geometricmd.curve_shorten.
compute_metric
(points, metric_function)[source]¶Takes a list of NumPy arrays describing points molecular configurations, evaluates the metric at each point and returns a list of metric values at those points.
Parameters: 


Returns:  A list of metric values at the corresponding points. 
Return type:  list 
geometricmd.curve_shorten.
compute_trajectory
(trajectory, local_num_nodes, energy, tol, filename, configuration, length_function=<function length>)[source]¶This function updates the trajectory object positions to represent the shortest curve.
Parameters: 


geometricmd.curve_shorten.
find_geodesic_midpoint
(start_point, end_point, number_of_inner_points, dimension, mass_matrix, molecule, energy, node_number, length_function)[source]¶This function computes the local geodesic curve joining start_point to end_point using the LBFGS method.
Parameters: 


Returns:  The node number for which the returned midpoint corresponds to. numpy.array :

Return type:  int 
geometricmd.curve_shorten.
generate_points
(x, start_point, end_point, rotation_matrix, total_number_of_points, co_dimension)[source]¶This function computes the local geodesic curve joining start_point to end_point using the LBFGS method.
Parameters: 


Returns:  The midpoint along the approximate local geodesic curve. 
Return type:  numpy.array 
geometricmd.curve_shorten.
get_rotation
(start_point, end_point, dimension)[source]¶Parameters: 


Returns:  The matrix representing the linear transformation from dimension dimensional space to the tangent space of the line joining start_point to end_point. 
Return type:  numpy.array 
geometricmd.curve_shorten.
length
(x, start_point, end_point, mass_matrix, rotation_matrix, total_number_of_points, co_dimension, metric)[source]¶This function computes the length of the local geodesic as a function of shifts from the line joining start_point to end_point. It also returns the gradient of this function for the LBFGS method.
Parameters: 


Returns:  The approximate length of the geodesic. numpy.array :

Return type:  float 
geometricmd.curve_shorten.
norm
(x, matrix)[source]¶Computes the value of sqrt(<x, matrix*x>).
Parameters: 


Returns:  The value of sqrt(<x, matrix*x>). 
Return type:  float 
geometricmd.curve_shorten.
norm_gradient
(x, matrix)[source]¶Computes the gradient of sqrt(<x, matrix*x>).
Parameters: 


Returns:  The gradient of sqrt(<x, matrix*x>). 
Return type:  numpy.array 