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 2.9.0 (current)
ioChem-BD handles results obtained from:
ADF 2009 to 2019
AMS 2020
Amber 18
CASTEP 2021
Gaussian ’09 to ’16
GROMACS 5.0
GronOR 21
GRRM 23
LAMMPS 30-Jul-2021
Molcas 8.0
Mopac 2016
Orca 3.0, 4.0, 5.0
QuantumESPRESSO 6.1
Turbomole 6.4
SIESTA 4.1.b4
VASP 5.3.2
Find below some examples used to check data capture and manipulation mechanisms coded inside ioChem-BD.
AMS / ADF
Calculation name |
Source files |
Properties |
Generated CML file |
CML derived content |
|---|---|---|---|---|
Keggin_anion |
ADF2010, OPT, BP86, TZ2P, COSMO |
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Keggin_anion |
ADF2009, SP, B3LYP, DZP, COSMO |
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W6O19 |
ADF2009, SP, CAMY-B3LYP, TZ2P, COSMO, TD-DFT, Excitations (10) |
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B2pin2 |
ADF2009, SP, BP86, Freqs |
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NMR |
ADF2009, NMR |
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Bis-porhyrine |
ADF2010, SP, SAOP, TZP, C2V, TD-DFT, CD, Excitations (80) |
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C16H31B2O6 |
ADF2009, OPT TS, BP86, TZP, Freqs |
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C2H21Mo24O77 |
ADF2010, OPT, BP86, TZP, ZORA, COSMO, Cs |
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ts1_freq |
ADF2010, SP, BP86, TZP, ZORA, Freqs |
Calculation name |
Source files |
Properties |
Generated CML file |
CML derived content |
|---|---|---|---|---|
Opt_Freq/Opt_Freq_PESpoint |
AMS 2021, Opt Freq PES point |
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Opt_Freq/Opt_Freq_No_Re-scan |
AMS 2021, Opt Freq No Re-scan |
|||
Opt_ Freq/Opt_Freq_Hessian_Calculate |
AMS 2021, Opt Freq Hessian Calculate |
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Opt_Freq/Opt_Freq_Raman |
AMS 2021, Opt Freq Raman |
|||
Opt_Freq/Opt_Freq_Re-scan |
AMS 2021, Opt Freq Re-scan |
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SinglePoint_diferent_basis/QZ4P |
AMS 2021, SinglePoint basis QZ4P |
|||
SinglePoint_diferent_basis/DZP |
AMS 2021, SinglePoint basis DZP |
|||
SinglePoint_diferent_basis/DZ |
AMS 2021, SinglePoint basis DZ |
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SinglePoint_diferent_basis/TZ2P |
AMS 2021, SinglePoint basis TZ2P |
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SinglePoint_diferent_basis/TZP |
AMS 2021, SinglePoint basis TZP |
|||
SinglePoint_diferent_basis/SZ |
AMS 2021, SinglePoint basis SZ |
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SinglePo int_diferent_solvent/DMSO_Klamt |
AMS 2021, SinglePoint sovent DMSO Klamt |
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SinglePoint_ diferent_solvent/Water_Allinger |
AMS 2021, SinglePoint sovent Water Allinger |
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Singl ePoint_diferent_solvent/No_Solv |
AMS 2021, SinglePoint sovent No Solv |
|||
SinglePoint_di ferent_solvent/Chloroform_Klamt |
AMS 2021, SinglePoint sovent Chloroform Klamt |
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SinglePo int_diferent_solvent/DMFA_Klamt |
AMS 2021, SinglePoint sovent DMFA Klamt |
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SinglePoi nt_diferent_solvent/Water_Klamt |
AMS 2021, SinglePoint sovent Water Klamt |
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Unrestricted/Unrestricted-2 |
