Gaussian Tips and Troubleshooting Guide

Gaussian Tips and Troubleshooting Guide

This guide compiles common errors encountered when running Gaussian calculations and provides practical solutions. Whether you’re optimizing geometries, computing frequencies, or running excited-state calculations, these tips should help you navigate the most frequent issues.

Tip: Use your browser’s search function (Ctrl+F / Cmd+F) to quickly find specific error messages. This guide is inspired by and builds upon resources from the computational chemistry community, particularly Zhe Wang’s comprehensive error guide.

Memory and Resource Issues

Insufficient Memory Errors

Common Error Messages:

• CISAX needs XXXXX more words of memory
• XXXXX words are not enough for AlAXAO
• galloc: could not allocate memory
• malloc failed: Resource temporarily unavailable

Solutions:

1. Increase memory allocation: Use the %mem directive at the top of your input file:

   %mem=8GB
   

   Note: Gaussian actually uses about 1 GB more than specified, so set %mem to at least 1 GB less than your job script’s memory allocation.

2. Reduce CPU cores: If memory is limited, reduce the number of processors:

   %nprocshared=4
   

   This reduces memory requirements per core.

3. Check job script settings: Ensure your job submission script (SLURM, PBS, etc.) allocates sufficient memory:

   #SBATCH --mem=16G  # Should be ~1GB more than %mem
   

Geometry Optimization Issues

Optimization Not Converging

Error Messages:

• Number of steps exceeded, NStep= 100
• Delta-x Convergence NOT Met
• Maximum of *** iterations exceeded in RedStp

Solutions:

1. Increase maximum cycles: Add opt=maxcycle=n where n is 2-3 times the current number of steps:

   # opt=calcfc opt=maxcycle=200
   

2. Try different optimization methods:
   • opt=RFO - Rational Function Optimization
   • opt=GDIIS - Geometry Direct Inversion in Iterative Subspace
   • opt=GEDIIS - Geometry Energy-Direct Inversion in Iterative Subspace
3. Switch coordinate system: If Z-matrix fails, try Cartesian coordinates:

   opt=cartesian
   

4. Check initial geometry: Verify your starting structure is reasonable. Use molecular visualization software (GaussView, Avogadro) to inspect the geometry.

5. Modify symmetry: Sometimes reducing symmetry helps:

   # symm=loose
   

Transition State Optimization Issues

Error Message:

• Wrong number of Negative eigenvalues: Desired= 1 Actual= 4

Solution: If you’re optimizing a transition state but get multiple negative frequencies, use:

opt=(ts,noeigen)

This skips the eigenvalue check. However, always verify your final structure has exactly one imaginary frequency!

Frequency Calculation Issues

Frequency Calculation Errors

Error Messages:

• Error in INITNF
• Linear search skipped for unknown reason
• Inconsistency: ModMin= N Eigenvalue= MM

Solutions:

1. Ensure optimization converged: Frequency calculations require a fully optimized geometry. Check that your optimization completed successfully.

2. Use freq=readfc: If you have a checkpoint file with force constants:

   # freq=readfc
   

3. Recalculate from scratch: Sometimes it’s best to re-optimize and then compute frequencies in a single job:

   # opt freq
   

SCF Convergence Issues

SCF Not Converging

Error Messages:

• Convergence failure -- run terminated
• SCF Done: E(RB3LYP) = ... A.U. after 50 cycles

Solutions:

1. Use convergence aids:

   scf=(conver=8,xqc)
   

   • conver=8 sets tighter convergence criteria
   • xqc uses quadratic convergence
2. Try different initial guess:

   guess=mix
   guess=huckel
   guess=read  # from checkpoint file
   

3. Use damping:

   scf=(conver=8,damp)
   

4. Check for problematic systems:
   • Open-shell systems may need stable=opt
   • Systems with near-degeneracies may need different methods

Post-HF Method Convergence

CCSD/CCSD(T) Not Converging

Error Messages:

• Error termination via Lnk1e in l913.exe (after CCSD iterations)
• Large amplitudes in the output

Solutions:

1. Increase maximum cycles:

   ccsd(t,maxcyc=100)
   

   Default is 50 cycles.

2. Check convergence trend: Look at the DE(Corr) values in the output. If they’re converging (approaching a stable value), increasing cycles should help.

3. Verify reference state: Ensure your HF reference is reasonable. Try:

   stable=opt
   

   before the CCSD calculation.

