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geoschem.go
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/*
Copyright © 2017 the InMAP authors.
This file is part of InMAP.
InMAP is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
InMAP is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with InMAP. If not, see <http://www.gnu.org/licenses/>.
*/
package inmap
import (
"fmt"
"io"
"math"
"os"
"strconv"
"strings"
"time"
"github.com/ctessum/atmos/seinfeld"
"github.com/ctessum/atmos/wesely1989"
"github.com/ctessum/cdf"
"github.com/ctessum/geom"
"github.com/ctessum/geom/index/rtree"
"github.com/ctessum/sparse"
)
const (
geosFormat = "20060102"
geosChemFormat = "20060102.150000"
)
// GEOSChem is an InMAP preprocessor for GEOS-Chem output.
// Information regarding GEOS-Chem output variables is available from
// http://wiki.seas.harvard.edu/geos-chem/index.php/List_of_GEOS-FP_met_fields
// and
// http://wiki.seas.harvard.edu/geos-chem/index.php/Species_in_GEOS-Chem.
type GEOSChem struct {
aVOC, bVOC, aSOA, bSOA, nox, no, no2, pNO, sox, pS, nh3, pNH, totalPM25 map[string]float64
noChemHour bool
start, end time.Time
chemRecordDeltaInterval, chemFileDeltaInterval time.Duration
recordDelta1h, recordDelta3h time.Duration
fileDelta24h, fileDelta3h time.Duration
landUse *sparse.DenseArray
nz int
dx, dy float64
xCenters, yCenters []float64
geosA1 string
geosA3Cld string
geosA3Dyn string
geosI3 string
geosA3MstE string
geosApBp string
geosChem string
// If dash is '-', GEOS-Chem chemical variable names are assumed to be in the
// form 'IJ-AVG-S__xxx'. If dash is '_', they are assumed to be in the form
// 'IJ_AVG_S_xxx'.
dash string
msgChan chan string
}
// NewGEOSChem initializes a GEOS-Chem preprocessor from the given
// configuration information.
//
// GEOSA1 is the location of the GEOS 1-hour time average files.
// [DATE] should be used as a wild card for the simulation date.
//
// GEOSA3Cld is the location of the GEOS 3-hour average cloud
// parameter files. [DATE] should be used as a wild card for
// the simulation date.
//
// GEOSA3Cld is the location of the GEOS 3-hour average dynamical
// parameter files. [DATE] should be used as a wild card for
// the simulation date.
//
// GEOSI3 is the location of the GEOS 3-hour instantaneous parameter
// files. [DATE] should be used as a wild card for
// the simulation date.
//
// GEOSA3MstE is the location of the GEOS 3-hour average moist parameters
// on level edges files. [DATE] should be used as a wild card for
// the simulation date.
//
// geosApBp is the location of the pressure level variable file.
// It is optional; if it is not specified the Ap and Bp information
// will be extracted from the geosChem file.
//
// GEOSChemOut is the location of GEOS-Chem output files.
// [DATE] should be used as a wild card for the simulation date.
//
// OlsonLandMap is the location of the GEOS-Chem Olson land use map file,
// which is described here:
// http://wiki.seas.harvard.edu/geos-chem/index.php/Olson_land_map
//
// startDate and endDate are the dates of the beginning and end of the
// simulation, respectively, in the format "YYYYMMDD".
//
// If dash is true, GEOS-Chem chemical variable names are assumed to be in the
// form 'IJ-AVG-S__xxx'. If dash is false, they are assumed to be in the form
// 'IJ_AVG_S_xxx'.
//
// If msgChan is not nil, status messages will be sent to it.
//
// chemRecordInterval is the time interval between different records in
// the GEOS-Chem output. It is specified by the user as a string
// (chemRecordStr), e.g. "3h" for 3 hours.
//
// chemFileInterval is the time interval of each file. It is specified
// as a string (chemFileStr), e.g. "3h" for 3 hours.
//
// If noChemHour is true, then the GEOS-Chem output files will be
// assumed to not contain a time dimension.
func NewGEOSChem(GEOSA1, GEOSA3Cld, GEOSA3Dyn, GEOSI3, GEOSA3MstE, GEOSApBp, GEOSChemOut, OlsonLandMap, startDate, endDate string, dash bool, chemRecordStr, chemFileStr string, noChemHour bool, msgChan chan string) (*GEOSChem, error) {
var d string
if dash {
d = "-"
} else {
d = "_"
}
gc := GEOSChem{
// These maps contain the GEOS-Chem variables that make
// up the chemical species groups, as well as the
// multiplication factors required to convert concentrations
// to mass fractions [μg/kg dry air].
// GEOS-Chem VOC species;
// Only includes anthropogenic precursors to SOA from
// anthropogenic (aSOA) and biogenic (bSOA) sources.
// Additional information available from:
// http://wiki.seas.harvard.edu/geos-chem/index.php/Species_in_GEOS-Chem.
