IQCAP -- Intelligent Quantum Chemistry Analysis Platform

1. Overview

IQCAP (Intelligent Quantum Chemistry Analysis Platform) is an automated quantum chemistry analysis platform designed for molecular design and materials research. Through a systematic modular architecture, it automates the complete pipeline from molecular structure input to electronic structure analysis and publication-quality visualization output, significantly improving computational efficiency and reproducibility.

Users only need to provide a molecular structure file (.xyz format) to automatically perform the following analyses:

Geometry optimization
Multi-charge-state single-point energy calculations (N / N+1 / N-1)
Electrostatic potential (ESP) surface mapping with three-view rendering
Frontier orbital (HOMO / LUMO) visualization
Fukui reactivity descriptors (f+, f-, f0, Df dual descriptor) with 2x2 panel rendering
NCI / RDG weak interaction analysis (isosurface + scatter plot)
Hirshfeld charge population
Mayer bond order analysis
Conceptual DFT (CDFT) reactivity indices
IGMH (Independent Gradient Model based on Hirshfeld partition) weak interaction analysis
IRI (Interaction Region Indicator) analysis
HS (Hirshfeld Surface) analysis with fingerprint plot and element contact area statistics
CDA (Charge Decomposition Analysis) with orbital interaction diagrams
Transition state search via NEB-CI / NEB-TS with automatic TS optimization and frequency verification
IRC (Intrinsic Reaction Coordinate) path tracing with publication-quality energy profile plots
Single-point energy refinement at higher theory levels for publication-quality barriers

The platform uses a modular design with good extensibility for integrating additional computational and analysis methods.

Important disclaimer: This software is a workflow orchestration and analysis platform. It invokes third-party programs for computation and visualization but does NOT include the third-party program binaries (ORCA, Multiwfn, VMD). Users must obtain and install those programs independently under their respective licenses.

2. Software Architecture

iqcap/
  IQCAP.png                Promotional banner (README)
  bin/
    iqcap-opt.sh                  Geometry optimization module
    iqcap-basic_elect_analysis.sh Basic electronic structure analysis
    iqcap-elect_interaction.sh    Weak Interaction Analysis (NCI/IGMH/IRI/HS/chgdiff/CDA)
    iqcap-ts.sh                   Transition State & Reaction Path Analysis Engine
    ...                           Auxiliary utilities (G, summary, report, plotting helpers)
  README.md                Software documentation (English)
  README_zh.md             Software documentation (Chinese)
  CHANGELOG.md             Version history
  LICENSE.txt              License declaration

2.1 Module Overview

Module	File	Description
Geometry Optimization	`iqcap-opt.sh`	Standalone geometry optimization, two-step optimization, or single-point-only preparation
Basic Electronic Analysis	`iqcap-basic_elect_analysis.sh`	Multi-state SP -> ESP/orbital/Fukui/NCI visualization -> charges/bond order -> CDFT
Weak Interaction Analysis	`iqcap-elect_interaction.sh`	NCI/IGMH/IRI/HS/chgdiff/CDA (IGMH/HS/chgdiff/CDA require fragment definition)
TS & Reaction Path Engine	`iqcap-ts.sh`	NEB-CI path search -> OptTS + freq verification -> IRC path -> energy profile

The main ground-state workflow is sequential: iqcap-opt.sh prepares the optimized structure, iqcap-basic_elect_analysis.sh performs the core electronic-structure analysis, and iqcap-elect_interaction.sh reuses the core workflow outputs (opt.xyz, *.molden.input, and related volumetric data when available).

Auxiliary utilities such as iqcap-G.sh, iqcap-summary.sh, and iqcap-report.sh are optional helpers and are not required for the core pipeline.

The TS & Reaction Path module is independent and operates on reactant/product XYZ files directly.

