abinit
無料Generate and manage ABINIT DFT calculations. Use when the user requests ABINIT, or needs DFPT phonons, GW calculations, or BSE optical spectra.
日本語の概要は準備中です。原文の説明を表示しています。
Density of states (DOS) workflow in VASP. Three-step process for accurate total and projected DOS, d-band center analysis.
日本語の概要は準備中です。原文の説明を表示しています。
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Compute total and projected density of states. Requires a three-step workflow: geometry optimization, self-consistent single point, and DOS analysis.
The tetrahedron method (ISMEAR=-5) gives the most accurate DOS but is incompatible with geometry optimization (forces are not well-defined). That is why a separate single point is needed.
from catgo.workflow import Workflow
from catgo.workflow.builtins import geo_opt, single_point, dos_analysis
wf = Workflow("RuO2 DOS")
struct = wf.add_task("structure_input", structure=structure_json)
# Step 1: Optimize geometry
opt = wf.add_task(geo_opt, structure=struct.output.structure,
ISIF=2, system_name="relax")
# Step 2: Single point with DOS settings
sp = wf.add_task(single_point, structure=opt.output.structure,
ISMEAR=-5, # Tetrahedron method with Blochl corrections
NEDOS=3001, # Dense energy grid (default is 301)
LORBIT=11, # Projected DOS per atom and orbital
LCHARG=True, # Write charge density
EDIFF=1e-6, # Tight convergence
system_name="DOS")
# Step 3: Analyze DOS
dos = wf.add_task(dos_analysis, data=sp.output.energy,
d_band=True, system_name="DOS_analysis")
wf.submit()
# Create workflow
catgo_workflow_engine(action="create", params={"name": "DOS calculation"})
# Step 1: Input structure
catgo_workflow_engine(action="add_task", params={
"workflow_id": "wf_xxx",
"task_type": "structure_input",
"structure": "<json>"
})
# Step 2: Geometry optimization
catgo_workflow_engine(action="add_task", params={
"workflow_id": "wf_xxx",
"task_type": "geo_opt",
"software": "vasp",
"structure": "{{t_001.output.structure}}",
"system_name": "relax"
})
# Step 3: Single point for DOS
catgo_workflow_engine(action="add_task", params={
"workflow_id": "wf_xxx",
"task_type": "single_point",
"software": "vasp",
"structure": "{{t_002.output.structure}}",
"ISMEAR": -5,
"NEDOS": 3001,
"LORBIT": 11,
"LCHARG": true,
"EDIFF": 1e-6,
"system_name": "DOS"
})
# Step 4: DOS analysis
catgo_workflow_engine(action="add_task", params={
"workflow_id": "wf_xxx",
"task_type": "dos_analysis",
"data": "{{t_003.output.energy}}",
"d_band": true,
"system_name": "DOS_analysis"
})
catgo_workflow_engine(action="submit", params={"workflow_id": "wf_xxx"})
| Parameter | Value | Purpose |
|---|---|---|
| ISMEAR | -5 | Tetrahedron method — accurate DOS integration |
| NEDOS | 3001 | Energy grid points (more = smoother DOS) |
| LORBIT | 11 | Write atom-projected and orbital-projected DOS |
| EMIN/EMAX | auto | Energy range (auto-detected from eigenvalues) |
| LCHARG | True | Write CHGCAR for post-processing |
The dos_analysis task computes the d-band center for transition metals:
d_band_center = integral(rho_d(E) * E dE) / integral(rho_d(E) dE)
This is valuable for catalysis studies (Norskov d-band model). The analysis automatically identifies transition metal atoms and extracts their d-orbital projected DOS.
For magnetic systems, set ISPIN=2 to get spin-up and spin-down DOS separately:
sp = wf.add_task(single_point, structure=opt.output.structure,
ISMEAR=-5, NEDOS=3001, LORBIT=11,
ISPIN=2,
MAGMOM="4*5.0 8*0.6", # Initial moments
system_name="DOS_spin")
LORBIT=11 writes per-atom projections. The dos_analysis task can extract DOS for specific atoms or orbitals. Common use cases:
If the structure is already optimized, skip step 1:
wf = Workflow("DOS only")
struct = wf.add_task("structure_input", structure=optimized_json)
sp = wf.add_task(single_point, structure=struct.output.structure,
ISMEAR=-5, NEDOS=3001, LORBIT=11,
system_name="DOS")
wf.submit()
| Problem | Fix |
|---|---|
| Noisy/spiky DOS | Increase NEDOS (try 5001), use ISMEAR=-5 |
| ISMEAR=-5 error | Need >= 3 k-points per direction. Increase k-mesh |
| No d-band center | dos_analysis only computes d-band for transition metals |
| DOS looks wrong | Check that SCF is converged (EDIFF=1e-6), check ISPIN for magnetic systems |
| Fermi level misplaced | VASP sets E_F automatically; verify with band structure |
The single_point task produces raw DOSCAR data. The dos_analysis task produces:
output.dos_data — total and projected DOS as plottable arraysまだレビューはありません。使ってみた感想をお寄せください。
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Generate and manage ABINIT DFT calculations. Use when the user requests ABINIT, or needs DFPT phonons, GW calculations, or BSE optical spectra.
日本語の概要は準備中です。原文の説明を表示しています。
Use when the user asks to place an adsorbate molecule on a surface, find adsorption sites, or set up a surface+adsorbate model for DFT.
日本語の概要は準備中です。原文の説明を表示しています。
Use when the user asks for adsorption energy, binding energy, or wants to compare how strongly a molecule binds to a surface.
日本語の概要は準備中です。原文の説明を表示しています。
Use when the user asks to analyze computational results: Gibbs free energy, OER/HER/CO2RR overpotentials, adsorption energy, convergence tests, DOS/d-band analysis, or Bader charge analysis.
日本語の概要は準備中です。原文の説明を表示しています。
Use AmberTools antechamber for molecular force field parameterization. Generates GAFF/GAFF2 parameters and AM1-BCC or RESP charges for use in AMBER or LAMMPS classical MD simulations.
日本語の概要は準備中です。原文の説明を表示しています。
One-shot recipes for adding, deleting, moving, and replacing individual atoms in the active CatGo viewer structure. Use whenever the user asks to "add an atom", "delete atoms", "remove this atom", "move atom N", "replace H with Li", or any single-atom edit — including "add a hydrogen on top of atom 12" / "delete atoms 5–9" / "swap the oxygen at site 3 for fluorine". Skips the discovery loop (no need to list structure tools or check adsorption sites first); goes straight to the matching `catgo_structure` action. Triggers in Chinese on 加原子, 删原子, 减原子, 移动原子, 替换原子, 增加氢, 删除氧, 把 ... 换成 ....
日本語の概要は準備中です。原文の説明を表示しています。