PTEROSOR/QUESTDB_website
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Merge branch 'master' into ADC

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This commit is contained in:
Mickaël Véril 2020-08-03 17:25:51 +02:00
commit fa31721e7b
20 changed files with 420 additions and 310 deletions
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47
content/dataset.html
View File

@ -99,12 +99,12 @@ draft: false
var data= await loadAllData()
window.defaultDats = []
for (const sub of Object.values(data)) {
for (const doi of uniq(sub.map(d => d.DOI.string))) {
const subdoi = sub.filter(d => d.DOI.string === doi)
for (const doi of uniq(sub.map(d => (d.DOI == null ? "" : d.DOI.string)))) {
const subdoi = sub.filter(d => (d.DOI == null ? "" : d.DOI.string) === doi)
for (mol of uniq(subdoi.map(d => d.molecule))) {
const submol = subdoi.filter(d => d.molecule === mol)
const source = submol.find((d) => {
if (d.DOI.string === "10.1021/acs.jctc.8b01205") {
if ((d.DOI == null ? "" : d.DOI.string) === "10.1021/acs.jctc.8b01205") {
return d.method.name === "CASPT2" && d.method.basis === "aug-cc-pVDZ"
} else {
return d.method.isTBE
@ -120,11 +120,24 @@ draft: false
window.defaultDats = window.defaultDats.concat(sub)
}
await doiCache.addRange(Array.from(new Set(window.defaultDats.map(d=>d.DOI.string))))
await doiCache.addRange(Array.from(new Set(window.defaultDats.filter(d=>d.DOI!==null).map(d=>d.DOI.string))))
window.defaultDats = window.defaultDats.sort((datfa,datfb)=>{
const puba = doiCache.get(datfa.DOI.string).format('data', { format: 'object' })[0]
const pubb = doiCache.get(datfb.DOI.string).format('data', { format: 'object' })[0]
return pubUtils.getIssuedDate(puba) - pubUtils.getIssuedDate(pubb)
const DOIa=datfa.DOI
const DOIb=datfb.DOI
if (DOIa == null && DOIb == null) {
return 0
}
else if (DOIa == null){
return 1
}
else if (DOIb == null){
return -1
}
else {
const puba = doiCache.get(DOIa.string).format('data', { format: 'object' })[0]
const pubb = doiCache.get(DOIb.string).format('data', { format: 'object' })[0]
return pubUtils.getIssuedDate(puba) - pubUtils.getIssuedDate(pubb)
}
})
processingIndicator.isActive = false
reloadCustomFiles()
@ -194,7 +207,8 @@ draft: false
const sets = await (async () => {
if (name === "DOI") {
const publis = await getPublis()
const sets = publis.sets
var sets = publis.sets
sets.set("","Unknow set")
return sets
}
else {
@ -238,7 +252,7 @@ draft: false
case "basis":
return data.method.basis
case "DOI":
return data.DOI.string
return data.DOI === null ? "" : data.DOI.string
default:
return data[name]
break;
@ -256,7 +270,7 @@ draft: false
if (!(sdatdic.has(key))) {
sdatdic.set(key, new Map())
}
const myT1s = T1ref.get(d.DOI.string).get(d.molecule)
const myT1s = T1ref.get(d.DOI == null ? "" : d.DOI.string).get(d.molecule)
for (const exc of d.excitations) {
var allowT1 = false
const T1Key = JSON.stringify((exc.initial, exc.final))
@ -367,14 +381,14 @@ draft: false
})
})
window.T1ref = new Map()
var dois = new Set(window.filtData.map((d) => d.DOI.string))
var dois = new Set(window.filtData.map((d) =>d.DOI===null ? "" : d.DOI.string))
var mols = new Set(window.filtData.map((d) => d.molecule))
await window.doiCache.addRange(dois)
for (const doi of dois) {
window.T1ref.set(doi, new Map())
for (const mol of mols) {
window.T1ref.get(doi).set(mol, new Map())
var TBESortdat = window.dats.filter(d => d.DOI.string === doi && d.molecule === mol).sort((d1, d2) => {
var TBESortdat = window.dats.filter(d => (d.DOI === null ? "" : d.DOI.string) === doi && d.molecule === mol).sort((d1, d2) => {
if (d1.method.isTBE && !d2.method.isTBE) {
return -1
} else if (!d1.method.isTBE && d2.method.isTBE) {
@ -398,7 +412,7 @@ draft: false
}
}
$(sel_ref).empty()
for (const el of uniq(window.filtData.map(d => [d.method, d.DOI.string]))) {
for (const el of uniq(window.filtData.map(d => [d.method, (d.DOI === null ? null : d.DOI.string)]))) {
op = $("<option/>", {
value: JSON.stringify(el)
}).text(el[0])
@ -413,10 +427,11 @@ draft: false
var data = $("#data")
$(data).empty();
if (window.filtData.length > 0) {
const sets = (await getPublis()).sets
var sets = (await getPublis()).sets
sets.set("","Unknow set")
for (const doi of doiCache.keys()) {
paperdata = window.filtData.filter((d) => {
return d.DOI.string == doi
return (d.DOI === null ? "" : d.DOI.string) == doi
})
var methods = uniq(paperdata.map(d => d.method))
const sortedMethods = methods.sort((a, b) => {
@ -451,7 +466,7 @@ draft: false
datadic = new Map()
for (const dat of paperdata) {
const key1 = dat.molecule;
const myT1s = T1ref.get(dat.DOI.string).get(dat.molecule)
const myT1s = T1ref.get(dat.DOI == null ? "" : dat.DOI.string).get(dat.molecule)
if (!datadic.has(key1)) {
datadic.set(key1, new Map())
}

