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ADF ADF ADF
  • Installation
    • Windows
    • Linux
    • MacOS
    • Package manager Install optional components
  • Tutorials
    • Getting started
    • All tutorials
  • AMS Driver
    • Geometry and System
    • Geometry Optimization
    • Molecular Dynamics
    • Nudged Elastic Band (NEB)
    • PES Exploration
    • PES Scan, Linear Transit
    • Transition State Search
    • Vibrational Spectroscopy
  • Engines
    • ADF Molecular DFT
    • BAND Periodic DFT
    • DFTB Semi-empirical
    • ForceField AMBER, UFF, APPLE&P...
    • GFNFF Force field
    • Hybrid QM/MM and mixed methods
    • ML Potential Machine Learning potentials
    • MOPAC Semi-empirical
    • Quantum ESPRESSO Periodic DFT
    • VASP Periodic DFT
    • ReaxFF Reactive force field
    • ASE engine Use any ASE calculator
  • Meso/Macro
    • COSMO-RS Thermodynamic properties of fluids
    • Bumblebee OLED device modeling
    • Microkinetics
    • Zacros Kinetic Monte Carlo
  • Tools
    • GUI Graphical User Interface
    • ParAMS Parametrization tool
    • Simple Active Learning On-the-fly training of ML
    • OLED Deposition and Properties Multiscale OLED modeling
    • Reactions Discovery Automatic reaction-discovery workflow
    • ACE Reaction Network Generation of reaction networks
    • Conformers Conformers generation
    • MD Trajectory Analysis Analysis of MD trajectories
    • ChemTraYzer2 Detect reactions from MD simulations
    • Utilities Various utility tools
  • Scripting
    • Python Scripting Examples Examples for Python scripting
    • PLAMS Python Library for Automating Molecular Simulations
    • amspython Python stack shipped with AMS
    • pyCRS Python Scripting with COSMO-RS
    • SCM Base Library Python library with core modules
    • reactmap Atom mapping between reactants and products
    • Command-line tools
    • ASE calculator
    • pyZacros Python Library Zacros (Kinetic Monte Carlo)
  • AMS2026.1
  • Other versions
  • ADF
  • Index
  • General
    • Introduction
    • What’s new in ADF 2026.1
    • Older releases
    • AMSification of ADF in AMS2020
    • Input, execution and output
    • Feature List
    • Technical remarks and Terminology
  • Input, execution, and output
    • Input
    • Execution
    • Structure of the Output
  • Coordinates, Basis sets, Fragments
    • Atomic coordinates
    • Basis sets and atomic fragments
    • Molecular fragments
  • Model Hamiltonians
    • Electronic Configuration
    • Density Functionals (XC)
    • Relativistic effects
    • Solvents and other environments
      • COSMO: Conductor-like Screening Model
      • SM12: Solvation Model 12
      • Quild
      • Hybrid Engine (QM/MM, QM/QM’)
      • DIM/QM: Discrete Interaction Model/Quantum Mechanics
      • QM/FQ: Quantum Mechanics/Fluctuating Charges (and Fluctuating Dipoles)
      • QM/ωFQ: Quantum Mechanics/Frequency-Dependent Fluctuating Charges (and Fluctuating Dipoles)
      • FDE: Frozen Density Embedding
      • 3D-RISM: 3D Reference Interaction Site Model
    • Electric Field: Homogeneous, Point Charges, Polarizability
  • Structure and Reactivity
  • Gradients, Hessian, Thermodynamics
  • Spectroscopic properties
    • Vibrational Spectroscopy
    • Time-dependent DFT
    • Excitation energies: UV/Vis, X-ray, CD, MCD
    • Excited state (geometry) optimizations
    • Vibrationally resolved electronic spectra
    • (Hyper-)Polarizabilities, ORD, magnetizabilities, Verdet constants
    • Ligand Field and Density Functional Theory (LFDFT)
    • NMR
      • NMR Chemical Shifts
      • Paramagnetic NMR Chemical Shifts
      • NMR spin-spin coupling constants
    • ESR/EPR
    • Nuclear Quadrupole Interaction (EFG)
    • Mössbauer spectroscopy
    • GW
  • Transport properties
    • Charge transfer integrals (transport properties)
    • Exciton transfer integrals
    • GREEN: Non-self-consistent Green’s function calculation
  • Analysis
    • Molecules built from fragments
    • Bond energy analysis
    • Localized Molecular Orbitals
    • Advanced charge density and bond order analysis
    • Controlling printed output
    • Results on Output
    • Densf: Volume Maps
    • DOS: Density of States
    • VCD Analysis: VCDtools
    • PyFrag: Activation Strain Model Analysis
  • Accuracy and Efficiency
    • Precision and Self-Consistency
      • SCF
      • Numerical Integration
      • Density fitting
      • Hartree-Fock RI scheme
      • MBPT scheme
      • Dependency (basis set, fit set)
    • Basis Set Superposition Error (BSSE)
    • Control of Program Flow
    • Technical Settings
  • Restarts
    • ADF Restart files
    • The restart key
    • Structure of the restart file
  • Recommendations and Troubleshooting
    • Recommendations
      • Precision
      • Electronic Configuration
      • What basis set should I use in ADF?
