abinit
FreeGenerate and manage ABINIT DFT calculations. Use when the user requests ABINIT, or needs DFPT phonons, GW calculations, or BSE optical spectra.
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Use when the user asks to test ENCUT convergence, k-point convergence, or any parameter sweep to determine converged computational settings.
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Before production calculations, verify that results are converged with respect to key numerical parameters. The two most important are:
Convergence is reached when the target property (energy, forces, band gap) changes by less than a threshold (typically 1 meV/atom for energy).
Convergence tests use a fan-out DAG: one input structure feeds into
multiple independent single_point calculations with different parameter
values.
+--> single_point(ENCUT=300)
|
structure_input ---+--> single_point(ENCUT=400)
|
+--> single_point(ENCUT=500)
|
+--> single_point(ENCUT=600)
|
+--> single_point(ENCUT=700)
Use single_point (not geo_opt) to isolate the parameter effect without
geometry changes confounding the comparison.
{"tool": "catgo_workflow_engine", "arguments": {
"action": "create", "name": "ENCUT convergence - TiO2"
}}
{"tool": "catgo_workflow_engine", "arguments": {
"action": "add_task", "workflow_id": "wf_conv",
"task_type": "single_point",
"params": {"software": "vasp", "ENCUT": 300, "system_name": "ENCUT=300"}
}}
{"tool": "catgo_workflow_engine", "arguments": {
"action": "add_task", "workflow_id": "wf_conv",
"task_type": "single_point",
"params": {"software": "vasp", "ENCUT": 400, "system_name": "ENCUT=400"}
}}
{"tool": "catgo_workflow_engine", "arguments": {
"action": "add_task", "workflow_id": "wf_conv",
"task_type": "single_point",
"params": {"software": "vasp", "ENCUT": 500, "system_name": "ENCUT=500"}
}}
Repeat for ENCUT = 600, 700, 800.
{"tool": "catgo_workflow_engine", "arguments": {
"action": "submit", "workflow_id": "wf_conv"
}}
{"tool": "catgo_workflow_engine", "arguments": {
"action": "get_result", "workflow_id": "wf_conv", "task_id": "task_encut300"
}}
{"tool": "catgo_analyze", "arguments": {
"action": "convergence", "workflow_id": "wf_conv"
}}
{"tool": "catgo_workflow_engine", "arguments": {
"action": "add_task", "workflow_id": "wf_conv",
"task_type": "single_point",
"params": {"software": "vasp", "ENCUT": 520, "KPOINTS": [2,2,1],
"system_name": "2x2x1"}
}}
{"tool": "catgo_workflow_engine", "arguments": {
"action": "add_task", "workflow_id": "wf_conv",
"task_type": "single_point",
"params": {"software": "vasp", "ENCUT": 520, "KPOINTS": [4,4,1],
"system_name": "4x4x1"}
}}
Repeat for 6x6x1, 8x8x1. Use the converged ENCUT from the previous test.
from catgo.workflow import Workflow
wf = Workflow("ENCUT convergence - TiO2")
inp = wf.add_task("structure_input", structure=tio2_json)
encut_values = [300, 400, 500, 600, 700, 800]
tasks = {}
for encut in encut_values:
tasks[encut] = wf.add_task("single_point",
structure=inp.output.structure,
software="vasp", ENCUT=encut,
system_name=f"ENCUT={encut}")
wf.submit()
wf = Workflow("KPOINTS convergence - TiO2 slab")
inp = wf.add_task("structure_input", structure=tio2_slab_json)
kpoints_list = [[2,2,1], [4,4,1], [6,6,1], [8,8,1], [10,10,1]]
for kp in kpoints_list:
label = f"{kp[0]}x{kp[1]}x{kp[2]}"
wf.add_task("single_point",
structure=inp.output.structure,
software="vasp", ENCUT=520, KPOINTS=kp,
system_name=label)
wf.submit()
| Property | Threshold | Typical Converged ENCUT |
|---|---|---|
| Total energy | 1 meV/atom | 1.3x max(ENMAX) in POTCAR |
| Forces | 5 meV/A | Same as energy |
| Band gap | 10 meV | May need higher ENCUT |
| Stress tensor | 0.1 kbar | Often needs 1.5x ENMAX |
| System | Starting ENCUT Range | Notes |
|---|---|---|
| Simple metals (Cu, Pt) | 300-500 | Usually converges quickly |
| Oxides (TiO2, RuO2) | 400-600 | O has high ENMAX |
| Nitrides, carbides | 400-600 | N, C have moderate ENMAX |
| F-containing | 500-800 | F has very high ENMAX |
This avoids the combinatorial explosion of testing all ENCUT x KPOINTS pairs.
single_point, not geo_opt. Geometry changes at different
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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.
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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.
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Use when the user asks for adsorption energy, binding energy, or wants to compare how strongly a molecule binds to a surface.
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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.
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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.
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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 ....
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