AMS 2021, Unrestricted-2 |
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Unres tricted/Unrestricted-2_symmetry |
AMS 2021, Unrestricted-2 symmetry |
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Unrestricted/Unrestricted+2 |
AMS 2021, Unrestricted+2 |
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Unres tricted/Unrestricted+2_symmetry |
AMS 2021, Unrestricted+2 symmetry |
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GeomOpt/GeomOpt_symmetry |
AMS 2021, Opt symmetry |
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GeomOpt/GeomOpt |
AMS 2021, Opt |
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GeomOpt/GeomOpt_no_min |
AMS 2021, Opt no min |
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SinglePoi nt_diferent_functional/GGA:mPBE |
AMS 2021, SinglePoint GGA:mPBE |
|||
SinglePo int_diferent_functional/GGA:PBE |
AMS 2021, SinglePoint GGA:PBE |
|||
SinglePoint_d iferent_functional/Hybrid:B3LYP |
AMS 2021, SinglePoint Hybrid:B3LYP |
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SinglePoi nt_diferent_functional/GGA:OPBE |
AMS 2021, SinglePoint GGA:OPBE |
|||
Sing lePoint_diferent_functional/LDA |
AMS 2021, SinglePoint LDA |
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SinglePoi nt_diferent_functional/GGA:BP86 |
AMS 2021, SinglePoint GGA:BP86 |
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SinglePoi nt_diferent_functional/GGA:BLYP |
AMS 2021, SinglePoint GGA:BLYP |
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Examples/CH2 |
AMS 2021, SinglePoint Unrestricted CH2 PBE TZ2P |
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Examples/Keggin |
AMS 2021, SinglePoint Excitations Keggin BP86 TZP |
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Examples/Ciclohexane |
AMS 2021,Opt Ciclohexane BP86 TZP 1H-NMR |
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Examples/CH4 |
AMS 2021, Opt BP86 TZP Cosmo Freq CH4 |
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Examples/Sn2_scan |
AMS 2021, Sn2 TS CH3Br-Cl B3LYP TZP Cosmo |
Gaussian ’09
Calculation name |
Source files |
Properties |
Generated CML file |
CML derived content |
|---|---|---|---|---|
ketone-qm |
MeCOMe, b3lyp, opt, freq |
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me-ccsdt |
methane, single point ccsd(t) |
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h2smd |
H2, b3lyp, opt, SMD |
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ketone-oniom |
MeCOMe, oniom(b3lyp:uff), opt, freq |
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PdPh3-pbed3 |
Pd(PPh3), pbepbe/d3, opt |
|||
meoh-dist |
MeOH, b97d/gen, modredund |
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tpcuts |
TpCu(N2)(CHCO2Me)(MeCO2Et), b97d, ts search, freq |
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meoh-scan |
MeOH, b97d/gen, scan |
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me-mp2 |
methane, single point mp2 |
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tpcuts2step |
TpCu(N2)(CHCO2Me)(MeCO2Et), b97d constr. opt + ts search, freq |
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me-mp5 |
methane, single point mp5 |
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cucl-pse4 |
CuCl, b3lyp/gen, opt, pseudo=read |
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cucurb |
alkyne+azide inside capsule, b97d, counterpoise calculation |
|||
a-siw12-2 |
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 |
