This is the technical documentation for features of Yup that an end-user is less likely to need or use. For example, the writing of a force field assembly module is not something that is done every day.

INTRODUCTION

Introduction: Introduction to the advanced features. Most users will not need to modify files directly, but if you do, you better read up on the format. YUP is also driven by a graphical interface but advanced features are accessible only through scripting. The scripting language is Python.

EXTENSIONS

Directory: Atoms can be organized into groups that can be further organized into more groups. Atoms (and Groups) can be organized in any hierarchy, can be added, modified and deleted. These pages describe the AtomMap module which implements a mapping type called AtomMap.
Vectors: Vectors and Arrays are required in many places. These pages describe the AtomVector type which is implemented as a Numeric and Mapping Type.
Energy: Detailed look at the individual terms of the potential energy function. The energy modules are bundled into a Potential object.
Model: A molecular model is represented by a Model object which is a bundle of AtomMaps, AtomVectors and Potential objects.

CREATE

Assembly: A force field assembly module defines methods to prepare and analyze a specific class of molecular model. This section explains how to write a force field assembler as well as how to use the sample assembler.

SIMULATE

Methods: The molecular mechanics methods available in the Taro and Yammp modules. This is the heart of YUP, where actual work gets done.

FILES

FPF: The Force Parameter (fp) file defines the names of Atom Inclusion and Exclusion Types and the force constants for each term of the force field.
AVF: The Atom Vector (av) file contains a name map and any number of atom vectors (coordinates, velocities, gradients, etc).
SWCH: The Swiss Cheese file

FFF: The Force Field (ff) file contains the definition of an assembled force field. The Taro module does not make use of a ff file but you can save the results of a force field assembly to a ff file. The ff file is an essential input file to the Yammp module where there is no force field assembly capability.

SCRIPTING

TaroScript: The taro module can be finely controlled with a script because of the low-level integration with the scripting language. Scripting can be avoided if you use the graphical user interface.
YammpScript: The yammp module is integrated with Python at a very high level so scripting is much more limited. Scripting can be avoided if you use the graphical script builder.

MISCELLANEOUS

Python: is the scripting (and programming) language for all modules. Tutorial and pointers to Python resources.
Utilities: The YUP Toolbox. There may already be a solution to your problem.

The links above will bring you to sub-sections of the technical documentation. In addition to the standard links to other sections, there will be links to sub-sections.