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ACDB2.0

The purpose of this database is to compile existing atmospheric cluster structures and thermochemical data under one common methodology.

Please cite:

  • J. Elm, ACS Omega, 2019, 4, 10965-10974
  • J. Kubecka, ACS Omega 2023, 8, 45115-45128
  • and the associated original literature if any of the structures or thermochemical properties from the database are used in your published research.

README content:

  • Subfolders (i.e. methods that were used to obtain the clusters)
  • Type of files (i.e. what is saved in each file)
  • How to download only specific subfolder!
  • Using the pickles files (i.e. how to utilize JKQC or manipulate with databases)

Subfolders

Articles

  • This folder contains over 46 articles and molecular clusters/data provided from them.
  • The newest folders contain metadata described in greater detail.
  • The old articles sometimes lack proper description.

Full_database

  • Full database contains 1269055 entries.

SP_energies

  • This folder contains SP energies calculated level of theory specified by each subfolder

  • See the levels.txt file for more details on program version and method input.

  • B97-3c/

    • contains 79738 entries
    • contains 227 different cluster types

  • DLPNO-CCSD-T_aug-cc-pVTZ_NormalPNO/

    • contains 6742 entries
    • contains 1833 different cluster types

  • DLPNO-CCSD-T_aug-cc-pVTZ_TightPNO/

    • contains 1210 entries
    • contains 383 different cluster types

  • G09-wB97X-D_6-31++Gxx/

    • contains 68708 entries
    • contains 1045 different cluster types

  • G16-wB97X-D_6-31++Gxx/

    • contains 107389 entries
    • contains 1806 different cluster types

  • GFN1-xTB/

    • contains 347819 entries
    • contains 468 different cluster types

  • ORCA-wB97X-D_6-311++Gxx/

    • contains 11804 entries
    • contains 102 different cluster types

  • r2SCAN-3c/

    • contains 276593 entries
    • contains 382 different cluster types

Equilibrium_TMD

  • This folder contains free energy properties for SP_electronic_energy//geom._optim.+TMD

  • Some monomers are missing, hence not all binding properties are provided

  • For all wB97X-D TMD, we use anharmonicity (-v 0.996) and low-vibrational (-fc 100) treatement

  • B97-3c__B97-3c/

    • contains 21350 entries
    • contains 155 different cluster types

  • B97-3c__GFB1-xTB/

    • contains 17082 entries
    • contains 91 different cluster types

  • DLPNO-CCSD-T_aug-cc-pVTZ_NormalPNO__G09-wB97X-D_6-31++Gxx/

    • contains 1957 entries
    • contains 811 different cluster types

  • DLPNO-CCSD-T_aug-cc-pVTZ_NormalPNO__G16-wB97X-D_6-31++Gxx/

    • contains 3316 entries
    • contains 993 different cluster types

  • DLPNO-CCSD-T_aug-cc-pVTZ_TightPNO__G09-wB97X-D_6-31++Gxx/

    • contains 118 entries
    • contains 107 different cluster types

  • DLPNO-CCSD-T_aug-cc-pVTZ_TightPNO__G16-wB97X-D_6-31++Gxx/

    • contains 972 entries
    • contains 320 different cluster types

  • G09-wB97X-D_6-31++Gxx__G09-wB97X-D_6-31++Gxx/

    • contains 44490 entries
    • contains 912 different cluster types

  • G16-wB97X-D_6-31++Gxx__G16-wB97X-D_6-31++Gxx/

    • contains 74488 entries
    • contains 1662 different cluster types

  • GFN1-xTB__GFB1-xTB/

    • contains 65014 entries
    • contains 91 different cluster types

  • r2SCAN-3c__GFB1-xTB/

    • contains 24878 entries
    • contains 91 different cluster types

FORCES

TO BE DONE

Files

  • databases:
    • database.pkl
      • all data collected from the given folder
      • database is often split into database_s.pkl files with maximum 10000 entries per file
    • database1DFT.pkl
      • 1 lowest (DFT[geometry+TMD]) Gibbs free energy structure per cluster from database.pkl
    • database1DLPNO.pkl
      • 1 lowest (DLPNO[SP corr]//DFT[geometry+TMD]) Gibbs free energy structure from database.pkl
  • structures:
    • structures1DFT.xyzs and structures1DLPNO.xyzs
      • structures from database1DFT.pkl and structures1DLPNO.pkl, respectively
  • properties:
    • properties1DFT.txt and properties1DLPNO.txt
      • properties from database1DFT.pkl and structures1DLPNO.pkl, respectively
      • QHA and anharmonicity corrections applied
      • these are in the following format: structure_name | dG(298.15K) | dH(298.15K) | dS(298.15K)
  • binding properties:
    • located only in the most outside folder
    • binding_properties3DFT.txt and binding_properties1DLPNO.txt
      • 1 lowest (DFT or DLPNO//DFT) Gibbs free energies of formation from database3DFT.pkl and database1DLPNO.pkl, respectively

DOWNLOADING FROM ACDB

If you are interested in e.g. this folder: https://github.com/elmjonas/ACDB/master/tree/database_v2/Articles/kubecka19_sa_gd then you must replace master/tree with trunk and use svn to downlaod the folder:

svn checkout https://github.com/elmjonas/ACDB/trunk/database_v2/Articles/kubecka19_sa_gd