2
content/publications.html
View File

@ -20,7 +20,7 @@ draft: false
window.onload = async function () {
var div = document.getElementById("publis_div")
const Cite = require("citation-js")
const sdois = uniq(Object.values(await loadAllData()).flat().map(d => d.DOI.string))
const sdois = uniq(Object.values(await loadAllData()).flat().filter(d => d.DOI !== null).map(d => d.DOI.string))
const spubliscite = await Cite.async(sdois)
const pubs = await getPublis()
const uospublis = spubliscite.format('data', { format: 'object' })

2
static/js/data.js
View File

@ -169,6 +169,8 @@ class excitationBase {
this.type.Value = this.type | excitationTypes.Rydberg
} else if (ty.includes(String.raw`\mathrm{V}`)) {
this.type.Value = this.type | excitationTypes.Valence
} else if (ty.toLowerCase()===excitationTypes.Double.description.string.toLowerCase()){
this.type.Value = this.type | excitationTypes.Double
}
}
}

47
tools/datafileBuilder.py
View File

@ -4,32 +4,39 @@ import re
from enum import IntEnum,auto,unique
import numpy as np
from pathlib import Path
from lib import LaTeX
from lib.dfbOptions import dfbOptions
from lib.Format import Format
from lib import LaTeX,formats,dfbOptions
from lib.formats import getFormatHandlers
from TexSoup import TexSoup,TexNode,TexCmd,TexEnv
from lib.data import dataFileBase,DataType,state
from collections import defaultdict
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--file', type=argparse.FileType('r'))
parser.add_argument("--list","-l",action="store_true", help='List all available format')
parser.add_argument('--debug', action='store_true', help='Debug mode')
args = parser.parse_args()
lines=args.file.readlines()
soup=TexSoup(lines)
opt=soup.dfbOptions
if type(opt) is TexNode and type(opt.expr) is TexEnv:
texOps=dfbOptions.readFromEnv(opt)
if args.list:
print("The list of avalable formats are:")
for formatName,_ in getFormatHandlers():
print(formatName)
elif args.file!=None:
lines=args.file.readlines()
soup=TexSoup(lines)
opt=soup.dfbOptions
if type(opt) is TexNode and type(opt.expr) is TexEnv:
texOps=dfbOptions.readFromEnv(opt)
else:
texOps=dfbOptions()
commands=[LaTeX.newCommand(cmd) for cmd in soup.find_all("newcommand")]
dat=LaTeX.tabularToData(soup.tabular,commands)
scriptpath=Path(sys.argv[0]).resolve()
datapath=scriptpath.parents[1]/"static"/"data"
if args.debug:
datapath=datapath/"test"
if not datapath.exists():
datapath.mkdir()
datalst=dataFileBase.readFromTable(dat,texOps,commands=commands)
for data in datalst:
data.toFile(datapath,texOps.suffix)
else:
texOps=dfbOptions()
commands=[LaTeX.newCommand(cmd) for cmd in soup.find_all("newcommand")]
dat=LaTeX.tabularToData(soup.tabular,commands)
scriptpath=Path(sys.argv[0]).resolve()
datapath=scriptpath.parents[1]/"static"/"data"
if args.debug:
datapath=datapath/"test"
if not datapath.exists():
datapath.mkdir()
datalst=dataFileBase.readFromTable(dat,texOps,commands=commands)
for data in datalst:
data.toFile(datapath,texOps.suffix)
parser.print_help()

9
tools/lib/Format.py
View File

@ -1,9 +0,0 @@
from enum import IntEnum,auto,unique
@unique
class Format(IntEnum):
LINE=auto()
COLUMN=auto()
DOUBLECOLUMN=auto()
EXOTICCOLUMN=auto()
TBE=auto()
DOUBLETBE=auto()