      • Relativistic methods
    • Troubleshooting
      • License file corrupt
      • Recover from Crash
      • Memory Management
      • SCF Convergence Guidelines for ADF
      • Geometry Optimization troubleshooting
      • Frequencies
      • Input ignored
      • SFO Populations
      • Error Aborts
      • Warnings
  • Appendices
    • Basis set file format
    • Elements of the Periodic Table
    • Multiplet States
    • Dirac program: relativistic core potentials
    • Symmetry
    • Binary result files
    • Error messages
    • Warnings
  • Required Citations
  • Examples
    • Example: r2SCAN-3c
    • Example: Asymptotically correct XC potentials: CO
    • Example: Meta-GGA energy functionals: OH
    • Example: Hartree-Fock: HI
    • Example: B3LYP: H2PO
    • Example: Long-range corrected GGA functional LCY-BP: H2O
    • Example: Range-separated functional CAMY-B3LYP: H2O
    • Example: Single point MP2
    • Example: Water Dimer SOS-AO-PARI-MP2
    • Example: Single point B2GPPLYP
    • Example: Water-MeOH - DODSCAN
    • Example: unrestricted MP2: Li
    • Example: RPA@PBE calculation: H2O
    • Example: RPASOX@PBE0 calculation: H2O
    • Example: Grimme Molecular Mechanics dispersion-corrected functionals (DFT-D3-BJ)
    • Example: Density-Dependent Dispersion Correction (dDsC): CH4-dimer
    • Example: DFT-ulg Dispersion Correction: Benzene dimer T-shaped
    • Example: ZORA Relativistic Effects: Au2
    • Example: Spin-Orbit coupling: Bi and Bi2
    • Example: Spin-Orbit unrestricted non-collinear: Tl
    • Example: Excitation energies including spin-orbit coupling: AuH
    • Example: ZORA, X2C and RA-X2C: HgI2 = Hg + I2
    • Example: spin-orbit coupled MP2: atomization energy I2
    • Example: Spin-Orbit spin-polarized start-up: Cr3
    • Example: COSMO: HCl
    • Example: solvation model SM12: Acetamide
    • Example: geometry optimization with SM12 using RESP charges
    • Example: Electric Field: PtCO
    • Example: Electric Field, Point Charge: N2
    • Example: 3D-RISM: Glycine
    • Example: 3D-RISM: Entropy
    • Example: FDE: H2O in water
    • Example: FDE freeze-and-thaw: HeCO2
    • Example: FDE energy: NH3-H2O
    • Example: FDE energy: unrestricted fragments: Ne-H2O
    • Example: FDE geometry optimization: H2O-Li(+)
    • Example: FDE NMR shielding: Acetonitrile in water
    • Example: FDE NMR spin-spin coupling: NH3-H2O
    • Example: Subsystem TDDFT, coupled FDE excitation energies
    • Example: FDE and COSMO: H2O-NH3
    • Example: FDE and COSMO: H2O-NH3
    • Example: DRF: H2O and H2O
    • Example: DRF: hyperpolarizability H2O in water
    • Example: DRF: scripting tool
    • Example: DRF2: Polarizability N2 on Ag68 + H2O
    • Example: CPIM: excitation energies N2 on silver cluster Ag68
    • Example: CPIM: polarizability N2 on silver cluster Ag68
    • Example: PIM: H2O on Ag2689
    • Example: PIM: Polarizability with local fields
    • Example: PIM: optimization N2 on silver cluster Ag68
    • Example: PIM: polarizability N2 on silver cluster Ag68
    • Example: PIM: Raman scattering N2 on silver cluster Ag68
    • Example: PIM: SEROA calculation N2 on silver cluster Ag68
    • Example: PIM: Multipole Method N2 on silver cluster Ag1415
    • Example: QM/FQ(Fμ): 2-Methyloxirane (QM) in Water
    • Example: QM/FQ(Fμ): geometry optimization
