diff --git a/modules/mol/mm/doc/simulation.rst b/modules/mol/mm/doc/simulation.rst index 1366dd81e110c2b8c6f5d6a81f784df1335d6e3b..f8e661932e721b4bce6f20cc0aa9bb0bedbcf12d 100644 --- a/modules/mol/mm/doc/simulation.rst +++ b/modules/mol/mm/doc/simulation.rst @@ -63,7 +63,7 @@ mapped back to the attached structure at any time. .. method:: Load(filename) Loads a dumped simulation from disk. You have to make sure, that the provided - settings are consistent with those from the saved simualtion. Undefined + settings are consistent with those from the saved simulation. Undefined behaviour must be expected otherwise. :param filename: Filename @@ -74,31 +74,38 @@ mapped back to the attached structure at any time. .. method:: ApplyLBFGS([tolerance=1.0,max_iterations=1000]) - Run minimization using the Limited-memory Broyden–Fletcher–Goldfarb–Shanno (L-BFGS) method. + Run minimization using the Limited-memory Broyden–Fletcher–Goldfarb–Shanno + (L-BFGS) method. - :param tolerance: Tolerance descrining abort criteria of minimization - :param max_iterations: Maximum number of minimization iterations + :param tolerance: Tolerance describing abort criteria of minimization. + The tolerance is interpreted as the root mean square + value of all force components. + :param max_iterations: Maximum number of minimization iterations :type tolerance: :class:`float` :type max_iterations: :class:`int` - .. method:: ApplySD(tolerance,max_iterations) + .. method:: ApplySD([tolerance=100,max_iterations=1000]) - Run minimization using the Steepest-Descend method. + Run minimization using the steepest descend method. - :param tolerance: Tolerance descrining abort criteria of minimization + :param tolerance: Tolerance describing abort criteria of minimization. + The tolerance is interpreted as the norm of the maximum + force acting onto the particles. :param max_iterations: Maximum number of minimization iterations :type tolerance: :class:`float` :type max_iterations: :class:`int` + :returns: :class:`bool` whether tolerance has been reached + .. method:: Steps(steps) Runs the simulation for **steps** number of steps. - :param steps: Number of steps - :types: :class:`int` + :param steps: Number of steps to perform + :type steps: :class:`int` .. method:: GetPositions([enforce_periodic_box = false, in_angstrom = true])