naphtha |
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butadiene/quartet/buta |
buta |
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butadiene/singlet/buta |
buta |
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butadiene/quintet/buta |
buta |
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butadiene/doublet/buta |
buta |
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butadiene/triplet/buta |
buta |
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benzene/exp/ab |
ab |
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benzene/cas44-44/benzene |
benzene |
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benzene/50Ang/cas44-66_S0T1_T/benzene |
benzene |
|||
benzene/50Ang/cas44-44_S0S0/benzene |
benzene |
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benzene/50Ang/cas44-66_S0S0/benzene |
benzene |
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dpp/dpp |
dpp |
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buta_ethe/butaethene |
butaethene |
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metalambda3/metalambda3 |
metalambda3 |
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ethene/dimer/cas22_50Ang/ethene |
ethene |
|||
ethene/dimer/triplet_50Ang/ethene |
ethene |
|||
ethene/dimer/hf_50Ang/ethene |
ethene |
|||
ethene/monomer/cas22/ethene |
ethene |
|||
ethene/monomer/hf/ethene |
ethene |
|||
ethene/monomer/triplet/ethene |
ethene |
GRRM 23
Calculation folder |
Source files |
Properties |
Generated CML file |
CML derived content |
|---|---|---|---|---|
FREQ |
Frequencies B3LYP H2CO |
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MIN |
Geometry optimization B3LYP H2CO |
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PT0 |
Path top structure SC-AFIR2 B3LYP H2CO |
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SADDLE |
Transition state optimization B3LYP H2CO |
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TS4 |
Transition state structure SC-AFIR2 B3LYP H2CO |
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IRC |
Intrinsic Reaction Coordinate B3LYP H2CO |
Turbomole 6.4
Calculation folder |
Source files* |
Properties |
Generated CML file |
CML derived content |
|---|---|---|---|---|
acetic/cc |
Single point MP2 CCSD CCSD(T) |
|||
acetic/freq |
Frequencies DFT (BP86 / def2-SVP) |
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acetic |
Geometry optimization DFT (BP86 / def2-SVP) |
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acrolein/cosmo |
Single point, cosmo HF |
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acrolein |
Single point, Excited states TD-DFT (B3-LYP , RPA) |
|||
biverdazyl |
Geom. Opt. S=1 DFT (PBE0) |
|||
dmabn/tddft/freq |
Frequencies DFT (BP86) |
|||
dmabn/tddft |
Geom. Opt. Exc. State DFT (BP86) |
|||
dmabn/tdhf |
Single point, Excited states HF |
|||
dmabn |
Restricted Geom opt. DFT (b-lyp) |
|||
FeOH2/quartet/TS |
Geometry opt. TS DFT (pbe0) |
|||
FeOH2/quartet |
Geometry opt. DFT (pbe0) |
|||
FeOH2/TS |
Geometry opt. TS DFT (pbe0) |
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FeOH2 |
Geometry opt. DFT (pbe0) |
|||
fetz/HS |
Geometry opt. TS DFT (pbe0) |
|||
fetz/IS |
Geom opt. + freq DFT (B3-LYP) |
|||
fetz/LS |
Geom opt. + freq DFT (B3-LYP) |
|||
fim |
Geom opt. DFT (BP86) |
|||
fluorophenol |
Geometry optimization DFT (BP86) |
|||
fluorophenol/nbo |
Single point DFT (BP86) |
|||
rubipy |
Single point DFT (pbe0, D3) |
|||