3. System Requirements

3.1 Operating System

Linux (recommended: Ubuntu 20.04+, CentOS 7+)
Bash 4.0 or higher

3.2 Third-Party Dependencies

Program	Version	Purpose
ORCA	5.0+	Quantum chemistry engine (geometry optimization, single-point calculations, NEB, IRC)
orca_2aim	Bundled with ORCA	Wavefunction file format conversion
orca_2mkl	Bundled with ORCA	Molden-format wavefunction export
Multiwfn	3.8+	Wavefunction analysis (ESP, orbitals, Fukui, NCI, IGMH, IRI, CDA, CDFT)
VMD	1.9.3+	Molecular and isosurface visualization (TachyonInternal ray tracing)

3.3 Python Environment

Python 3.6 or higher
Required packages:

Package	Purpose
numpy	Fukui cube file arithmetic, NCI data masking
scipy	Grid interpolation for differential charge density (chgdiff module)
Pillow	TGA-to-PNG conversion, colorbar annotation, panel composition
matplotlib	NCI/RDG/IGMH/IRI scatter plots, CDA orbital interaction diagrams

Installation:

pip install numpy scipy Pillow matplotlib

4. Input and Output

4.1 Input

Molecular structure file: Standard XYZ format (.xyz) containing atom count, comment line, and atomic coordinates
Command-line arguments: Charge/spin multiplicity, compute resources, module switches, visualization parameters, etc.

4.2 Output

Output Type	File Format	Description
Optimized structure	`opt.xyz`	Molecular coordinates after geometry optimization convergence
Wavefunction files	`.molden.input`, `.wfn`	Wavefunction data readable by Multiwfn
Volumetric data	`.cub` / `.cube`	3D grid data for electron density, ESP, orbitals, Fukui, NCI
Visualization images	`.png`	High-resolution (2400x1800) publication-quality images with colorbar annotations
Analysis logs	`.txt`, `.out`	Hirshfeld charges, Mayer bond orders, CDFT indices, CDA data
Scatter plots	`.png`	NCI/IGMH/IRI sign(lambda2)*rho vs RDG/dg/IRI scatter plots
Fingerprint plot	`.png`	HS d_i vs d_e fingerprint scatter plot (viridis colormap)
Contact area statistics	`.txt`, `.png`	HS element contact area table and pie chart
Orbital diagrams	`.png`	CDA orbital interaction energy-level diagrams
Energy profiles	`.png`	TS energy barrier diagrams with multi-unit annotations
IRC path plots	`.png`	Reaction coordinate vs energy along the IRC
Energy data	`.csv`, `.txt`	Barrier energies in Hartree / eV / kcal/mol / kJ/mol
TS validation panel	`.png`	Combined vibrational spectrum, imaginary-mode view, and IRC curve
Mode projection plot	`.png`	Decomposition of the imaginary mode onto internal coordinates (bond lengths/angles)
IRC internal coordinates	`.png`	Evolution of key bond lengths/angles along the IRC path
NEB convergence diagnostics	`.png`	Convergence history of band and climbing-image forces and barrier height
IRC animation	`.gif`	Animated structural change along the IRC (front/side/top views)

5. Functional Modules

5.1 Core Ground-State Workflow (`iqcap-opt.sh` + `iqcap-basic_elect_analysis.sh`)

5.1.1 Geometry Optimization (`iqcap-opt.sh`)

DFT-level geometry optimization using ORCA
Supports direct publication-quality optimization, low+high two-step optimization, and single-point-only preparation modes
Writes optimization/opt.xyz and downstream-reusable wavefunction artifacts when available

5.1.2 Multi-Charge-State Single-Point Calculations (`iqcap-basic_elect_analysis.sh`)

Automatic single-point calculations for N (neutral), N+1 (anion), and N-1 (cation) states
Automatic spin multiplicity inference with electron-count parity validation

5.1.3 ESP Surface Mapping

Maps electrostatic potential onto the molecular density isosurface
Generates three-view renders (front/side/top) with BGR colorbar, isovalue annotation, and surface extrema

