MTK++ Latest version: 0.2.0

Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes
MTKpp::dcParser Class Reference

Reads divcon output files and write divcon input files. More...

#include <mtkpp/src/Parsers/dcParser.h>

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List of all members.

Public Member Functions

 dcParser ()
 dcParser Constructor
virtual ~dcParser ()
 dcParser Destructor
void Read (const std::string &i, molecule *m)
 Read DivCon formatted file.
double ReadHOF (const std::string &i)
 Read DivCon formatted file.
double ReadElecEnergy (const std::string &i)
 Parse electronic energy from the divcon output file.
void setHamiltonian (std::string ham)
void setOptimizer (std::string opt)
void setMaxOpt (int i)
void setChargeModel (std::string chg)
void setFrequency ()
void setThermo ()
void setCluster (int i)
void setDBuff1 (double d)
void setDBuff2 (double d)
void setNoOverlap ()
void setStandard ()
void doScrf ()
void setScrfScale (double i)
void setDirect (int i)
void setResidue (int i)
void setPDump (int i)
void setDump (int i)
void setShift (double d)
void setCutBond (double d)
void setGuess ()
void setNMR ()
void setCalNuc (unsigned int i)
void setPWD ()
void setPWDatom ()
void setPWDresidue ()
void setPrtSub ()
void setPrtVec ()
void setPrtCoords ()
void setPrtPar ()
void setPrtVdw ()
void setAddMM ()
void setNoMM ()
void setCoord (std::string coordSystem)
void setFullSCF ()
void setMaxIt (int i)
void setDouble (int d)
void setIntegrals (std::string s)
void setTempK (double k)
void setMaxTime (int s)
void setMinR (double d)
void setCutRepul (double d)
void setChkRes ()
void setDos ()
void setDipole ()
void setIP ()
void setHomoLumo ()
void setScreen ()
void setZMake ()
void setQMAlign ()
void setImult (int i)
void setUhf (int i)
void setExternal (int i)
void Write (const std::string &i, collection *c, bool &success)
 Write DivCon input file.
void Write (const std::string &i, molecule *m, bool &success)
 Write DivCon input file.
void Write (const std::string &i, molecule *m, std::vector< vector3d > &coordinates, bool &success)
 Write DivCon input file.
virtual void Read ()
 Read function.
virtual void Write ()
 Write function.
std::ofstream & OpenFile (std::string fileName)
 Write function.
std::string determineElement (std::string &name)
 Preceive element symbol from the atom name.
void setError (int i)
 Error handling within Parsers.
bool getError ()
 Error handling within dcParser.
void setErrorMessage (std::string s)
 Error handling within Parsers.
std::string getErrorMessage ()
 Error handling within Parsers.

Protected Types

typedef std::vector< molecule * >
::iterator 
molIterator
 molecule iterator
typedef std::vector
< submolecule * >::iterator 
sMolIterator
 submolecule iterator
typedef std::vector< atom * >
::iterator 
AtomIterator
 atom iterator
typedef std::vector
< std::string >::iterator 
strIterator
 string iterator

Protected Member Functions

void readCoordinates (std::ifstream &idc, molecule *m)
 Read coordinate section of a divcon output.
void readQMQSAR (std::ifstream &idc, molecule *m)
 Read qmqsar section of a divcon output.
void readNMR (std::ifstream &idc, molecule *m)
 Read nmr section of a divcon output.
bool check ()
 Do some error checking before writing the file.
void openInputFile (const std::string &i)
 Open Input File.
void writeHead ()
 Write Head of a DivCon Input File.
void writeCoords ()
 Write Coordinate section of a DivCon Input File.
void writeCoords (std::vector< vector3d > &coordinates)
 Write Coordinate section of a DivCon Input File.
void writeTail ()
 Write Tail of a DivCon Input File.

