ohmms Users' guides

Jeongnim Kim

NCSA and MCC, UIUC

Kaden Hazzard

The Ohio State University

$Revision: 1.5 $

$Date: 2004/08/22 00:06:11 $

Abstract

This document describes the input xml elements to run ohmms and derived applications. The reference pages for Free-energy Monte Carlo simulations are written by Kaden Hazzard.


Table of Contents

1. Proposal for ohmms DTD (schema)
Introduction
Basic elements: parameter and attrib
Common attribute names
2. Changes from previous schema
Summary of the changes
Transformations of old xml files
I. Reference Pages for ohmms dtd/schema
acceptor - Decides whether or not to accept a proposed particle configuration change.
application - A description of an application used to perform a simulation
atom - A generic atomic data-type.
attrib - An attribute of a particle set.
ensemble - A method to propagate a particle set.
filename - A file.
freemc - Executes a simulation of free energies using the Wang-Landau method
group - A generic group of one datatype or one kind.
keyword - keywords to classify the project.
kpoint - A description of k-points for quantum Hamiltonians.
loop - A description of how to move a particle set.
mcupdate - Attempts particle configuration moves until one is accepted.
mdsim - An execution thread of a simulation
nebsim - An execution of Nudged-Elastic-Band simulations
neb - A set of controlling parameters for NEB.
parameter - A generic parameter of a simple type.
particlelayout - A description of a particle layout.
particleset - A set of particles with/without a unitcell.
particlesets - A list of any number of particle sets.
potential - A model Hamiltonian.
process - An execution thread of a simulation
project - A description of a simulation or a process of a simulation
random - A description of the random number generator(s)
record - A description of how to report the calculations.
simulation - A start of a simulation
stepper - Generates candidate particle configuration changes by displacing atoms.
summary - A description of a simulation
transform - A transformation on a particle set.
unitcell - A unitcell definition.

List of Figures

1.1. UML diagram representing simulation element
1.2. UML diagram representing process element

List of Tables

1.1. Common attribute names and general meanings
2.1. Changes excluding those due to the upper/lower case changes
3. Transformations on the particle sets

List of Examples

1. Using atom element in particleset.
2. Usage of filename
3. Using group element in particleset.
4. Generation of MP mesh
5. A list of k-points and weights
6. A list of k-points and weights II
7. How to set up k-points for a band structure calculation