By Martin J. Field
This publication is aa-ight. it's extra approximately find out how to use their library for molecular simulation than it's approximately writing your individual from scratch. however it has a couple of reliable insights. total, it is a strong one for the gathering of molecular simulation books if that is your factor. :)
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Additional info for A Practical Introduction to the Simulation of Molecular Systems
2 with different values of the safety factor. In the second part (lines 26–61), the connectivity for the molecule is generated with a ‘reasonable’ value of the safety factor and the values of the internal coordinates printed out. Lines 6–7 create molecule whose connectivity is to be analysed. Line 10 defines a table to which the results of the first part of the program will be output. In the pDynamo library, the Python print keyword is never used directly. Instead all output is handled through instances of subclasses of the class LogFileWriter.
There are several alternative coordinate systems that can be used to define the atom positions. For the most part in this book, Cartesian coordinates are employed. These give the absolute position of an atom in three-dimensional space in terms of its x, y and z coordinates. Other schemes include crystallographic coordinates in which the atom positions are given in a coordinate system that is based upon the crystallographic symmetry of the system and internal coordinates that define the position of an atom by its position relative to a number of other atoms (usually three).
Method Center Determine a centre for the coordinates. Center ( ) is the instance of Coordinates3 for which the centre is to be calculated. is an instance of the class Vector3 that contains the coordinates of the centre. 44 Coordinates and coordinate manipulations Method InertiaMatrix Determine the inertia matrix for the coordinates. InertiaMatrix ( ) is an instance of Coordinates3. is an instance of the class Matrix33 that contains the matrix of inertia. Method Rotate Rotate the coordinates given a rotation matrix.