18
tools/lib/LaTeX.py
View File

@ -138,4 +138,20 @@ def tabularToData(table,commands=None):
table=np.array(lnewtable,TexNode)
return table
else:
raise ValueError("Only tabular LaTeX environment is supported")
raise ValueError("Only tabular LaTeX environment is supported")
def extractMath(TexMath,Soup=False,commands=[]):
if not Soup and len(commands)>0:
raise ValueError("Commandw are only usable when Soup is True")
math=TexMath.find("$")
lst=list(math.contents)
mystr=str(lst[0])
if not Soup:
return mystr
mathsoup=None
try:
mathsoup=TexSoup(mystr)
except:
raise ValueError(f"Error when parsing latex math: {mystr}")
newCommand.runAll(mathsoup,commands)
return mathsoup

1
tools/lib/__init__.py
View File

@ -0,0 +1 @@
from .dfbOptions import dfbOptions

291
tools/lib/data.py
View File

@ -1,10 +1,10 @@
from collections import OrderedDict
from TexSoup import TexSoup
from .LaTeX import newCommand
from .LaTeX import newCommand,extractMath
from .utils import getValFromCell,checkFloat
from TexSoup import TexNode,TexEnv
from enum import IntEnum,auto,unique,IntFlag
from .Format import Format
from .formats import getFormatHandlers
import re
import numpy as np
import json
@ -25,6 +25,27 @@ class state:
class DataType(IntEnum):
ABS=auto()
FLUO=auto()
def datafileSelector(dataType):
switcher={
DataType.ABS:AbsDataFile,
DataType.FLUO:FluoDataFile,
}
return switcher[dataType]
def getSubtablesRange(table,firstindex=2,column=0,count=1):
subtablesRange=list()
i=firstindex+count
while i<np.size(table,0):
if str(table[i,column])!="":
subtablesRange.append(range(firstindex,i))
firstindex=i
i+=count
else:
i+=1
subtablesRange.append(range(firstindex,np.size(table,0)))
return subtablesRange
class dataFileBase(object):
def __init__(self):
self.molecule = ''
@ -46,17 +67,7 @@ class dataFileBase(object):
def convertState(StateTablelist,initialState,default=DataType.ABS,commands=[]):
tmplst=[]
for TexState in StateTablelist:
math=TexState.find("$")
lst=list(math.contents)
mystr=str(lst[0])
mathsoup=None
try:
mathsoup=TexSoup(mystr)
except:
print(f"Error when parsing latex state: {mystr}")
exit(-1)
newCommand.runAll(mathsoup,commands)
st=str(mathsoup)
st=str(extractMath(TexState,Soup=True,commands=commands))
m=re.match(r"^\^(?P<multiplicity>\d)(?P<symm>[^\s\[(]*)\s*(?:\[(?:\\mathrm{)?(?P<special>\w)(?:})\])?\s*(:?\((?P<type>[^\)]*)\))?",st)
seq=m.group("multiplicity","symm")
mul=int(m.group("multiplicity"))
@ -78,253 +89,13 @@ class dataFileBase(object):
return lst
@staticmethod
def readFromTable(table,TexOps, commands=[]):
def getSubtableIndex(table,firstindex=2,column=0,count=1):
subtablesindex=list()
i=firstindex+count
while i<np.size(table,0):
if str(table[i,column])!="":
subtablesindex.append((firstindex,i-1))
firstindex=i
i+=count
else:
i+=1
subtablesindex.append((firstindex,np.size(table,0)))
return subtablesindex
datalist=list()
switcher={
DataType.ABS:AbsDataFile,
DataType.FLUO:FluoDataFile,
}
if TexOps.format==Format.LINE:
for col in range(1,np.size(table,1)):
col=table[:,col]
mymolecule=str(col[0])
mymethod=method(str(col[2]),str(col[1]))
initialState=TexOps.initialStates[mymolecule]
finsts=dataFileBase.convertState(table[3:,0],initialState,default=TexOps.defaultType,commands=commands)
datacls=dict()
for index,cell in enumerate(col[3:]):
if str(cell)!="":
val,unsafe=getValFromCell(cell)
finst=finsts[index]
dt=finst[1]
if dt in datacls:
data=datacls[dt]
else:
cl=switcher[dt]
data=cl()
datacls[dt]=data
data.molecule=mymolecule
data.method=mymethod
