Gromacs
2024.4
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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. | |
real * | xc_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. | |
std::vector< gmx::RVec > | referencePositions |
Rotation group reference positions, perhaps centered. | |
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? | |
real * | mc |
Collective masses. | |
real * | mc_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. | |
real * | m_loc |
Masses of the current local atoms. | |
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. | |
real * | slab_weights |
Sum of gaussian weights in a slab. | |
real * | slab_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 | |
real * | gn_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_slabdata * | slab_data |
Holds atom positions and gaussian weights of atoms belonging to a slab. | |
gmx_potfit * | PotAngleFit |
Used for fit type 'potential'. | |