USING THE PICKLED FILES

In order to use any database, you can:

USING JKQC

First, donwload JKCS:

cd <App_dir>

git clone https://github.com/kubeckaj/JKCS2.1.git

  1. Then, setup JKCS and python environment for JKQC with correct python (see the online manual):

 sh setup.sh -help

 sh setup.sh -python python3.9 -module "module load python3.9" -r

  1. It will add one line to your ~/.bashrc file, therefore source it

source ~/.bashrc

  1. Now you should be able to use JKQC, e.g.:

JKQC -help

JKQC DATABASE.PKL -b -el

JKQC DATABASE.PKL -xyz

(see other functionalities: https://jkcs.readthedocs.io/en/latest/)

USING YOUR OWN PYTHON SCRIPT

Theoretically, you can use only your own python but I really recommend to setup your python environment via JKCS (step 1-3 above). Then run:

JKpython

After activating the correct python environment, use python to analyse/use the data:

$USER/: python

import pandas as pd

clusters_dataframe = pd.read_pickle("DATABASE.PKL")

STUCTURES NAMES

Water:

  • w=water

Positive charges:

  • 1p=proton (+)
  • 1am1p=ammonium cat (+)
  • 1dma1p=dimethylammonium cat. (+)
  • 1gly1p=glycinium cat. (+)
  • 1gd1p=guanidium cat. (+)
  • na=sodium cat. (+)

Bases:

  • am=ammonia
  • bda=butane-1,4-diamine
  • buta=butamine
  • dbma=dibuthylmethylamine
  • dea=diethylmine
  • dma=dimethylamine
  • dmea=dimethylethylamine
  • dpenta=dipentamine
  • dpropa=dipropamine
  • eda=ethylendiamine
  • gd=guanidine
  • dhexa=dihexamine
  • ibuta=isobutylamine
  • ipropa=iso-propylamine
  • ipropea=iso-propylethylamine
  • ma=methylamine
  • mda=methylethylendiamine
  • mea=monoethylamine
  • nona=nonamine
  • pda=propan-1,3-diamine
  • propa=propamine
  • put=putrescine
  • pz=piperazine
  • sbuta=sec-butamine
  • tbuta=tributylamine
  • tibuta=triisobutylamine
  • tea=triethylamine
  • tma=trimethylamine
  • tpropa=tripropamine
  • diAAmda=N,N-dimethylethylendiamine
  • diABmda=N,N-dimethylethylendiamine
  • triAABmda=trimethylethylendiamine
  • teAABBmda=tetramethylethylendiamine
  • IIebuta=2-ethylbutylamine

Anorganic acids:

  • sa=sulfuric acid
  • cba=carboxylic acid
  • cbt=carboxylate (-)
  • cna=cabonic acid
  • cnt=carbonate (-)
  • b=bisulphate (-)
  • brd=bromide (-)
  • id=iodide (-)
  • pha=phosforic acid
  • msa=methanesulfonic acid
  • mb=methanebisulfate (-)
  • hcl=hydrogenchloride
  • cl=chloride (-)
  • cla=chloric acid
  • pcla=perchloric acid
  • nta=nitric acid
  • nt=nitrate (-)

Iodine-containing:

  • it=iodine tatraoxide
  • ip=iodine pentoxide
  • ica=iodic acid
  • isa=iodous acid

Organics:

  • gly=glycine
  • glyt=glycinate an. (-)
  • homF=C6H8O7
  • homJ=C10H16O8
  • fd=formaldehyde
  • ml=methanol
  • pxml=methanolperoxide/methyl hydroperoxide
  • mf=methyl formate
  • etox=ethylene oxide
  • acal=acetaldehyde
  • acan=acetic anhydride
  • dme=dimethylether
  • acon=acetone

Organic acids:

  • ABisopooh = 1,2-isoprene hydroxy hydroperoxide
  • aca=acetic acid
  • acc=acetic an. (-)
  • bza=benzoic acid
  • bzc=benzoic an. (-)
  • ca=caric acid
  • cc=caric an. (-)
  • dhppa=2,2-dihydroxypropanoic acid
  • fa=formic acid
  • fc=formic an. (-)
  • hgta=3-hydroxy-glutaric acid
  • hptmf=hydroperoxymethyl thioformate
  • lca=lactic acid
  • maa=maleic acid
  • mbtca=3-methyl-1,2,3-butanetricarboxylic acid
  • mbtcc=3-methyl-1,2,3-butanetricarboxylic an. (-)
  • mca=malic acid
  • moa=malonic acid
  • oa=oxalic acid
  • oc=oxalic an. (-)
  • pa=pinic acid
  • poa=pinonic acid
  • paca=phenylacetic acid
  • pc=pinic an. (-)
  • ppa=propionic acid
  • pta=phtalic acid
  • pua=pyruvic acid
  • pue=pyruvate an. (-)
  • pxfa=peroxyformic acid
  • pxaca=peroxyacetic acid
  • sua=succinic acid
  • suc=succinic an. (-)
  • tba=terebic acid
  • tbc=terebic an. (-)
  • tpa=terpenylic acid
  • tpc=terpenylic an. (-)
  • tta=tartaric acid
  • ttc=tartaric an. (-)