water/spectrum |
Single point, Excited states TD-DFT (PBE0) |
|||
water |
Single point MP2-F12 |
* B = basis , C1 = control, C2 = coord, E = energy, O = job.last (or module output file)
Orca 3.0.1
Calculation name |
Source files |
Properties |
Generated CML file |
CML derived content |
|---|---|---|---|---|
FeOH2/quartet |
Geometry optimization DFT (pbe0) Geometry optimization quartet |
|||
FeOH2/quartet/TS |
Geometry optimization TSDFT (pbe0) Geometry optimization TS quartet |
`CML < https://www.iochem-bd.org/data-conversion/v1.0.0/orca/FeOH2/quartet/TS/feoh2.out.xml>`__ |
||
FeOH2/sextet |
Geometry optimization DFT (pbe0) Geometry optimization sextet |
|||
FeOH2/sextet/TS |
Geometry optimization TSDFT (pbe0) Geometry optimization TS sextet |
|||
acrolein |
Single point, Excited statesTDDFT (B3LYP) Excited states with TDDFT |
|||
acrolein/geom_opt |
Geometry optimization DFT (TPSS) Geometry optimization |
`CML < https://www.iochem-bd.org/data-conversion/v1.0.0/orca/acrolein/geom_opt/acro.out.xml>`__ |
||
acrolein/geom_opt/D3_cosmo |
Geometry optimization, COSMODFT (TPSS D3) Geometry optimization + Dispersion correction + COSMO |
|||
acrolein/bp |
Single point, Excited statesTDDFT (BP86) Excited states with TDDFT (TDA, default) |
|||
acrolein/bp/no_tda |
Single point, Excited statesTDDFT (BP86) Excited states with TDDFT (no TDA) |
|||
ch4 |
Single pointDFT (VWN5) NMR shifts |
|||
rubipy |
Single pointDFT (PBE0 D3) Non standard integration grid, dispersion correction and use of ECP |
|||
rubipy/standard_grid |
Single pointDFT (PBE0 D3) Standard integration grid, dispersion correction and use of ECP |
|||
acetic |
Geometry optimizationDFT (BP86) Geometry optimization |
|||
acetic/cc |
Single pointMP2 CCSD CCSD(T) Post Hartree-Fock methods |
|||
acetic/freq |
Geom. Opt + freqDFT (BP86) Frequencies |
|||
siwyig |
Broken symmetryDFT (B3LYP) Spin flip (BS approach) |
|||
biverdazyl |
Geometry optimizationDFT (PBE0) Geom. Opt for S=1; spin populations |
|||
water/restr_geom |
Restricted geometry optimizationHF Restr. Geom opt. Fixing an angle |
|||
water/f12 |
Single pointMP2-F12 MP2-F12 |
|||
water/spectrum |
Single point, Excited statesTDDFT (PBE0) Excited singlet and triplet states |
|||
fetz/LS |
Geom. Opt + freqDFT (B3LYP D3) Geom. Opt. + freq + D3 |
|||
fetz/IS |
Geom. Opt + freqDFT (B3LYP D3) generating spin state report |
|||
fetz/HS |
Geom. Opt + freqDFT (B3LYP D3) generating spin state report |
|||
fluorophenol |
Geometry optimizationDFT (BP86) population analysis + electrostatic moments |
|||
fetacn |
Geometry optimizationDFT (B3LYP*) non standard DFT functionals |
|||
fetacn |
Geometry optimizationDFT (B3LYP modified) non standard DFT functionals (50% Fock) |
|||
fim |
Geometry optimizationDFT (BP86 D3) Geometry optimization with dispersion |
|||
fim/tddft |
Single point Excited stateTDDFT (B3LYP) Excited states with TDDFT |
|||
dmabn |
Geometry optimizationHF Hartree-Fock geometry optimization |
|||
dmabn/tdhf |
Single point, Excited statesTDHF Time dependent HF for excited states |
|||
dmabn/tddft |
Geometry optimization, Excited StateDFT (BP86) Geometry optimization in the excited state |
` CML <https://www.iochem-bd.org/data-conversion/v1.0.0/orca/dmabn/tddft/dmabn.out.xml>`__ |
||
dmabn/tddft/freq |
Geometry optimization Minimum, Excited stateDFT (BP86) Frequencies excited state |
`CML < https://www.iochem-bd.org/data-conversion/v1.0.0/orca/dmabn/tddft/freq/dmabn.out.xml>`__ |