5.1.4 Frontier Orbital Visualization

Exports HOMO and LUMO orbital cube files with positive/negative isosurface rendering
Composes annotated side-by-side panel (with isovalue and phase legend)

5.1.5 Fukui Reactivity Descriptors

Computes f+, f-, f0, and Df (dual descriptor) via multi-charge-state density differences
Generates annotated 2x2 panel image

5.1.6 NCI / RDG Weak Interaction Analysis

Computes RDG isosurface colored by sign(lambda2)*rho
Generates three-view isosurface renders and scatter plot

5.1.7 Charge and Bond Order Analysis

Hirshfeld charge population
Mayer bond order

5.1.8 Conceptual DFT (CDFT)

Computes chemical potential, hardness, electrophilicity, and related CDFT indices via Multiwfn

5.2 Weak Interaction Analysis (iqcap-elect_interaction.sh)

5.2.1 chgdiff (Differential Charge Density)

Computes Δρ = ρ(AB) − ρ(A) − ρ(B) between fragment 1 and fragment 2
Three-view images (front/side/top) with Fukui-style yellow-blue coloring

5.2.2 NCI / RDG Analysis

Noncovalent interaction isosurface and scatter plot (no fragment definition required)

5.2.3 IGMH Analysis

Independent Gradient Model based on Hirshfeld partition
User-defined molecular fragment specification
Generates dg_inter isosurface three-view renders (BGR coloring) and scatter plot

5.2.4 IRI Analysis

Interaction Region Indicator (fine grid, smooth isosurface)
Simultaneously visualizes covalent and weak interactions

5.2.5 HS (Hirshfeld Surface) Analysis

Constructs the Hirshfeld surface for a user-defined fragment and maps promolecular electron density onto it
Three-view renders (front/side/top) with BWR colorbar (blue = weak, white = moderate, red = strong interaction)
Fingerprint scatter plot (d_i vs d_e, viridis colormap) for interaction characterization
Element contact area statistics with pie chart and tabulated data
Only requires atomic coordinates (no wavefunction needed), very fast even for large systems

5.2.6 CDA (Charge Decomposition Analysis)

Automatic fragment geometry extraction and fragment single-point calculations
Computes d (charge donation), b (back-donation), r (polarization)
Generates full orbital interaction energy-level diagram and focused publication diagram (HOMO-2 to LUMO+2)
Renders 3D isosurface images of key orbitals

5.3 Transition State & Reaction Path Engine (iqcap-ts.sh)

5.3.1 Endpoint Optimization

Optional geometry optimization of reactant and product at the calculation level
Ensures consistent energy surface for NEB and barrier calculations

5.3.2 NEB Path Search

NEB-CI (Climbing Image NEB, default) or NEB-TS for transition state guess
NEB-CI drives the highest-energy image toward the true saddle point
Configurable number of interpolation images and convergence criteria

5.3.3 TS Optimization and Frequency Verification

ORCA OptTS with automatic numerical Hessian for initial TS search direction
Combined OptTS + NumFreq for efficiency
Automatic verification: confirms exactly one imaginary frequency (true first-order saddle point)

5.3.4 IRC Path Tracing

Intrinsic Reaction Coordinate in both directions from the TS
Confirms the TS connects the expected reactant and product
Extracts IRC endpoint structures for energy comparison

5.3.5 Single-Point Energy Refinement

SP calculations on reactant, TS, product, and IRC endpoints
Supports a higher theory level than geometry optimization (e.g., DLPNO-CCSD(T)/def2-TZVPP//B3LYP-D3/def2-TZVP)
Outputs energy barriers in Hartree, eV, kcal/mol, and kJ/mol

5.3.6 Energy Profile Visualization

Publication-quality energy profile diagram with barrier annotations
Forward barrier (ΔE‡), reverse barrier (ΔE‡_rev), and reaction energy (ΔE_rxn)
Dual-unit display (kcal/mol and kJ/mol)
IRC path plot showing energy vs reaction coordinate

5.3.7 TS Structure Rendering

VMD three-view rendering of the optimized TS structure
Annotated with imaginary frequency value

5.3.8 TS Validation and Diagnostics

TS validation panel combining vibrational spectrum, 2D projection of the imaginary mode, and IRC energy curve.
Imaginary-mode projection onto internal coordinates (bond lengths/angles) to highlight which bonds stretch, compress, or bend.
IRC internal-coordinate plots for key bond lengths/angles vs IRC step to aid mechanism analysis.
NEB convergence diagnostics panel showing band and climbing-image force convergence and barrier-height convergence.
Automatic IRC animation GIFs for three orthogonal views.

