Container of atom group data (allow collection of aggregated atomic data) More...
#include <colvarproxy.h>
Inheritance diagram for colvarproxy_atom_groups:
Public Member Functions | |
| colvarproxy_atom_groups () | |
| Constructor. | |
| virtual | ~colvarproxy_atom_groups () |
| Destructor. | |
| int | reset () |
| Clear atom group data. | |
| virtual int | scalable_group_coms () |
| Whether this proxy implementation has capability for scalable groups. More... | |
| virtual int | init_atom_group (std::vector< int > const &atoms_ids) |
| Prepare this group for collective variables calculation, selecting atoms by internal ids (0-based) More... | |
| virtual void | clear_atom_group (int index) |
| Used by the atom_group class destructor. More... | |
| int | get_atom_group_id (int index) const |
| Get the numeric ID of the given atom group (for the MD program) | |
| cvm::real | get_atom_group_mass (int index) const |
| Get the mass of the given atom group. | |
| cvm::real | get_atom_group_charge (int index) const |
| Get the charge of the given atom group. | |
| cvm::rvector | get_atom_group_com (int index) const |
| Read the current position of the center of mass given atom group. | |
| cvm::rvector | get_atom_group_total_force (int index) const |
| Read the current total force of the given atom group. | |
| void | apply_atom_group_force (int index, cvm::rvector const &new_force) |
| Request that this force is applied to the given atom group. | |
| cvm::rvector | get_atom_group_velocity (int) |
| Read the current velocity of the given atom group. | |
| std::vector< int > const * | get_atom_group_ids () const |
| size_t | get_num_active_atom_groups () const |
| Return number of atom groups with positive reference count. | |
| std::vector< cvm::real > * | modify_atom_group_masses () |
| std::vector< cvm::real > * | modify_atom_group_charges () |
| std::vector< cvm::rvector > * | modify_atom_group_positions () |
| std::vector< cvm::rvector > * | modify_atom_group_total_forces () |
| std::vector< cvm::rvector > * | modify_atom_group_applied_forces () |
| void | compute_rms_atom_groups_applied_force () |
| Compute the root-mean-square of the applied forces. | |
| void | compute_max_atom_groups_applied_force () |
| Compute the maximum norm among all applied forces. | |
| cvm::real | rms_atom_groups_applied_force () const |
| Get the root-mean-square of the applied forces. | |
| cvm::real | max_atom_groups_applied_force () const |
| Get the maximum norm among all applied forces. | |
Protected Member Functions | |
| int | add_atom_group_slot (int atom_group_id) |
| Used by all init_atom_group() functions: create a slot for an atom group not requested yet. | |
Protected Attributes | |
| std::vector< int > | atom_groups_ids |
| Array of 0-based integers used to uniquely associate atom groups within the host program. | |
| std::vector< size_t > | atom_groups_refcount |
| Keep track of how many times each group is used by a separate cvc. | |
| std::vector< cvm::real > | atom_groups_masses |
| Total masses of the atom groups. | |
| std::vector< cvm::real > | atom_groups_charges |
| Total charges of the atom groups (allow redefinition during a run, as done e.g. in LAMMPS) | |
| std::vector< cvm::rvector > | atom_groups_coms |
| Current centers of mass of the atom groups. | |
| std::vector< cvm::rvector > | atom_groups_total_forces |
| Most recently updated total forces on the com of each group. | |
| std::vector< cvm::rvector > | atom_groups_new_colvar_forces |
| Forces applied from colvars, to be communicated to the MD integrator. | |
| cvm::real | atom_groups_rms_applied_force_ |
| Root-mean-square of the applied group forces. | |
| cvm::real | atom_groups_max_applied_force_ |
| Maximum norm among all applied group forces. | |
Detailed Description
Container of atom group data (allow collection of aggregated atomic data)
Member Function Documentation
◆ clear_atom_group()
|
virtual |
Used by the atom_group class destructor.
Reimplemented in colvarproxy_namd.
◆ init_atom_group()
|
virtual |
Prepare this group for collective variables calculation, selecting atoms by internal ids (0-based)
Reimplemented in colvarproxy_namd.
◆ scalable_group_coms()
|
virtual |
Whether this proxy implementation has capability for scalable groups.
Reimplemented in colvarproxy_namd.
The documentation for this class was generated from the following files:
- colvarproxy.h
- colvarproxy.cpp
