OHMind-Multiwfn MCP Server

Wavefunction analysis and electronic structure post-processing tools using Multiwfn.

Overview
Server Configuration
Tools Reference
Usage Examples
Results Format
Troubleshooting
See Also

Overview

The OHMind-Multiwfn MCP server provides 16 tools for wavefunction analysis and electronic structure post-processing. It analyzes ORCA output files to extract orbital energies, electron density information, population analysis, and generates visualizations.

Server Details

Property	Value
Server Name	`OHMind-Multiwfn`
Entry Point	`python -m OHMind_agent.MCP.Multiwfn.server`
Tool Count	16
Dependencies	Multiwfn executable

Capabilities

Orbital analysis (HOMO/LUMO energies, compositions)
Population analysis (Mulliken, Hirshfeld, ADCH, RESP)
Electron density analysis (AIM, ELF, LOL)
Weak interaction analysis (NCI, RDG, IGMH)
Bond analysis and bond orders
Aromaticity analysis (NICS)
Spectrum simulation (UV-Vis, IR, NMR)
Orbital visualization (2D/3D)

Server Configuration

Starting the Server

# stdio transport (default)
python -m OHMind_agent.MCP.Multiwfn.server --transport stdio

# HTTP transport
python -m OHMind_agent.MCP.Multiwfn.server --transport streamable-http --port 8104

Environment Variables

Variable	Purpose	Required
`PYTHONPATH`	Path to OHMind project	Yes
`MULTIWFN_PATH`	Path to Multiwfn executable	Yes
`MULTIWFN_WORK_DIR`	Working directory	Yes
`QM_WORK_DIR`	QM results directory	For finding ORCA files

mcp.json Configuration

{
  "OHMind-Multiwfn": {
    "command": "python",
    "args": ["-m", "OHMind_agent.MCP.Multiwfn.server", "--transport", "stdio"],
    "env": {
      "PYTHONPATH": "/path/to/OHMind",
      "MULTIWFN_PATH": "/path/to/Multiwfn",
      "MULTIWFN_WORK_DIR": "/OHMind_workspace/Multiwfn",
      "QM_WORK_DIR": "/OHMind_workspace/ORCA"
    }
  }
}

Tools Reference

Core Analysis Tools

`AnalyzeWavefunction`

Basic wavefunction analysis for a given input file.

Parameters:

Name	Type	Required	Description
`input_file`	string	Yes	Path to wavefunction file (fchk/wfn/gbw/out)

Returns: Wavefunction diagnostics and summary

`OrbitalAnalysis`

Analyze HOMO, LUMO, and other molecular orbitals.

Parameters:

Name	Type	Required	Description
`input_file`	string	Yes	Path to `.out` or `.gbw` file, OR results_directory
`orbital_number`	string	No	`"HOMO"`, `"LUMO"`, `"HOMO-1"`, `"LUMO+1"`, or integer
`composition_method`	string	No	`"Mulliken"`, `"Hirshfeld"`, `"NAO"`, `"Becke"`

Returns: Orbital energies, compositions, and properties

Example:

{
  "input_file": "/OHMind_workspace/ORCA/results",
  "orbital_number": "LUMO",
  "composition_method": "Mulliken"
}

`PopulationAnalysis`

Calculate atomic charges using various methods.

Parameters:

Name	Type	Required	Description
`input_file`	string	Yes	Path to wavefunction file
`methods`	array	No	Charge methods to use

Available Methods:

Method	Description
`mulliken`	Mulliken population analysis
`hirshfeld`	Hirshfeld charges
`adch`	ADCH charges
`resp`	RESP charges
`cm5`	CM5 charges
`mbis`	MBIS charges

Returns: Charges per atom for each method

`ElectronDensityAnalysis`

Analyze electron density using various methods.

Parameters:

Name	Type	Required	Description
`input_file`	string	Yes	Path to wavefunction file
`analysis_type`	string	Yes	Analysis type

Analysis Types:

Type	Description
`aim`	Atoms in Molecules (Bader) analysis
`elf`	Electron Localization Function
`lol`	Localized Orbital Locator
`laplacian`	Laplacian of electron density

Returns: Electron density analysis results

`BondAnalysis`

Analyze chemical bonds and bond orders.

Parameters:

Name	Type	Required	Description
`input_file`	string	Yes	Path to wavefunction file
`bond_order_type`	string	No	`"mayer"`, `"wiberg"`, `"fuzzy"`

Returns: Bond orders and strength descriptors

Interaction Analysis Tools

`WeakInteractionAnalysis`

Analyze noncovalent interactions.