6. Usage Examples

6.1 Basic Analysis (Core Workflow)

# Step 1: geometry optimization
bash iqcap-opt.sh --mode 1 --xyz 0.xyz --n-charge 0 --n-mult 1

# Step 2: electronic-structure analysis on the optimized geometry
bash iqcap-basic_elect_analysis.sh --xyz 0.xyz --n-charge 0 --n-mult 1

# Two-step optimization for difficult systems
bash iqcap-opt.sh --mode 2 --xyz molecule.xyz --n-charge 0 --n-mult 1

# Re-render figures only from an existing calculation
bash iqcap-basic_elect_analysis.sh --xyz 0.xyz --plot-only

# ESP and orbitals only, skip Fukui / molecule-view / charge / bond-order output
bash iqcap-basic_elect_analysis.sh --no-fukui-plot --no-mol-view --no-charges --no-bondorder

# Custom compute resources
bash iqcap-opt.sh --mode 1 --xyz molecule.xyz --nprocs 32 --maxcore 8192
bash iqcap-basic_elect_analysis.sh --xyz molecule.xyz --nprocs 32 --maxcore 8192

# Show version information
bash iqcap-opt.sh --version
bash iqcap-basic_elect_analysis.sh --version

6.2 Differential Charge Density (chgdiff)

# H2O: fragment 1 = atoms 1-2 (O, first H), fragment 2 = atom 3 (second H)
bash iqcap-elect_interaction.sh --only-chgdiff --frag1-atoms "1-2" --frag2-atoms "3"

# Custom fragment indices
bash iqcap-elect_interaction.sh --only-chgdiff --frag1-atoms "1,3,5" --frag2-atoms "2,4,6" --chgdiff-iso 0.0008

6.3 Weak Interactions and Charge Decomposition

# Water dimer (6 atoms): fragment 1 = atoms 1-3, fragment 2 = atoms 4-6
bash iqcap-elect_interaction.sh --frag1-atoms "1-3" --frag2-atoms "4-6"

# HS only (Hirshfeld Surface analysis)
bash iqcap-elect_interaction.sh --only-hs --frag1-atoms "1-3" --frag2-atoms "4-6"

# CDA only, skip NCI/IGMH/IRI/HS/chgdiff
bash iqcap-elect_interaction.sh --only-CDA --frag1-atoms "1-3" --frag2-atoms "4-6"

# Custom IGMH isosurface
bash iqcap-elect_interaction.sh --frag1-atoms "1-3" --frag2-atoms "4-6" \
    --igmh-iso 0.005 --igmh-color-min -0.03 --igmh-color-max 0.015

# Show version information
bash iqcap-elect_interaction.sh --version

6.4 Transition State & Reaction Path Analysis

# Full pipeline: NEB-CI -> OptTS + Freq -> IRC -> SP -> energy profile
bash iqcap-ts.sh --reactant reactant.xyz --product product.xyz

# Provide a TS guess directly (skip NEB)
bash iqcap-ts.sh --reactant reactant.xyz --product product.xyz \
    --ts-guess ts_guess.xyz

# Use NEB-TS instead of NEB-CI
bash iqcap-ts.sh --neb-method NEB-TS --neb-nimages 12

# Fast testing with low-precision DFT (default)
bash iqcap-ts.sh --reactant reactant.xyz --product product.xyz

# Production run with high-level SP refinement
bash iqcap-ts.sh --reactant reactant.xyz --product product.xyz \
    --opt-level "B3LYP D3 def2-TZVP(-f) def2/J RIJCOSX" \
    --sp-level "DLPNO-CCSD(T) def2-TZVPP def2-TZVPP/C tightSCF"

