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gmx_enfrotgrp Struct Reference
+ Collaboration diagram for gmx_enfrotgrp:

Description

Enforced rotation data for a single rotation group.

Public Attributes

const t_rotgrp * rotg = nullptr
 Input parameters for this group.
 
int groupIndex
 Index of this group within the set of groups.
 
real degangle
 Rotation angle in degrees.
 
matrix rotmat
 Rotation matrix.
 
std::unique_ptr
< gmx::LocalAtomSet
atomSet
 The atoms subject to enforced rotation.
 
rvec vec
 The normalized rotation vector.
 
real V
 Rotation potential for this rotation group.
 
rvec * f_rot_loc
 Array to store the forces on the local atoms resulting from enforced rotation potential.
 
realxc_ref_length
 Length of each x_rotref vector after x_rotref has been put into origin.
 
rvec xc_center
 Center of the rotation group positions, may be mass weighted.
 
rvec xc_ref_center
 Center of the rotation group reference positions.
 
rvec * xc
 Current (collective) positions.
 
ivec * xc_shifts
 Current (collective) shifts.
 
ivec * xc_eshifts
 Extra shifts since last DD step.
 
rvec * xc_old
 Old (collective) positions.
 
rvec * xc_norm
 Normalized form of the current positions.
 
rvec * xc_ref_sorted
 Reference positions (sorted in the same order as xc when sorted)
 
int * xc_sortind
 Where is a position found after sorting?
 
realmc
 Collective masses.
 
realmc_sorted
 Collective masses sorted.
 
real invmass
 one over the total mass of the rotation group
 
real torque_v
 Torque in the direction of rotation vector.
 
real angle_v
 Actual angle of the whole rotation group.
 
real weight_v
 Weights for angle determination.
 
rvec * xr_loc
 Local reference coords, correctly rotated.
 
rvec * x_loc_pbc
 Local current coords, correct PBC image.
 
realm_loc
 Masses of the current local atoms.
 
int nslabs_alloc
 For this many slabs memory is allocated.
 
int slab_first
 Lowermost slab for that the calculation needs to be performed at a given time step.
 
int slab_last
 Uppermost slab ...
 
int slab_first_ref
 First slab for which ref. center is stored.
 
int slab_last_ref
 Last ...
 
int slab_buffer
 Slab buffer region around reference slabs.
 
int * firstatom
 First relevant atom for a slab.
 
int * lastatom
 Last relevant atom for a slab.
 
rvec * slab_center
 Gaussian-weighted slab center.
 
rvec * slab_center_ref
 Gaussian-weighted slab center for the reference positions.
 
realslab_weights
 Sum of gaussian weights in a slab.
 
realslab_torque_v
 Torque T = r x f for each slab. torque_v = m.v = angular momentum in the direction of v.
 
real max_beta
 min_gaussian from t_rotgrp is the minimum value the gaussian must have so that the force is actually evaluated. max_beta is just another way to put it
 
realgn_atom
 Precalculated gaussians for a single atom.
 
int * gn_slabind
 Tells to which slab each precalculated gaussian belongs.
 
rvec * slab_innersumvec
 Inner sum of the flexible2 potential per slab; this is precalculated for optimization reasons.
 
gmx_slabdataslab_data
 Holds atom positions and gaussian weights of atoms belonging to a slab.
 
gmx_potfitPotAngleFit
 Used for fit type 'potential'.
 

The documentation for this struct was generated from the following file: