Index

A

A (ves.potentials.MullerBrownPotential attribute) a (ves.potentials.MullerBrownPotential attribute) animate_traj() (ves.visualization.VisualizePotential1D method) (ves.visualization.VisualizePotential2D method) animate_traj_projection_x() (ves.visualization.VisualizePotential2D method)

animate_traj_projection_y() (ves.visualization.VisualizePotential2D method) axis (ves.basis.LegendreBasis1D attribute) (ves.basis.NNBasis1D attribute) (ves.bias.HarmonicBias_SingleParticle_1D attribute) (ves.bias.HarmonicBias_SingleParticle_1D_ForceModule attribute)

B

b (ves.potentials.MullerBrownPotential attribute)

beta (ves.bias.VESBias_SingleParticle_1D attribute) Bias (class in ves.bias)

C

c (ves.potentials.MullerBrownPotential attribute)

CatchBondPotential2D (class in ves.potentials)

D

degree (ves.basis.LegendreBasis1D attribute) (ves.basis.LegendreBasis2DPathCV attribute) (ves.basis.LegendreBasis2DRadialCV attribute)

Delta (ves.potentials.SzaboBerezhkovskiiPotential attribute) DoubleWellPotential1D (class in ves.potentials) DoubleWellPotential2D (class in ves.potentials)

F

force (ves.bias.Bias property) (ves.bias.NNBias property) (ves.potentials.Potential1D attribute) (ves.potentials.Potential2D attribute)

forward() (ves.basis.LegendreBasis1D method) (ves.basis.LegendreBasis2DPathCV method) (ves.basis.LegendreBasis2DRadialCV method) (ves.basis.NNBasis1D method) (ves.bias.HarmonicBias_SingleParticle_1D_ForceModule method)

G

gamma_i (ves.basis.LegendreBasis2DPathCV attribute)

H

HarmonicBias_SingleParticle_1D (class in ves.bias)

HarmonicBias_SingleParticle_1D_ForceModule (class in ves.bias)

I

init_ves() (ves.langevin_dynamics.SingleParticleSimulation method)

K

k (ves.bias.HarmonicBias_SingleParticle_1D attribute) (ves.bias.HarmonicBias_SingleParticle_1D_ForceModule attribute)

kappa (ves.basis.LegendreBasis2DPathCV attribute)

L

lam (ves.basis.LegendreBasis2DPathCV attribute) layers (ves.basis.NNBasis1D attribute) legendre_polynomial() (ves.basis.LegendreBasis1D class method) (ves.basis.LegendreBasis2DPathCV class method) (ves.basis.LegendreBasis2DRadialCV class method)

LegendreBasis1D (class in ves.basis) LegendreBasis2DPathCV (class in ves.basis) LegendreBasis2DRadialCV (class in ves.basis)

M

max (ves.basis.LegendreBasis1D attribute) (ves.basis.NNBasis1D attribute) min (ves.basis.LegendreBasis1D attribute) (ves.basis.NNBasis1D attribute) model (ves.bias.NNBias attribute) model_loc (ves.bias.HarmonicBias_SingleParticle_1D attribute) (ves.bias.NNBias attribute) (ves.bias.StaticBias_SingleParticle attribute) (ves.bias.VESBias_SingleParticle_1D attribute) module ves ves.basis ves.bias ves.config_creation ves.langevin_dynamics ves.potentials ves.target ves.utils ves.visualization

MullerBrownPotential (class in ves.potentials)

N

NNBasis1D (class in ves.basis)

NNBias (class in ves.bias)

O

Omega2 (ves.potentials.SzaboBerezhkovskiiPotential attribute) omega2 (ves.potentials.SzaboBerezhkovskiiPotential attribute)

optimizer_params (ves.bias.VESBias_SingleParticle_1D attribute) optimizer_type (ves.bias.VESBias_SingleParticle_1D attribute)

