 'N'
+  },
+  atomic_unit_of_force: {
+    dimension: 'force',