cct.gamess
Class Gamess

java.lang.Object
  cct.gamess.Gamess

public class Gamess
extends java.lang.Object

Title:

Description:

Copyright: Copyright (c) 2006

Company: ANU

Field Summary

(package private) java.util.ArrayList<GamessAtom>	atoms
(package private) int	AxisOrder
(package private) java.util.HashMap	basisGroup
(package private) static java.lang.String	basisSection
(package private) static java.util.HashMap<java.lang.String,GamessSwitch>	basisSwitches
(package private) static int	CART
(package private) static java.lang.String	cidetSection
(package private) static java.lang.String	cidrtSection
(package private) static java.lang.String	ciinpSection
(package private) static java.lang.String	cisortSection
(package private) static java.lang.String	commentSection
(package private) static java.lang.String	controlSection
(package private) static java.util.HashMap<java.lang.String,GamessSwitch>	controlSwitches
(package private) static java.lang.String	cphfSection
(package private) java.util.HashMap<java.lang.String,java.util.HashMap>	currentVars
(package private) static java.lang.String	dataSection
(package private) static float	DEGREES_TO_RADIANS
(package private) static java.lang.String	detSection
(package private) static java.lang.String	dipdrSection
(package private) static java.lang.String	disbsSection
(package private) static java.lang.String	disrepSection
(package private) static java.lang.String	drcSection
(package private) static java.lang.String	drtSection
(package private) static java.lang.String	ecpSection
(package private) static java.lang.String	efieldSection
(package private) static java.lang.String	efragSection
(package private) static java.lang.String	eldensSection
(package private) static java.lang.String	elfldgSection
(package private) static java.lang.String	elmonSection
(package private) static java.lang.String	elpotSection
(package private) static java.lang.String	endSection
(package private) static java.lang.String	ffcalcSection
(package private) static java.lang.String	fgrrplSection
(package private) static java.lang.String	forceSection
(package private) static java.lang.String	fragnameSection
(package private) static java.lang.String	gradSection
(package private) static java.lang.String	gridSection
(package private) static java.lang.String	guessSection
(package private) static java.lang.String	gugdiaSection
(package private) static java.lang.String	gugdm2Section
(package private) static java.lang.String	gugdmSection
(package private) static java.lang.String	gugemSection
(package private) static java.lang.String	hessSection
(package private) static int	HINT
(package private) static java.lang.String	intgrlSection
(package private) static java.lang.String	ircSection
(package private) static java.lang.String	lagranSection
(package private) static java.lang.String	libeSection
(package private) static java.lang.String	localSection
(package private) static int	LOOKING_FOR_SECTION
(package private) static int	LOOKING_FOR_SWITCH
(package private) static int	LOOKING_FOR_SWITCH_VALUE
(package private) static java.lang.String	massSection
(package private) static java.lang.String	mcqdptSection
(package private) static java.lang.String	mcscfSection
(package private) static java.lang.String	molgrfSection
(package private) static java.lang.String	morokmSection
(package private) static java.lang.String	mp2Section
(package private) static java.lang.String	newcavSection
(package private) static double	ONE_BOHR
(package private) static java.lang.String	pcmcavSection
(package private) static java.lang.String	pcmSection
(package private) static java.lang.String	pdcSection
(package private) static java.lang.String	pointsSection
(package private) static int	READING_COMMENT
(package private) static java.lang.String	scfmiSection
(package private) static java.lang.String	scfSection
(package private) static java.lang.String	scrfSection
(package private) static java.util.HashMap<java.lang.String,java.util.HashMap>	sectionVarsReference
(package private) static java.lang.String	statptSection
(package private) static java.lang.String	stoneSection
(package private) static java.lang.String	surfSection
(package private) java.lang.String	SymmetrySymbol
(package private) static java.lang.String	systemSection
(package private) static java.util.HashMap<java.lang.String,GamessSwitch>	systemSwitches
(package private) static java.lang.String	tdhfSection
(package private) java.lang.String	Title
(package private) static java.lang.String	transSection
(package private) static java.lang.String	transtSection
(package private) static java.lang.String	trfdm2Section
(package private) static java.lang.String	trudgeSection
(package private) static java.lang.String	trurstSection
(package private) static java.lang.String	twoeiSection
(package private) static int	UNIQUE
(package private) static java.util.HashSet	validSections
(package private) static java.util.HashSet	validSymmetrySymbols
(package private) static java.lang.String	vecSection
(package private) static java.lang.String	vibSection
(package private) static java.lang.String	zmatSection
(package private) static int	ZMT
(package private) static int	ZMTMPC