P

p (ves.target.Target_x property) plot_potential() (ves.visualization.VisualizePotential1D method) (ves.visualization.VisualizePotential2D method) plot_projection_x() (ves.visualization.VisualizePotential2D method) plot_projection_y() (ves.visualization.VisualizePotential2D method) potential() (ves.potentials.CatchBondPotential2D method) (ves.potentials.DoubleWellPotential1D method) (ves.potentials.DoubleWellPotential2D method) (ves.potentials.MullerBrownPotential method) (ves.potentials.Potential1D method) (ves.potentials.Potential2D method) (ves.potentials.SingleWellPotential1D method) (ves.potentials.SingleWellPotential2D method) (ves.potentials.SlipBondPotential2D method) (ves.potentials.SzaboBerezhkovskiiPotential method)

Potential1D (class in ves.potentials) Potential2D (class in ves.potentials)

R

read_traj() (ves.utils.TrajectoryReader method)

S

s0 (ves.bias.HarmonicBias_SingleParticle_1D attribute) (ves.bias.HarmonicBias_SingleParticle_1D_ForceModule attribute) scatter_traj() (ves.visualization.VisualizePotential1D method) (ves.visualization.VisualizePotential2D method) scatter_traj_projection_x() (ves.visualization.VisualizePotential2D method) scatter_traj_projection_y() (ves.visualization.VisualizePotential2D method) singleParticle1D_init_coord() (in module ves.config_creation)

singleParticle2D_init_coord() (in module ves.config_creation) SingleParticleSimulation (class in ves.langevin_dynamics) SingleWellPotential1D (class in ves.potentials) SingleWellPotential2D (class in ves.potentials) SlipBondPotential2D (class in ves.potentials) StaticBias_SingleParticle (class in ves.bias) SzaboBerezhkovskiiPotential (class in ves.potentials)

T

target (ves.bias.VESBias_SingleParticle_1D attribute) Target_Uniform_HardSwitch_x (class in ves.target) Target_x (class in ves.target) training (ves.basis.LegendreBasis1D attribute) (ves.basis.LegendreBasis2DPathCV attribute) (ves.basis.LegendreBasis2DRadialCV attribute) (ves.basis.NNBasis1D attribute) (ves.bias.HarmonicBias_SingleParticle_1D_ForceModule attribute)

TrajectoryReader (class in ves.utils)

U

update() (ves.bias.Bias method) (ves.bias.VESBias_SingleParticle_1D method)

update_steps (ves.bias.VESBias_SingleParticle_1D attribute)

V

V_module (ves.bias.StaticBias_SingleParticle attribute) (ves.bias.VESBias_SingleParticle_1D attribute) ves module ves.basis module ves.bias module ves.config_creation module ves.langevin_dynamics module

ves.potentials module ves.target module ves.utils module ves.visualization module VESBias_SingleParticle_1D (class in ves.bias) visualize_free_energy_2D() (in module ves.visualization) VisualizePotential1D (class in ves.visualization) VisualizePotential2D (class in ves.visualization)

W

weights (ves.basis.LegendreBasis1D attribute) (ves.basis.LegendreBasis2DPathCV attribute) (ves.basis.LegendreBasis2DRadialCV attribute)

X

x (ves.target.Target_x property) x0 (ves.potentials.SzaboBerezhkovskiiPotential attribute) x_bar (ves.potentials.MullerBrownPotential attribute)

x_i (ves.basis.LegendreBasis2DPathCV attribute) x_max (ves.basis.LegendreBasis2DRadialCV attribute) x_min (ves.basis.LegendreBasis2DRadialCV attribute)

Y

y_bar (ves.potentials.MullerBrownPotential attribute) y_i (ves.basis.LegendreBasis2DPathCV attribute)

y_max (ves.basis.LegendreBasis2DRadialCV attribute) y_min (ves.basis.LegendreBasis2DRadialCV attribute)