Protected Attributes

collectionpCollection
 collection pointer
moleculepMolecule
 molecule pointer
submoleculepSubMolecule
 submolecule pointer
atompAtom
 atom pointer
std::string inputFileName
 divcon input file name
std::string outputFileName
 divcon output file name
std::ofstream inputFileStream
 Input File Stream.
std::string coord
 cartesion/internal
bool bStandard
 standard (no DnC)
bool bCluster
 DnC calculation.
double dBuff1
 size of first buffer in DnC
double dBuff2
 size of second buffer in DnC
bool bResidue
 store residue pointers
bool bDirect
 calculate integrals on the fly
std::string hamiltonian
 Which Hamiltonian to use.
bool bChargeModel
 Turn on a charge model.
std::string chargeModel
 Which Charge model to use.
bool bCutBond
 Use a cutoff for repulsion integrals.
double cutbond
 size of cutoff
bool bShift
 use shift (helps convergence)
double shift
 size of shift
bool bGuess
 Use a guess file.
bool bPDump
 output density matrix file
int pDump
bool bDump
 output restart coordinate file
int dump
 output restart coordinate file every n step
bool bDouble
 double scf
int iDouble
bool bMaxOpt
 maximum number of optimization steps
unsigned int maxopt
 maximum number of optimization steps
bool bOpt
 optimize structure
std::string optimizer
 which optimizer
bool bScrf
 run solvent calculation
double scrfScale
 run solvent calculation
bool bWater
 solvent is water
bool bOctanol
 solvent is octanol
bool bNoOverlap
bool bScreen
 Output screen info.
bool bVdw
bool bDipole
 calculate dipoles
bool bFreq
 calculate frequencies
bool bThermo
 calculate thermochemical properties
bool bNMR
 calculate NMR shieldings
int calnum
 which nmr nuclei to calculate
bool bPwd
 do energy decomposition
bool bPwdAtom
 do energy decomposition at atomic level
bool bPwdResidue
 do energy decomposition at residue level
bool bPrtSub
 print subsystem info
bool bPrtVec
 print eigenvector info
bool bPrtCoords
 print coordinates
bool bPrtPar
 print parameter info
bool bPrtVdw
 print van der Waals info
bool bAddMM
 add MM correction [default]
bool bNoMM
 no MM correction
bool bFullSCF
bool bMaxIt
int maxIt
bool bCutRepul
double cutRepul
bool bIntegrals
std::string integrals
bool bTempK
double tempK
bool bMaxTime
int maxTime
bool bMinR
double minR
bool bQMAlign
bool bChkRes
bool bDOS
bool bIP
bool bHomoLumo
bool bZmake
int imult
bool bUhf
bool bExternal
std::ofstream outputFileStream
 Output File Stream.
bool bError
 Error occured.
std::string errorMessage
 Error message.
unsigned int NUM_INDENTS_PER_SPACE

Detailed Description

Reads divcon output files and write divcon input files.

Author:
Martin Peters
Date:
2005

DivCon Input Options


Member Typedef Documentation

typedef std::vector<molecule*>::iterator MTKpp::dcParser::molIterator [protected]

molecule iterator

typedef std::vector<submolecule*>::iterator MTKpp::dcParser::sMolIterator [protected]

submolecule iterator

typedef std::vector<atom*>::iterator MTKpp::dcParser::AtomIterator [protected]

atom iterator

typedef std::vector<std::string>::iterator MTKpp::dcParser::strIterator [protected]

string iterator


Constructor & Destructor Documentation

MTKpp::dcParser::dcParser ( )
MTKpp::dcParser::~dcParser ( ) [virtual]

dcParser Destructor


Member Function Documentation

void MTKpp::dcParser::Read ( const std::string &  i,
molecule m 
)
double MTKpp::dcParser::ReadHOF ( const std::string &  i)

Read DivCon formatted file.

Parameters:
iInput file
ccollection pointer
mmolecule id

Parse heat of formation from the divcon output file

Parameters:
iInput file
Returns:
Heat of Formation

References MTKpp::baseParser::setError(), MTKpp::baseParser::setErrorMessage(), and MTKpp::splitString().

double MTKpp::dcParser::ReadElecEnergy ( const std::string &  i)

Parse electronic energy from the divcon output file.

Parameters:
iInput file
Returns:
Electronc energy

References MTKpp::baseParser::setError(), MTKpp::baseParser::setErrorMessage(), and MTKpp::splitString().

