About

ioChem-BD captures the most relevant information derived from computational chemistry software packages and translate it to style-agnostic data formats such as XML, and particularly to CML (Chemical Markup Language). Such tagged data format serves as the base platform for querying its content to look for specific information. This base CML format is also being used to generate automated reports, graphs and further data processing. Our goal is to use this data assets to manage and query the Big Data generated in this specific field of chemistry.

This document collects a number of cases that ioChem-BD can handle. Find below the original input and output files that were uploaded, and the files generated upon processing either as the raw CML file, as the HTML5 file used for data visualisation, or as the JCAMP-DX file for vibrational spectrum representation.

We kindly ask the interested reader to browse the "Conversion Templates Reference" site (Documentation menu) for a detailed description of what and from where data fields are captured, and how the HTML5 file is generated for visualisation. Note that ioChem-BD captures many data fields but for only few of them the HTML5 representation is generated. Given the dynamic architecture of iochem-BD, generating new capture templates and/or new representation templates is extremely flexible, so new templates can be written and implemented at any time without disrupting normal operation. Contact us for further requests.

Release v1.1.0 (current)

iochem-BD handles results obtained from:

Find below some examples used to check data capture and manipulation mechanisms coded inside ioChem-BD.

ADF

Calculation name Source files Properties Generated CML file CML derived content
Keggin_anion Input / Output ADF2010, OPT, BP86, TZ2P, COSMO CML HTML5
Keggin_anion Input / Output ADF2009, SP, B3LYP, DZP, COSMO CML HTML5
W6O19 Input / Output ADF2009, SP, CAMY-B3LYP, TZ2P, COSMO, TD-DFT, Excitations (10) CML HTML5
B2pin2 Input / Output ADF2009, SP, BP86, Freqs CML HTML5 JCAMP-DX
NMR Input / Output ADF2009, NMR CML HTML5
Bis-porhyrine Input / Output ADF2010, SP, SAOP, TZP, C2V, TD-DFT, CD, Excitations (80) CML HTML5
C16H31B2O6 Input / Output ADF2009, OPT TS, BP86, TZP, Freqs CML HTML5 JCAMP-DX
C2H21Mo24O77 Input / Output ADF2010, OPT, BP86, TZP, ZORA, COSMO, Cs CML HTML5
ts1_freq Input / Output ADF2010, SP, BP86, TZP, ZORA, Freqs CML HTML5 JCAMP-DX

Gaussian '09

Calculation name Source files Properties Generated CML file CML derived content
ketone-qm Input / Output MeCOMe, b3lyp, opt, freq CML HTML5 JCAMP-DX
me-ccsdt Input / Output methane, single point ccsd(t) CML HTML5
h2smd Input / Output H2, b3lyp, opt, SMD CML HTML5
ketone-oniom Input / Output MeCOMe, oniom(b3lyp:uff), opt, freq CML HTML5 JCAMP-DX
PdPh3-pbed3 Input / Output Pd(PPh3), pbepbe/d3, opt CML HTML5 JCAMP-DX
meoh-dist Input / Output MeOH, b97d/gen, modredund CML HTML5
tpcuts Input / Output TpCu(N2)(CHCO2Me)(MeCO2Et), b97d, ts search, freq CML HTML5 JCAMP-DX
meoh-scan Input / Output MeOH, b97d/gen, scan CML HTML5
me-mp2 Input / Output methane, single point mp2 CML HTML5
tpcuts2step Input / Output TpCu(N2)(CHCO2Me)(MeCO2Et), b97d constr. opt + ts search, freq CML HTML5 JCAMP-DX
me-mp5 Input / Output methane, single point mp5 CML HTML5
cucl-pse4 Input / Output CuCl, b3lyp/gen, opt, pseudo=read CML HTML5
cucurb Input / Output alkyne+azide inside capsule, b97d, counterpoise calculation CML HMTL5
a-siw12-2 Input / Output CML HTML5