# Skip endpoint optimization (pre-optimized structures)
bash iqcap-ts.sh --skip-opt-endpoints

# IRC only (with existing TS)
bash iqcap-ts.sh --ts-guess ts.xyz --no-neb --no-optts --no-freq

6.5 Complete Workflow Example

# Step 1: Prepare molecular structure file
# Save molecular coordinates in XYZ format as 0.xyz

# Step 2: Optimize the geometry
bash iqcap-opt.sh --mode 1 --xyz 0.xyz --n-charge 0 --n-mult 1

# Step 3: Run the basic electronic-structure workflow
bash iqcap-basic_elect_analysis.sh --xyz 0.xyz --n-charge 0 --n-mult 1

# Step 4: Run weak interaction analysis (for intermolecular interaction analysis)
bash iqcap-elect_interaction.sh --frag1-atoms "1-3" --frag2-atoms "4-6"

# Step 5: Run transition state and reaction path analysis (independent workflow)
cd reaction_dir/
bash iqcap-ts.sh --reactant reactant.xyz --product product.xyz

# Output results are saved in subdirectories of the current directory

7. Command-Line Reference

iqcap-opt.sh

Parameter	Type	Default	Description
`--mode`	INT	1	`1` = direct optimization, `2` = low+high two-step optimization, `3` = single-point-only preparation
`--xyz`	FILE	0.xyz	Input structure file
`--output-dir`	DIR	optimization	Output directory
`--n-charge`	INT	0	Molecular charge
`--n-mult`	INT	1	Spin multiplicity
`--nprocs`	INT	16	Number of parallel processes
`--maxcore`	INT	4096	Memory per process (MB)
`--opt-low`	STR	`B3LYP D3 def2-SVP def2/J RIJCOSX opt`	Low-level optimization for mode 2
`--opt-pub`	STR	`B3LYP D3 def2-TZVP(-f) def2/J RIJCOSX opt`	Publication-level optimization
`--sp-level`	STR	`B3LYP D3 def2-TZVP(-f) def2/J RIJCOSX tightSCF`	Single-point level for mode 3
`-V, --version`	FLAG	-	Show version information
`-h, --help`	FLAG	-	Show help message

iqcap-basic_elect_analysis.sh

Parameter	Type	Default	Description
`--xyz`	FILE	0.xyz	Reference XYZ file
`--sp-level`	STR	`B3LYP D3 def2-TZVP(-f) def2/J RIJCOSX tightSCF`	ORCA single-point theory level
`--n-charge`	INT	0	Neutral-state charge
`--n-mult`	INT	1	Neutral-state multiplicity
`--nprocs`	INT	16	Number of parallel processes
`--maxcore`	INT	4096	Memory per process (MB)
`--no-multiwfn`	FLAG	-	Skip all Multiwfn-based analyses
`--no-cdft`	FLAG	-	Skip conceptual DFT analysis
`--no-esp-plot`	FLAG	-	Skip ESP rendering
`--no-mol-view`	FLAG	-	Skip pure molecule three-view rendering
`--no-homo-lumo-plot`	FLAG	-	Skip HOMO/LUMO rendering
`--no-fukui-plot`	FLAG	-	Skip Fukui rendering
`--no-charges`	FLAG	-	Skip Hirshfeld charges
`--no-bondorder`	FLAG	-	Skip Mayer bond-order analysis
`--plot-only`	FLAG	-	Re-render from existing data without recomputation
`--esp-iso`	FLOAT	0.001	ESP density isosurface
`--mo-iso`	FLOAT	0.03	Orbital isosurface value
`--fukui-iso`	FLOAT	0.003	Fukui isosurface value
`-V, --version`	FLAG	-	Show version information
`-h, --help`	FLAG	-	Show help message

