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2025-dev-20241003-bd59e46
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Gromacs
2025-dev-20241003-bd59e46
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Collaboration diagram for gmx_enfrotgrp: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'. | |
1.8.5