Yammp Shell
Introduction

Yammp Shell (ysh) commands are usually saved as text files and redirected to the standard input of mimesis. In the following, shell commands are set in teletype font; variables are italized; choices are separated by |, preset or default values are set in bold type and ellipses ... indicate more of the previous object. Text between # and the end of the line are ignored.

Words can be abbreviated to no fewer than four characters provided there is no ambiguity in doing so. Command words are case-sensitive. Commands cannot be split (they must be written complete in one line) and each line may contain only one command. The entire script is translated first and if there are no syntax errors the assembled commands are then executed. Ysh is not an interactive command language, interpretation of the script stops at the first syntax error and mimesis is stopped. Nevertheless, there are a couple of interactive commands; these are for programming support.


Simple Commands
Modify the Molecular Environment
Modify the Linesearch Methods for Energy Minimization
Modify the Energy Minimization Methods
Modify the Molecular Dynamics Methods
Modify the Monte Carlo Methods
Modify the Non-Bond Terms During a Simulation
Modify Bond Constraints for Molecular Dynamics
Modify the CONTRA-MD Method
Defining and Invoking Macros
Control Structures
Examples

 


des format
arc format
yammp shell
exam commands
intro
arc
arcedit
arctransform
checkspider
des
elec2vlat

exam
mimesis
mkchainarc
mkchaindes
mkd3c
mkd3d
mkr2cc
mksnac
mksnad
xmd3
xmr2
ympf

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