    • Example: QM/FQ(Fμ): polarizability 2-Methyloxirane (AORESPONSE)
    • Example: QM/FQ(Fμ): polarizability 2-Methyloxirane (RESPONSE)
    • Example: QM/FQ(Fμ): excitations 2-Methyloxirane
    • Example: QM/FDE/FQ: excitations of acrolein in water
    • Example: QM/wFQ(Fμ): 2-Methyloxirane (QM) with Sodium nanoparticle
    • Example: QM/wFQ(Fμ): 2-Methyloxirane (QM) on a carbon sheet
    • Example: QM/wFQ(Fμ): 2-Methyloxirane (QM) with Silver nanoparticle
    • Example: QM/wFQ(Fμ): 2-Methyloxirane (QM) with Gold nanoparticle
    • Example: Geometry Optimization: H2O
    • Example: Restraint Geometry Optimization: H2O
    • Example: Constraint Geometry Optimization: H2O
    • Example: Initial Hessian
    • Example: Geometry optimization with an external electric field or point charges: LiF
    • Example: LT, Frequencies, TS, and IRC: HCN
    • Example: TS search using partial Hessian: C2H6 internal rotation
    • Example: Relativistic ZORA TS search: CH4 + HgCl2 <==> CH3HgCl + HCl
    • Example: TS reaction coordinate: F- + CH3Cl
    • Example: (non-)Linear Transit: H2O
    • Example: Total Energy calculation: H2O
    • Example: Multiplet States: [Cr(NH3)6]3+
    • Example: Calculation of S2: CuH+
    • Example: Localized Hole: N2+
    • Example: Broken spin-symmetry: Fe4S4
    • Example: Core-electron binding energies (CEBE): NNO
    • Example: CEBE 1s Iodine in HI
    • Example: Constrained DFT: H2O+ … H2O
    • Example: ROKS: O2
    • Example: ROKS: SF
    • Example: Numerical Frequencies: NH3
    • Example: Numerical Frequencies, spin-orbit coupled ZORA: UF6
    • Example: Numerical Frequencies, accurate Hartree-Fock: H2O
    • Example: Analytic Frequencies: CN
    • Example: Analytic Frequencies: CH4
    • Example: Analytic Frequencies: HI
    • Example: Mobile Block Hessian (MBH): Ethanol
    • Example: Mobile Block Hessian: CH4
    • Example: Raman: NH3
    • Example: Raman: HI
    • Example: Resonance Raman, excited state finite lifetime: HF
    • Example: Vibrational Raman optical activity (VROA): H2O2
    • Example: Resonance VROA: H2O2
    • Example: Raman and VROA for approximate modes
    • Example: Vibrational Circular Dichroism (VCD): NHDT
    • Example: unrestricted VCD: CHFClBr
    • Example: Excitation energies and polarizability: Au2
    • Example: Excitation energies open shell molecule: CN
    • Example: Spin-flip excitation energies: SiH2
    • Example: TDHF excitation energies: N2
    • Example: excitation energies CAM-B3LYP: Pyridine
    • Example: CAMY-B3LYP excitation energies: H2O
    • Example: Full XC kernel in excitation energy calculation: H2O+
    • Example: Use of xcfun in excitation energy calculations: H2O
    • Example: Core excitation energies: TiCl4
    • Example: X-Ray Absorption and Emission Quadrupole Oscillator strengths at the Cl K-edge: TiCl4
    • Example: (Core) Excitation energies including spin-orbit coupling: Ne
    • Example: Excitation energies perturbative spin-orbit coupling: AgI
    • Example: ROKS-TDA-SOC: Cd+
    • Example: ROKS_TDA_SOC: NpF6
    • Example: Excitation energies including spin-orbit coupling for open shell: PbF
    • Example: Circular Dichroism (CD) spectrum: DMO
    • Example: CD spectrum with spin-orbit coupling: C2H3I
    • Example: CD spectrum, hybrid functional: Twisted ethene
    • Example: MCD: H2O