// We assume condensable vapor from SOA has molar mass of 70.
aVOC: map[string]float64{
"IJ" + d + "AVG" + d + "S__BENZ": ppbcToUgKg(78.11, 6),
"IJ" + d + "AVG" + d + "S__TOLU": ppbcToUgKg(92.14, 7),
"IJ" + d + "AVG" + d + "S__XYLE": ppbcToUgKg(106.16, 8),
"IJ" + d + "AVG" + d + "S__NAP": ppbcToUgKg(128.1705, 10),
"IJ" + d + "AVG" + d + "S__POG1": ppbvToUgKg(12),
"IJ" + d + "AVG" + d + "S__POG2": ppbvToUgKg(12),
},
bVOC: map[string]float64{
"IJ" + d + "AVG" + d + "S__ISOP": ppbcToUgKg(68.12, 5),
"IJ" + d + "AVG" + d + "S__LIMO": ppbvToUgKg(136.23),
"IJ" + d + "AVG" + d + "S__MTPA": ppbvToUgKg(136.23),
"IJ" + d + "AVG" + d + "S__MTPO": ppbvToUgKg(136.23),
},
// SOA species (anthropogenic only)
aSOA: map[string]float64{
"IJ" + d + "AVG" + d + "S__ASOA1": ppbvToUgKg(150),
"IJ" + d + "AVG" + d + "S__ASOA2": ppbvToUgKg(150),
"IJ" + d + "AVG" + d + "S__ASOA3": ppbvToUgKg(150),
"IJ" + d + "AVG" + d + "S__ASOAN": ppbvToUgKg(150),
},
// SOA species (biogenic only)
bSOA: map[string]float64{
"IJ" + d + "AVG" + d + "S__TSOA0": ppbvToUgKg(150),
"IJ" + d + "AVG" + d + "S__TSOA1": ppbvToUgKg(150),
"IJ" + d + "AVG" + d + "S__TSOA2": ppbvToUgKg(150),
"IJ" + d + "AVG" + d + "S__TSOA3": ppbvToUgKg(150),
"IJ" + d + "AVG" + d + "S__SOAGX": ppbvToUgKg(58),
"IJ" + d + "AVG" + d + "S__SOAMG": ppbvToUgKg(72),
"IJ" + d + "AVG" + d + "S__SOAIE": ppbvToUgKg(118),
"IJ" + d + "AVG" + d + "S__SOAME": ppbvToUgKg(102),
"IJ" + d + "AVG" + d + "S__LVOCOA": ppbvToUgKg(154),
"IJ" + d + "AVG" + d + "S__ISN1OA": ppbvToUgKg(226),
},
// NOx species. We are only interested in the mass
// of Nitrogen, rather than the mass of the whole molecule, so
// we use the molecular weight of Nitrogen.
nox: map[string]float64{
"IJ" + d + "AVG" + d + "S__NO": ppbvToUgKg(mwN),
"IJ" + d + "AVG" + d + "S__NO2": ppbvToUgKg(mwN),
},
// pNO is the Nitrogen fraction of the particulate
// NO species.
pNO: map[string]float64{
"IJ" + d + "AVG" + d + "S__NIT": ppbvToUgKg(mwN),
"IJ" + d + "AVG" + d + "S__NITs": ppbvToUgKg(mwN),
},
// SOx species. We are only interested in the mass
// of Sulfur, rather than the mass of the whole molecule, so
// we use the molecular weight of Sulfur.
sox: map[string]float64{
"IJ" + d + "AVG" + d + "S__SO2": ppbvToUgKg(mwS),
},
// pS is the MADE particulate Sulfur species; sulfur fraction
// sulfate (SO4) plus sulfate on the surface of sea ice (SO4s).
pS: map[string]float64{
"IJ" + d + "AVG" + d + "S__SO4": ppbvToUgKg(mwS),
"IJ" + d + "AVG" + d + "S__SO4s": ppbvToUgKg(mwS),
"IJ" + d + "AVG" + d + "S__DMS": ppbvToUgKg(mwS),
},
// NH3 is ammonia. We are only interested in the mass
// of Nitrogen, rather than the mass of the whole molecule, so
// we use the molecular weight of Nitrogen.
nh3: map[string]float64{"IJ" + d + "AVG" + d + "S__NH3": ppbvToUgKg(mwN)},
// pNH is the Nitrogen fraction of the particulate
// ammonia species.
pNH: map[string]float64{"IJ" + d + "AVG" + d + "S__NH4": ppbvToUgKg(mwN)},
// totalPM25 is total mass of PM2.5.