||
ni7 |
Single pointDFT (TPSSh) g tensor and ZFS |
|||
ReCO2 |
Single point Excited stateTDDFT (PBE0 D3) Excited states with TDDFT + dispersion correction |
Molcas 8.0
Calculation name |
Source files |
Properties |
Generated CML file |
CML derived content |
|---|---|---|---|---|
biverdazyl/raspt2 |
single point RASSCF/RASPT2 D2h symmetry |
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biverdazyl/caspt2 |
single point CASSCF/CASPT2 D2h symmetry |
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acetic |
geometry optimization B3LYP |
|||
acetic/cc |
single point MP2, CCSD CCSD(T) post Hartree Fock methods |
|||
acetic/freq |
opt + freq B3LYP |
|||
acetic/caspt2 |
single point CASSCF/CASPT2, medium cholesky |
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hf/pcm |
single point with PCM and symmetry C2 |
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hf/kirkwood |
single point with cavity solvent model and symmetry C2 |
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fluorophenol |
Single point; atomic charges and polarizabilities |
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water |
Restricted geometry optimization |
|||
acrolein/b3lyp_opt |
geometry optimization B3LYP |
|||
acrolein/opbe_opt |
geometry optimization OPBE |
|||
acrolein/casscf_opt |
geometry optimization CASSCF |
|||
acrolein/pbe0_cosmo_opt |
geometry optimization PBE0 with PCM |
|||
acrolein/mo62x_opt |
geometry optimization M062X |
|||
acrolein/caspt2 |
CASSCF/CASPT2 for five roots |
` CML <https://www.iochem-bd.org/data-conversion/v1.0.0/molcas/acrolein/caspt2/acrolein.output.xml>`__ |
||
FeOH2/sextet_TS |
TS optimization with CASPT2 + frequencies |
|||
FeOH2/sextet |
CASPT2 geometry optimization |
|||
FeOH2/quartet |
CASPT2 geometry optimization |
|||
FeOH2/sextet_freq |
TS optimization with CASPT2 + frequencies |
|||
ethane/staggered |
Single point; atomic charges and polarizabilities |
|||
ethane/eclipsed |
Single point; atomic charges and polarizabilities |
|||
dmabn/geom_opt |
geometry optimization B3LYP |
|||
dmabn/spectrum |
Excited states and oscilator strengths |
|||
rubipy |
spin polarized B3LYP |
SIESTA 4.1.b4
Calculation name |
Source files |
Properties |
Auto-generated CML file |
CML derived content |
|---|---|---|---|---|
32_h2o |
32 water molecules for simplex minimization |
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ar2_vdw |
Unconverged optimization of the Argon dimer with vdW-DF |
|||
batio3 |
Barium titanate cubic structure |
|||
benzene |
Benzene molecule |
|||
bessel |
Water molecule with Bessel orbitals |
|||
carbon_nanoscroll |
80-5-20 carbon nanoscroll |
|||
ch4 |
FCC Methane with vdW pre-packaged molecules |
|||
chargeconf-h2o |
Water molecule with charge confinement |
|||
constant_volume |
MgCO3 SZ in variable primitive cell with constant volume |
|||
fe |
BCC iron, non-linear partial-core correction, Pulay mixing |
|||
fe_broyden |
BCC iron, non-linear partial-core correction, Broyden mixing |
|||
fe_clust_noncollinear |
Linear Fe3 cluster, LDA |
|||
fe_clust_noncollinear-gga |
Linear Fe3 cluster, GGA |
|||
fe_cohp |
BCC iron, non-linear partial-core correction, COOP curves |
|||
fe_noncol_kp |
Linear Fe3 cluster with k-points |
|||
fen |
Bulk FeN in ZB structure , COOP curves |
|||
fire_benzene |
Benzene molecule with FIRE optimizer |
|||
floating |
Water molecule with Floating H orbitals |
|||
ge111 |