Constructor Summary

Gamess()

Method Summary

void	applySymmetry(java.lang.String symbol, int axisOrder, java.util.ArrayList<GamessAtom> points)
static void	fromZMatrixToCartesians(java.util.ArrayList<GamessAtom> atoms) Expects bond length in angstroms
static int	getAtomicNumber(java.lang.String symbol)
java.util.HashMap	getControlSection()
void	getMolecularInterface(MoleculeInterface molec)
static void	main(java.lang.String[] args)
void	parseGamessInput(java.lang.String inputfile)
void	parseGamessInput(java.lang.String inputfile, int fileType)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ONE_BOHR

static final double ONE_BOHR

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Constant Field Values

DEGREES_TO_RADIANS

static final float DEGREES_TO_RADIANS

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Constant Field Values

LOOKING_FOR_SECTION

static final int LOOKING_FOR_SECTION

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Constant Field Values

LOOKING_FOR_SWITCH

static final int LOOKING_FOR_SWITCH

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Constant Field Values

LOOKING_FOR_SWITCH_VALUE

static final int LOOKING_FOR_SWITCH_VALUE

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Constant Field Values

READING_COMMENT

static final int READING_COMMENT

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Constant Field Values

endSection

static final java.lang.String endSection

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Constant Field Values

commentSection

static final java.lang.String commentSection

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Constant Field Values

UNIQUE

static final int UNIQUE

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Constant Field Values

HINT

static final int HINT

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Constant Field Values

CART

static final int CART

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Constant Field Values

ZMT

static final int ZMT

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Constant Field Values

ZMTMPC

static final int ZMTMPC

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Constant Field Values

controlSection

static final java.lang.String controlSection

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Constant Field Values

systemSection

static final java.lang.String systemSection

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Constant Field Values

basisSection

static final java.lang.String basisSection

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Constant Field Values

dataSection

static final java.lang.String dataSection

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Constant Field Values

zmatSection

static final java.lang.String zmatSection

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Constant Field Values

libeSection

static final java.lang.String libeSection

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Constant Field Values

scfSection

static final java.lang.String scfSection

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Constant Field Values

scfmiSection

static final java.lang.String scfmiSection

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Constant Field Values

mp2Section

static final java.lang.String mp2Section

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Constant Field Values

guessSection

static final java.lang.String guessSection

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Constant Field Values

vecSection

static final java.lang.String vecSection

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Constant Field Values

statptSection

static final java.lang.String statptSection

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Constant Field Values

trudgeSection

static final java.lang.String trudgeSection

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Constant Field Values

trurstSection

static final java.lang.String trurstSection

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Constant Field Values

forceSection

static final java.lang.String forceSection

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Constant Field Values

cphfSection

static final java.lang.String cphfSection

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Constant Field Values

hessSection

static final java.lang.String hessSection

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Constant Field Values

gradSection

static final java.lang.String gradSection

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Constant Field Values

dipdrSection

static final java.lang.String dipdrSection

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Constant Field Values

vibSection

static final java.lang.String vibSection

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Constant Field Values

massSection

static final java.lang.String massSection

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Constant Field Values

ircSection

static final java.lang.String ircSection

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Constant Field Values

drcSection

static final java.lang.String drcSection

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Constant Field Values

surfSection

static final java.lang.String surfSection

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Constant Field Values

localSection

static final java.lang.String localSection

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Constant Field Values

twoeiSection

static final java.lang.String twoeiSection

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Constant Field Values

elmonSection

static final java.lang.String elmonSection

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Constant Field Values

elpotSection

static final java.lang.String elpotSection

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Constant Field Values

eldensSection

static final java.lang.String eldensSection

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Constant Field Values

elfldgSection

static final java.lang.String elfldgSection

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Constant Field Values

pointsSection

static final java.lang.String pointsSection

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Constant Field Values

gridSection

static final java.lang.String gridSection

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Constant Field Values

pdcSection

static final java.lang.String pdcSection