// It is calculated based on the formula at:
// http://wiki.seas.harvard.edu/geos-chem/index.php/Particulate_matter_in_GEOS-Chem
totalPM25: map[string]float64{
"IJ" + d + "AVG" + d + "S__NH4": ppbvToUgKg(18) * 1.33,
"IJ" + d + "AVG" + d + "S__NIT": ppbvToUgKg(62) * 1.33,
"IJ" + d + "AVG" + d + "S__SO4": ppbvToUgKg(96) * 1.33,
"IJ" + d + "AVG" + d + "S__BCPI": ppbvToUgKg(12),
"IJ" + d + "AVG" + d + "S__BCPO": ppbvToUgKg(12),
"IJ" + d + "AVG" + d + "S__POA1": ppbvToUgKg(12) * 1.4,
"IJ" + d + "AVG" + d + "S__POA2": ppbvToUgKg(12) * 1.4,
"IJ" + d + "AVG" + d + "S__OPOA1": ppbvToUgKg(12) * 2.1,
"IJ" + d + "AVG" + d + "S__OPOA2": ppbvToUgKg(12) * 2.1,
"IJ" + d + "AVG" + d + "S__TSOA0": ppbvToUgKg(150) * 1.16,
"IJ" + d + "AVG" + d + "S__TSOA1": ppbvToUgKg(150) * 1.16,
"IJ" + d + "AVG" + d + "S__TSOA2": ppbvToUgKg(150) * 1.16,
"IJ" + d + "AVG" + d + "S__TSOA3": ppbvToUgKg(150) * 1.16,
"IJ" + d + "AVG" + d + "S__ASOAN": ppbvToUgKg(150) * 1.16,
"IJ" + d + "AVG" + d + "S__ASOA1": ppbvToUgKg(150) * 1.16,
"IJ" + d + "AVG" + d + "S__ASOA2": ppbvToUgKg(150) * 1.16,
"IJ" + d + "AVG" + d + "S__ASOA3": ppbvToUgKg(150) * 1.16,
"IJ" + d + "AVG" + d + "S__SOAGX": ppbvToUgKg(58) * 1.16,
"IJ" + d + "AVG" + d + "S__INDIOL": ppbvToUgKg(102) * 1.16,
"IJ" + d + "AVG" + d + "S__SOAMG": ppbvToUgKg(72) * 1.16,
"IJ" + d + "AVG" + d + "S__SOAIE": ppbvToUgKg(118) * 1.16,
"IJ" + d + "AVG" + d + "S__SOAME": ppbvToUgKg(102) * 1.16,
"IJ" + d + "AVG" + d + "S__LVOCOA": ppbvToUgKg(154) * 1.16,
"IJ" + d + "AVG" + d + "S__ISN1OA": ppbvToUgKg(226) * 1.16,
"IJ" + d + "AVG" + d + "S__DST1": ppbvToUgKg(29),
"IJ" + d + "AVG" + d + "S__DST2": ppbvToUgKg(29) * 0.38,
"IJ" + d + "AVG" + d + "S__SALA": ppbvToUgKg(31.4) * 1.86,
},
geosA1: GEOSA1,
geosA3Cld: GEOSA3Cld,
geosA3Dyn: GEOSA3Dyn,
geosI3: GEOSI3,
geosA3MstE: GEOSA3MstE,
geosApBp: GEOSApBp,
geosChem: GEOSChemOut,
dash: d,
msgChan: msgChan,
noChemHour: noChemHour,
}
var err error
gc.start, err = time.Parse(inDateFormat, startDate)
if err != nil {
return nil, fmt.Errorf("inmap: GEOS-Chem preprocessor start time: %v", err)
}
gc.end, err = time.Parse(inDateFormat, endDate)
if err != nil {
return nil, fmt.Errorf("inmap: GEOS-Chem preprocessor end time: %v", err)
}
gc.chemRecordDeltaInterval, err = time.ParseDuration(chemRecordStr)
if err != nil {
return nil, fmt.Errorf("inmap: GEOS-Chem preprocessor recordDelta: %v", err)
}
gc.recordDelta1h, err = time.ParseDuration("1h")
if err != nil {
return nil, fmt.Errorf("inmap: GEOS-Chem preprocessor recordDelta: %v", err)
}
gc.recordDelta3h, err = time.ParseDuration("3h")
if err != nil {
return nil, fmt.Errorf("inmap: GEOS-Chem preprocessor recordDelta: %v", err)
}
gc.chemFileDeltaInterval, err = time.ParseDuration(chemFileStr)
if err != nil {
return nil, fmt.Errorf("inmap: GEOS-Chem preprocessor fileDelta: %v", err)
}
gc.fileDelta24h, err = time.ParseDuration("24h")
if err != nil {
return nil, fmt.Errorf("inmap: GEOS-Chem preprocessor fileDelta: %v", err)
}
gc.fileDelta3h, err = time.ParseDuration("3h")
if err != nil {
return nil, fmt.Errorf("inmap: GEOS-Chem preprocessor fileDelta: %v", err)
}
gc.nz, err = gc.Nz()
if err != nil {
return nil, err
}
gc.dx, err = gc.DX()
if err != nil {
return nil, err
}
gc.dy, err = gc.DY()
if err != nil {
return nil, err
}
gc.xCenters, err = gc.XCenters()
if err != nil {
return nil, err
}
gc.yCenters, err = gc.YCenters()
if err != nil {
return nil, err
}
file, err := os.Open(OlsonLandMap)
if err != nil {
return nil, err
}
defer file.Close()
cfile, err := cdf.Open(file)
if err != nil {
return nil, fmt.Errorf("inmap: Olson land use file: %v", err)
}
gc.landUse, err = gc.largestLandUse(cfile)
if err != nil {
return nil, err
}
return &gc, nil
}
// ppbcToUgKg returns a multiplier to convert a concentration in
// ppbc (parts per billion carbon) dry air to a mass fraction
// [micrograms per kilogram dry air]
// for a chemical species with the given molecular weight
// (mw, g/mol) and number of carbons (nc).
func ppbcToUgKg(mw, nc float64) float64 {
return mw / nc / MWa
}
// ppbvToUgKg returns a multiplier to convert a concentration in
// ppbv dry air to a mass fraction [micrograms per kilogram dry air]
// for a chemical species with the given molecular weight in g/mol.
func ppbvToUgKg(mw float64) float64 {
return mw / MWa
}
func (gc *GEOSChem) readA3Dyn(varName string) NextData {
conv := geosLayerConvert(gc.nz)
return conv(nextDataNCF(gc.geosA3Dyn, geosFormat, varName, gc.start, gc.end, gc.recordDelta3h, gc.fileDelta24h, readNCF, gc.msgChan))
}
func (gc *GEOSChem) readA3MstE(varName string) NextData {
conv := geosLayerConvert(gc.nz)
return conv(nextDataNCF(gc.geosA3MstE, geosFormat, varName, gc.start, gc.end, gc.recordDelta3h, gc.fileDelta24h, readNCF, gc.msgChan))
}
func (gc *GEOSChem) readA3Cld(varName string) NextData {
conv := geosLayerConvert(gc.nz)
return conv(nextDataNCF(gc.geosA3Cld, geosFormat, varName, gc.start, gc.end, gc.recordDelta3h, gc.fileDelta24h, readNCF, gc.msgChan))
}
func (gc *GEOSChem) readA1(varName string) NextData {
// All variables in A1 are 2-d, so we don't need to perform a layer conversion.
