abacustest-prepare-inputs

name	abacustest-prepare-inputs
description	Batch configure structure files (CIF/POSCAR/STRU, etc.) as ABACUS input files for various calculation types (SCF, relax, cell-relax, MD, band), and download ABACUS recommended pseudopotential and orbital libraries (APNS-v1). Use when: user wants to batch prepare ABACUS inputs from structure files, download recommended pseudopotentials and orbital libraries, set up DFT+U/magnetic calculations with recommended parameters.
metadata	{"openclaw":{"emoji":"📝","requires":{"pip":["abacustest"]}}}

abacustest Model: Inputs

This skill has two main functions:

1. Download recommended pseudopotentials and orbitals for ABACUS
2. Generate ABACUS input files from structure files with recommended parameters

---

Part 1: Download Recommended Pseudopotentials & Orbitals

ABACUS requires pseudopotential files (.upf) for all calculations, and orbital files (.orb) for LCAO basis calculations. This skill can download the official APNS (Atomic Pseudopotential & Numerical Basis Set) library.

⚠️ IMPORTANT: Always Confirm Before Downloading

DO NOT download automatically. The pseudopotential/orbital library is large (~several MB). Always confirm with the user first:

⚠️ Pseudopotential/Orbital Library Download

The APNS v1 library contains:
- Pseudopotentials (.upf files) for most elements (H to Rn)
- Orbital files (.orb files) for LCAO calculations
- Total size: ~50 MB
- Download time: Varies by network connection

Before proceeding, please confirm:

□ Do you already have pseudopotentials/orbitals installed?
  → If yes, skip download and set ABACUS_PP_PATH/ABACUS_ORB_PATH environment variables

□ Do you want to download the recommended APNS v1 library?
  → If yes, I will run: abacustest model inputs --download-pporb apns-v1
  → After download, you'll need to move files to a shared location and set environment variables

□ Or do you have a preferred pseudopotential library?
  → If yes, please provide the path

Please confirm before I proceed with the download.

When to Offer Download

Only suggest downloading when:

1. User explicitly asks to download pseudopotentials/orbitals
2. User has no existing PP/orbital setup (no --pp/--orb args, no env vars)
3. User confirms they want to proceed

Download Command (After Confirmation)

abacustest model inputs --download-pporb apns-v1

What Gets Downloaded

• Pseudopotentials (pp/): .upf files for most elements
• Orbitals (orb/): .orb files for LCAO calculations
• Version: APNS v1 (ABACUS recommended)

Setup After Download

After downloading, move the files to a shared location and set environment variables:

# Move to a shared location (example)
mv ABACUS-APNS-PPORBs-v1 /shared/ABACUS-APNS-v1/

# Add to your shell config (~/.bashrc or ~/.zshrc)
export ABACUS_PP_PATH=/shared/ABACUS-APNS-v1/pp
export ABACUS_ORB_PATH=/shared/ABACUS-APNS-v1/orb

# Apply changes
source ~/.bashrc  # or source ~/.zshrc

Verify Setup

# Check environment variables
echo $ABACUS_PP_PATH
echo $ABACUS_ORB_PATH

# List available pseudopotentials
ls $ABACUS_PP_PATH/*.upf | head -5

Once set up, you won't need to specify --pp or --orb paths for future calculations.

---

Part 2: Generate ABACUS Input Files

Convert structure files (CIF, POSCAR, STRU) to complete ABACUS input directories with recommended parameters.

⚠️ Before You Start: Check Pseudopotential & Orbital Paths

ABACUS requires pseudopotential files for all calculations. Before generating inputs, follow this checklist:

┌─────────────────────────────────────────────────────────────┐
│  Step 1: Did you provide --pp/--orb command-line arguments? │
│  └─ Yes → Use provided paths, skip to Step 4               │
│  └─ No  → Continue to Step 2                               │
├─────────────────────────────────────────────────────────────┤
│  Step 2: Check if environment variables are set:            │
│  $ echo $ABACUS_PP_PATH                                     │
│  $ echo $ABACUS_ORB_PATH                                    │
│  └─ Set → Proceed using environment variable paths          │
│  └─ Not set → Continue to Step 3                            │
├─────────────────────────────────────────────────────────────┤
│  Step 3: No paths found! Options:                           │
│  a) Download recommended PP/orbital:                        │
│     abacustest model inputs --download-pporb apns-v1        │
│  b) Ask user: "Where are your pseudopotentials located?"    │
│  c) Skip PP/orbital linking (manual editing required)       │
├─────────────────────────────────────────────────────────────┤
│  Step 4: Generate inputs with confirmed paths               │
└─────────────────────────────────────────────────────────────┘

Basic Usage

# From CIF file
abacustest model inputs -f structure.cif

# From VASP POSCAR
abacustest model inputs -f POSCAR --ftype poscar

# From ABACUS STRU
abacustest model inputs -f stru.cif --ftype abacus

# Batch process multiple files
abacustest model inputs -f *.cif

Generated Output

For each structure, a directory is created containing:

000000/
├── INPUT           # Calculation parameters
├── STRU            # Structure file
├── KPT             # K-point settings
├── *.upf           # Pseudopotential links
├── *.orb           # Orbital links (if LCAO)
└── run.sh          # Run script

---

Calculation Types & Recommended Parameters

Use --jtype to specify the calculation type. The skill automatically sets appropriate parameters for each type.