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Constant Field Values

molgrfSection

static final java.lang.String molgrfSection

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Constant Field Values

stoneSection

static final java.lang.String stoneSection

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Constant Field Values

morokmSection

static final java.lang.String morokmSection

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Constant Field Values

ffcalcSection

static final java.lang.String ffcalcSection

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Constant Field Values

tdhfSection

static final java.lang.String tdhfSection

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Constant Field Values

efragSection

static final java.lang.String efragSection

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Constant Field Values

fragnameSection

static final java.lang.String fragnameSection

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Constant Field Values

fgrrplSection

static final java.lang.String fgrrplSection

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Constant Field Values

pcmSection

static final java.lang.String pcmSection

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Constant Field Values

pcmcavSection

static final java.lang.String pcmcavSection

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Constant Field Values

newcavSection

static final java.lang.String newcavSection

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Constant Field Values

disbsSection

static final java.lang.String disbsSection

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Constant Field Values

disrepSection

static final java.lang.String disrepSection

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Constant Field Values

scrfSection

static final java.lang.String scrfSection

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Constant Field Values

ecpSection

static final java.lang.String ecpSection

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Constant Field Values

efieldSection

static final java.lang.String efieldSection

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Constant Field Values

intgrlSection

static final java.lang.String intgrlSection

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Constant Field Values

transSection

static final java.lang.String transSection

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Constant Field Values

ciinpSection

static final java.lang.String ciinpSection

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Constant Field Values

detSection

static final java.lang.String detSection

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Constant Field Values

cidetSection

static final java.lang.String cidetSection

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Constant Field Values

drtSection

static final java.lang.String drtSection

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Constant Field Values

cidrtSection

static final java.lang.String cidrtSection

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Constant Field Values

mcscfSection

static final java.lang.String mcscfSection

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Constant Field Values

mcqdptSection

static final java.lang.String mcqdptSection

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Constant Field Values

cisortSection

static final java.lang.String cisortSection

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Constant Field Values

gugemSection

static final java.lang.String gugemSection

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Constant Field Values

gugdiaSection

static final java.lang.String gugdiaSection

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Constant Field Values

gugdmSection

static final java.lang.String gugdmSection

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Constant Field Values

gugdm2Section

static final java.lang.String gugdm2Section

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Constant Field Values

lagranSection

static final java.lang.String lagranSection

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Constant Field Values

trfdm2Section

static final java.lang.String trfdm2Section

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Constant Field Values

transtSection

static final java.lang.String transtSection

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Constant Field Values

validSections

static final java.util.HashSet validSections

sectionVarsReference

static java.util.HashMap<java.lang.String,java.util.HashMap> sectionVarsReference

controlSwitches

static java.util.HashMap<java.lang.String,GamessSwitch> controlSwitches

basisSwitches

static java.util.HashMap<java.lang.String,GamessSwitch> basisSwitches

systemSwitches

static java.util.HashMap<java.lang.String,GamessSwitch> systemSwitches

validSymmetrySymbols

static final java.util.HashSet validSymmetrySymbols

Title

java.lang.String Title

SymmetrySymbol

java.lang.String SymmetrySymbol

AxisOrder

int AxisOrder

currentVars

java.util.HashMap<java.lang.String,java.util.HashMap> currentVars

atoms

java.util.ArrayList<GamessAtom> atoms

basisGroup

java.util.HashMap basisGroup

Constructor Detail

Gamess

public Gamess()

Method Detail

getMolecularInterface

public void getMolecularInterface(MoleculeInterface molec)
                           throws java.lang.Exception

Throws:

java.lang.Exception

parseGamessInput

public void parseGamessInput(java.lang.String inputfile)
                      throws java.lang.Exception

Throws:

java.lang.Exception

parseGamessInput

public void parseGamessInput(java.lang.String inputfile,
                             int fileType)
                      throws java.lang.Exception

Throws:

java.lang.Exception

getControlSection

public java.util.HashMap getControlSection()

main

public static void main(java.lang.String[] args)

applySymmetry

public void applySymmetry(java.lang.String symbol,
                          int axisOrder,
                          java.util.ArrayList<GamessAtom> points)
                   throws java.lang.Exception

Throws:

java.lang.Exception

fromZMatrixToCartesians

public static void fromZMatrixToCartesians(java.util.ArrayList<GamessAtom> atoms)
                                    throws java.lang.Exception

Expects bond length in angstroms

Parameters:

atoms - ArrayList

Throws:

java.lang.Exception

getAtomicNumber

public static int getAtomicNumber(java.lang.String symbol)