return nextDataNCF(gc.geosA1, geosFormat, varName, gc.start, gc.end, gc.recordDelta1h, gc.fileDelta24h, readNCF, gc.msgChan)
}
func (gc *GEOSChem) readI3(varName string) NextData {
conv := geosLayerConvert(gc.nz)
return conv(nextDataNCF(gc.geosI3, geosFormat, varName, gc.start, gc.end, gc.recordDelta3h, gc.fileDelta24h, readNCF, gc.msgChan))
}
func (gc *GEOSChem) readChem(varName string) NextData {
if gc.noChemHour {
return nextDataNCF(gc.geosChem, geosChemFormat, varName, gc.start, gc.end, gc.chemRecordDeltaInterval, gc.chemFileDeltaInterval, readNCFNoHour, gc.msgChan)
}
return nextDataNCF(gc.geosChem, geosChemFormat, varName, gc.start, gc.end, gc.chemRecordDeltaInterval, gc.chemFileDeltaInterval, readNCF, gc.msgChan)
}
func (gc *GEOSChem) readApBp(varName string) NextData {
if gc.geosApBp != "" {
return nextDataConstantNCF(strings.ToLower(varName), gc.geosApBp)
}
return nextDataNCF(gc.geosChem, geosChemFormat, varName, gc.start, gc.end, gc.recordDelta3h, gc.fileDelta3h, readNCFNoHour, gc.msgChan)
}
func (gc *GEOSChem) readChemGroupAlt(varGroup map[string]float64) NextData {
if gc.noChemHour {
return nextDataGroupAltNCF(gc.geosChem, geosChemFormat, varGroup, gc.ALT(), gc.start, gc.end, gc.chemRecordDeltaInterval, gc.chemFileDeltaInterval, readNCFNoHour, gc.msgChan)
}
return nextDataGroupAltNCF(gc.geosChem, geosChemFormat, varGroup, gc.ALT(), gc.start, gc.end, gc.chemRecordDeltaInterval, gc.chemFileDeltaInterval, readNCF, gc.msgChan)
}
func (gc *GEOSChem) readChemGroupSTP(varGroup map[string]float64) NextData {
if gc.noChemHour {
return nextDataGroupSTPNCF(gc.geosChem, geosChemFormat, varGroup, gc.start, gc.end, gc.chemRecordDeltaInterval, gc.chemFileDeltaInterval, readNCFNoHour, gc.msgChan)
}
return nextDataGroupSTPNCF(gc.geosChem, geosChemFormat, varGroup, gc.start, gc.end, gc.chemRecordDeltaInterval, gc.chemFileDeltaInterval, readNCF, gc.msgChan)
}
var geosLayerConvert = func(nz int) func(NextData) NextData {
const (
geosLayers = 72
geosChemShortLayers = 47
)
if nz == geosLayers {
// If GEOS-Chem is using the full 72 layers, we don't need to perform a
// conversion.
return func(d NextData) NextData { return d }
} else if nz != geosChemShortLayers {
panic(fmt.Errorf("inmap preprocessor: invalid number of GEOS layers (%d); should be 72 or 47", nz))
}
// GEOS always has 72 unstaggered layers, but sometimes GEOS-Chem only uses 47.
// layerMap is a mapping between the 72 and 47 layer versions for
// unstaggered variables.
var layerMap = map[int]int{
0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8,
9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15,
16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22,
23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 29: 29,
30: 30, 31: 31, 32: 32, 33: 33, 34: 34, 35: 35, 36: 36,
37: 36, 38: 37, 39: 37, 40: 38, 41: 38, 42: 39, 43: 39,
44: 40, 45: 40, 46: 40, 47: 40, 48: 41, 49: 41, 50: 41,
51: 41, 52: 42, 53: 42, 54: 42, 55: 42, 56: 43, 57: 43,
58: 43, 59: 43, 60: 44, 61: 44, 62: 44, 63: 44, 64: 45,
65: 45, 66: 45, 67: 45, 68: 46, 69: 46, 70: 46, 71: 46,
}
// layerCount is the number of GEOS layers in each chemistry layer.
layerCount := make(map[int]float64)
for _, iChem := range layerMap {
layerCount[iChem] += float64(1)
}
// staggeredLayerMap is the map between the 73 and 48 staggered layers in
// GEOS and GEOS-Chem.
staggeredLayerMap := make(map[int]int)
for iG, iChem := range layerMap {
if _, ok := staggeredLayerMap[iChem]; !ok {
staggeredLayerMap[iChem] = iG
} else if iG < staggeredLayerMap[iChem] {
// We want to assign the lowest matching GEOS level to each GEOS-Chem
// level.
staggeredLayerMap[iChem] = iG
}
}
staggeredLayerMap[47] = 72 // This is the model top edge.
return func(in NextData) NextData {
return func() (*sparse.DenseArray, error) {
d, err := in()
if err != nil {
return nil, err
}
if len(d.Shape) < 3 {
return d, nil // not a 3-d array.
