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dftbplus

Generate and manage DFTB+ calculations. Use when the user requests DFTB+, tight-binding DFT, SCC-DFTB, or needs fast approximate DFT for large systems or MD.

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Hello-QM/catgo-LRG星标 208(GitHub 208 + cccskills 0)

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包含的文件(1)

  • SKILL.md4.3 KB

SKILL.md(原文)

安装前可以查看交给 AI 代理的指令内容。

DFTB+

When to Use

  • User explicitly requests DFTB+ or tight-binding DFT
  • User needs fast DFT-level calculations for large systems (1000-10000 atoms)
  • User wants SCC-DFTB molecular dynamics at DFT accuracy
  • User needs a quick pre-screening before expensive DFT
  • User has Slater-Koster parameters available for the elements of interest

Prerequisites

  1. DFTB+ binary accessible on HPC (dftb+ --version)
  2. Slater-Koster files available (3ob for organic/bio, matsci for inorganic, mio for general)
  3. Structure loaded in viewer — verify with catgo_view(action="get_state")
  4. Confirm SK parameter coverage for all elements in the structure

Workflow Steps

1. Verify structure

catgo_view(action="get_state")

2. Create workflow

catgo_workflow_engine(action="create", params={"name": "DFTB+ optimization"})

3. Add DFTB+ task via shell

CatGo does not yet have a native DFTB+ engine. Use task_type: "shell".

catgo_workflow_engine(action="add_task", params={
  "workflow_id": "wf_xxx",
  "task_type": "shell",
  "name": "dftb_relax",
  "command": "dftb+ > dftb.out 2>&1",
  "input_files": {
    "dftb_in.hsd": "<HSD input content>",
    "geo.gen": "<geometry in GEN format>"
  },
  "system_name": "MoS2_relax"
})

When a @register_engine("dftbplus") is added, use task_type: "geo_opt" with software: "dftbplus".

Input File Template — SCC-DFTB SCF

Geometry = GenFormat {
  <<< geo.gen
}

Driver = {}

Hamiltonian = DFTB {
  Scc = Yes
  SccTolerance = 1e-5
  MaxSccIterations = 200

  SlaterKosterFiles = Type2FileNames {
    Prefix = "/path/to/skfiles/3ob-3-1/"
    Separator = "-"
    Suffix = ".skf"
  }

  MaxAngularMomentum {
    Ti = "d"
    O  = "p"
  }

  KPointsAndWeights = SupercellFolding {
    <k1> 0 0
    0 <k2> 0
    0 0 <k3>
    0.0 0.0 0.0
  }

  Filling = Fermi {
    Temperature [K] = 300
  }
}

Options {
  WriteDetailedOut = Yes
}

Analysis {
  CalculateForces = Yes
}

Relaxation Input

Replace Driver = {} with:

Driver = ConjugateGradient {
  MaxForceComponent = 1e-3   # Ha/Bohr (~0.05 eV/Ang)
  MaxSteps = 500
  LatticeOpt = No            # Yes for bulk cell optimization
}

GEN Format (Geometry File)

<natoms> S                    # S=supercell (periodic), C=cluster
Ti O                          # Element labels
1  1  0.000  0.000  0.000     # index, type, x, y, z (Angstrom or Bohr)
2  2  1.479  1.479  0.000
0.0 0.0 0.0                   # Origin
<a1x> <a1y> <a1z>             # Lattice vectors (only for S type)
<a2x> <a2y> <a2z>
<a3x> <a3y> <a3z>

Parameter Guidance

ParameterTypical valueNotes
SccTolerance1e-5SCC charge convergence; tighten for forces
MaxAngularMomentumPer elementMust match SK files (s/p/d/f)
SlaterKosterFiles3ob / matsci / mioCheck element coverage at dftb.org
MaxForceComponent1e-3 Ha/Bohr~0.05 eV/Ang; 1e-4 for high accuracy
Filling Temperature300 KElectronic smearing; increase for metals

Slater-Koster Parameter Sets

SetElementsBest for
3ob-3-1H, C, N, O, S, P, Zn, ...Organic, biochemistry
matsci-0-3Si, Ge, C, ...Semiconductors, materials
mio-1-1H, C, N, O, S, PGeneral organic
tiorg-0-1Ti, C, H, N, O, STiO2 + organics

Common Pitfalls

  1. Missing SK files — DFTB+ silently produces wrong results if SK files are incomplete. Verify all element pairs exist.
  2. MaxAngularMomentum mismatch — must exactly match what the SK file provides (check SK file header)
  3. No SK files for element pair — DFTB+ cannot treat arbitrary element combinations. Check dftb.org/parameters.
  4. Units — DFTB+ uses atomic units internally (Bohr, Hartree). GEN files use Angstrom by default.
  5. Dispersion missing — add Dispersion = DftD3 {} for van der Waals systems
  6. Spin polarization — add SpinPolarisation = Colinear { ... } for magnetic systems; not all SK sets support it

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