iqcap-elect_interaction.sh

Parameter	Type	Default	Description
`--frag1-atoms`	STR	-	Fragment 1 atom indices (required for IGMH/HS/chgdiff/CDA)
`--frag2-atoms`	STR	-	Fragment 2 atom indices
`--only-CDA`	FLAG	-	Run CDA only
`--only-chgdiff`	FLAG	-	Run chgdiff only
`--only-hs`	FLAG	-	Run HS only
`--igmh-iso`	FLOAT	0.01	IGMH isosurface value
`--iri-iso`	FLOAT	1.0	IRI isosurface value
`--hs-color-min`	FLOAT	0.0	HS color scale lower bound (promol. density)
`--hs-color-max`	FLOAT	0.015	HS color scale upper bound (promol. density)
`--no-igmh`	FLAG	-	Skip IGMH analysis
`--no-iri`	FLAG	-	Skip IRI analysis
`--no-hs`	FLAG	-	Skip HS analysis
`--no-cda`	FLAG	-	Skip CDA analysis
`-V, --version`	FLAG	-	Show version information
`-h, --help`	FLAG	-	Show help message

iqcap-ts.sh

Parameter	Type	Default	Description
`--reactant`	FILE	reactant.xyz	Reactant structure file
`--product`	FILE	product.xyz	Product structure file
`--ts-guess`	FILE	-	TS initial guess (skips NEB)
`--charge`	INT	0	Molecular charge
`--mult`	INT	1	Spin multiplicity
`--nprocs`	INT	16	Number of parallel processes
`--maxcore`	INT	4096	Memory per process (MB)
`--opt-level`	STR	PBE D3 def2-SVP def2/J	ORCA theory for geometry/NEB/TS/IRC
`--sp-level`	STR	(same as opt-level)	ORCA theory for SP energy refinement
`--neb-method`	STR	NEB-CI	NEB-CI or NEB-TS
`--neb-nimages`	INT	8	Number of NEB interpolation images
`--neb-maxiter`	INT	500	Max NEB iterations
`--irc-maxiter`	INT	50	Max IRC steps per direction
`--irc-stepsize`	FLOAT	0.3	IRC step size (Bohr·amu^0.5)
`--irc-maxdisp`	FLOAT	0.5	Max IRC displacement per step
`--skip-opt-endpoints`	FLAG	-	Skip endpoint optimization
`--no-neb`	FLAG	-	Skip NEB (requires --ts-guess)
`--no-irc`	FLAG	-	Skip IRC path tracing
`--no-sp-refine`	FLAG	-	Skip SP energy refinement
`--no-eprofile`	FLAG	-	Skip energy profile plot
`--no-irc-plot`	FLAG	-	Skip IRC path plot
`--no-ts-render`	FLAG	-	Skip VMD TS rendering
`--no-ts-panel`	FLAG	-	Skip TS validation panel
`--no-mode-proj`	FLAG	-	Skip imaginary-mode projection plot
`--no-irc-coords`	FLAG	-	Skip IRC internal-coordinates plot
`--no-neb-conv`	FLAG	-	Skip NEB convergence diagnostics plot
`--no-irc-anim`	FLAG	-	Skip IRC animation GIFs
`--mol-zoom`	FLOAT	1.00	VMD zoom factor for TS renders
`--monitor-bonds`	STR	-	Comma-separated atom pairs to track along IRC, e.g. `"1-2,2-3"`
`--vmd-bin`	PATH	auto-detect	Override VMD executable path
`-V, --version`	FLAG	-	Show version information
`-h, --help`	FLAG	-	Show help message

8. Version Information

Current version: v1.5.0
Release date: 2026-03-02
Development language: Bash / Python 3
Total lines of code: approximately 13,300

