Qbics Manual

• In the left panel, you can find a quick overview of the main sections of the manual

• Below, you can find a detailed table of contents.

Program

• Compiling Qbics
  • Download Source Code
  • Preparations
  • One-Key Build: Quick Way
  • One-Key Build: More Options
  • Build from Lean Source Code
  • Build GPU Version of Qbics
  • Build MPI Version of Qbics
  • Additional Modules of Plumed
  • Possible Issues
• Installing Qbics
  • General Considerations
  • GPU Version
  • MPI Version
• Running Qbics
  • Command Line Arguments
  • Run Qbics on a Single Node with GPU
  • Run Qbics on Multiple Nodes

Input

• Input File Format
• Input Library
  • Tutorials
  • Keywords

Tutorial

• Density Functional Theory Calculations
  • Example: Single Point Energy of Water
  • More Basis Set Configurations
  • Example: Heavy Elements with Pseudopotential
  • Example: Set Special SCF Initial Guess
  • SCF Convergence Condition
• Semi-empirical Quantum Chemistry Methods
  • Example: xTB for Ligand-protecing Gold Clusters
  • Example: AM1 and PM3 for An Organic Anion
• Molecular Mechanics Calculations
  • Topology and Parameters
  • Solvated Protein 5VBM
  • Oragnic Molecule 92V
• Geometry Optimization
  • Example: DFT for CH₃CH₂SO₃H
  • Example: xTB Pre-optimization befor DFT Geomtry Optimization
  • Example: DFT Geomtry Optimization with Constraints
  • Example: MM for Solvated Protein 5VBM
• Standard Molecular Dynamics Simulations
  • Example: NVT MD for Solvated Protein 5VBM
  • Example: NVE MD for Bullvalene
• Transition State Search
  • Example: NEB and QST2/Dimer for Amine-Catalyzed Aldol Reaction
  • Example: dMECP for F^-+CH₃Cl = CH₃F+Cl^-
• Energy Decomposition Analysis
  • Example: EDA for (H₂SO₄)(NH₃)
  • Example: EDA for (Ca²⁺)(SO₄^2-)(H₂O)₅
• TSO-DFT (1): Excited States
  • Example: HCHO n→π* Excitation Energy
  • Example: HCHO n²→(π*)² Excitation Energy
  • Example: HCHO n→π* Excited State Geometry
  • Example: HCCH Non-linear Excited State Geometry
• TSO-DFT (2): Diabatic States
  • Example: Definition of Diabatic States of NaCl
  • Example: Reactant and Product Diabatic States of F^-+CH₃Cl
• Metadynamics for Calculating Free Energy Surface
  • Example: Conformation Change of Dialaline
  • Example: Proton Transfer of Malonaldehyde

Keywords

• basis
  • Using Built-in Basis Sets
  • Explicit Basis Set Definitions
  • Using Self-defined Basis Set Files
  • Define Different Basis Sets for Different Elements
  • Theoretical Background
  • Input Examples
• basinfo
  • Options
  • Theoretical Background
  • Input Examples
• charmm
  • Options
  • Theoretical Background
  • Input Examples
• eda
  • Options
  • Theoretical Background
  • Input Examples
• grimmedisp
  • Options
  • Theoretical Background
  • Input Examples
• md
  • Options
  • Theoretical Background
  • Input Examples
• mecp
  • Options
  • Theoretical Background
  • Input Examples
• mol and mol2
  • Explicit XYZ Coordinates
  • XYZ File Name
  • PDB File Name
  • Theoretical Background
  • Input Examples
• msdft
  • Options
  • Theoretical Background
  • Input Examples
• nddo
  • Options
  • Theoretical Background
  • Input Examples
• nosi
• nosi_dets_mwfn
• opt
  • Options
  • Theoretical Background
  • Input Examples
• output
  • Options
• pcm
  • Options
  • Theoretical Background
  • Input Examples
• pifep
  • Options
  • Theoretical Background
  • Input examples
  • Checkpoint and restart
  • Code Execution in Parallel
• pseudopotential
  • Using Built-in Pseudopotentials
  • Explicit Pseudopotential Definitions
  • Using Self-defined Pseudopotential Files
  • Theoretical Background
  • Input Examples
• qmmm
  • Options
  • Theoretical Background
  • Input Examples
• scf
  • Options
  • Theoretical Background
  • Input Examples
• scfguess
  • Options
  • Theoretical Background
  • Input Examples
• tddft
  • Options
  • Theoretical Background
  • Input Examples
• thermo
  • Options
  • Theoretical Background
  • Input Examples
• wfn
  • Options
  • Theoretical Background
  • Input Examples
• xtb
  • Options
  • Theoretical Background
  • Input Examples

Development

• Developing Tools
  • Auxiliary Development Tools
  • Source Code Editor
  • Static Analysis
  • Documentation
• Code Styles
  • Code Format
  • C++ Version
  • File Structures
  • Naming
  • Class and Structure Format
  • Flow Control
  • Usage of const
  • Function Design
  • Numbers
  • Forbidden C++ Features
  • Comments
  • Exceptions
• Domain Logic
  • General Rules
  • General Libraries
  • kiseki
  • Input Design
  • Quantum Chemistry Coding
  • Molecular Mechanics Coding
• Git Commands

Quick Links

• Quick Links