--jtype	Description	Key Parameters
scf	Self-consistent field (default)	ecutwfc 80, kspacing 0.14, scf_thr 1e-8
relax	Ionic relaxation	force_thr_ev 0.01, relax_method cg
cell-relax	Cell relaxation	stress_thr 0.5, cal_stress 1
md	Molecular dynamics	md_type nvt, md_dt 1.0, md_tfirst 300
band	Band structure	Generates SCF + NSCF + Band sequence

Example:

# SCF calculation (default)
abacustest model inputs -f Fe.cif

# Relaxation
abacustest model inputs -f Fe.cif --jtype relax

# Molecular dynamics
abacustest model inputs -f Fe.cif --jtype md

---

Parameter Reference

Required Parameters

Parameter	Description	Example
-f	Structure file(s)	-f Fe.cif
--ftype	File type	cif, poscar, abacus

Calculation Settings

Parameter	Description	Options	Default
--jtype	Calculation type	scf, relax, cell-relax, md, band	scf
--lcao	Use LCAO basis	-	No (PW)
--kpt	K-point setting	6 6 6 or single value	Auto

Spin & Magnetic Settings

Parameter	Description	Example
--nspin	Spin type: 1=no spin, 2=spin-polarized, 4=non-collinear+SOC	--nspin 2
--soc	Enable spin-orbit coupling	--soc (requires --nspin 4)
--init_mag	Initial magnetic moments (element value pairs)	--init_mag Fe 2.0 Mn -1.5
--afm	Antiferromagnetic ordering (alternates signs)	--afm

Examples:

# Spin-polarized with magnetic moment
abacustest model inputs -f Fe.cif --nspin 2 --init_mag Fe 2.5

# Antiferromagnetic (alternating +2.0, -2.0)
abacustest model inputs -f Fe2.cif --nspin 2 --init_mag Fe 2.0 --afm

# SOC calculation (non-collinear)
abacustest model inputs -f Pt.cif --nspin 4 --soc

DFT+U Settings

Parameter	Description	Example
--dftu	Enable DFT+U correction	--dftu
--dftu_param	Hubbard U values (element value pairs)	--dftu_param Fe 4.0 Ti 1.0

Example:

# DFT+U with default U values (d=4eV, f=6eV)
abacustest model inputs -f FeO.cif --dftu

# Specify custom U values
abacustest model inputs -f FeO.cif --dftu --dftu_param Fe 4.0 O 1.0

---

Pseudopotential & Orbital Paths

Why Paths Matter

• Pseudopotentials (.upf): Required for ALL ABACUS calculations. Define the electron-ion interaction.
• Orbitals (.orb): Required only for LCAO basis calculations (--lcao). Define the atomic orbital basis functions.

How Paths Are Resolved

The skill looks for pseudopotential/orbital paths in this order:

1. Command-line arguments (highest priority):

   abacustest model inputs -f Fe.cif --pp /my/pp/path --orb /my/orb/path
   

2. Environment variables:

   export ABACUS_PP_PATH=/shared/ABACUS-APNS-v1/pp
   export ABACUS_ORB_PATH=/shared/ABACUS-APNS-v1/orb
   abacustest model inputs -f Fe.cif
   

3. No path provided (lowest priority):

   • If neither --pp/--orb nor environment variables are set, the skill will generate STRU files without pseudopotential/orbital paths.
   • You must manually add them to the STRU file before running ABACUS.

Recommendation

Set up environment variables once (see Part 1) so you don't need to specify paths every time:

# Add to ~/.bashrc or ~/.zshrc
export ABACUS_PP_PATH=/shared/ABACUS-APNS-v1/pp
export ABACUS_ORB_PATH=/shared/ABACUS-APNS-v1/orb

---

Other Options

Parameter	Description	Example
--copy_pp_orb	Copy files instead of symlinking	--copy_pp_orb
--folder-syntax	Custom output directory naming	'{x[:-4]}'
--overwrite	Overwrite existing directories	--overwrite
--input	Use custom INPUT template	--input my_input.txt

Examples:

# Custom directory names (Fe.cif → Fe/)
abacustest model inputs -f *.cif --folder-syntax '{x[:-4]}'

# Copy PP files (for portability)
abacustest model inputs -f Fe.cif --copy_pp_orb

# Overwrite existing output
abacustest model inputs -f Fe.cif --overwrite

---

Common Errors

Missing Pseudopotentials

# Warning: some elements have no pseudopotentials
abacustest model inputs -f Fe.cif

Fix: Set ABACUS_PP_PATH or use --pp:

abacustest model inputs -f Fe.cif --pp /path/to/pp

DFT+U Parameter Format

# Error: parameters should be in pairs
abacustest model inputs -f FeO.cif --dftu --dftu_param Fe

Fix: Provide element-value pairs:

abacustest model inputs -f FeO.cif --dftu --dftu_param Fe 4.0

SOC Without nspin=4

# Warning: SOC requires nspin=4
abacustest model inputs -f Pt.cif --soc --nspin 2

Fix:

abacustest model inputs -f Pt.cif --soc --nspin 4