Referenced by Read().

void MTKpp::dcParser::setHamiltonian ( std::string  ham) [inline]
  • Hamiltonians
    1. MNDO
    2. AM1
    3. PM3
    4. PM3 ZnB : biological Zinc paramters to be used in pm3
    5. MNDO/d
    6. PDDG-PM3

References hamiltonian.

Referenced by MTKpp::DivConInterface::Minimize(), and MTKpp::DivConInterface::runNMR().

void MTKpp::dcParser::setOptimizer ( std::string  opt) [inline]
  • Geometry optimizations
    1. steep: steepest descent
    2. conjgrad: conjgrate gradient
    3. bfgs:
    4. lbfgs: limited memory BFGS

References bOpt, and optimizer.

Referenced by MTKpp::DivConInterface::Minimize().

void MTKpp::dcParser::setMaxOpt ( int  i) [inline]
  • geometry optimizations
    1. maxopt: do a maximum of X cycles of geometry optimization
    2. snapgeom: print out every optimization step into separate files
    3. lsearch: linear search in lbfgs
    4. diagterm: initial diagonal term in lbfgs opt
    5. force-it: force geometry opt criteria to be satisfied

References bMaxOpt, and maxopt.

Referenced by MTKpp::DivConInterface::Minimize().

void MTKpp::dcParser::setChargeModel ( std::string  chg) [inline]
  • geometry optimizations
    1. ts: transition state geometry calculation
    2. tsprfo: baker method
    3. tsqna: quasi-newton method
    4. tsnr: pure newton method
    5. nomodefollow: mode following not activated in ts search
  • Gradient
    1. gradient: output final gradient
    2. central: use central difference in gradient calculation
    3. inter: include only intermolecular contributions
    4. recipintra: consider intramolecular contributions void setGradient(); void setCentral(); void setInter(); void setRecipintra();
  • Convergence criteria
    1. descf: user defined scf energy criterion [descf == ecrit]
    2. dpscf: user defined scf density criterion [dpscf == dcrit]
    3. etest: energy criterion
    4. gtest: gradient criterion
    5. ecrit: energy criterion
    6. dcrit: density matrix criterion

void setDESCF(double d); void setDPSCF(double d); void setETEST(double d); void setGTEST(double d); void setECRIT(double d); void setDCRIT(double d);

  • Charge Models Available
    1. mulliken: use mulliken for scrf/pme calculations
    2. cm1: use mulliken for scrf/pme calculations
    3. cm2: use mulliken for scrf/pme calculations

References bChargeModel, and chargeModel.

Referenced by MTKpp::DivConInterface::Minimize().

void MTKpp::dcParser::setFrequency ( ) [inline]

freq: carry out frequency analysis

References bFreq.

void MTKpp::dcParser::setThermo ( ) [inline]

thermo: report thermodynamic quantities from freq calculations

References bThermo.

void MTKpp::dcParser::setCluster ( int  i) [inline]
  • Subsetting
    1. cluster: cluster bases subsetting
    2. dbuff1: buffer 1 size
    3. dbuff2: buffer 2 size
    4. no-overlap: off diagonal terms of density matrix are set to zero
    5. atgrid: atom wise grid based subsetting
    6. resgrid: residue wise grid based subsetting
    7. mixgrid: residue wise, grid based subsetting for core and atom wise for grid based subsetting for buffers
    8. combsub: combination subsetting
    9. standard: no divide-and-conquer

void setAtGrid(); void setResGrid(); void setMixGrid(); void setCombSub();

References bCluster, and bStandard.

