Logo

About UAMMD-structured

  • What is UAMMD-structured and what is not?
  • UAMMD-structured compilation and installation
    • Installing from conda (recommended)
      • Floating precision variants
    • Installing from source
      • Getting the source code
      • Getting the build dependencies
      • Compiling UAMMD-structured
      • Additional Compilation Options
        • Floating precision
        • CUDA architectures
        • Not building UAMMDlauncher and the library
        • Unity builds
        • Debian Package
        • Building the conda package
    • Testing
  • First Example

UAMMD-structured Guide

  • Simulation
  • Execution
  • Input
    • Data Entry
    • Input Formats
    • Example
  • System
    • Handling Errors
  • Global
    • Fundamental
    • Units
    • Types
    • Ensemble
  • State
  • Integrators
  • Topology
    • Structure
    • Force Field
  • Simulation Steps

Global Data

  • Fundamental
    • None
    • Time
    • DynamicallyBondedPatchyParticles
  • Units
    • None
    • KcalMol_A
  • Types
    • Basic
    • Polarizable
  • Ensemble
    • NVT
    • NVTlambda

Integrators

  • Minimization
    • SteepestDescent
  • NVE
    • Verlet
      • VelocityVerlet
  • NVT
    • Brownian
      • EulerMaruyama
      • EulerMaruyamaRigidBody
      • EulerMaruyamaRigidBodyPatchesState
    • Langevin
      • BBK
      • GJF
    • DPD
      • Verlet
    • SPH
      • Verlet
    • BDHIOpenBoundary
      • Cholesky
      • Lanczos
    • BDHITriplyPeriodic
      • ForceCouplingMethod
      • PositivelySplitEwald
      • FluctuatingImmersedBoundary
    • BDHIDoublyPeriodic
      • DPStokes
      • Quasi2D
    • FluctuatingHydrodynamics
      • CompressibleInertialCoupling
      • IncompressibleInertialCoupling
    • Magnetic
      • Brownian
      • Fixed
      • ForceCouplingMethod
  • Special
    • None

Interactors

  • Bonds
    • Bond1
      • FixedHarmonic
      • ConstantForce
      • LambdaFixedHarmonicAnisotropic
      • FixedHarmonicAnisotropic
    • Bond2
      • Harmonic
        • HarmonicCommon_K
        • HarmonicCommon_K_r0
      • HarmonicAnisotropic
      • LambdaHarmonic
      • Fene
        • FeneCommon_K_R0
        • FeneCommon_r0_K_R0
      • Morse
        • MorseCommon_D
        • MorseCommon_r0_E_D
      • Gaussian
        • GaussianCommon_E_r0_D
      • Steric
        • Steric6
        • Steric12
        • Steric6Common_epsilon_sigma
      • LennardJones
        • LennardJonesType1
        • LennardJonesType2
        • LennardJonesType3
        • LennardJonesType1Common_epsilon
      • LennardJonesKaranicolasBrooks
        • LennardJonesKaranicolasBrooksCommon_epsilon
      • LennardJonesGaussian
        • LennardJonesGaussianCommon_epsilon_D
      • LennardJonesSoftCore
        • LennardJonesSoftCoreType1
        • LennardJonesSoftCoreType2
        • LennardJonesSoftCoreType1Common_epsilon
      • DebyeHuckel
      • MaxDistanceRestraint
      • HelixExponential
      • HelixCosine
    • Bond3
      • KratkyPorod
        • KratkyPorodCommon_K
      • HarmonicAngular
        • HarmonicAngularCommon_K
        • HarmonicAngularCommon_K_theta0
      • BestChenHummerAngular
    • Bond4
      • Dihedral
        • DihedralCommon_n_K_phi0
        • Dihedral4
      • IDP_Fourier
  • Single
    • External
      • ConstantForce
      • ConstantTorque
      • SphericalShell
      • Plates
      • ExternalTabulated
      • PolarizationTabulated
      • ConstantMagneticField
      • ACMagneticField
      • HelixBoundaries
    • Surface
      • SurfaceLennardJones
        • SurfaceLennardJonesType1
        • SurfaceLennardJonesType2
      • SurfaceWCA
        • SurfaceWCAType1
        • SurfaceWCAType2
      • SurfaceGeneralLennardJones
        • SurfaceGeneralLennardJonesType1
        • SurfaceGeneralLennardJonesType2
      • SurfaceAnchorage
      • ParabolaSurface
      • Absorbed
  • NonBonded
    • Short Range
      • LennardJones
        • LennardJonesType1
        • LennardJonesType2
        • LennardJonesType3
      • GeneralLennardJones
        • GeneralLennardJonesType1
        • GeneralLennardJonesType2
        • GeneralLennardJonesType3
      • SplitLennardJones
      • Steric
        • Steric6
        • Steric12
      • WCA (Weeks-Chandler-Andersen)
        • WCAType1
        • WCAType2
        • WCAType3
      • SoftCore
        • LennardJonesSoftCoreType1
        • LennardJonesSoftCoreType2
      • DebyeHuckel
      • DLVO
      • KimHummer
      • Zhang
      • DipolarMagnetic
      • Clashed
    • Electrostatics
  • Set
    • Set1
      • FixedHarmonicAnisotropicCenterOfMass
      • ConstantForceOverCenterOfMass
      • ConstantTorqueOverCenterOfMass
    • Set2
      • HarmonicBondBetweenCentersOfMass
      • ConstantForceBetweenCentersOfMass
      • ConstantTorqueBetweenCentersOfMass
  • Atomic Force Microscopy
    • SphericalTip
    • SphericallyBluntedConicTip