data.excitations.append(excitationValue(initialState,finst[0],val,type=finst[2],isUnsafe=unsafe))
for value in datacls.values():
datalist.append(value)
return datalist
elif TexOps.format==Format.COLUMN:
subtablesindex=getSubtableIndex(table)
for first, last in subtablesindex:
for col in range(2,np.size(table,1)):
datacls=dict()
col=table[:,col]
mymolecule=str(table[first,0])
initialState=TexOps.initialStates[mymolecule]
mymethod=method(str(col[1]),str(col[0]))
finsts=dataFileBase.convertState(table[first:last+1,1],initialState,default=TexOps.defaultType,commands=commands)
for index,cell in enumerate(col[first:last+1]):
if str(cell)!="":
val,unsafe=getValFromCell(cell)
finst=finsts[index]
dt=finst[1]
if dt in datacls:
data=datacls[dt]
else:
cl=switcher[dt]
data=cl()
data.molecule=mymolecule
data.method=mymethod
datacls[dt]=data
data.excitations.append(excitationValue(initialState,finst[0],val,type=finst[2]))
for value in datacls.values():
datalist.append(value)
return datalist
elif TexOps.format==Format.DOUBLECOLUMN:
datacls=dict()
subtablesMol=getSubtableIndex(table)
for firstMol, lastMol in subtablesMol:
mymolecule=str(table[firstMol,0])
moltable=table[firstMol:lastMol+1,:]
subtablestrans=getSubtableIndex(moltable,firstindex=0,column=1,count=2)
for firstTrans,lastTrans in subtablestrans:
mytrans=moltable[firstTrans:lastTrans+1,:]
mytransdesc=mytrans[0:2,1]
for i in range(2):
try:
mathsoup=TexSoup(mytransdesc[i])
except:
print(f"Error when parsing latex state: {str(mytransdesc[i])}")
exit(-1)
newCommand.runAll(mathsoup,commands)
mytransdesc[i]=str(mathsoup)
for colindex in range(3,np.size(table,1)):
col=mytrans[:,colindex]
mybasis=str(table[1,colindex])
for index,cell in enumerate(col):
methodnameAT1=str(mytrans[index,2])
PTString=r"($\%T_1$)"
HasT1=methodnameAT1.endswith(PTString)
if HasT1:
methodname=methodnameAT1[:-len(PTString)]
else:
methodname=str(methodnameAT1)
mymethod=method(methodname,mybasis)
strcell=str(cell)
if strcell!="":
if HasT1:
m=re.match(r"^(?P<value>[-+]?\d+\.?\d*)\s*(?:\((?P<T1>\d+\.?\d*)\\\%\))?",strcell)
val,unsafe=getValFromCell(TexSoup(m.group("value")))
T1=m.group("T1")
else:
m=re.match(r"^[-+]?\d+\.?\d*",strcell)
val,unsafe=getValFromCell(TexSoup(m.group(0)))
T1=None
if (mymolecule,mymethod.name,mymethod.basis) in datacls:
data=datacls[(mymolecule,mymethod.name,mymethod.basis)]
else:
data=AbsDataFile()
data.molecule=mymolecule
data.method=mymethod
datacls[(mymolecule,mymethod.name,mymethod.basis)]=data
infin=mytransdesc[0].split(r"\rightarrow")
for i,item in enumerate(infin):
m=re.match(r"^(?P<number>\d)\\[,:;\s]\s*\^(?P<multiplicity>\d)(?P<sym>\S*)",item.strip())
infin[i]=state(m.group("number"),m.group("multiplicity"),m.group("sym"))
data.excitations.append(excitationValue(infin[0],infin[1],val,type=mytransdesc[1],isUnsafe=unsafe,T1=T1))
for value in datacls.values():
datalist.append(value)
return datalist
elif TexOps.format==Format.EXOTICCOLUMN:
import json
subtablesindex=getSubtableIndex(table)
for first, last in subtablesindex:
valDic=dict()
mymolecule=str(table[first,0])
initialState=TexOps.initialStates[mymolecule]
for col in range(2,np.size(table,1)):
col=table[:,col]
basis=str(col[0])
mymethcell=list(col[1])
if isinstance(mymethcell[0],TexNode) and mymethcell[0].name=="$":
kindSoup=TexSoup("".join(list(mymethcell[0].expr.all)))
newCommand.runAll(kindSoup,commands)
kind=str(kindSoup)
methodnameSoup=TexSoup(mymethcell[1].value)
newCommand.runAll(methodnameSoup,commands)
methodname=str(methodnameSoup)
else:
kind=""
methtex=col[1]
newCommand.runAll(methtex,commands)