Referenced by setDBuff1(), and setDBuff2().

void MTKpp::dcParser::setDBuff1 ( double  d) [inline]

References dBuff1, and setCluster().

void MTKpp::dcParser::setDBuff2 ( double  d) [inline]

References dBuff2, and setCluster().

void MTKpp::dcParser::setNoOverlap ( ) [inline]

References bNoOverlap.

void MTKpp::dcParser::setStandard ( ) [inline]

References bCluster, and bStandard.

void MTKpp::dcParser::doScrf ( ) [inline]
  • Self Consistent Reaction Field:
    1. scrf: requests a scrf calculation with Delphi
    2. scrf-inside: only fill cavities with a continuum
    3. drad: used with scrf-inside
    4. indi: internal dielectric set to X
    5. exdi: external dielectric set to X
    6. scale: grid space set to X grid per angstrom
    7. perfill: molecule occupies X % of the grid
    8. ion: ion strength set to X
    9. probrab: probe radius set to X
    10. water: use water params for scrf calculation (Gnp)
    11. octanol: use octanol params for scrf calculation (Gnp)
    12. divpb: use divpb instead of delphi for scrf calculation
    13. soldmx: use guess dmx for scrf calculation

References bScrf.

void MTKpp::dcParser::setScrfScale ( double  i) [inline]

References scrfScale.

void MTKpp::dcParser::setDirect ( int  i) [inline]

direct: do not store 2-e integrals in scf calculations

References bDirect.

Referenced by MTKpp::DivConInterface::Minimize(), and MTKpp::DivConInterface::runNMR().

void MTKpp::dcParser::setResidue ( int  i) [inline]

residue: store residue pointers (needed for D&C)

References bResidue.

void MTKpp::dcParser::setPDump ( int  i) [inline]

pdump: write a restart density matrix every X scf cycles

References bPDump, and pDump.

void MTKpp::dcParser::setDump ( int  i) [inline]

dump: write a restart file every X opt cycles

References bDump, and dump.

void MTKpp::dcParser::setShift ( double  d) [inline]

shift: initial dynamic level shift set to X

References bShift, and shift.

void MTKpp::dcParser::setCutBond ( double  d) [inline]

trajectory: dump coordinates to a trajectory file at restart points

cutbond: cutoff bonding beyond X Angstroms

References bCutBond, and cutbond.

void MTKpp::dcParser::setGuess ( ) [inline]

1SCF: perform only one scf iteration

guess: build initial density matrix from one or more dmx files

References bGuess.

void MTKpp::dcParser::setNMR ( ) [inline]

vdw: calculate van der Waals interactions

  • nmr
    1. nmr: nmr shielding calculation

References bNMR.

Referenced by setCalNuc().

void MTKpp::dcParser::setCalNuc ( unsigned int  i) [inline]
  • nmr
    1. calnuc = 1 proton calculation
    2. calnuc = 2 carbon calculation

References calnum, and setNMR().

Referenced by MTKpp::DivConInterface::runNMR().

void MTKpp::dcParser::setPWD ( ) [inline]
  • PairWise Energy Decomposition
    1. pwd: perform a pwd

References bPwd.

void MTKpp::dcParser::setPWDatom ( ) [inline]
  • PairWise Energy Decomposition
    1. pwd_atom: perform a pwd and output atom info only

References bPwdAtom.

void MTKpp::dcParser::setPWDresidue ( ) [inline]
  • PairWise Energy Decomposition
    1. pwd_residue: perform a pwd and output residue only

References bPwdResidue.

void MTKpp::dcParser::setPrtSub ( ) [inline]
  • Output
    1. prtsub: prints subsystem atom list

References bPrtSub.

void MTKpp::dcParser::setPrtVec ( ) [inline]
  • Output
    1. prtvec: prints final eigenvectors

References bPrtVec.

void MTKpp::dcParser::setPrtCoords ( ) [inline]
  • Output
    1. prtcoords: prints atomic coordinates

References bPrtCoords.

void MTKpp::dcParser::setPrtPar ( ) [inline]
  • Output
    1. prtpar: prints semi-empirical parameters

References bPrtPar.

void MTKpp::dcParser::setPrtVdw ( ) [inline]
  • Output
    1. prtvdwaals: output van der Waals radii

References bPrtVdw.

void MTKpp::dcParser::setAddMM ( ) [inline]

addmm: adds MM correction to peptide rotational barrier [default]

References bAddMM.

void MTKpp::dcParser::setNoMM ( ) [inline]

nomm: does not use addmm

References bNoMM.

void MTKpp::dcParser::setCoord ( std::string  coordSystem) [inline]
  • Coordinate System
    1. cartesian: requires x,y,z data
    2. internal: requires a z-matrix