4. Try different basis set: Sometimes a smaller or different basis set helps establish convergence.

File and I/O Errors

Disk Space Issues

Error Messages:

• Erroneous write. write 122880 instead of 4239360
• writwa: No space left on device
• Erroneous write during file extend

Solutions:

1. Check disk space:

   df -h
   du -sh ~/scratch/
   

2. Clean up scratch directory: Remove old checkpoint files and temporary files.

3. Use smaller basis set: For very large calculations, consider using a smaller basis set or reducing system size.

4. Set scratch directory: Ensure GAUSS_SCRDIR points to a directory with sufficient space:

   export GAUSS_SCRDIR=/path/to/large/disk/scratch
   

Checkpoint File Issues

Error Messages:

• Error termination in NtrErr: Operation on file out of range
• Error imposing constraints

Solutions:

1. Regenerate checkpoint file: The checkpoint file may be corrupted or incomplete. Re-run the calculation that generates the needed data.

2. Don’t rely on incomplete checkpoints: If a previous job failed or was killed, don’t try to read from its checkpoint file.

Input File Errors

Z-Matrix and Coordinate Errors

Error Messages:

• End of file in Zsymb
• Found a string as input
• There are no atoms in this input structure
• Symbol not found in Z-matrix
• Variable index is out of range
• Determination of dummy atom variables in z-matrix conversion failed

Solutions:

1. Check input format: Ensure proper spacing and formatting in your Z-matrix or Cartesian coordinates.

2. Use Cartesian coordinates: If Z-matrix conversion fails, switch to Cartesian:

   # opt=cartesian
   

3. Verify atom definitions: Check that all atoms are properly defined and variables are correctly referenced.

4. Use GaussView or similar: Generate input files using molecular visualization software to avoid formatting errors.

Method-Specific Issues

DFT Functional Limitations

Error Message:

• No func 3rd derivs with HSE (or similar for other functionals)

Explanation: Some functionals don’t support third-order derivatives needed for hyperpolarizability calculations.

Solutions:

1. For polarizability only: Use polar=Numerical:

   # polar=Numerical
   

   This calculates polarizability α but may fail for hyperpolarizability β.

2. Use different functional: Switch to a functional that supports third-order derivatives (most standard functionals do).

3. Check output: Sometimes the desired property (e.g., α) is calculated before the error occurs, so check earlier in the output file.

System and Permission Errors

Gaussian Installation Issues

Error Messages:

• Files in the Gaussian directory are world accessible. This must be fixed.
• failed to open execfile

Solutions:

1. Fix permissions:

   chmod -R 750 /path/to/Gaussian
   

2. Check Linda vs. OpenMP: If using nprocl, ensure your system supports Linda. Otherwise, use nprocshared:

   %nprocshared=8  # instead of nprocl
   

3. Verify environment variables: Check that g09root or g16root and GAUSS_EXEDIR are set correctly.

General Best Practices

Input File Organization

1. Always include route section: Start with # followed by method and keywords
2. Use title line: Provide a descriptive title
3. Specify charge and multiplicity: Essential for proper calculation
4. Use checkpoint files: Include %chk=filename.chk for recovery

Example Well-Structured Input:

%mem=8GB
%nprocshared=4
%chk=water_opt.chk
# opt freq b3lyp/6-31g(d)

Water optimization

0 1
O    0.000000    0.000000    0.117300
H    0.000000    0.757200   -0.469200
H    0.000000   -0.757200   -0.469200

Monitoring Calculations

1. Watch output in real-time: Use tail -f to monitor progress:

   tail -f jobname.log
   

2. Check for convergence: Look for “Optimization completed” or “Normal termination”

3. Save intermediate results: Use checkpoint files to restart or extract data

Performance Tips

1. Use appropriate basis sets: Don’t use larger basis sets than necessary
2. Parallelize wisely: More cores don’t always mean faster (memory trade-off)
3. Use efficient methods: Consider opt=calcfc to calculate force constants once
4. Chain calculations: Use geom=allcheck to continue from previous calculations

Quick Reference: Common Fixes

Additional Resources

• Gaussian Official Documentation
• Gaussian User’s Reference
• Zhe Wang’s Gaussian Error Guide
• Crawford Group Computational Chemistry Resources

Getting Help

If you encounter errors not covered here:

1. Check the full output file: Errors often have context earlier in the file
2. Search error messages: Many errors are documented online
3. Consult colleagues: Often someone has seen the same issue
4. Gaussian support: For licensed users, contact Gaussian Inc. support

Remember: Computational chemistry calculations can be finicky. When in doubt, start simpler (smaller basis set, fewer atoms) and work your way up!