USPEX 10.6 manual
1
Features, aims and history of USPEX
▶
1.1
Overview
1.2
Features of USPEX
1.3
Key USPEX papers
1.4
Version history
2
Getting started
▶
2.1
How to obtain USPEX
2.2
Necessary citations
2.3
Bug reports
2.4
On which machines USPEX can be run
2.5
Codes that can work with USPEX
2.6
How to install USPEX
2.7
How to run USPEX
2.8
Running USPEX examples: a mini-tutorial
3
Overview of input and output files
▶
3.1
Input files
3.2
Output files
4
Input options. The
INPUT.txt
file
▶
4.1
Type of calculation and system specification
4.2
Population
4.3
Survival of the fittest and selection
4.4
Structure generation and variation operators
4.5
Constraints
4.6
Cell
4.7
Restart
4.8
Details of
ab initio
calculations
4.9
Fingerprint settings
4.10
Antiseed settings
4.11
Space group determination
4.12
Keywords for developers
4.13
Seldom used keywords
5
Additional input for special cases
▼
5.1
Variable-composition seraches: predicting novel compunds and their structures
5.2
Optimization of thermoelectric properties
5.3
Defining Arbitrary Properties as Fitness Functions in USPEX
5.4
Interfacing USPEX with Arbitrary External Codes (DFT / MD / ML Engines)
5.5
Activating the Database Structure Importer
5.6
Molecular crystals and polymers
5.7
Surfaces
5.8
Two dimensional (2D) crystals
5.9
Clusters
5.10
Evolutionary metadynamics code
5.11
Particle swarm optimization (PSO) code
6
Prediction of phase transition pathways
▶
6.1
Pmapaths: geometric method for predicting solid-solid phase transition mechanisms
6.2
Variable-cell nudged elastic band (VCNEB) method
6.3
Transition path sampling (TPS) method
7
Online utilities
▶
7.1
Structure characterization
7.2
Properties calculations
7.3
Molecular crystals
7.4
Surfaces
7.5
Miscellaneous
8
Frequently asked questions
▶
8.1
How can I visualize the results?
8.2
How can I avoid trapping?
8.3
What is a single-block calculation?
8.4
How to predict structures based on known fragments?
8.5
How do I use the seed technique?
8.6
How do I play with the compositions?
8.7
How do I set up a passwordless connection from a local machine to a remote cluster?
8.8
How do I set up a calculation using a job submission script?
9
Appendices
▶
9.1
List of Examples
9.2
Test runs
9.3
Sample
INPUT.txt
files
9.4
List of space groups
9.5
List of layer groups
9.6
List of plane groups
9.7
List of point groups
9.8
Table of univalent covalent radii used in USPEX
9.9
Table of default chemical
valences
used in USPEX
9.10
Table of default
goodBonds
used in USPEX
10
Bibliography
5 Additional input for special cases