methodname=str(methtex)
mymethod=method(methodname,basis)
methkey=json.dumps(mymethod.__dict__)
finsts=dataFileBase.convertState(table[first:last+1,1],initialState,default=TexOps.default,commands=commands)
for index,cell in enumerate(col[first:last+1]):
if str(cell)!="":
val,unsafe=getValFromCell(cell)
finst=finsts[index]
dt=finst[1]
if dt in valDic:
dtDic=valDic[dt]
else:
dtDic=dict()
valDic[dt]=dtDic
if not methkey in dtDic:
dtDic[methkey]=dict()
dataDic=dtDic[methkey]
exkey=(json.dumps(finst[0].__dict__,),finst[2])
if not exkey in dataDic:
dataDic[exkey]=dict()
if kind=='':
dataDic[exkey][kind]=(val,unsafe)
else:
dataDic[exkey][kind]=val
#data.excitations.append(excitationValue(initialState,finst[0],val,type=finst[2]))
for dt,methdic in valDic.items():
for methstring,exdic in methdic.items():
data=switcher[dt]()
data.molecule=mymolecule
methdic=json.loads(methstring)
data.method=method(methdic["name"],methdic["basis"])
for exstr,values in exdic.items():
stDict=json.loads(exstr[0])
ty=exstr[1]
st=state(stDict["number"],stDict["multiplicity"],stDict["symetry"])
T1=values["\\%T_1"] if "\\%T_1" in values else None
oF= values["f"] if "f" in values else None
val,unsafe=values[""]
data.excitations.append(excitationValue(initialState,st,val,type=ty,T1=T1,isUnsafe=unsafe,oscilatorForces=oF))
datalist.append(data)
return datalist
elif TexOps.format==Format.TBE:
subtablesindex=getSubtableIndex(table)
for first, last in subtablesindex:
datacls=dict()
mymolecule=str(table[first,0])
initialState=TexOps.initialStates[mymolecule]
mymethod=(method("TBE(FC)"),method("TBE"))
finsts=dataFileBase.convertState(table[first:last+1,1],initialState,default=TexOps.defaultType,commands=commands)
for index,row in enumerate(table[first:last+1,]):
oscilatorForces=checkFloat(str(row[2]))
T1 = checkFloat(str(row[3]))
val,unsafe = getValFromCell(row[4])
corr,unsafecorr = getValFromCell(row[7])
finst=finsts[index]
dt=finst[1]
if dt in datacls:
datamtbe = datacls[dt]
else:
cl=switcher[dt]
datamtbe=[]
for met in mymethod:
data=cl()
data.molecule=mymolecule
data.method=met
datamtbe.append(data)
datacls[dt]=datamtbe
vs=[val,corr]
uns=[unsafe,unsafecorr]
for i in range(2):
datamtbe[i].excitations.append(excitationValue(initialState,finst[0],vs[i],type=finst[2],T1=T1,oscilatorForces=oscilatorForces,isUnsafe=uns[i]))
for value in datacls.values():
for dat in value:
datalist.append(dat)
return datalist
elif TexOps.format==Format.DOUBLETBE:
datacls=dict()
subtablesMol=getSubtableIndex(table)
for firstMol, lastMol in subtablesMol:
data=AbsDataFile()
data.molecule=str(table[firstMol,0])
data.method=method("TBE","CBS")
for mytrans in table[firstMol:lastMol+1]:
try:
mathsoup=TexSoup(mytrans[1])
except:
print(f"Error when parsing latex state: {str(mytransdesc[i])}")
exit(-1)
newCommand.runAll(mathsoup,commands)
mytransdesc=str(mathsoup)
infin=mytransdesc.split(r"\rightarrow")
for i,item in enumerate(infin):
m=re.match(r"^(?P<number>\d)\\[,:;\s]\s*\^(?P<multiplicity>\d)(?P<sym>\S*)",item.strip())
infin[i]=state(m.group("number"),m.group("multiplicity"),m.group("sym"))
cell=mytrans[6]
val,unsafe=getValFromCell(cell)
data.excitations.append(excitationValue(infin[0],infin[1],val,isUnsafe=unsafe))
datalist.append(data)
return datalist
for formatName,Cls in getFormatHandlers():
if formatName.lower()==TexOps.format.lower():
handler=Cls(TexOps,commands)
break
else:
raise ValueError()
return handler.readFromTable(table)
def getMetadata(self):
dic=OrderedDict()
dic["Molecule"]=self.molecule