Parameters:

Name	Type	Required	Description
`input_file`	string	Yes	Path to wavefunction file
`analysis_type`	string	Yes	Analysis type

Analysis Types:

Type	Description
`rdg`	Reduced Density Gradient
`nci`	Non-Covalent Interaction
`igmh`	Independent Gradient Model based on Hirshfeld
`iri`	Interaction Region Indicator

Returns: Weak interaction analysis results

`AromaticityAnalysis`

Calculate aromaticity indices.

Parameters:

Name	Type	Required	Description
`input_file`	string	Yes	Path to wavefunction file
`ring_atoms`	array	Yes	Atom indices defining the ring

Returns: NICS values and related aromaticity measures

`EnergyDecomposition`

Energy decomposition analysis.

Parameters:

Name	Type	Required	Description
`input_file`	string	Yes	Path to wavefunction file
`method`	string	No	`"lmo-eda"`, `"sapt"`

Returns: Energy decomposition results

Spectrum Simulation Tools

`SimulateSpectrum`

Simulate various spectra from computed properties.

Parameters:

Name	Type	Required	Description
`input_file`	string	Yes	Path to wavefunction/output file
`spectrum_type`	string	Yes	Spectrum type
`broadening`	float	No	Peak broadening parameter

Spectrum Types:

Type	Description
`uv-vis`	UV-Visible absorption
`ir`	Infrared
`raman`	Raman
`nmr`	NMR
`ecd`	Electronic Circular Dichroism
`vcd`	Vibrational Circular Dichroism

Returns: Simulated spectrum data

Visualization Tools

`GenerateCubeFiles`

Generate cube files for densities and orbitals.

Parameters:

Name	Type	Required	Description
`input_file`	string	Yes	Path to wavefunction file
`property`	string	Yes	Property to generate
`orbital_number`	integer	No	Orbital index for orbital cubes

Properties:

density - Electron density
orbital - Molecular orbital
elf - Electron Localization Function
lol - Localized Orbital Locator

Returns: Path to generated cube file

`VisualizeOrbitals`

High-level orbital visualization orchestration.

Parameters:

Name	Type	Required	Description
`input_file`	string	Yes	Path to wavefunction file
`orbitals`	array	Yes	Orbital numbers to visualize
`output_format`	string	No	Output format (`"png"`, `"cube"`)

Returns: Paths to visualization files

`QuickVisualizeHOMOLUMO`

Convenience tool to quickly visualize HOMO/LUMO.

Parameters:

Name	Type	Required	Description
`input_file`	string	Yes	Path to wavefunction file

Returns: HOMO and LUMO visualization files

`RenderOrbitals2D`

2D slice plotting of orbitals/densities.

Parameters:

Name	Type	Required	Description
`cube_file`	string	Yes	Path to cube file
`plane`	string	No	Slice plane (`"xy"`, `"xz"`, `"yz"`)
`slice_position`	float	No	Position along perpendicular axis

Returns: 2D plot image

`RenderOrbitals3D`

3D orbital rendering with VMD/Tachyon style.

Parameters:

Name	Type	Required	Description
`cube_file`	string	Yes	Path to cube file
`isovalue`	float	No	Isosurface value
`style`	string	No	Rendering style

Returns: 3D render image

MD Analysis Tools

`MDAnalysis`

Post-processing of MD trajectories.

Parameters:

Name	Type	Required	Description
`trajectory`	string	Yes	Path to trajectory file
`topology`	string	Yes	Path to topology file
`analysis_type`	string	Yes	`"rdf"`, `"coordination"`, `"hbond"`

Returns: MD analysis results

Advanced Analysis Tools

`AdNDPAnalysis`

Adaptive Natural Density Partitioning analysis.

Parameters:

Name	Type	Required	Description
`input_file`	string	Yes	Path to wavefunction file

Returns: AdNDP bonding analysis

Usage Examples

Charge and Reactive Hot-Spot Analysis

For the optimized cation geometry from my QM calculation (assume I have 
already generated a suitable wavefunction file), use your Multiwfn tools 
to analyze charge distribution and identify likely degradation hot spots 
under alkaline conditions.

Report which atoms or fragments are most positively charged or otherwise reactive.

Orbital Visualization

Starting from the wavefunction of a candidate cation, generate HOMO and 
LUMO visualizations (both 2D slices and 3D renders).

Describe where the LUMO is localized and what that suggests about 
degradation pathways.

HOMO/LUMO Energy Analysis

For the ORCA calculation results in /OHMind_workspace/ORCA, analyze the 
HOMO and LUMO energies using Mulliken composition analysis.

