PPSTM

Official Resources

• Source Repository: https://github.com/Probe-Particle/PPSTM
• Documentation: Included in repository
• License: Open source

Overview

PPSTM (Probe-Particle STM) is a simulation code for various scanning tunneling microscopy (STM) techniques, including STM imaging, scanning tunneling spectroscopy (STS), and inelastic electron tunneling spectroscopy (IETS). It uses the probe-particle model to simulate tip-sample interactions with sub-molecular resolution.

Scientific domain: Scanning probe microscopy, surface science, spectroscopy
Target user community: Researchers simulating and interpreting STM/STS/IETS experiments at surfaces

Theoretical Methods

• Probe-particle model for tip-sample interaction
• Bardeen tunneling theory
• Tersoff-Hamann approximation
• Inelastic tunneling (IETS)
• Local density of states (LDOS) mapping
• Tight-binding or DFT input for electronic structure

Capabilities (CRITICAL)

• STM image simulation (constant-current and constant-height)
• Scanning tunneling spectroscopy (STS/dI/dV maps)
• Inelastic electron tunneling spectroscopy (IETS)
• AFM image simulation (via ppafm)
• Sub-molecular resolution imaging
• Tip tilting effects
• Vibrational mode imaging (IETS)
• Fourier-transformed STS analysis
• Support for DFT and tight-binding inputs

Sources: GitHub repository, Comput. Phys. Commun. 305, 109341 (2024)

Key Strengths

Probe-Particle Model:

• Realistic tip geometry
• Tilting and flexibility
• Beyond Tersoff-Hamann
• Sub-molecular resolution
• Efficient computation

Comprehensive SPM:

• STM, STS, IETS in one code
• AFM via ppafm integration
• Multiple imaging modes
• Fourier analysis
• Comparison with experiment

Flexible Input:

• DFT-calculated orbitals
• Tight-binding models
• Wannier functions
• Various file formats

Inputs & Outputs

• Input formats:

  • DFT orbital data (VASP, QE, FHI-aims, CP2K)
  • Tight-binding models
  • Probe-particle parameters
  • Bias voltage settings

• Output data types:

  • STM images (2D maps)
  • STS/dI/dV spectra and maps
  • IETS spectra and maps
  • AFM images (via ppafm)
  • Fourier-transformed data

Interfaces & Ecosystem

• ppafm: AFM simulation companion code
• VASP: DFT orbital input
• Quantum ESPRESSO: DFT orbital input
• FHI-aims: DFT orbital input
• CP2K: DFT orbital input
• Python: Scripting and visualization

Performance Characteristics

• Speed: Fast (seconds to minutes per image)
• Accuracy: Good for qualitative comparison
• System size: Hundreds of atoms
• Memory: Moderate

Computational Cost

• STM image: Seconds to minutes
• STS map: Minutes to hours
• IETS: Hours (needs vibrational modes)
• Typical: Very efficient

Limitations & Known Constraints

• Model-based: Not fully ab initio tunneling
• Tip model: Simplified probe-particle
• No full NEGF: Approximate tunneling
• Vibrational modes: Need external calculation
• Documentation: Could be more extensive

Comparison with Other Codes

• vs cp2k-spm-tools: PPSTM uses probe-particle model, cp2k-spm uses CP2K directly
• vs STMng: PPSTM is more established and open-source
• vs ppafm: PPSTM focuses on STM/STS, ppafm on AFM
• Unique strength: Comprehensive STM/STS/IETS simulation with probe-particle model, multiple DFT code interfaces

Application Areas

On-Surface Molecules:

• PTCDA, pentacene STM images
• Molecular orbital imaging
• Tip-dependent contrast
• Bond-resolved imaging

2D Materials:

• Graphene moiré patterns
• TMD defect imaging
• Twisted bilayer STM
• Charge density waves

Vibrational Spectroscopy:

• Single-molecule IETS
• Vibrational mode mapping
• Isotope effects
• Tip-enhanced spectroscopy

Surface Reactions:

• Reaction intermediate imaging
• On-surface synthesis
• Catalytic site identification
• Adsorption geometry

Best Practices

Tip Parameters:

• Calibrate probe-particle stiffness
• Test tip radius and shape
• Compare with experimental contrast
• Consider tip functionalization

DFT Input:

• Use well-converged orbitals
• Include enough vacuum for surface
• Appropriate k-point sampling
• Check LDOS quality

IETS Calculations:

• Need accurate vibrational modes
• Calibrate inelastic coupling
• Compare with experimental IETS
• Consider temperature broadening

Community and Support

• Open source on GitHub
• Active development (Probe-Particle team)
• Published in Comput. Phys. Commun. (2024)
• Used by multiple SPM groups worldwide
• Tutorial examples provided

Verification & Sources

Primary sources:

1. GitHub repository: https://github.com/Probe-Particle/PPSTM
2. N. Oinonen et al., Comput. Phys. Commun. 305, 109341 (2024)
3. P. Hapala et al., Phys. Rev. B 90, 085421 (2014)

Confidence: VERIFIED

Verification status: ✅ VERIFIED

• Source code: ACCESSIBLE (GitHub)
• Documentation: Included in repository
• Community support: Active (SPM community)
• Academic citations: >500 (method papers)
• Active development: Ongoing
• Specialized strength: STM/STS/IETS simulation with probe-particle model, multi-DFT-code interface