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| colvarproxy_system () |
| | Constructor.
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virtual | ~colvarproxy_system () |
| | Destructor.
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| virtual int | set_unit_system (std::string const &units, bool check_only) |
| | Request to set the units used internally by Colvars. More...
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cvm::real | angstrom_to_internal (cvm::real l) const |
| | Convert a length from Angstrom to internal.
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cvm::real | internal_to_angstrom (cvm::real l) const |
| | Convert a length from internal to Angstrom.
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cvm::real | boltzmann () const |
| | Boltzmann constant, with unit the same as energy / K.
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cvm::real | target_temperature () const |
| | Current target temperature of the simulation (K units)
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virtual int | set_target_temperature (cvm::real T) |
| | Set the current target temperature of the simulation (K units)
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double | dt () const |
| | Time step of the simulation (fs units)
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virtual int | set_integration_timestep (cvm::real dt) |
| | Set the current integration timestep of the simulation (fs units)
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| virtual cvm::real | rand_gaussian (void) |
| | Pseudo-random number with Gaussian distribution. More...
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| virtual void | add_energy (cvm::real energy) |
| | Pass restraint energy value for current timestep to MD engine. More...
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| virtual cvm::rvector | position_distance (cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) const |
| | Get the PBC-aware distance vector between two positions. More...
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void | update_pbc_lattice () |
| | Recompute PBC reciprocal lattice (assumes XYZ periodicity)
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void | reset_pbc_lattice () |
| | Set the lattice vectors to zero.
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| virtual void | request_total_force (bool yesno) |
| | Tell the proxy whether total forces are needed (they may not always be available) More...
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| virtual bool | total_forces_enabled () const |
| | Are total forces being used? More...
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| virtual bool | total_forces_same_step () const |
| | Are total forces from the current step available? More...
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| virtual int | get_molid (int &molid) |
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| virtual int | get_alch_lambda (cvm::real *lambda) |
| | Get value of alchemical lambda parameter from back-end (if available) More...
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void | set_alch_lambda (cvm::real lambda) |
| | Set value of alchemical lambda parameter to be sent to back-end at end of timestep.
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| virtual int | send_alch_lambda () |
| | Send cached value of alchemical lambda parameter to back-end (if available) More...
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| virtual int | get_dE_dlambda (cvm::real *dE_dlambda) |
| | Get energy derivative with respect to lambda (if available) More...
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virtual int | apply_force_dE_dlambda (cvm::real *force) |
| | Apply a scalar force on dE_dlambda (back-end distributes it onto atoms)
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virtual int | get_d2E_dlambda2 (cvm::real *d2E_dlambda2) |
| | Get energy second derivative with respect to lambda (if available)
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| virtual cvm::real | get_accelMD_factor () const |
| | Get weight factor from accelMD. More...
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virtual bool | accelMD_enabled () const |
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std::string | units |
| | Name of the unit system used internally by Colvars (by default, that of the back-end). Supported depending on the back-end: real (A, kcal/mol), metal (A, eV), electron (Bohr, Hartree), gromacs (nm, kJ/mol) Note: calls to back-end PBC functions assume back-end length unit We use different unit from back-end in VMD bc using PBC functions from colvarproxy base class Colvars internal units are user specified, because the module exchanges info in unknown composite dimensions with user input, while it only exchanges quantities of known dimension with the back-end (length and forces)
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cvm::real | indirect_lambda_biasing_force |
| | Force to be applied onto alch. lambda, propagated from biasing forces on dE_dlambda.
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cvm::real | cached_alch_lambda |
| | Next value of lambda to be sent to back-end.
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bool | cached_alch_lambda_changed |
| | Whether lambda has been set and needs to be updated in backend.
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cvm::real | boltzmann_ |
| | Boltzmann constant in internal Colvars units.
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cvm::real | target_temperature_ |
| | Most up to date target temperature (K units); default to 0.0 if undefined.
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double | timestep_ |
| | Current integration timestep (engine units); default to 1.0 if undefined.
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| cvm::real | angstrom_value_ |
| | Value of 1 Angstrom in the internal (front-end) Colvars unit for atomic coordinates. More...
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cvm::real | kcal_mol_value_ |
| | Value of 1 kcal/mol in the internal Colvars unit for energy.
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bool | total_force_requested |
| | Whether the total forces have been requested.
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Boundaries_type | boundaries_type |
| | Type of boundary conditions.
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cvm::rvector | unit_cell_x |
| | Bravais lattice vectors.
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cvm::rvector | unit_cell_y |
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cvm::rvector | unit_cell_z |
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cvm::rvector | reciprocal_cell_x |
| | Reciprocal lattice vectors.
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cvm::rvector | reciprocal_cell_y |
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cvm::rvector | reciprocal_cell_z |
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Methods for accessing the simulation system (PBCs, integrator, etc)