Germanium 111 slab with 2x8 reconstruction |
|||
ge_fatbands_so |
Bulk Ge with SOC and various types of WFS output |
|||
graphite_vdw_df |
Unconverged graphite with vdw-DF |
|||
h2_bessel |
H2 molecule with a Bessel orbital in the middle |
|||
h2o |
Water molecule |
|||
h2o_2 |
Water molecule, changing the numbering of atoms |
|||
h2o_4 |
Cluster of 4 water molecules, compute mu |
|||
h2o_am05 |
Water molecule optimization with the AM05 functional |
|||
h2o_basis |
Water molecule with various basis generation options |
|||
h2o_coop |
Water molecule, COOP curves |
|||
h2o_dipole |
Dipole correction of a water molecule from DOI:10.1103/PhysRevB.59.12301 |
|||
h2o_dipole2 |
Dipole correction of a water molecule from DOI:10.1103/PhysRevB.59.12301 |
|||
h2o_filteret_basis |
Water molecule using a Filteret basis set |
|||
h2o_findp_bug |
Pre-findp bug example |
|||
h2o_netcdf |
NetCDF DMHS history of a water molecule |
|||
h2o_op_broyden |
Broyden optimization of a water molecule |
|||
h2o_orderN |
Order-N optimization of a water molecule |
|||
h2o_radialgrid |
Example of accurate radial grid use |
|||
h2o_reparam |
Pseudopotential reparametrization of a water molecule |
|||
h3po4_1 |
H3PO4 molecule optimization changing species ordering |
|||
h3po4_2 |
H3PO4 molecule optimization changing species ordering |
|||
h3po4_3 |
H3PO4 molecule optimization changing species ordering |
|||
h_chain |
Hydrogen chain |
|||
h_chain2 |
Hydrogen chain with 2 atoms per cell and SZ basis |
|||
md_anneal |
Harris-functional annealing of a primitive c-Si supercell |
|||
md_nose |
Nosé MD of a MgCO3 primitive cell |
|||
md_npr |
Nosé-Parinello-Rahman MD of a MgCO3 primitive cell |
|||
md_pr |
Parinello-Rahman MD of a MgCO3 primitive cell |
|||
md_verlet |
Verlet MD of a MgCO3 primitive cell |
|||
mgc-force |
One-shot forces of a MgCO3 primitive cell |
|||
mgco3 |
Default MD of a MgCO3 primitive cell |
|||
mix_broyden |
Linear Fe3 cluster, Broyden mixing |
|||
mix_linear |
Linear Fe3 cluster, linear mixing |
|||
mix_pulay |
Linear Fe3 cluster, Pulay mixing |
|||
mno_ldau |
Ferromagnetic Manganese oxide, LDA+U |
|||
n_chain |
Nitrogen atom chain |
|||
nanotube-c-5-0 |
Metallic (5,0) carbon nanotube |
|||
oxyn |
Molecule made up of ON hybrids |
|||
pb_bulk |
Bulk lead |
|||
pb_bulk_1000 |
Bulk lead |
|||
pb_filter_cutoff |
Bulk lead, cutoff-filtered |
|||
pb_filter_tol |
Bulk lead, tolerance-filtered |
|||
scfmix |
Linear Fe3 cluster, various mixing methods |
|||
si-optical |
Optical properties of bulk Si |
|||
si001 |
Si(100), asymmetric 2x1 reconstruction |
|||
si64 |
Untitled |
|||
si64_coop |
Cubic supercell of 64 Si atoms, COOP curves |
|||
si_bandpoints |
Bulk Silicon to test BandPoints |
|||
si_coop |
Si chain for the calculation of COOP curves |
|||
si_fatbands |
Bulk Silicon with various types of WFS output |
|||
si_pdos_kgrid |
bulk silicon with extra sampling for PDOS |
|||
sic-slab |
Hydrogen/SiC surface |
|||
sih |
Hydrogen in a supercell of 64 Silicon atoms |
|||
sih-mrrr |
Hydrogen in a supercell of 64 Silicon atoms, MRRR diagonalizer |
|||
sih_fire |
Hydrogen in a supercell of 64 Silicon atoms, FIRE quenching |
|||
sih_op_broyden |
Hydrogen in a supercell of 64 Silicon atoms, Broyden optimization |
|||
var_cell |
Broyden optimization of MgCO3 in a variable primitive cell |
|||
wannier |
Occupied bonding Wannier functions of Silicon |
|||
zmatrix |
Convoluted example of zmatrix input |