References coord.

void MTKpp::dcParser::setFullSCF ( ) [inline]

fullscf: performs full diagonalizations in SCF

References bFullSCF.

void MTKpp::dcParser::setMaxIt ( int  i) [inline]

maxit: maximum number of scf iterations is 100

References bMaxIt, and maxIt.

void MTKpp::dcParser::setDouble ( int  d) [inline]

double: do a double scf step for every scf iteration

References bDouble, and iDouble.

void MTKpp::dcParser::setIntegrals ( std::string  s) [inline]

intgls: stewart/talman to be used [talman]

References bIntegrals, and integrals.

Referenced by setQMAlign().

void MTKpp::dcParser::setTempK ( double  k) [inline]

tempk: set temperature to X

References bTempK, and tempK.

void MTKpp::dcParser::setMaxTime ( int  s) [inline]

tmax: request a maximum CPU time of X seconds

References bMaxTime, and maxTime.

void MTKpp::dcParser::setMinR ( double  d) [inline]

rmin: minimum distance between atoms is X

References bMinR, and minR.

void MTKpp::dcParser::setCutRepul ( double  d) [inline]

cutrepul: cut off for repulsion integrals

References bCutRepul, and cutRepul.

void MTKpp::dcParser::setChkRes ( ) [inline]

chkres: check inter-residue distances for each residue

References bChkRes.

void MTKpp::dcParser::setDos ( ) [inline]

dos: density of states

References bDOS.

void MTKpp::dcParser::setDipole ( ) [inline]

dipole: calculates dipole moment

References bDipole.

void MTKpp::dcParser::setIP ( ) [inline]

ip: calculate ionization potential

References bIP.

void MTKpp::dcParser::setHomoLumo ( ) [inline]

homolumo: calculates homo-lumo gap

References bHomoLumo.

void MTKpp::dcParser::setScreen ( ) [inline]

screen: output info to screen

References bScreen.

void MTKpp::dcParser::setZMake ( ) [inline]

zmake: generates a z-matrix

References bZmake.

void MTKpp::dcParser::setQMAlign ( ) [inline]

qmailgn: generate output for QM-QSAR

References bQMAlign, and setIntegrals().

void MTKpp::dcParser::setImult ( int  i) [inline]

imult: sets multiplicity

References imult.

void MTKpp::dcParser::setUhf ( int  i) [inline]

uhf: sets uhf

References bUhf.

void MTKpp::dcParser::setExternal ( int  i) [inline]

External: sets multiplicity

References bExternal.

void MTKpp::dcParser::Write ( const std::string &  i,
collection c,
bool &  success 
)

Write DivCon input file.

rotate: rotational angle for barrier is X

push: push cluster groups apart

Parameters:
iInput file
ccollection pointer
successsuccess boolean

References MTKpp::baseName(), check(), inputFileName, openInputFile(), pCollection, pMolecule, writeCoords(), writeHead(), and writeTail().

Referenced by MTKpp::DivConInterface::Minimize(), and MTKpp::DivConInterface::runNMR().

void MTKpp::dcParser::Write ( const std::string &  i,
molecule m,
bool &  success 
)

Write DivCon input file.

Parameters:
iInput file
mmolecule pointer
successsuccess boolean

References MTKpp::molecule::getCoordinates(), and MTKpp::baseParser::Write().

void MTKpp::dcParser::Write ( const std::string &  i,
molecule m,
std::vector< vector3d > &  coordinates,
bool &  success 
)

Write DivCon input file.

Parameters:
iInput file
mmolecule pointer
coordinatesVector of coordinates which overrides the molecules coordinates
successsuccess boolean

References check(), openInputFile(), pCollection, pMolecule, writeCoords(), writeHead(), and writeTail().

void MTKpp::dcParser::readCoordinates ( std::ifstream &  idc,
molecule m 
) [protected]
void MTKpp::dcParser::readQMQSAR ( std::ifstream &  idc,
molecule m 
) [protected]

Read qmqsar section of a divcon output.