}
if len(d.Shape) != 3 {
panic(fmt.Errorf("inmap preprocessor: GEOS array is more than 3 dimensions (%d)", len(d.Shape)))
}
switch d.Shape[0] {
case 72:
return geosLayerConvertUnstaggered(d, layerMap, layerCount), nil
case 73:
return geosLayerConvertStaggered(d, staggeredLayerMap), nil
case 1: // only one vertical layer (not 3-d)
return d, nil
default:
panic(fmt.Errorf("inmap preprocessor: invalid vertical dimension %d", d.Shape[0]))
}
}
}
}
// geosLayerConvertUnstaggered sets the GEOS-Chem layer values
// to the average of the GEOS layer values that fall within them.
func geosLayerConvertUnstaggered(in *sparse.DenseArray, layerMap map[int]int, layerCount map[int]float64) *sparse.DenseArray {
o := sparse.ZerosDense(47, in.Shape[1], in.Shape[2])
for iG, iChem := range layerMap {
count := layerCount[iChem]
for j := 0; j < in.Shape[1]; j++ {
for i := 0; i < in.Shape[2]; i++ {
o.AddVal(in.Get(iG, j, i)/count, iChem, j, i)
}
}
}
return o
}
// geosLayerConvertStaggered sets the GEOS-Chem layer values
// to the GEOS layer values that have coinciding edges with them.
func geosLayerConvertStaggered(in *sparse.DenseArray, staggeredLayerMap map[int]int) *sparse.DenseArray {
o := sparse.ZerosDense(48, in.Shape[1], in.Shape[2])
for iChem, iG := range staggeredLayerMap {
for j := 0; j < in.Shape[1]; j++ {
for i := 0; i < in.Shape[2]; i++ {
o.Set(in.Get(iG, j, i), iChem, j, i)
}
}
}
return o
}
// Nx helps fulfill the Preprocessor interface by returning
// the number of grid cells in the West-East direction.
func (gc *GEOSChem) Nx() (int, error) {
f, ff, err := ncfFromTemplate(gc.geosA3Dyn, geosFormat, gc.start)
if err != nil {
return -1, err
}
defer f.Close()
v := "RH"
dims := ff.Header.Lengths(v)
if len(dims) == 0 {
return -1, fmt.Errorf("geos: missing variable %s", v)
}
return dims[3], nil
}
// Ny helps fulfill the Preprocessor interface by returning
// the number of grid cells in the South-North direction.
func (gc *GEOSChem) Ny() (int, error) {
f, ff, err := ncfFromTemplate(gc.geosA3Dyn, geosFormat, gc.start)
if err != nil {
return -1, err
}
defer f.Close()
v := "RH"
dims := ff.Header.Lengths(v)
if len(dims) == 0 {
return -1, fmt.Errorf("geos: missing variable %s", v)
}
return dims[2], nil
}
// Nz helps fulfill the Preprocessor interface by returning
// the number of grid cells in the below-above direction.
func (gc *GEOSChem) Nz() (int, error) {
// We get Nz from the GEOS-Chem output to make sure we're using the
// GEOS-Chem number of layers rather than the GEOS number of layers.
f, ff, err := ncfFromTemplate(gc.geosChem, geosChemFormat, gc.start)
if err != nil {
return -1, err
}
defer f.Close()
v := "IJ" + gc.dash + "AVG" + gc.dash + "S__SO2"
dims := ff.Header.Lengths(v)
if len(dims) == 0 {
return -1, fmt.Errorf("geoschem: missing variable %s", v)
} else if len(dims) == 4 {
dims = dims[1:4] // Sometimes GEOS-Chem files also have a time dimension.
}
return dims[0], nil
}
// Return the first set of values of a variable from a chemistry file.
func (gc *GEOSChem) chemFirstValues(v string) ([]float64, error) {
f, ff, err := ncfFromTemplate(gc.geosChem, geosChemFormat, gc.start)
if err != nil {
return nil, err
}
defer f.Close()
data, err := readNCFNoHour(v, ff, 0)
if err != nil {
// If variable not in file, try all lowercase.
data, err = readNCFNoHour(strings.ToLower(v), ff, 0)
if err != nil {
return nil, err
}
}
return data.Elements, nil
}
// Return an attribute from a chemistry file.
func (gc *GEOSChem) chemAttribute(a string) (float64, error) {
f, ff, err := ncfFromTemplate(gc.geosChem, geosChemFormat, gc.start)
if err != nil {
return math.NaN(), err
}
defer f.Close()
attr := ff.Header.GetAttribute("", a)
return float64(attr.([]float32)[0]), nil
}
// XCenters returns the x-coordinates of the grid points.
func (gc *GEOSChem) XCenters() ([]float64, error) { return gc.chemFirstValues("LON") }
// YCenters returns the y-coordinates of the grid points.
func (gc *GEOSChem) YCenters() ([]float64, error) { return gc.chemFirstValues("LAT") }
// DX returns the longitude grid spacing.
func (gc *GEOSChem) DX() (float64, error) { return gc.chemAttribute("Delta_Lon") }
// DY returns the latitude grid spacing.
func (gc *GEOSChem) DY() (float64, error) { return gc.chemAttribute("Delta_Lat") }
// PBLH helps fulfill the Preprocessor interface.
func (gc *GEOSChem) PBLH() NextData { return gc.readA1("PBLH") }
// Height returns a functions that calculates layer heights at each
// time step using the hyposometric equation.
