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 v2.7.2 (current)¶
ioChem-BD handles results obtained from:
- ADF 2009 to 2019
- Amber 18
- Gaussian ’09 to ’16
- GROMACS 5.0
- GronOR 21
- LAMMPS 30-Jul-2021
- Molcas 8.0
- Mopac 2016
- Orca 3.0, 4.0, 5.0
- QuantumESPRESSO 6.1
- Turbomole 6.4
- VASP 5.3.2
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 |
GronOR 21.00¶
Note: In this specific package, the CML file is generated by GronOR not by the ioChem-BD conversion tools.
| Calculation folder | Source files* | Properties | Generated CML file | CML derived content |
|---|---|---|---|---|
| naphthalene/naphtha | Input / Output | naphtha | CML | HTML5 |
| butadiene/quartet/buta | Input / Output | buta | CML | HTML5 |
| butadiene/singlet/buta | Input / Output | buta | CML | HTML5 |
| butadiene/quintet/buta | Input / Output | buta | CML | HTML5 |
| butadiene/doublet/buta | Input / Output | buta | CML | HTML5 |
| butadiene/triplet/buta | Input / Output | buta | CML | HTML5 |
| benzene/exp/ab | Input / Output | ab | CML | HTML5 |
| benzene/cas44-44/benzene | Input / Output | benzene | CML | HTML5 |
| benzene/50Ang/cas44-66_S0T1_T/benzene | Input / Output | benzene | CML | HTML5 |
| benzene/50Ang/cas44-44_S0S0/benzene | Input / Output | benzene | CML | HTML5 |
| benzene/50Ang/cas44-66_S0S0/benzene | Input / Output | benzene | CML | HTML5 |
| dpp/dpp | Input / Output | dpp | CML | HTML5 |
| buta_ethe/butaethene | Input / Output | butaethene | CML | HTML5 |
| metalambda3/metalambda3 | Input / Output | metalambda3 | CML | HTML5 |
| ethene/dimer/cas22_50Ang/ethene | Input / Output | ethene | CML | HTML5 |
| ethene/dimer/triplet_50Ang/ethene | Input / Output | ethene | CML | HTML5 |
| ethene/dimer/hf_50Ang/ethene | Input / Output | ethene | CML | HTML5 |
| ethene/monomer/cas22/ethene | Input / Output | ethene | CML | HTML5 |
| ethene/monomer/hf/ethene | Input / Output | ethene | CML | HTML5 |
| ethene/monomer/triplet/ethene | Input / Output | ethene | 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¶
| 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 |