Turbomole 6.4

Calculation folder
Source files* Properties Generated CML file CML derived content
acetic/cc B / C1 / C2 / E / O Single point MP2 CCSD CCSD(T) CML HTML5
acetic/freq B / C1 / C2 / E / O Frequencies DFT (BP86 / def2-SVP) CML HTML5 JCAMP-DX
acetic B / C1 / C2 / E / O Geometry optimization DFT (BP86 / def2-SVP) CML HTML5
acrolein/cosmo B / C1 / C2 / E / O Single point, cosmo HF CML HTML5
acrolein B / C1 / C2 / E / O Single point, Excited states TD-DFT (B3-LYP , RPA) CML HTML5
biverdazyl B / C1 / C2 / E / O Geom. Opt. S=1 DFT (PBE0) CML HTML5
dmabn/tddft/freq B / C1 / C2 / E / O Frequencies DFT (BP86) CML HTML5 JCAMP-DX
dmabn/tddft B / C1 / C2 / E / O Geom. Opt. Exc. State DFT (BP86) CML HTML5
dmabn/tdhf B / C1 / C2 / E / O Single point, Excited states HF CML HTML5
dmabn B / C1 / C2 / E / O Restricted Geom opt. DFT (b-lyp) CML HTML5
FeOH2/quartet/TS B / C1 / C2 / E / O Geometry opt. TS DFT (pbe0) CML HTML5 JCAMP-DX
FeOH2/quartet B / C1 / C2 / E / O Geometry opt. DFT (pbe0) CML HTML5 JCAMP-DX
FeOH2/TS B / C1 / C2 / E / O Geometry opt. TS DFT (pbe0) CML HTML5 JCAMP-DX
FeOH2 B / C1 / C2 / E / O Geometry opt. DFT (pbe0) CML HTML5 JCAMP-DX
fetz/HS B / C1 / C2 / E / O Geometry opt. TS DFT (pbe0) CML HTML5 JCAMP-DX
fetz/IS B / C1 / C2 / E / O Geom opt. + freq DFT (B3-LYP) CML HTML5 JCAMP-DX
fetz/LS B / C1 / C2 / E / O Geom opt. + freq DFT (B3-LYP) CML HTML5
fim B / C1 / C2 / E / O Geom opt. DFT (BP86) CML HTML5
fluorophenol B / C1 / C2 / E / O Geometry optimization DFT (BP86) CML HTML5
fluorophenol/nbo B / C1 / C2 / E / O Single point DFT (BP86) CML HTML5
rubipy B / C1 / C2 / E / O Single point DFT (pbe0, D3) CML HTML5
water/spectrum B / C1 / C2 / E / O Single point, Excited states TD-DFT (PBE0) CML HTML5
water B / C1 / C2 / E / O Single point MP2-F12 CML HTML5

* B = basis , C1 = control, C2 = coord, E = energy, O = job.last (or module output file)

Vasp 5.3.2

Calculation name Source files Properties Generated CML file CML derived content
Comming soon

Orca 3.0.1

Calculation name Source files Properties Generated CML file CML derived content
FeOH2/quartetInput / OutputGeometry optimization DFT (pbe0) Geometry optimization quartetCMLHTML5 JCAMP-DX
FeOH2/quartet/TSInput / OutputGeometry optimization TSDFT (pbe0) Geometry optimization TS quartetCMLHTML5 JCAMP-DX
FeOH2/sextetInput / OutputGeometry optimization DFT (pbe0) Geometry optimization sextetCMLHTML5 JCAMP-DX
FeOH2/sextet/TSInput / OutputGeometry optimization TSDFT (pbe0) Geometry optimization TS sextetCMLHTML5 JCAMP-DX
acroleinInput / OutputSingle point, Excited statesTDDFT (B3LYP) Excited states with TDDFTCMLHTML5
acrolein/geom_optInput / OutputGeometry optimization DFT (TPSS) Geometry optimizationCMLHTML5
acrolein/geom_opt/D3_cosmoInput / OutputGeometry optimization, COSMODFT (TPSS D3) Geometry optimization + Dispersion correction + COSMOCMLHTML5
acrolein/bpInput / OutputSingle point, Excited statesTDDFT (BP86) Excited states with TDDFT (TDA, default)CMLHTML5
acrolein/bp/no_tdaInput / OutputSingle point, Excited statesTDDFT (BP86) Excited states with TDDFT (no TDA)CMLHTML5
ch4Input / OutputSingle pointDFT (VWN5) NMR shiftsCMLHTML5
rubipyInput / OutputSingle pointDFT (PBE0 D3) Non standard integration grid, dispersion correction and use of ECPCMLHTML5
rubipy/standard_gridInput / OutputSingle pointDFT (PBE0 D3) Standard integration grid, dispersion correction and use of ECPCMLHTML5
aceticInput / OutputGeometry optimizationDFT (BP86) Geometry optimizationCMLHTML5
acetic/ccInput / OutputSingle pointMP2 CCSD CCSD(T) Post Hartree-Fock methodsCMLHTML5
acetic/freqInput / OutputGeom. Opt + freqDFT (BP86) Frequencies CMLHTML5 JCAMP-DX
siwyigInput / OutputBroken symmetryDFT (B3LYP) Spin flip (BS approach)CMLHTML5
biverdazylInput / OutputGeometry optimizationDFT (PBE0) Geom. Opt for S=1; spin populationsCMLHTML5
water/restr_geomInput / OutputRestricted geometry optimizationHF Restr. Geom opt. Fixing an angleCMLHTML5
water/f12Input / OutputSingle pointMP2-F12 MP2-F12CMLHTML5
water/spectrumInput / OutputSingle point, Excited statesTDDFT (PBE0) Excited singlet and triplet statesCMLHTML5
fetz/LSInput / OutputGeom. Opt + freqDFT (B3LYP D3) Geom. Opt. + freq + D3CMLHTML5 JCAMP-DX
fetz/ISInput / OutputGeom. Opt + freqDFT (B3LYP D3) generating spin state reportCMLHTML5 JCAMP-DX
fetz/HSInput / OutputGeom. Opt + freqDFT (B3LYP D3) generating spin state reportCMLHTML5 JCAMP-DX
fluorophenolInput / OutputGeometry optimizationDFT (BP86) population analysis + electrostatic momentsCMLHTML5
fetacnInput / OutputGeometry optimizationDFT (B3LYP*) non standard DFT functionalsCMLHTML5
fetacnInput / OutputGeometry optimizationDFT (B3LYP modified) non standard DFT functionals (50% Fock)CMLHTML5
fimInput / OutputGeometry optimizationDFT (BP86 D3) Geometry optimization with dispersionCMLHTML5
fim/tddftInput / OutputSingle point Excited stateTDDFT (B3LYP) Excited states with TDDFTCMLHTML5
dmabnInput / OutputGeometry optimizationHF Hartree-Fock geometry optimizationCMLHTML5
dmabn/tdhfInput / OutputSingle point, Excited statesTDHF Time dependent HF for excited statesCMLHTML5
dmabn/tddftInput / OutputGeometry optimization, Excited StateDFT (BP86) Geometry optimization in the excited stateCMLHTML5
dmabn/tddft/freqInput / OutputGeometry optimization Minimum, Excited stateDFT (BP86) Frequencies excited stateCMLHTML5 JCAMP-DX
ni7Input / OutputSingle pointDFT (TPSSh) g tensor and ZFSCMLHTML5
ReCO2Input / OutputSingle point Excited stateTDDFT (PBE0 D3) Excited states with TDDFT + dispersion correctionCMLHTML5