func (gc *GEOSChem) Height() NextData {
TFunc := gc.T() // Temperature [K]
PFunc := gc.P() // Pressure [Pa]
return func() (*sparse.DenseArray, error) {
T, err := TFunc()
if err != nil {
return nil, err
}
P, err := PFunc()
if err != nil {
return nil, err
}
layerHeights := sparse.ZerosDense(T.Shape[0]+1, T.Shape[1], T.Shape[2])
for k := 1; k < T.Shape[0]+1; k++ { // The height of layer zero is zero.
for j := 0; j < T.Shape[1]; j++ {
for i := 0; i < T.Shape[2]; i++ {
p := P.Get(k, j, i) // Pressure [Pa]
pBelow := P.Get(k-1, j, i) // Pressure [Pa]
t := T.Get(k-1, j, i) // tL in units on K
h := -1 * math.Log(p/pBelow) * rr * t / g // in meters
layerHeights.Set(h+layerHeights.Get(k-1, j, i), k, j, i)
}
}
}
return layerHeights, nil
}
}
// ALT helps fulfill the Preprocessor interface, returning
// inverse air density [m3/kg].
func (gc *GEOSChem) ALT() NextData {
densityFunc1 := gc.readChem("TIME" + gc.dash + "SER__AIRDEN") // Air density in molec/cm3.
densityFunc2 := gc.readChem("BXHGHT_S__AIRNUMDE") // Alternate: Dry air density in molec/cm3.
return func() (*sparse.DenseArray, error) {
density, err := densityFunc1()
if err != nil {
if err == io.EOF {
return nil, err
}
holdErr := err
density, err = densityFunc2()
if err != nil {
if err == io.EOF {
return nil, err
}
return nil, fmt.Errorf("%s; %s", holdErr, err)
}
}
alt := sparse.ZerosDense(density.Shape...)
for i, val := range density.Elements {
alt.Elements[i] = 1 / (val * (MWa / avNum) * 1000.)
}
return alt, nil
}
}
// U helps fulfill the Preprocessor interface.
func (gc *GEOSChem) U() NextData { return stagger(gc.readA3Dyn("U"), 2) } // (unstaggered)
// V helps fulfill the Preprocessor interface.
func (gc *GEOSChem) V() NextData { return stagger(gc.readA3Dyn("V"), 1) } // (unstaggered)
// W helps fulfill the Preprocessor interface.
func (gc *GEOSChem) W() NextData {
omegaFunc := gc.readA3Dyn("OMEGA") // Vertical pressure velocity [Pa/s] (unstaggered).
PFunc := gc.P()
TFunc := gc.T()
return func() (*sparse.DenseArray, error) {
omega, err := omegaFunc()
if err != nil {
return nil, err
}
P, err := PFunc()
if err != nil {
return nil, err
}
T, err := TFunc()
if err != nil {
return nil, err
}
w := sparse.ZerosDense(omega.Shape...)
for k := 0; k < omega.Shape[0]; k++ {
for j := 0; j < omega.Shape[1]; j++ {
for i := 0; i < omega.Shape[2]; i++ {
dz := -1 * math.Log(P.Get(k+1, j, i)/P.Get(k, j, i)) * rr * T.Get(k, j, i) / g // in meters
wVal := omega.Get(k, j, i) / (P.Get(k+1, j, i) - P.Get(k, j, i)) / dz
w.Set(wVal, k, j, i)
}
}
}
return staggerWorker(w, 0), nil
}
}
// AVOC helps fulfill the Preprocessor interface.
func (gc *GEOSChem) AVOC() NextData { return gc.readChemGroupSTP(gc.aVOC) }
// BVOC helps fulfill the Preprocessor interface.
func (gc *GEOSChem) BVOC() NextData { return gc.readChemGroupSTP(gc.bVOC) }
// NOx helps fulfill the Preprocessor interface.
func (gc *GEOSChem) NOx() NextData { return gc.readChemGroupSTP(gc.nox) }
// SOx helps fulfill the Preprocessor interface.
func (gc *GEOSChem) SOx() NextData { return gc.readChemGroupSTP(gc.sox) }
// NH3 helps fulfill the Preprocessor interface.
func (gc *GEOSChem) NH3() NextData { return gc.readChemGroupSTP(gc.nh3) }
// ASOA helps fulfill the Preprocessor interface.
func (gc *GEOSChem) ASOA() NextData { return gc.readChemGroupSTP(gc.aSOA) }
// BSOA helps fulfill the Preprocessor interface.
func (gc *GEOSChem) BSOA() NextData { return gc.readChemGroupSTP(gc.bSOA) }
// PNO helps fulfill the Preprocessor interface.
func (gc *GEOSChem) PNO() NextData { return gc.readChemGroupSTP(gc.pNO) }
// PS helps fulfill the Preprocessor interface.
func (gc *GEOSChem) PS() NextData { return gc.readChemGroupSTP(gc.pS) }
// PNH helps fulfill the Preprocessor interface.
func (gc *GEOSChem) PNH() NextData { return gc.readChemGroupSTP(gc.pNH) }
// TotalPM25 helps fulfill the Preprocessor interface.
func (gc *GEOSChem) TotalPM25() NextData { return gc.readChemGroupSTP(gc.totalPM25) }
// SurfaceHeatFlux helps fulfill the Preprocessor interface by returning
// sensible heat flux from turbulence [W/m2].
func (gc *GEOSChem) SurfaceHeatFlux() NextData { return gc.readA1("HFLUX") }
// UStar helps fulfill the Preprocessor interface by returning
// friction velocity [m/s].
