From 23460b79826ccd0947128fd08b3bd7af5ec81bf3 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 7 May 2015 11:59:47 +0200
Subject: [PATCH] properly describe the abort criteria in minimization
algorithms plus some typos
---
modules/mol/mm/doc/simulation.rst | 25 ++++++++++++++++---------
1 file changed, 16 insertions(+), 9 deletions(-)
diff --git a/modules/mol/mm/doc/simulation.rst b/modules/mol/mm/doc/simulation.rst
index 1366dd81e..f8e661932 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])
--
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