gpumdkit-analyzers

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Use when analyzing, validating, or filtering molecular dynamics structures. Provides composition analysis, outlier detection, chemical species identification, charge balance check, distance calculations, property filtering, and probability density analysis. Use when user asks about: structure analysis, data quality, minimum distance, composition, charge balance, outlier detection, or structure filtering.

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GPUMDkit Analyzers

Available Tools

Tool	Command	Description
Composition Analysis	`-analyze_comp`	Group structures by composition
Outlier Detection	Menu 502	Find high-error structures
Chemical Species	`-chem_species` or Menu 503	List unique elements
Charge Balance	`-cbc`	Check oxidation-state balance
Property Range	`-range`	Energy/force/virial statistics
Distance Filter	`-filter_dist` or Menu 506	Filter by minimum distance (no PBC)
Distance Filter (PBC)	`-filter_dist_pbc`	Filter by minimum distance with PBC
Minimum Distance	`-min_dist`	Calculate min distances (no PBC)
Minimum Distance (PBC)	`-min_dist_pbc`	Calculate min distances (with PBC)
Probability Density	`-pda` or Menu 508	3D diffusion channel analysis

Command Reference

Composition Analysis

# Analyze composition of extxyz file
gpumdkit.sh -analyze_comp train.xyz

# Output: Table of unique compositions with counts
# Interactive: Select compositions to export as separate files

Property Range Analysis

# Analyze energy range
gpumdkit.sh -range train.xyz energy

# Analyze force range
gpumdkit.sh -range train.xyz force

# Analyze virial range
gpumdkit.sh -range train.xyz virial

# With histogram plot
gpumdkit.sh -range train.xyz force hist

Minimum Distance

# Fast calculation (no PBC)
gpumdkit.sh -min_dist dump.xyz

# Accurate calculation (with PBC)
gpumdkit.sh -min_dist_pbc dump.xyz

# Output: Table of minimum distances for all element pairs

Charge Balance Check

# Check charge balance
gpumdkit.sh -cbc train.xyz

# Output:
# - balanced.xyz (charge-balanced structures)
# - unbalanced.xyz (unbalanced structures)
# - indices.txt (summary)

Chemical Species Identification

# List unique elements
gpumdkit.sh -chem_species train.xyz

# Interactive mode also works:
# gpumdkit.sh  # Select: 5) Analyzer -> 503

# Output: Sorted list of all elements in the file

Structure Filtering

By Minimum Distance (No PBC)

gpumdkit.sh -filter_dist dump.xyz 1.5
# Output: filtered_<file>.xyz, filtered_out_<file>.xyz

By Minimum Distance (With PBC)

gpumdkit.sh -filter_dist_pbc dump.xyz 1.5
# More accurate for periodic systems

By Element-Pair Distance Range

# Filter structures where Li-Li distance is between 1.9 and 2.0 Angstrom
gpumdkit.sh -filter_range dump.xyz Li Li 1.9 2.0

# Output: filtered_<elem1>_<elem2>_<min>_<max>.xyz

By Box Size

# Filter structures with box edge > 20 Angstrom
gpumdkit.sh -filter_box dump.xyz 20

# Output: filtered_by_box.xyz

By Property Value

# Keep structures with force < 20 eV/Angstrom
gpumdkit.sh -filter_value train.xyz force 20

# Output: filtered.xyz

Outlier Detection

# Find outlier structures based on RMSE
gpumdkit.sh  # Select: 5) Analyzer -> 502

# Required files in current directory:
# - train.xyz
# - energy_train.out
# - force_train.out
# - stress_train.out

# Output: selected.xyz (high-error), remained.xyz (low-error)

Probability Density Analysis

# Calculate 3D probability density of mobile ions
gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25

# Parameters:
# - Reference structure (POSCAR)
# - Trajectory file (extxyz)
# - Mobile species (e.g., Li)
# - Grid interval (e.g., 0.25 Angstrom)

# Output: probability_density_<interval>.vasp (CHGCAR format)
# Can be visualized with VESTA or similar software

Common Workflows

Data Quality Check

# 1. Check composition
gpumdkit.sh -analyze_comp train.xyz

# 2. Check minimum distances
gpumdkit.sh -min_dist_pbc train.xyz

# 3. Check force range
gpumdkit.sh -range train.xyz force

# 4. Check for outliers
gpumdkit.sh  # Select: 5) Analyzer -> 502

Structure Filtering Pipeline

# 1. Filter by distance
gpumdkit.sh -filter_dist_pbc dump.xyz 1.5

# 2. Filter by box size
gpumdkit.sh -filter_box filtered.xyz 20

# 3. Filter by force value
gpumdkit.sh -filter_value filtered_by_box.xyz force 15

Diffusion Channel Analysis

# 1. Calculate probability density
gpumdkit.sh -pda LLZO.vasp dump.xyz Li 0.25

# 2. Visualize with VESTA or similar
# Open probability_density_0.25.vasp

Additional Tools

Time Monitoring

# Monitor GPUMD progress
gpumdkit.sh -time gpumd

# Monitor NEP training progress
gpumdkit.sh -time nep

CLI Flag Reference

Flag	Description	Syntax
`-analyze_comp`	Composition analysis	`gpumdkit.sh -analyze_comp <file>`
`-range`	Property range	`gpumdkit.sh -range <file> <prop>`
`-min_dist`	Min distance (no PBC)	`gpumdkit.sh -min_dist <file>`
`-min_dist_pbc`	Min distance (PBC)	`gpumdkit.sh -min_dist_pbc <file>`
`-chem_species`	Chemical species list	`gpumdkit.sh -chem_species <file>`
`-cbc`	Charge balance	`gpumdkit.sh -cbc <file>`
`-filter_dist`	Filter by minimum distance	`gpumdkit.sh -filter_dist <file> <min_dist>`
`-filter_dist_pbc`	Filter by minimum distance with PBC	`gpumdkit.sh -filter_dist_pbc <file> <min_dist>`
`-filter_range`	Filter by distance range	`gpumdkit.sh -filter_range <file> <e1> <e2> <min> <max>`
`-filter_box`	Filter by box size	`gpumdkit.sh -filter_box <file> <limit>`
`-filter_value`	Filter by property	`gpumdkit.sh -filter_value <file> <prop> <thresh>`
`-time`	Time monitoring	`gpumdkit.sh -time <gpumd

Dependencies

Tool	Required Packages
All Python scripts	`ase`, `numpy`
Distance calculations	`scipy`
Charge balance	`pymatgen`, `tqdm`
Property range	`matplotlib`
Probability density	`pymatgen`

Detailed Documentation

See analyzer_scripts.md for comprehensive guide.