9. Key Technical Features

End-to-end automation: From XYZ structure input to publication-quality image output with no manual intervention
Intelligent parameter inference: Automatic spin multiplicity inference for multi-charge states with electron-count parity validation
Publication-quality visualization: All images rendered at 2400x1800 resolution with orthographic projection ray tracing, automatic colorbar, annotation, and legend
Modular architecture: Independent module switches for on-demand composition
Fault tolerance and self-checking: Automatic dependency detection, input parameter validation, and convergence verification
Cross-platform compatibility: Supports multiple Multiwfn/VMD naming conventions with automatic executable path resolution

Name		Name	Last commit message	Last commit date
Latest commit History 34 Commits
bin		bin
function		function
tests		tests
.gitignore		.gitignore
CHANGELOG.md		CHANGELOG.md
IQCAP.png		IQCAP.png
IQCAP_v1.5.0_Documentation.pdf		IQCAP_v1.5.0_Documentation.pdf
IQCAP_v1.5.0_SourceCode.pdf		IQCAP_v1.5.0_SourceCode.pdf
LICENSE.txt		LICENSE.txt
README.md		README.md
README_zh.md		README_zh.md
cleanup_large_files.sh		cleanup_large_files.sh
colour.py		colour.py
gen_doc_pdf.py		gen_doc_pdf.py
gen_source_pdf.py		gen_source_pdf.py

Folders and files

Latest commit

History

Repository files navigation

IQCAP -- Intelligent Quantum Chemistry Analysis Platform

1. Overview

2. Software Architecture

2.1 Module Overview

3. System Requirements

3.1 Operating System

3.2 Third-Party Dependencies

3.3 Python Environment

4. Input and Output

4.1 Input

4.2 Output

5. Functional Modules

5.1 Core Ground-State Workflow (iqcap-opt.sh + iqcap-basic_elect_analysis.sh)

5.1.1 Geometry Optimization (iqcap-opt.sh)

5.1.2 Multi-Charge-State Single-Point Calculations (iqcap-basic_elect_analysis.sh)

5.1.3 ESP Surface Mapping

5.1.4 Frontier Orbital Visualization

5.1.5 Fukui Reactivity Descriptors

5.1.6 NCI / RDG Weak Interaction Analysis

5.1.7 Charge and Bond Order Analysis

5.1.8 Conceptual DFT (CDFT)

5.2 Weak Interaction Analysis (iqcap-elect_interaction.sh)

5.2.1 chgdiff (Differential Charge Density)

5.2.2 NCI / RDG Analysis

5.2.3 IGMH Analysis

5.2.4 IRI Analysis

5.2.5 HS (Hirshfeld Surface) Analysis

5.2.6 CDA (Charge Decomposition Analysis)

5.3 Transition State & Reaction Path Engine (iqcap-ts.sh)

5.3.1 Endpoint Optimization

5.3.2 NEB Path Search

5.3.3 TS Optimization and Frequency Verification

5.3.4 IRC Path Tracing

5.3.5 Single-Point Energy Refinement

5.3.6 Energy Profile Visualization

5.3.7 TS Structure Rendering

5.3.8 TS Validation and Diagnostics

6. Usage Examples

6.1 Basic Analysis (Core Workflow)

6.2 Differential Charge Density (chgdiff)

6.3 Weak Interactions and Charge Decomposition

6.4 Transition State & Reaction Path Analysis

6.5 Complete Workflow Example

7. Command-Line Reference

iqcap-opt.sh

iqcap-basic_elect_analysis.sh

iqcap-elect_interaction.sh

iqcap-ts.sh

8. Version Information

9. Key Technical Features

About

Resources

License

Uh oh!

Stars

Watchers

Forks

Releases

Packages 0

Uh oh!

Contributors

Uh oh!

Languages

5.1 Core Ground-State Workflow (`iqcap-opt.sh` + `iqcap-basic_elect_analysis.sh`)

5.1.1 Geometry Optimization (`iqcap-opt.sh`)

5.1.2 Multi-Charge-State Single-Point Calculations (`iqcap-basic_elect_analysis.sh`)

Packages