Report the orbital energies in eV and explain what the HOMO-LUMO gap 
implies for the molecule's reactivity.

Spectrum Simulation

Take a representative structure from an MD snapshot of my membrane system 
and use Multiwfn to simulate an approximate UV-Vis or IR spectrum, 
highlighting features that correlate with specific structural motifs.

Comprehensive Electronic Analysis

Using your Multiwfn tools, perform a comprehensive electronic analysis 
of this cation:

1) Calculate Hirshfeld and ADCH charges
2) Analyze the LUMO orbital composition
3) Identify any weak interactions using NCI analysis
4) Generate a 3D visualization of the LUMO

Summarize which parts of the molecule are most vulnerable to nucleophilic attack.

Results Format

Output Directory Structure

Multiwfn results are saved to $MULTIWFN_WORK_DIR/:

$MULTIWFN_WORK_DIR/
├── <job-name>/
│   ├── input.*           # Input files
│   ├── analysis.log      # Analysis log
│   ├── *.dat             # Data files
│   ├── *.cube            # Cube files
│   └── *.png             # Visualization images

Output File Types

Extension	Contents
`.dat`	Numerical data (charges, energies)
`.cube`	3D volumetric data
`.png`	Visualization images
`.log`	Analysis log

Visualization Output

Cube files can be visualized with external tools:

VMD (Visual Molecular Dynamics)
PyMOL
Avogadro
Custom Python scripts with matplotlib

Troubleshooting

Common Issues

Multiwfn Not Found

Error: Multiwfn executable not found

Solution: Set the Multiwfn path:

export MULTIWFN_PATH=/path/to/Multiwfn

Input File Not Found

Error: Could not find wavefunction file

Solutions:

Check if ORCA calculation completed successfully
Verify QM_WORK_DIR is set correctly
Use full path to the .out or .gbw file

Analysis Failed

Error: Multiwfn analysis failed

Solutions:

Check Multiwfn log for error messages
Verify input file format is supported
Ensure sufficient disk space

Visualization Error

Error: Could not generate visualization

Solutions:

Check if cube file was generated
Verify matplotlib is installed
Check display settings for 3D rendering

Supported Input Formats

Format	Extension	Source
ORCA output	`.out`	ORCA calculation
ORCA wavefunction	`.gbw`	ORCA calculation
Gaussian fchk	`.fchk`	Gaussian
Molden	`.molden`	Various
WFN/WFX	`.wfn`, `.wfx`	Various

Debug Mode

Run the server with verbose logging:

PYTHONPATH=/path/to/OHMind \
  MULTIWFN_PATH=/path/to/Multiwfn \
  MULTIWFN_WORK_DIR=/OHMind_workspace/Multiwfn \
  python -m OHMind_agent.MCP.Multiwfn.server --transport stdio 2>&1 | tee multiwfn_debug.log

OHMind-Multiwfn MCP Server

Table of Contents

Overview

Server Details

Capabilities

Server Configuration

Starting the Server

Environment Variables

mcp.json Configuration

Tools Reference

Core Analysis Tools

AnalyzeWavefunction

OrbitalAnalysis

PopulationAnalysis

ElectronDensityAnalysis

BondAnalysis

Interaction Analysis Tools

WeakInteractionAnalysis

AromaticityAnalysis

EnergyDecomposition

Spectrum Simulation Tools

SimulateSpectrum

Visualization Tools

GenerateCubeFiles

VisualizeOrbitals

QuickVisualizeHOMOLUMO

RenderOrbitals2D

RenderOrbitals3D

MD Analysis Tools

MDAnalysis

Advanced Analysis Tools

AdNDPAnalysis

Usage Examples

Charge and Reactive Hot-Spot Analysis

Orbital Visualization

HOMO/LUMO Energy Analysis

Spectrum Simulation

Comprehensive Electronic Analysis

Results Format

Output Directory Structure

Output File Types

Visualization Output

Troubleshooting

Common Issues

Multiwfn Not Found

Input File Not Found

Analysis Failed

Visualization Error

Supported Input Formats

Debug Mode

See Also

`AnalyzeWavefunction`

`OrbitalAnalysis`

`PopulationAnalysis`

`ElectronDensityAnalysis`

`BondAnalysis`

`WeakInteractionAnalysis`

`AromaticityAnalysis`

`EnergyDecomposition`

`SimulateSpectrum`

`GenerateCubeFiles`

`VisualizeOrbitals`

`QuickVisualizeHOMOLUMO`

`RenderOrbitals2D`

`RenderOrbitals3D`

`MDAnalysis`

`AdNDPAnalysis`