Molcas 8.0 (BETA)

Calculation name Source files Properties Generated CML file CML derived content
biverdazyl/raspt2Input / Outputsingle point RASSCF/RASPT2 D2h symmetryCMLHTML5
biverdazyl/caspt2Input / Outputsingle point CASSCF/CASPT2 D2h symmetryCMLHTML5
aceticInput / Outputgeometry optimization B3LYPCMLHTML5
acetic/ccInput / Outputsingle point MP2, CCSD CCSD(T) post Hartree Fock methodsCMLHTML5
acetic/freqInput / Outputopt + freq B3LYPCMLHTML5 JCAMP-DX
acetic/caspt2Input / Outputsingle point CASSCF/CASPT2, medium choleskyCMLHTML5
hf/pcmInput / Outputsingle point with PCM and symmetry C2CMLHTML5
hf/kirkwoodInput / Outputsingle point with cavity solvent model and symmetry C2CMLHTML5
fluorophenolInput / OutputSingle point; atomic charges and polarizabilitiesCMLHTML5
waterInput / OutputRestricted geometry optimizationCMLHTML5
acrolein/b3lyp_optInput / Outputgeometry optimization B3LYPCMLHTML5
acrolein/opbe_optInput / Outputgeometry optimization OPBECMLHTML5
acrolein/casscf_optInput / Outputgeometry optimization CASSCFCMLHTML5
acrolein/pbe0_cosmo_optInput / Outputgeometry optimization PBE0 with PCMCMLHTML5
acrolein/mo62x_optInput / Outputgeometry optimization M062XCMLHTML5
acrolein/caspt2Input / OutputCASSCF/CASPT2 for five rootsCMLHTML5
FeOH2/sextet_TSInput / OutputTS optimization with CASPT2 + frequenciesCMLHTML5
FeOH2/sextetInput / OutputCASPT2 geometry optimizationCMLHTML5
FeOH2/quartetInput / OutputCASPT2 geometry optimizationCMLHTML5
FeOH2/sextet_freqInput / OutputTS optimization with CASPT2 + frequenciesCMLHTML5 JCAMP-DX
ethane/staggeredInput / OutputSingle point; atomic charges and polarizabilitiesCMLHTML5
ethane/eclipsedInput / OutputSingle point; atomic charges and polarizabilitiesCMLHTML5
dmabn/geom_optInput / Outputgeometry optimization B3LYPCMLHTML5
dmabn/spectrumInput / OutputExcited states and oscilator strengthsCMLHTML5
rubipyInput / Outputspin polarized B3LYP CMLHTML5