Cerius2 Builders

Contents

Release 4.5, June 2000
(Last full revision March 1997)

1. Introduction

Who should use this documentation

How to find information

Using other Cerius2 documentation

Additional information sources

Typographical conventions

2. Crystal Builder

Building and unbuilding crystals

Building a molecular crystal using general symmetry positions

Building a crystal from a 2D periodic model

Building an ionic crystal using space groups

Changing lattice vectors

Creating superstructures from crystals

Generating a primitive superlattice

Generating a noncrystalline superstructure

Generating a superstructure from a facetted crystal

Unbuilding a crystal

Displaying crystals

Displaying several cells

Drawing Miller planes

Displaying crystal facets

Calculating cell formula, density, and volume

Finding symmetry in a crystal

3. Surface Builder

Building and unbuilding surfaces

Cleaving a surface from a crystal

Building a surface from a nonperiodic model

Building a surface by adding atoms

Changing surface lattice vectors

Creating a surface superstructure

Unbuilding a surface

Displaying surfaces

4. Interface Builder

About the interface builder

Creating an interface

Defining the sides of the interface

Concepts and general procedure

Specifying the sides of the interface

Building the interface

Editing the interface after it is build

Creating a periodic model from an interface

Creating a crystal from an interface

Creating a surface from an interface

5. Polymer Builder

Monomer units

Specifying monomer units

Monomer files

Creating or editing monomers

Editing monomers

Using monomers created with other programs

Homopolymers

Building homopolymers

Tacticity

Monomer head/tail orientation

Torsion angles

Random copolymers

Building random copolymers

Random copolymer preferences

Reactivities

Block copolymers

Editing polymers

Monomer and polymer display

6. Amorphous Builder

How the amorphous builder works

Building amorphous structures

Building amorphous structures using the default settings

Building amorphous structures using custom settings

Cloning to create starting models

Specifying what torsions to rotate during building

Defining rotatable torsions and torsion rules

Finding unique rotatable torsions

Specifying torsion rotation methods

Entering data in the state table

Editing the state table, specifying rotation methods

Saving state table data

A. References

B. Files

State table (.ris) file

RIS file format

Example file