func (gc *GEOSChem) UStar() NextData { return gc.readA1("USTAR") }
// T helps fulfill the Preprocessor interface by returning temperature [K].
func (gc *GEOSChem) T() NextData { return gc.readI3("T") }
// P helps fulfill the Preprocessor interface by returning pressure [Pa].
func (gc *GEOSChem) P() NextData {
PSFunc := gc.readI3("PS") // Surface pressure [hPa]
apFunc := gc.readApBp("Ap") // Hybrid-grid A parameter [hPa]
bpFunc := gc.readApBp("Bp") // Hypbrid-grid b parameter [-]
return func() (*sparse.DenseArray, error) {
PS, err := PSFunc()
if err != nil {
return nil, err
}
ap, err := apFunc()
if err != nil {
return nil, err
}
bp, err := bpFunc()
if err != nil {
return nil, err
}
p := sparse.ZerosDense(ap.Shape[0], PS.Shape[0], PS.Shape[1])
for k := 0; k < ap.Shape[0]; k++ {
for j := 0; j < PS.Shape[0]; j++ {
for i := 0; i < PS.Shape[1]; i++ {
const hPa2Pa = 100.0 // Convert hPa to Pa.
p.Set((PS.Get(j, i)*bp.Get(k)+ap.Get(k))*hPa2Pa, k, j, i) // Pressure [Pa]
}
}
}
return p, nil
}
}
// HO helps fulfill the Preprocessor interface by returning hydroxyl
// radical concentration [ppmv].
func (gc *GEOSChem) HO() NextData {
HOFunc1 := gc.readChem("TIME" + gc.dash + "SER__OH") // OH density (molec / cm3)
f := gc.readChem("CHEM_L_S__OH") // Alternate OH density (molec / cm3)
HOFunc2 := func() (*sparse.DenseArray, error) {
data, err := f()
if err != nil {
return nil, err
}
if data.Shape[0] != 59 { // Sometimes this variable has 59 layers instead of 72. TODO: Why?
return data, nil
}
out := sparse.ZerosDense(72, data.Shape[1], data.Shape[2])
for k := 0; k < data.Shape[0]; k++ {
for j := 0; j < data.Shape[1]; j++ {
for i := 0; i < data.Shape[2]; i++ {
out.Set(data.Get(k, j, i), k, j, i)
}
}
}
return out, nil
}
altFunc := gc.ALT()
return func() (*sparse.DenseArray, error) {
HO, err := HOFunc1()
if err != nil {
if err == io.EOF {
return nil, err
}
errHold := err
HO, err = HOFunc2()
if err != nil {
return nil, fmt.Errorf("%s; %s", errHold, err)
}
}
alt, err := altFunc()
if err != nil {
return nil, err
}
const cm3perm3 = 100. * 100. * 100.
const airFactor = MWa / avNum * cm3perm3 // kg/molec.* cm3/m3
ho := sparse.ZerosDense(HO.Shape...)
for i, hoV := range HO.Elements {
// molec HO / cm3 * m3 / kg air * kg air/molec. air* cm3/m3 * ppm
ho.Elements[i] = hoV * alt.Elements[i] * airFactor * 1.0e6
}
return ho, nil
}
}
// H2O2 helps fulfill the Preprocessor interface by returning
// hydrogen peroxide concentration [ppmv].
func (gc *GEOSChem) H2O2() NextData {
H2O2Func := gc.readChem("IJ" + gc.dash + "AVG" + gc.dash + "S__H2O2") // H2O2 concentration [ppbv].
return func() (*sparse.DenseArray, error) {
H2O2, err := H2O2Func()
if err != nil {
return nil, err
}
return H2O2.ScaleCopy(1.0e-3), nil
}
}
// Z0 helps fulfill the Preprocessor interface by returning
// momentum roughness length [m].
func (gc *GEOSChem) Z0() NextData { return gc.readA1("Z0M") }
// SeinfeldLandUse helps fulfill the Preprocessor interface by
// returning land use categories as
// specified in github.com/ctessum/atmos/seinfeld.
func (gc *GEOSChem) SeinfeldLandUse() NextData {
// TODO (CT): Account for the fact that a single grid cell can have multiple land uses.
snowFunc := gc.readA1("FRSNO") // Fraction land covered by snow
return geosChemSeinfeldLandUse(snowFunc, gc.landUse)
}
func geosChemSeinfeldLandUse(snowFunc NextData, landUse *sparse.DenseArray) NextData {
return func() (*sparse.DenseArray, error) {
snowFrac, err := snowFunc() // Fraction land covered by snow
if err != nil {
return nil, err
}
o := sparse.ZerosDense(snowFrac.Shape...)
for j := 0; j < snowFrac.Shape[0]; j++ {
for i := 0; i < snowFrac.Shape[1]; i++ {
snowV := snowFrac.Get(j, i)
if snowV > 0.5 { // We assume that snow and desert have similar deposition properties.
o.Set(float64(seinfeld.Desert), j, i)
}
o.Set(float64(geosChemSeinfeld[f2i(landUse.Get(j, i))]), j, i)
}
}
return o, nil
}
}
// geosChemSeinfeld provides a mapping between GEOSChem use categories
// described in http://wiki.seas.harvard.edu/geos-chem/index.php/Olson_land_map
// and the land use categories as
// specified in github.com/ctessum/atmos/seinfeld.
