Welcome to PYGAMD’s documentation!

General introduction

• Introduction
• Installation
  • Source code
• Usage
• Units
  • Fundamental Units
  • Temperature units (thermal energy)
  • Charge units
  • Common derived units
  • Example physical units

Modules (NUMBA)

• System info
  • Data format
    • MST format
  • Data input
    • snapshot
    • MST reader
  • Data output
    • Collective information
    • MST dump
    • XML dump
  • Group
    • chare.particle_set
• Application
  • Modules management
    • application.dynamics
  • Multi-stage simulation
  • Two-dimensional simulation
• Force field
  • Non-bonded interactions
    • Non-bonded functions
    • Self-defined functions
    • Non-bonded functions for charged beads
    • Self-defined functions for charged beads
  • Bonded interactions
    • Bond interactions
    • Angle bending
    • Dihedral torsion
• Integration
  • NVT ensemble
    • NVT
    • GWVV
    • BD
• Modules
  • Dissipative particle dynamics
    • DPD force
    • GWVV integration

Modules (CUDA)

• Data
  • Data format
    • XML format
  • Data input
    • Reader
    • XML reader
    • Binary reader
  • Data output
    • Common functions for Data output
    • Collective information
    • MOL2 dump
    • XML dump
    • DCD trajectory dump
    • Binary dump
• System
  • Import libraries
    • import cuda lib (Linux)
    • import hip lib (Linux)
    • import cuda lib (Windows)
  • Information
    • Perform configuration
    • All information
  • Particle list
    • Neighbor list
    • Cell list
  • Particle set
    • ParticleSet
    • ParticleSet
    • ParticleSet
    • ParticleSet
  • Dynamic Particle Set
    • DynamicParticleSet
    • DynamicParticleSet
  • Information computation
    • ComputeInfo
  • Memory sorting
    • Sort
• Application
  • Modules management
    • Application
  • Multi-stage simulation
  • Two-dimensional simulation
• Force field
  • Short range non-bonded interactions
    • Lennard-Jones (LJ) interaction
    • Shift Lennard-Jones (LJ) interaction
    • Linear molecule \(\pi\)-\(\pi\) interaction
    • Generalized exponential model
    • Lennard-Jones and Ewald (short range) interaction
    • Lennard-Jones and Coulomb shift interaction
    • Pair interaction
  • Bonded interactions
    • Bond stretching
    • Angle bending
    • Dihedral torsion
  • Numerical interaction
    • Theory description
    • Non-bonded interaction
    • Bond interaction
    • Angle interaction
    • Dihedral interaction
    • Self-defined functions
  • Coulomb interaction
    • Ewald summation theory
    • Ewald (short-range)
    • Ewald for DPD (short-range)
    • PPPM (long-range)
    • ENUF (long-range)
  • Read force parameters
    • Force field format
    • Use force fields
    • Use GROMACS force fields
    • Convert GROMACS files
• Integration
  • NVE ensemble
    • NVE thermostat
    • NVE for rigid body
    • NVE for rigid body with tunable freedoms
  • NVT ensemble
    • Nose Hoover thermostat
    • Nose Hoover chain thermostat
    • Berendsen thermostat
    • Andersen thermostat
    • Langevin dynamic thermostat
    • NVT for rigid body
    • Langevin dynamic for rigid body
  • NPT ensemble
    • Andersen barostat
    • NPT for rigid body
    • Martyna-Tobias-Klein barostat
    • Martyna-Tobias-Klein barostat for rigid body
• Constraint
  • Variant
    • Variant Const
    • Variant Linear
    • Variant Sin
    • Variant Well
    • Variant Rsqrt
  • Space constraint
    • Bounce back condition
    • LJ surface force
  • Remove CM momentum
    • ZeroMomentum
    • ZeroMomentum
  • Constant chemical potential
    • CCPMD
  • Bond constraint
    • BondConstraint
  • Virtual site
    • Vsite
• External field
  • External force
    • ExternalForce
  • Axial stretching
    • AxialStretching
  • RNEMD
    • RNEMD
• Modules
  • MD-SCF
    • MDSCF force
    • MDSCF electrostatic force
  • Polymerization
    • Polymerization model
    • Depolymerization model
  • Anisotropic particle
    • Gay-Berne model
    • Soft anisotropic model
  • Dissipative particle dynamics
    • DPD force
    • GWVV integration
    • Coulomb interaction in DPD
  • Particle type change
    • ChangeType

Plug-Ins

• molgen
  • Description of molgen
  • Molecule definition
    • Molecule
    • Molecule
  • Objects definition
    • Object
    • Object
  • Generator definition
    • Generators
• dataTackle
  • Load dataTackle
  • Usage
  • Functions
    • 1 Rg^2:
    • 2 Ed^2:
    • 3 RDF:
    • 4 bond_distri:
    • 5 angle_distri:
    • 6 dihedral_distri:
    • 7 stress tensor:
    • 8 density:
    • 9 unwrapping:
    • 10 MSD:
    • 11 RDF-CM:
    • 12 MSD-CM:
    • 13 ents:
    • 14 strfac:
    • 15 domain size:
    • 16 dynamic strfac:
    • 17 config check:
    • 18 RDF between types:
    • 19 MST conversion:

Announcement

• License

Indices and tables

• Index

• Module Index

• Search Page