    • Example: MCD including zero-field splitting: H2O
    • Example: CV(n)-DFT excitation energies: Formamide
    • Example: HDA excitation energies: NH3
    • Example: HDA spin-orbit coupled excitation energies: H2O
    • Example: TD-DFT+TB excitation energies: beta-Carotene
    • Example: TDDFT-aas: Singlet excited state geometry optimization
    • Example: sTDA excitation energies: Adenine
    • Example: sTDDFT excitation energies: Adenine
    • Example: sTDA excitation energies RS functional: Bimane
    • Example: sTDA excitation energies wB97: TCNE-Benzene
    • Example: Excited state geometry optimization: N2
    • Example: Excited state geometry optimization with a constraint: CH2O
    • Example: Spin-flip excited state geometry optimization: CH2
    • Example: Numerical Frequencies of an excited state: PH2
    • Example: TD-DFT+TB: Singlet excited state geometry optimization
    • Example: TD-DFT+TB: Triplet excited state geometry optimization
    • Example: TD-DFT+TB: Open shell excited state geometry optimization
    • Example: Franck-Condon Factors: NO2
    • Example: Vibronic-Structure Tracking: Naphthalene
    • Example: Vibronic Density of States
    • Example: Polarizabilities including spin-orbit coupling: AgI
    • Example: damped first hyperpolarizability: LiH
    • Example: damped second hyperpolarizability: LiH
    • Example: Verdet constants: H2O
    • Example: Dispersion Coefficients: HF
    • Example: Optical Rotation Dispersion (ORD): DMO
    • Example: ORD, lifetime effects (key AORESPONSE): DMO
    • Example: Polarizability: first order perturbed density
    • Example: Hyperpolarizabilities of He and H2
    • Example: Damped Verdet constants: Propene
    • Example: Static magnetizability: H2O
    • Example: Dynamic magnetizability: H2O
    • Example: Time-dependent current-density-functional theory: C2H4:
    • Example: Damped complex polarizabilities with POLTDDFT: Au10
    • Example: POLTDDFT with hybrid functional: NH3
    • Example: POLTDDFT with range-separated functional: C2F4-C2H2
    • Example: Ligand Field DFT: Co 2+
    • Example: Ligand Field DFT: f-d transitions in Pr 3+
    • Example: LFDFT: g-tensor of Co(acacen)
    • Example: LFDFT: g-tensor of Cu(H2O)6
    • Example: LFDFT: XMCD 3d-4f transitions in Er 3+
    • Example: NMR Chemical Shifts: HBr
    • Example: NMR Chemical Shifts: HgMeBr
    • Example: NMR Chemical Shifts, SAOP potential: CH4
    • Example: NMR Nucleus-independent chemical shifts (NICS): PF3
    • Example: NMR with B3LYP: PF3
    • Example: Partial ZORA analysis: NMR chemical shift
    • Example: open shell NMR (pNMR) shielding: O2
    • Example: NMR Spin-spin coupling constants: C2H2
    • Example: NMR Spin-spin coupling constants, hybrid PBE0: HF
    • Example: NMR Spin-spin coupling constants, finite nucleus: PbH4
    • Example: ESR g-tensor, A-tensor, Q-tensor, D-tensor: HfV
    • Example: ESR g-tensor, A-tensor, self consistent spin-orbit coupling: VO
    • Example: ESR g-tensor, A-tensor, perturbative spin-orbit coupling: HgF
    • Example: ESR spin-restricted and spin-unrestricted: TiF3
    • Example: ESR, X2C and RA-X2C: PdH
    • Example: Zero-field splitting (ZFS), ESR D-tensor: NH
    • Example: ZFS D tensor, including direct electron spin-spin part: Phenylnitrene
    • Example: Mössbauer spectroscopy: Ferrocene