Data Structures

  • VerletConditionalListSet
    • Condition
      • all
      • intramolecular-intermolecular
      • non excluded
      • non excl intra - non excl inter
      • non excl intra - non excl inter - non excl charged
      • non excl intra - non excl inter - non excl inter charged
      • intermolecular different type

Simulation Steps

  • SimulationUtils
    • UtilsStep
      • InfoStep
      • SortStep
    • FlowControl
      • AFMMaxForce
      • LambdaCycle
      • LambdaActivation
  • SimulationOutput
    • WriteStep
      • WriteStep
      • WritePatchyParticlesStep
  • SimulationMeasures
    • ParticlesListMeasure
      • DistancesMeasure
      • AnglesMeasure
      • DihedralsMeasure
      • PotentialMeasure
      • ContactsMeasure
    • MechanicalMeasure
      • StressMeasure
      • HessianMeasure
      • PairwiseForceMeasure
      • ForceBetweenSetsMeasure
    • ThermodynamicMeasure
      • ThermodynamicQuantityMeasure
      • ThermodynamicIntegration
      • InteractorsListEnergyMeasure
    • GeometricalMeasure
      • MeanRadius
      • GyrationRadius
      • MeanSquareDisplacement
      • MeanAngularCorrelation
      • CenterOfMassPosition
      • EscapeTime
      • Height
      • DistanceBetweenCentersOfMass
    • MagneticMeasure
      • MeasureMeanMagnetization
      • MeasureTotalMagnetization
    • ExperimentMeasures
      • AFMMeasure

Utilities

  • Groups
  • Scheduling the components
  • Batching

pyUAMMD

  • Introduction
  • Installation
    • Installing from conda (recommended)
    • Installing from source
      • Building UAMMD-structured and pyUAMMD
      • Building pyUAMMD when UAMMD-structured is already installed

Implementation

  • Input
  • Design
    • Simulation
    • System
    • Global
    • State
    • Integrators
    • Topology
      • Structure
      • Force Field
  • Extending UAMMD-structured
    • Extending ParticleData
    • Extending Global
      • Fundamental
      • Units
      • Types
      • Ensemble
    • Extending Interactor
      • Generic Interactor
      • Potentials
        • Bonds
        • External
        • Surface
        • NonBonded
    • Extending Integrator
    • Extending SimulationStep
  • Information for developers
    • Github actions

Online Examples

  • Online Examples
UAMMD-structured
  • NVT
  • BDHITriplyPeriodic
  • View page source

BDHITriplyPeriodic

  • ForceCouplingMethod
  • PositivelySplitEwald
  • FluctuatingImmersedBoundary
Previous Next

© Copyright 2023, Pablo Ibáñez-Freire.

Built with Sphinx using a theme provided by Read the Docs.