Parameters:
idcinput file stream
mmolecule pointer

Referenced by Read().

void MTKpp::dcParser::readNMR ( std::ifstream &  idc,
molecule m 
) [protected]

Read nmr section of a divcon output.

Parameters:
idcinput file stream
mmolecule pointer

References MTKpp::atom::addProperty(), MTKpp::molecule::getAtom(), pAtom, and MTKpp::splitString().

Referenced by Read().

bool MTKpp::dcParser::check ( ) [protected]
void MTKpp::dcParser::openInputFile ( const std::string &  i) [protected]

Open Input File.

References inputFileStream.

Referenced by Write().

void MTKpp::dcParser::writeHead ( ) [protected]
void MTKpp::dcParser::writeCoords ( ) [protected]
void MTKpp::dcParser::writeCoords ( std::vector< vector3d > &  coordinates) [protected]
void MTKpp::dcParser::writeTail ( ) [protected]

Write Tail of a DivCon Input File.

References bCluster, bGuess, bNMR, MTKpp::molecule::getNumAtoms(), inputFileStream, outputFileName, and pMolecule.

Referenced by Write().

void MTKpp::baseParser::Read ( ) [virtual, inherited]

Read function.

Referenced by MTKpp::acParser::Read(), and MTKpp::molParser::Read().

void MTKpp::baseParser::Write ( ) [virtual, inherited]
std::ofstream & MTKpp::baseParser::OpenFile ( std::string  fileName) [inherited]

Write function.

References MTKpp::baseParser::outputFileStream.

Referenced by main().

std::string MTKpp::baseParser::determineElement ( std::string &  name) [inherited]

Preceive element symbol from the atom name.

References MTKpp::GetAlphaChar(), and MTKpp::removeCharacter().

Referenced by MTKpp::pdbParser::Read(), and MTKpp::prepParser::readFragment().

void MTKpp::baseParser::setError ( int  i) [inline, inherited]
bool MTKpp::baseParser::getError ( ) [inline, inherited]

Error handling within dcParser.

Returns:
error

References MTKpp::baseParser::bError.

Referenced by main().

void MTKpp::baseParser::setErrorMessage ( std::string  s) [inline, inherited]
std::string MTKpp::baseParser::getErrorMessage ( ) [inline, inherited]

Error handling within Parsers.

Returns:
error message

References MTKpp::baseParser::errorMessage.

Referenced by main().


Member Data Documentation

collection pointer

Referenced by check(), dcParser(), Write(), writeCoords(), and writeHead().

molecule pointer

Referenced by check(), dcParser(), Write(), writeCoords(), writeHead(), and writeTail().

submolecule pointer

Referenced by check(), dcParser(), readCoordinates(), and writeCoords().

atom pointer

Referenced by check(), dcParser(), readCoordinates(), readNMR(), and writeCoords().

std::string MTKpp::dcParser::inputFileName [protected]

divcon input file name

Referenced by dcParser(), and Write().

std::string MTKpp::dcParser::outputFileName [protected]

divcon output file name

Referenced by dcParser(), Read(), and writeTail().

std::ofstream MTKpp::dcParser::inputFileStream [protected]

Input File Stream.

Referenced by openInputFile(), writeCoords(), writeHead(), and writeTail().

std::string MTKpp::dcParser::coord [protected]

cartesion/internal

Referenced by dcParser(), setCoord(), and writeHead().

bool MTKpp::dcParser::bStandard [protected]

standard (no DnC)

Referenced by dcParser(), setCluster(), setStandard(), and writeHead().

bool MTKpp::dcParser::bCluster [protected]

DnC calculation.

Referenced by dcParser(), setCluster(), setStandard(), writeHead(), and writeTail().

double MTKpp::dcParser::dBuff1 [protected]

size of first buffer in DnC

Referenced by dcParser(), and setDBuff1().

double MTKpp::dcParser::dBuff2 [protected]

size of second buffer in DnC

Referenced by dcParser(), and setDBuff2().

bool MTKpp::dcParser::bResidue [protected]

store residue pointers

Referenced by dcParser(), setResidue(), writeCoords(), and writeHead().

bool MTKpp::dcParser::bDirect [protected]

calculate integrals on the fly

Referenced by dcParser(), setDirect(), and writeHead().

std::string MTKpp::dcParser::hamiltonian [protected]

Which Hamiltonian to use.