6
tools/lib/dfbOptions.py
View File

@ -1,12 +1,12 @@
from TexSoup import TexSoup,TexCmd
from .Format import Format
from . import formats
from .data import dataFileBase,DataType,state
from collections import defaultdict
class dfbOptions(object):
def __init__(self):
self.defaultType=DataType.ABS
self.format=Format.LINE
self.format="line"
self.suffix=None
self.initialStates=defaultdict(lambda : state(1,1,"A_1"))
@ -23,7 +23,7 @@ class dfbOptions(object):
if dfbFormatNode!=None:
dfbFormat=dfbFormatNode.expr
if type(dfbFormat) is TexCmd:
dfb_Opt.format=Format[dfbFormat.args[0].value.upper()]
dfb_Opt.format=dfbFormat.args[0].value
dfbSuffixNode=lateEnv.suffix
if dfbSuffixNode!=None:

3
tools/lib/formats/__init__.py Normal file
View File

@ -0,0 +1,3 @@
from .formatHandlerBase import formatHandlerBase
from .formatName import formatName
from .getFormatHandlers import getFormatHandlers

41
tools/lib/formats/default/TBEHandler.py Normal file
View File

@ -0,0 +1,41 @@
from ..formatHandlerBase import formatHandlerBase
from ..formatName import formatName
from ...data import dataFileBase,DataType,method,excitationValue,datafileSelector,getSubtablesRange
from ...utils import getValFromCell, checkFloat
@formatName("TBE")
class TBEHandler(formatHandlerBase):
def readFromTable(self,table):
datalist=list()
subtablesRange=getSubtablesRange(table)
for myrange in subtablesRange:
datacls=dict()
mymolecule=str(table[myrange[0],0])
initialState=self.TexOps.initialStates[mymolecule]
mymethod=(method("TBE(FC)"),method("TBE"))
finsts=dataFileBase.convertState(table[myrange,1],initialState,default=self.TexOps.defaultType,commands=self.commands)
for index,row in enumerate(table[myrange,]):
oscilatorForces=checkFloat(str(row[2]))
T1 = checkFloat(str(row[3]))
val,unsafe = getValFromCell(row[4])
corr,unsafecorr = getValFromCell(row[7])
finst=finsts[index]
dt=finst[1]
if dt in datacls:
datamtbe = datacls[dt]
else:
cl=datafileSelector(dt)
datamtbe=[]
for met in mymethod:
data=cl()
data.molecule=mymolecule
data.method=met
datamtbe.append(data)
datacls[dt]=datamtbe
vs=[val,corr]
uns=[unsafe,unsafecorr]
for i in range(2):
datamtbe[i].excitations.append(excitationValue(initialState,finst[0],vs[i],type=finst[2],T1=T1,oscilatorForces=oscilatorForces,isUnsafe=uns[i]))
for value in datacls.values():
for dat in value:
datalist.append(dat)
return datalist

6
tools/lib/formats/default/__init__.py Normal file
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from .lineHandler import lineHandler
from .columnHandler import columnHandler
from .doubleColumnHandler import doubleColumnHandler
from .TBEHandler import TBEHandler
from .doubleTBEHandler import doubleTBEHandler
from .exoticColumnHandler import exoticColumnHandler

35
tools/lib/formats/default/columnHandler.py Normal file
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from ..formatHandlerBase import formatHandlerBase
from ..formatName import formatName
from ...data import dataFileBase,DataType,method,excitationValue,datafileSelector,getSubtablesRange
from ...utils import getValFromCell
import numpy as np
@formatName("column")
class columnHandler(formatHandlerBase):
def readFromTable(self,table):
datalist=list()
subtablesRange=getSubtablesRange(table)
for myrange in subtablesRange:
for col in range(2,np.size(table,1)):
datacls=dict()
col=table[:,col]
mymolecule=str(table[myrange[0],0])
initialState=self.TexOps.initialStates[mymolecule]
mymethod=method(str(col[1]),str(col[0]))
finsts=dataFileBase.convertState(table[myrange,1],initialState,default=self.TexOps.defaultType,commands=self.commands)
for index,cell in enumerate(col[myrange]):
if str(cell)!="":
val,unsafe=getValFromCell(cell)
finst=finsts[index]
dt=finst[1]
if dt in datacls:
data=datacls[dt]
else:
cl=datafileSelector(dt)
data=cl()
data.molecule=mymolecule
data.method=mymethod
datacls[dt]=data
data.excitations.append(excitationValue(initialState,finst[0],val,type=finst[2]))
for value in datacls.values():
datalist.append(value)
return datalist

