Conversion test dataset

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: Text to CML 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 v2.0.0 (current)

iochem-BD handles results obtained from:

  • ADF 2009, 2010, 2011, 2012, 2013, 2014
  • Gaussian ’09
  • Turbomole 6.4
  • VASP 5.3.2
  • Orca 3.0.1

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/quartet Input / Output Geometry optimization DFT (pbe0) Geometry optimization quartet CML HTML5 JCAMP-DX
FeOH2/quartet/TS Input / Output Geometry optimization TSDFT (pbe0) Geometry optimization TS quartet CML HTML5 JCAMP-DX
FeOH2/sextet Input / Output Geometry optimization DFT (pbe0) Geometry optimization sextet CML HTML5 JCAMP-DX
FeOH2/sextet/TS Input / Output Geometry optimization TSDFT (pbe0) Geometry optimization TS sextet CML HTML5 JCAMP-DX
acrolein Input / Output Single point, Excited statesTDDFT (B3LYP) Excited states with TDDFT CML HTML5
acrolein/geom_opt Input / Output Geometry optimization DFT (TPSS) Geometry optimization CML HTML5
acrolein/geom_opt/D3_cosmo Input / Output Geometry optimization, COSMODFT (TPSS D3) Geometry optimization + Dispersion correction + COSMO CML HTML5
acrolein/bp Input / Output Single point, Excited statesTDDFT (BP86) Excited states with TDDFT (TDA, default) CML HTML5
acrolein/bp/no_tda Input / Output Single point, Excited statesTDDFT (BP86) Excited states with TDDFT (no TDA) CML HTML5
ch4 Input / Output Single pointDFT (VWN5) NMR shifts CML HTML5
rubipy Input / Output Single pointDFT (PBE0 D3) Non standard integration grid, dispersion correction and use of ECP CML HTML5
rubipy/standard_grid Input / Output Single pointDFT (PBE0 D3) Standard integration grid, dispersion correction and use of ECP CML HTML5
acetic Input / Output Geometry optimizationDFT (BP86) Geometry optimization CML HTML5
acetic/cc Input / Output Single pointMP2 CCSD CCSD(T) Post Hartree-Fock methods CML HTML5
acetic/freq Input / Output Geom. Opt + freqDFT (BP86) Frequencies CML HTML5 JCAMP-DX
siwyig Input / Output Broken symmetryDFT (B3LYP) Spin flip (BS approach) CML HTML5
biverdazyl Input / Output Geometry optimizationDFT (PBE0) Geom. Opt for S=1; spin populations CML HTML5
water/restr_geom Input / Output Restricted geometry optimizationHF Restr. Geom opt. Fixing an angle CML HTML5
water/f12 Input / Output Single pointMP2-F12 MP2-F12 CML HTML5
water/spectrum Input / Output Single point, Excited statesTDDFT (PBE0) Excited singlet and triplet states CML HTML5
fetz/LS Input / Output Geom. Opt + freqDFT (B3LYP D3) Geom. Opt. + freq + D3 CML HTML5 JCAMP-DX
fetz/IS Input / Output Geom. Opt + freqDFT (B3LYP D3) generating spin state report CML HTML5 JCAMP-DX
fetz/HS Input / Output Geom. Opt + freqDFT (B3LYP D3) generating spin state report CML HTML5 JCAMP-DX
fluorophenol Input / Output Geometry optimizationDFT (BP86) population analysis + electrostatic moments CML HTML5
fetacn Input / Output Geometry optimizationDFT (B3LYP*) non standard DFT functionals CML HTML5
fetacn Input / Output Geometry optimizationDFT (B3LYP modified) non standard DFT functionals (50% Fock) CML HTML5
fim Input / Output Geometry optimizationDFT (BP86 D3) Geometry optimization with dispersion CML HTML5
fim/tddft Input / Output Single point Excited stateTDDFT (B3LYP) Excited states with TDDFT CML HTML5
dmabn Input / Output Geometry optimizationHF Hartree-Fock geometry optimization CML HTML5
dmabn/tdhf Input / Output Single point, Excited statesTDHF Time dependent HF for excited states CML HTML5
dmabn/tddft Input / Output Geometry optimization, Excited StateDFT (BP86) Geometry optimization in the excited state CML HTML5
dmabn/tddft/freq Input / Output Geometry optimization Minimum, Excited stateDFT (BP86) Frequencies excited state CML HTML5 JCAMP-DX
ni7 Input / Output Single pointDFT (TPSSh) g tensor and ZFS CML HTML5
ReCO2 Input / Output Single point Excited stateTDDFT (PBE0 D3) Excited states with TDDFT + dispersion correction CML HTML5

Molcas 8.0 (BETA)

Calculation name Source files Properties Generated CML file CML derived content
biverdazyl/raspt2 Input / Output single point RASSCF/RASPT2 D2h symmetry CML HTML5
biverdazyl/caspt2 Input / Output single point CASSCF/CASPT2 D2h symmetry CML HTML5
acetic Input / Output geometry optimization B3LYP CML HTML5
acetic/cc Input / Output single point MP2, CCSD CCSD(T) post Hartree Fock methods CML HTML5
acetic/freq Input / Output opt + freq B3LYP CML HTML5 JCAMP-DX
acetic/caspt2 Input / Output single point CASSCF/CASPT2, medium cholesky CML HTML5
hf/pcm Input / Output single point with PCM and symmetry C2 CML HTML5
hf/kirkwood Input / Output single point with cavity solvent model and symmetry C2 CML HTML5
fluorophenol Input / Output Single point; atomic charges and polarizabilities CML HTML5
water Input / Output Restricted geometry optimization CML HTML5
acrolein/b3lyp_opt Input / Output geometry optimization B3LYP CML HTML5
acrolein/opbe_opt Input / Output geometry optimization OPBE CML HTML5
acrolein/casscf_opt Input / Output geometry optimization CASSCF CML HTML5
acrolein/pbe0_cosmo_opt Input / Output geometry optimization PBE0 with PCM CML HTML5
acrolein/mo62x_opt Input / Output geometry optimization M062X CML HTML5
acrolein/caspt2 Input / Output CASSCF/CASPT2 for five roots CML HTML5
FeOH2/sextet_TS Input / Output TS optimization with CASPT2 + frequencies CML HTML5
FeOH2/sextet Input / Output CASPT2 geometry optimization CML HTML5
FeOH2/quartet Input / Output CASPT2 geometry optimization CML HTML5
FeOH2/sextet_freq Input / Output TS optimization with CASPT2 + frequencies CML HTML5 JCAMP-DX
ethane/staggered Input / Output Single point; atomic charges and polarizabilities CML HTML5
ethane/eclipsed Input / Output Single point; atomic charges and polarizabilities CML HTML5
dmabn/geom_opt Input / Output geometry optimization B3LYP CML HTML5
dmabn/spectrum Input / Output Excited states and oscilator strengths CML HTML5
rubipy Input / Output spin polarized B3LYP CML HTML5