    • Example: Mössbauer with X2C: Hg compounds
    • Example: G0W0@PBE calculation: H2O
    • Example: G0W0@PBE0 calculation: O3
    • Example: G0W0@PBE0 calculation: Phenol
    • Example: evGW@M06-2X calculation: H2O
    • Example: qsGW calculation: N2
    • Example: qsGW with frozen core: Br2
    • Example: G3W2 calculation: H2O
    • Example: GW with DRF: CH2O in Water
    • Example: Charge transfer integrals: AT base pair
    • Example: Charge transfer integrals with FDE: water dimer
    • Example: Charge transfer integrals with FOCDFT
    • Example: Charge Recombination Calculation of Toluene and TCNE
    • Example: XCDFT: Charge Separation of an ethylene dimer
    • Example: Exciton transfer integrals with FOCDFT
    • Example: DOS and transmission: Aluminium
    • Example: Gold electrodes
    • Example: Benzenedithiol junction: Wide-Band-Limit
    • Example: Benzenedithiol junction
    • Example: Compound Fragments: Ni(CO)4
    • Example: Fragments: PtCl4H2 2-
    • Example: Spin-unrestricted Fragments: H2
    • Example: Bond Energy analysis open-shell fragments: PCCP
    • Example: Analysis of NaCl using ionic fragments: Na+ and Cl-
    • Example: Electron Pair bonding in NaCl: open shell fragments
    • Example: Bond Energy analysis meta-GGA, (meta-)hybrids: Zn2, Cr2, CrH
    • Example: unrestricted EDA: Cu(C2H4)2
    • Example: unrestricted fragments: CH3I
    • Example: Spin-Orbit SFO analysis: TlH
    • Example: Activation Strain Model Analysis using PyFrag
    • Example: (Perturbed) localized molecular orbitals in twisted Ethene
    • Example: Rose localization and TD-DFT: C2F4-C2H4
    • Example: Charge model 5 (CM5)
    • Example: Bond Orders
    • Example: NOCV: ethylene – Ni-diimina
    • Example: NOCV: H+ – CO
    • Example: NOCV: CH2 – Cr(CO)5
    • Example: NOCV: CH3 – CH3
    • Example: QTAIM Analysis
    • Example: QTAIM Reactivity
    • Example: IQA/QTAIM analysis
    • Example: QTAIM Aromaticity indices
    • Example: Density of States: Cu4CO
    • Example: adf2aim: convert an ADF adf.rkf to WFN format (for Bader analysis)
    • Example: NBO analysis: adfnbo, gennbo
    • Example: NBO analysis: EFG
    • Example: NBO analysis: NMR chemical shift
    • Example: NBO analysis: NMR spin-spin coupling
    • Example: Multiple excited state gradients: H2O
    • Example: Calculation of overlap of primitive basis functions
    • Example: Basis Set Superposition Error (BSSE): Cr(CO)5 +CO
    • Example: Troubleshooting SCF convergence: Ti2O4
    • Example: Rescan frequencies: NH3
    • Example: Multiresolution
    • Example: Restart analytical Hessian calculation
    • Example: Single point for multiple xyz files: Bakerset
    • Example: Basis set and integration accuracy convergence test: Methane
    • Example: amsprep: Replace atom with ligand
  • Keywords
  • KF output files
  • FAQ
  1. Documentation /
  2. ADF /
  3. Coordinates, Basis sets, Fragments

Coordinates, Basis sets, Fragments¶

See also:
ADF-GUI tutorial: building molecules , basis set effects , fragments
  • Atomic coordinates
  • Basis sets and atomic fragments
  • Molecular fragments
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Structure of the Output
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Atomic coordinates

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