var geosChemSeinfeld = []seinfeld.LandUseCategory{
seinfeld.Desert, // 0 Water
seinfeld.Deciduous, // 1 Urban
seinfeld.Grass, // 2 Shrub
seinfeld.Desert, // 3 ---
seinfeld.Desert, // 4 ---
seinfeld.Desert, // 5 ---
seinfeld.Evergreen, // 6 Trop. evergreen
seinfeld.Desert, // 7 ---
seinfeld.Desert, // 8 Desert
seinfeld.Desert, // 9 ---
seinfeld.Desert, // 10 ---
seinfeld.Desert, // 11 ---
seinfeld.Desert, // 12 ---
seinfeld.Desert, // 13 ---
seinfeld.Desert, // 14 ---
seinfeld.Desert, // 15 ---
seinfeld.Shrubs, // 16 Scrub
seinfeld.Desert, // 17 Ice
seinfeld.Desert, // 18 ---
seinfeld.Desert, // 19 ---
seinfeld.Evergreen, // 20 Conifer
seinfeld.Evergreen, // 21 Conifer
seinfeld.Evergreen, // 22 Conifer
seinfeld.Evergreen, // 23 Conifer/Deciduous
seinfeld.Deciduous, // 24 Deciduous/Conifer
seinfeld.Deciduous, // 25 Deciduous
seinfeld.Deciduous, // 26 Deciduous
seinfeld.Evergreen, // 27 Conifer
seinfeld.Deciduous, // 28 Dwarf forest
seinfeld.Deciduous, // 29 Trop. broadleaf
seinfeld.Deciduous, // 30 Agricultural
seinfeld.Deciduous, // 31 Agricultural
seinfeld.Deciduous, // 32 Dec. woodland
seinfeld.Deciduous, // 33 Trop. rainforest
seinfeld.Desert, // 34 ---
seinfeld.Desert, // 35 ---
seinfeld.Grass, // 36 Rice paddies
seinfeld.Shrubs, // 37 agric
seinfeld.Shrubs, // 38 agric
seinfeld.Shrubs, // 39 agric.
seinfeld.Shrubs, // 40 shrub/grass
seinfeld.Shrubs, // 41 shrub/grass
seinfeld.Shrubs, // 42 shrub/grass
seinfeld.Shrubs, // 43 shrub/grass
seinfeld.Shrubs, // 44 shrub/grass
seinfeld.Shrubs, // 45 wetland
seinfeld.Shrubs, // 46 scrub
seinfeld.Shrubs, // 47 scrub
seinfeld.Shrubs, // 48 scrub
seinfeld.Shrubs, // 49 scrub
seinfeld.Desert, // 50 Desert
seinfeld.Desert, // 51 Desert
seinfeld.Desert, // 52 Steppe
seinfeld.Desert, // 53 Tundra
seinfeld.Deciduous, // 54 rainforest
seinfeld.Deciduous, // 55 mixed wood/open
seinfeld.Deciduous, // 56 mixed wood/open
seinfeld.Deciduous, // 57 mixed wood/open
seinfeld.Deciduous, // 58 mixed wood/open
seinfeld.Deciduous, // 59 mixed wood/open
seinfeld.Evergreen, // 60 conifers
seinfeld.Evergreen, // 61 conifers
seinfeld.Evergreen, // 62 conifers
seinfeld.Evergreen, // 63 Wooded tundra
seinfeld.Grass, // 64 Moor
seinfeld.Desert, // 65 coastal
seinfeld.Desert, // 66 coastal
seinfeld.Desert, // 67 coastal
seinfeld.Desert, // 68 coastal
seinfeld.Desert, // 69 desert
seinfeld.Desert, // 70 ice
seinfeld.Desert, // 71 salt flats
seinfeld.Grass, // 72 wetland
seinfeld.Desert, // 73 water
}
// WeselyLandUse helps fulfill the Preprocessor interface by
// returning land use categories as
// specified in github.com/ctessum/atmos/wesely1989.
func (gc *GEOSChem) WeselyLandUse() NextData {
// TODO (CT): Account for the fact that a single grid cell can have multiple land uses.
snowFunc := gc.readA1("FRSNO") // Fraction land covered by snow
return geosChemSeinfeldLandUse(snowFunc, gc.landUse)
}
func geosChemWeselyLandUse(snowFunc NextData, landUse *sparse.DenseArray) NextData {
return func() (*sparse.DenseArray, error) {
snowFrac, err := snowFunc() // Fraction land covered by snow
if err != nil {
return nil, err
}
o := sparse.ZerosDense(snowFrac.Shape...)
for j := 0; j < snowFrac.Shape[0]; j++ {
for i := 0; i < snowFrac.Shape[1]; i++ {
snowV := snowFrac.Get(j, i)
if snowV > 0.5 { // We assume that snow and Barren have similar deposition properties.
o.Set(float64(wesely1989.Barren), j, i)
}
o.Set(float64(geosChemWesely[f2i(landUse.Get(j, i))]), j, i)
}
}
return o, nil
}
}
// geosChemWesely provides a mapping between GEOSChem use categories
// described in http://wiki.seas.harvard.edu/geos-chem/index.php/Olson_land_map
// and the land use categories as
// specified in github.com/ctessum/atmos/wesely1989.
var geosChemWesely = []wesely1989.LandUseCategory{
wesely1989.Water, // 0 Water
wesely1989.Urban, // 1 Urban
wesely1989.RockyShrubs, // 2 Shrub
wesely1989.Barren, // 3 ---
wesely1989.Barren, // 4 ---
wesely1989.Barren, // 5 ---
wesely1989.Coniferous, // 6 Trop. evergreen