| Atab (defined in Step_t) | Step_t | |
| cleanup_force (defined in Step_t) | Step_t | |
| cleanup_vel (defined in Step_t) | Step_t | |
| coef (defined in Step_t) | Step_t | |
| compute (defined in Step_t) | Step_t | |
| dif_beta (defined in Step_t) | Step_t | |
| dif_p (defined in Step_t) | Step_t | |
| dif_q (defined in Step_t) | Step_t | |
| doFixedAtoms (defined in Step_t) | Step_t | |
| done (defined in Step_t) | Step_t | |
| doRigidWaters (defined in Step_t) | Step_t | |
| drudeBond (defined in Step_t) | Step_t | |
| dt_over_qmass (defined in Step_t) | Step_t | |
| dt_over_qmass_com (defined in Step_t) | Step_t | |
| dt_over_qmass_dbond (defined in Step_t) | Step_t | |
| dt_tau (defined in Step_t) | Step_t | |
| errmsg (defined in Step_t) | Step_t | |
| eta (defined in Step_t) | Step_t | |
| eta_com (defined in Step_t) | Step_t | |
| eta_dbond (defined in Step_t) | Step_t | |
| f_com (defined in Step_t) | Step_t | |
| f_dbond (defined in Step_t) | Step_t | |
| fdf (defined in Step_t) | Step_t | |
| h_mass (defined in Step_t) | Step_t | |
| half_vel (defined in Step_t) | Step_t | |
| is_drude (defined in Step_t) | Step_t | |
| mass_com (defined in Step_t) | Step_t | |
| mass_dbond (defined in Step_t) | Step_t | |
| nh_qmass (defined in Step_t) | Step_t | |
| nonPolarized (defined in Step_t) | Step_t | |
| num_com (defined in Step_t) | Step_t | |
| num_dbond (defined in Step_t) | Step_t | |
| num_drudeBond (defined in Step_t) | Step_t | |
| num_nonPolarized (defined in Step_t) | Step_t | |
| o_mass (defined in Step_t) | Step_t | |
| old_f (defined in Step_t) | Step_t | |
| orderk (defined in Step_t) | Step_t | |
| param (defined in Step_t) | Step_t | |
| pos_com (defined in Step_t) | Step_t | |
| pos_dbond (defined in Step_t) | Step_t | |
| qmass_com (defined in Step_t) | Step_t | |
| qmass_dbond (defined in Step_t) | Step_t | |
| ra (defined in Step_t) | Step_t | |
| random (defined in Step_t) | Step_t | |
| rb (defined in Step_t) | Step_t | |
| rc (defined in Step_t) | Step_t | |
| refpos (defined in Step_t) | Step_t | |
| scal_inv_mass (defined in Step_t) | Step_t | |
| scal_inv_mass_com (defined in Step_t) | Step_t | |
| scal_inv_mass_dbond (defined in Step_t) | Step_t | |
| search_direction (defined in Step_t) | Step_t | |
| sham (defined in Step_t) | Step_t | |
| starting_position (defined in Step_t) | Step_t | |
| system (defined in Step_t) | Step_t | |
| tempkonst (defined in Step_t) | Step_t | |
| tempkonst_com (defined in Step_t) | Step_t | |
| tempkonst_dbond (defined in Step_t) | Step_t | |
| twice_desired_ke (defined in Step_t) | Step_t | |
| twice_desired_ke_com (defined in Step_t) | Step_t | |
| twice_desired_ke_dbond (defined in Step_t) | Step_t | |
| twoke (defined in Step_t) | Step_t | |
| twoke_bath (defined in Step_t) | Step_t | |
| twoke_com (defined in Step_t) | Step_t | |
| twoke_dbond (defined in Step_t) | Step_t | |
| u (defined in Step_t) | Step_t | |
| vel_com (defined in Step_t) | Step_t | |
| vel_dbond (defined in Step_t) | Step_t | |
| xi (defined in Step_t) | Step_t | |
| xi_com (defined in Step_t) | Step_t | |
| xi_dbond (defined in Step_t) | Step_t |
1.3.9.1