62
tools/lib/formats/default/doubleColumnHandler.py Normal file
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from ..formatHandlerBase import formatHandlerBase
from ..formatName import formatName
from ...data import dataFileBase,DataType,method,excitationValue,datafileSelector,AbsDataFile,getSubtablesRange,state
from ...LaTeX import newCommand,extractMath
import re
from TexSoup import TexSoup
import numpy as np
from ...utils import getValFromCell
@formatName("doubleColumn")
class doubleColumnHandler(formatHandlerBase):
def readFromTable(self,table):
datalist=list()
datacls=dict()
subtablesMol=getSubtablesRange(table)
for rangeMol in subtablesMol:
mymolecule=str(table[rangeMol[0],0])
moltable=table[rangeMol,:]
subtablestrans=getSubtablesRange(moltable,firstindex=0,column=1,count=2)
for rangeTrans in subtablestrans:
mytrans=moltable[rangeTrans,:]
mytransdesc=mytrans[0:2,1]
for i in range(2):
mathsoup=extractMath(mytransdesc[i],Soup=True,commands=self.commands)
mytransdesc[i]=str(mathsoup)
for colindex in range(3,np.size(table,1)):
col=mytrans[:,colindex]
mybasis=str(table[1,colindex])
for index,cell in enumerate(col):
methodnameAT1=str(mytrans[index,2])
PTString=r"($\%T_1$)"
HasT1=methodnameAT1.endswith(PTString)
if HasT1:
methodname=methodnameAT1[:-len(PTString)]
else:
methodname=str(methodnameAT1)
mymethod=method(methodname,mybasis)
strcell=str(cell)
if strcell!="":
if HasT1:
m=re.match(r"^(?P<value>[-+]?\d+\.?\d*)\s*(?:\((?P<T1>\d+\.?\d*)\\\%\))?",strcell)
val,unsafe=getValFromCell(TexSoup(m.group("value")))
T1=m.group("T1")
else:
m=re.match(r"^[-+]?\d+\.?\d*",strcell)
val,unsafe=getValFromCell(TexSoup(m.group(0)))
T1=None
if (mymolecule,mymethod.name,mymethod.basis) in datacls:
data=datacls[(mymolecule,mymethod.name,mymethod.basis)]
else:
data=AbsDataFile()
data.molecule=mymolecule
data.method=mymethod
datacls[(mymolecule,mymethod.name,mymethod.basis)]=data
infin=mytransdesc[0].split(r"\rightarrow")
for i,item in enumerate(infin):
m=re.match(r"^(?P<number>\d)\\[,:;\s]\s*\^(?P<multiplicity>\d)(?P<sym>\S*)",item.strip())
infin[i]=state(m.group("number"),m.group("multiplicity"),m.group("sym"))
data.excitations.append(excitationValue(infin[0],infin[1],val,type=mytransdesc[1],isUnsafe=unsafe,T1=T1))
for value in datacls.values():
datalist.append(value)
return datalist

28
tools/lib/formats/default/doubleTBEHandler.py Normal file
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from ..formatHandlerBase import formatHandlerBase
from ..formatName import formatName
from ...data import dataFileBase,DataType,method,excitationValue,datafileSelector,getSubtablesRange,AbsDataFile,state
from ...utils import getValFromCell, checkFloat
from ...LaTeX import newCommand,extractMath
from TexSoup import TexSoup
import re
@formatName("doubleTBE")
class doubleTBEHandler(formatHandlerBase):
def readFromTable(self,table):
datalist=list()
subtablesMol=getSubtablesRange(table)
for rangeMol in subtablesMol:
data=AbsDataFile()
data.molecule=str(table[rangeMol[0],0])
data.method=method("TBE","CBS")
for mytrans in table[rangeMol]:
mathsoup=extractMath(mytrans[1],Soup=True,commands=self.commands)
mytransdesc=str(mathsoup)
infin=mytransdesc.split(r"\rightarrow")
for i,item in enumerate(infin):
m=re.match(r"^(?P<number>\d)\\[,:;\s]\s*\^(?P<multiplicity>\d)(?P<sym>\S*)",item.strip())
infin[i]=state(m.group("number"),m.group("multiplicity"),m.group("sym"))
cell=mytrans[6]
val,unsafe=getValFromCell(cell)
data.excitations.append(excitationValue(infin[0],infin[1],val,isUnsafe=unsafe))
datalist.append(data)
return datalist

