Index

_

__init__() (trimem.core.BondParams method) (trimem.core.BondType method) (trimem.core.ContinuationParams method) (trimem.core.EnergyManager method) (trimem.core.EnergyParams method) (trimem.core.HalfedgeHandle method) (trimem.core.NeighbourList method) (trimem.core.Point method) (trimem.core.SurfaceRepulsionParams method) (trimem.core.TriMesh method) (trimem.core.VertexProperties method)

A

a0 (trimem.core.BondParams property) area (trimem.core.VertexProperties property)

area() (in module trimem.core) area_frac (trimem.core.EnergyParams property) avg_tri_props() (in module trimem.core)

B

bending (trimem.core.VertexProperties property) bond_params (trimem.core.EnergyParams property)

BondParams (class in trimem.core) BondType (class in trimem.core)

C

callback() (trimem.mc.evaluators.EnergyEvaluators method) (trimem.mc.evaluators.TimingEnergyEvaluators method) CheckpointReader (class in trimem.mc.output.checkpoint) CheckpointWriter (class in trimem.mc.output.checkpoint) cli() (in module trimem.mc.app) config() (in module trimem.mc.app)

config_to_params() (in module trimem.mc.config) continuation_params (trimem.core.EnergyParams property) ContinuationParams (class in trimem.core) copy() (trimem.mc.mesh.Mesh method) create_backup() (in module trimem.mc.output.util) curvature (trimem.core.VertexProperties property) curvature_frac (trimem.core.EnergyParams property)

D

delta (trimem.core.ContinuationParams property) dihedral_angle() (in module trimem.core)

dihedral_angle_grad() (in module trimem.core) distance_matrix() (trimem.core.NeighbourList method)

E

edge_length() (in module trimem.core) edge_length_grad() (in module trimem.core) edges_length() (in module trimem.core) energy() (trimem.core.EnergyManager method)

EnergyEvaluators (class in trimem.mc.evaluators) EnergyManager (class in trimem.core) EnergyParams (class in trimem.core) eparams (trimem.core.EnergyManager property) exclusion_level (trimem.core.SurfaceRepulsionParams property)

F

f (trimem.mc.mesh.Mesh property) face_area() (in module trimem.core) face_area_grad() (in module trimem.core) face_volume() (in module trimem.core)

face_volume_grad() (in module trimem.core) flip() (in module trimem.core) fun() (trimem.mc.evaluators.EnergyEvaluators method) fv_indices() (trimem.core.TriMesh method)

G

get_step_counters() (in module trimem.mc.hmc) grad() (trimem.mc.evaluators.EnergyEvaluators method)

gradient() (in module trimem.core) (trimem.core.EnergyManager method)

H

halfedge_handle() (trimem.core.TriMesh method)

HalfedgeHandle (class in trimem.core) HMC (class in trimem.mc.hmc)

I

info() (trimem.mc.hmc.HMC method) (trimem.mc.hmc.MeshFlips method)

initial_props (trimem.core.EnergyManager property)

K

kappa_a (trimem.core.EnergyParams property) kappa_b (trimem.core.EnergyParams property) kappa_c (trimem.core.EnergyParams property)

kappa_r (trimem.core.EnergyParams property) kappa_t (trimem.core.EnergyParams property) kappa_v (trimem.core.EnergyParams property)

L

lam (trimem.core.ContinuationParams property) lc0 (trimem.core.BondParams property)

lc1 (trimem.core.BondParams property) (trimem.core.SurfaceRepulsionParams property)

M

make_nlist() (in module trimem.core) make_output() (in module trimem.mc.output.util) Mesh (class in trimem.mc.mesh) MeshFlips (class in trimem.mc.hmc) MeshHMC (class in trimem.mc.hmc) MeshMonteCarlo (class in trimem.mc.hmc) module trimem trimem.core trimem.mc trimem.mc.app trimem.mc.config trimem.mc.evaluators trimem.mc.hmc trimem.mc.mesh trimem.mc.output trimem.mc.output.checkpoint trimem.mc.output.util trimem.mc.output.vtu trimem.mc.output.xdmf trimem.mc.output.xyz trimem.mc.util

N

n_edges() (trimem.core.TriMesh method) n_search (trimem.core.SurfaceRepulsionParams property)

n_vertices() (trimem.core.TriMesh method) NeighbourList (class in trimem.core) next_halfedge_handle() (trimem.core.TriMesh method)

O

opposite_halfedge_handle() (trimem.core.TriMesh method)

P

pflip() (in module trimem.core) Point (class in trimem.core) point_distances() (trimem.core.NeighbourList method)

points() (trimem.core.TriMesh method) print_config() (in module trimem.mc.config) print_info() (trimem.core.EnergyManager method) properties() (trimem.core.EnergyManager method)

R

r (trimem.core.BondParams property) (trimem.core.SurfaceRepulsionParams property) read() (trimem.mc.output.checkpoint.CheckpointReader method) read_checkpoint() (in module trimem.mc.util) read_config() (in module trimem.mc.config) read_mesh() (in module trimem.core) read_trimesh() (in module trimem.mc.mesh) repulse_params (trimem.core.EnergyParams property)

repulsion (trimem.core.VertexProperties property) rlist (trimem.core.SurfaceRepulsionParams property) run() (in module trimem.mc.app) (in module trimem.mc.util) (trimem.mc.hmc.HMC method) (trimem.mc.hmc.MeshFlips method) (trimem.mc.hmc.MeshMonteCarlo method) run_mc() (in module trimem.mc.util) run_minim() (in module trimem.mc.util)

S

setup_energy_manager() (in module trimem.mc.util) step() (trimem.mc.hmc.HMC method) (trimem.mc.hmc.MeshFlips method) (trimem.mc.hmc.MeshHMC method) (trimem.mc.hmc.MeshMonteCarlo method)

SurfaceRepulsionParams (class in trimem.core)

T

tethering (trimem.core.VertexProperties property) TimingEnergyEvaluators (class in trimem.mc.evaluators) trimem module trimem.core module trimem.mc module trimem.mc.app module trimem.mc.config module trimem.mc.evaluators module trimem.mc.hmc module trimem.mc.mesh module

trimem.mc.output module trimem.mc.output.checkpoint module trimem.mc.output.util module trimem.mc.output.vtu module trimem.mc.output.xdmf module trimem.mc.output.xyz module trimem.mc.util module TriMesh (class in trimem.core) type (trimem.core.BondParams property)

U

update_config_defaults() (in module trimem.mc.config)

update_reference_properties() (trimem.core.EnergyManager method) update_repulsion() (trimem.core.EnergyManager method)

V

VertexProperties (class in trimem.core) volume (trimem.core.VertexProperties property)

volume_frac (trimem.core.EnergyParams property) VtuWriter (class in trimem.mc.output.vtu)

W

write() (trimem.mc.output.checkpoint.CheckpointWriter method) write_checkpoint_handle() (in module trimem.mc.util) write_default_config() (in module trimem.mc.config)

write_points_cells() (trimem.mc.output.vtu.VtuWriter method) (trimem.mc.output.xdmf.XdmfWriter method) (trimem.mc.output.xyz.XyzWriter method)

X

x (trimem.mc.mesh.Mesh property)

XdmfWriter (class in trimem.mc.output.xdmf) XyzWriter (class in trimem.mc.output.xyz)