MOPAC Output Parser

A Python script to parse MOPAC output files (.out) and extract key computational chemistry data including energy, atomic charges, dipole moment, molecular formula, and geometry.

Features

• Energy Extraction: Parses final heat of formation or total energy
• Atomic Charges: Extracts NET ATOMIC CHARGES with atom numbers, symbols, and charge values
• Dipole Moment: Extracts dipole components and total (if available)
• Molecular Formula: Derives or extracts the empirical formula
• Geometry: Extracts the last Cartesian coordinates and saves as Gaussian input file (.gjf)
• Batch Processing: Processes all .out files in the current directory
• Output Formats:
  • JSON file with extracted data (energy, charges, dipole, formula)
  • Individual .gjf files for each geometry

Requirements

• Python 3.x
• Standard library modules: re, os, json

Usage

1. Place your MOPAC .out files in the same directory as the script
2. Run the script:

python mopac_parser.py

3. The script will:
   • Process all .out files in the directory
   • Print summary information for each file
   • Save extracted data to parsed_results.json
   • Save geometries to individual .gjf files

Output Files

parsed_results.json

Contains extracted data for all processed files:

{
    "filename.out": {
        "energy": 2093.54508,
        "charges": [
            {
                "atom": 1,
                "symbol": "C",
                "charge": -0.479686
            }
        ],
        "dipole": null,
        "formula": "C31 H64  =    95 atoms"
    }
}

filename.gjf

Gaussian input files with the extracted geometry:

%chk=filename.chk
# pm7

Geometry from filename.out

0 1
C 7.193082 1.842861 0.030668
H 7.451486 2.497367 0.855113
...

Script Structure

The script uses a MOPACParser class with the following methods:

• read_file(): Reads the .out file content
• extract_energy(): Finds final energy values
• extract_charges(): Parses atomic charges section
• extract_dipole_moment(): Extracts dipole data
• extract_geometry(): Parses Cartesian coordinates
• extract_molecular_formula(): Gets or derives formula
• parse(): Orchestrates all extractions

Error Handling

• Checks for file existence
• Handles missing data gracefully (returns None for unavailable data)
• Continues processing other files if one fails
• Validates coordinate parsing

Example Output

Parsed vvc.out: Formula = C31 H64  =    95 atoms, Energy = 2093.54508, Dipole total = N/A
Geometry saved to vvc.gjf
All results saved to parsed_results.json

Notes

• The script extracts the last occurrence of geometry sections
• Charges and geometry are distinguished by line format (6 parts for charges, 5 for geometry)
• Dipole moment is extracted if present in the output
• The .gjf files use PM7 method with charge 0 and multiplicity 1