73
tools/lib/formats/default/exoticColumnHandler.py Normal file
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from ..formatHandlerBase import formatHandlerBase
from ..formatName import formatName
from ...data import dataFileBase,DataType,method,excitationValue,datafileSelector,getSubtablesRange,state
from ...utils import getValFromCell
from TexSoup import TexSoup,TexNode
from ...LaTeX import newCommand
import numpy as np
import json
@formatName("exoticColumn")
class exoticColumnHandler(formatHandlerBase):
def readFromTable(self,table):
datalist=list()
subtablesRange=getSubtablesRange(table)
for myrange in subtablesRange:
valDic=dict()
mymolecule=str(table[myrange[0],0])
initialState=self.TexOps.initialStates[mymolecule]
for col in range(2,np.size(table,1)):
col=table[:,col]
basis=str(col[0])
mymethcell=list(col[1])
if isinstance(mymethcell[0],TexNode) and mymethcell[0].name=="$":
kindSoup=TexSoup("".join(list(mymethcell[0].expr.all)))
newCommand.runAll(kindSoup,self.commands)
kind=str(kindSoup)
methodnameSoup=TexSoup(mymethcell[1].value)
newCommand.runAll(methodnameSoup,self.commands)
methodname=str(methodnameSoup)
else:
kind=""
methtex=col[1]
newCommand.runAll(methtex,self.commands)
methodname=str(methtex)
mymethod=method(methodname,basis)
methkey=json.dumps(mymethod.__dict__)
finsts=dataFileBase.convertState(table[myrange,1],initialState,default=self.TexOps.defaultType,commands=self.commands)
for index,cell in enumerate(col[myrange]):
if str(cell)!="":
val,unsafe=getValFromCell(cell)
finst=finsts[index]
dt=finst[1]
if dt in valDic:
dtDic=valDic[dt]
else:
dtDic=dict()
valDic[dt]=dtDic
if not methkey in dtDic:
dtDic[methkey]=dict()
dataDic=dtDic[methkey]
exkey=(json.dumps(finst[0].__dict__,),finst[2])
if not exkey in dataDic:
dataDic[exkey]=dict()
if kind=='':
dataDic[exkey][kind]=(val,unsafe)
else:
dataDic[exkey][kind]=val
#data.excitations.append(excitationValue(initialState,finst[0],val,type=finst[2]))
for dt,methdic in valDic.items():
for methstring,exdic in methdic.items():
data=datafileSelector(dt)()
data.molecule=mymolecule
methdic=json.loads(methstring)
data.method=method(methdic["name"],methdic["basis"])
for exstr,values in exdic.items():
stDict=json.loads(exstr[0])
ty=exstr[1]
st=state(stDict["number"],stDict["multiplicity"],stDict["symetry"])
T1=values["\\%T_1"] if "\\%T_1" in values else None
oF= values["f"] if "f" in values else None
val,unsafe=values[""]
data.excitations.append(excitationValue(initialState,st,val,type=ty,T1=T1,isUnsafe=unsafe,oscilatorForces=oF))
datalist.append(data)
return datalist

33
tools/lib/formats/default/lineHandler.py Normal file
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from ..formatHandlerBase import formatHandlerBase
from ..formatName import formatName
from ...data import dataFileBase,DataType,method,excitationValue,datafileSelector
from ...utils import getValFromCell
import numpy as np
@formatName("line")
class lineHandler(formatHandlerBase):
def readFromTable(self,table):
datalist=list()
for col in range(1,np.size(table,1)):
col=table[:,col]
mymolecule=str(col[0])
mymethod=method(str(col[2]),str(col[1]))
initialState=self.TexOps.initialStates[mymolecule]
finsts=dataFileBase.convertState(table[3:,0],initialState,default=self.TexOps.defaultType,commands=self.commands)
datacls=dict()
for index,cell in enumerate(col[3:]):
if str(cell)!="":
val,unsafe=getValFromCell(cell)
finst=finsts[index]
dt=finst[1]
if dt in datacls:
data=datacls[dt]
else:
cl=datafileSelector(dt)
data=cl()
datacls[dt]=data
data.molecule=mymolecule
data.method=mymethod
data.excitations.append(excitationValue(initialState,finst[0],val,type=finst[2],isUnsafe=unsafe))
for value in datacls.values():
datalist.append(value)
return datalist

10
tools/lib/formats/formatHandlerBase.py Normal file
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from abc import ABCMeta
from abc import abstractmethod
class formatHandlerBase(object):
__metaclass__ = ABCMeta
def __init__(self,TexOps, commands=[]):
self.TexOps=TexOps
self.commands=commands
@abstractmethod
def readFromTable(self,table):
raise NotImplementedError()

5
tools/lib/formats/formatName.py Normal file
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def formatName(name):
def formatWrapped(Cls):
Cls.__formatName__=name
return Cls
return formatWrapped

11
tools/lib/formats/getFormatHandlers.py Normal file
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import inspect
from . import formatHandlerBase
def getFormatHandlers(includeUnnamed=False):
from . import default
for clsName,Cls in inspect.getmembers(default,inspect.isclass):
if issubclass(Cls,formatHandlerBase):
if hasattr(Cls,"__formatName__"):
yield (Cls.__formatName__,Cls)
elif(includeUnnamed):
yield (None,Cls)