Referenced by check(), dcParser(), setHamiltonian(), and writeHead().

Turn on a charge model.

Referenced by dcParser(), setChargeModel(), and writeHead().

std::string MTKpp::dcParser::chargeModel [protected]

Which Charge model to use.

Referenced by dcParser(), setChargeModel(), and writeHead().

bool MTKpp::dcParser::bCutBond [protected]

Use a cutoff for repulsion integrals.

Referenced by dcParser(), setCutBond(), and writeHead().

double MTKpp::dcParser::cutbond [protected]

size of cutoff

Referenced by dcParser(), setCutBond(), and writeHead().

bool MTKpp::dcParser::bShift [protected]

use shift (helps convergence)

Referenced by dcParser(), setShift(), and writeHead().

double MTKpp::dcParser::shift [protected]

size of shift

Referenced by dcParser(), setShift(), and writeHead().

bool MTKpp::dcParser::bGuess [protected]

Use a guess file.

Referenced by dcParser(), setGuess(), writeHead(), and writeTail().

bool MTKpp::dcParser::bPDump [protected]

output density matrix file

Referenced by dcParser(), setPDump(), and writeHead().

int MTKpp::dcParser::pDump [protected]

Referenced by dcParser(), setPDump(), and writeHead().

bool MTKpp::dcParser::bDump [protected]

output restart coordinate file

Referenced by dcParser(), setDump(), and writeHead().

int MTKpp::dcParser::dump [protected]

output restart coordinate file every n step

Referenced by dcParser(), setDump(), and writeHead().

bool MTKpp::dcParser::bDouble [protected]

double scf

Referenced by dcParser(), and setDouble().

int MTKpp::dcParser::iDouble [protected]

Referenced by dcParser(), and setDouble().

bool MTKpp::dcParser::bMaxOpt [protected]

maximum number of optimization steps

Referenced by dcParser(), and setMaxOpt().

unsigned int MTKpp::dcParser::maxopt [protected]

maximum number of optimization steps

Referenced by dcParser(), setMaxOpt(), and writeHead().

bool MTKpp::dcParser::bOpt [protected]

optimize structure

Referenced by dcParser(), setOptimizer(), and writeHead().

std::string MTKpp::dcParser::optimizer [protected]

which optimizer

Referenced by dcParser(), setOptimizer(), and writeHead().

bool MTKpp::dcParser::bScrf [protected]

run solvent calculation

Referenced by dcParser(), doScrf(), and writeHead().

double MTKpp::dcParser::scrfScale [protected]

run solvent calculation

Referenced by dcParser(), setScrfScale(), and writeHead().

bool MTKpp::dcParser::bWater [protected]

solvent is water

Referenced by dcParser(), and writeHead().

bool MTKpp::dcParser::bOctanol [protected]

solvent is octanol

Referenced by dcParser(), and writeHead().

bool MTKpp::dcParser::bNoOverlap [protected]

Referenced by dcParser(), setNoOverlap(), and writeHead().

bool MTKpp::dcParser::bScreen [protected]

Output screen info.

Referenced by dcParser(), setScreen(), and writeHead().

bool MTKpp::dcParser::bVdw [protected]

Referenced by dcParser().

bool MTKpp::dcParser::bDipole [protected]

calculate dipoles

Referenced by dcParser(), setDipole(), and writeHead().

bool MTKpp::dcParser::bFreq [protected]

calculate frequencies

Referenced by dcParser(), setFrequency(), and writeHead().

bool MTKpp::dcParser::bThermo [protected]

calculate thermochemical properties

Referenced by dcParser(), setThermo(), and writeHead().

bool MTKpp::dcParser::bNMR [protected]

calculate NMR shieldings

Referenced by dcParser(), setNMR(), writeHead(), and writeTail().

int MTKpp::dcParser::calnum [protected]

which nmr nuclei to calculate

Referenced by dcParser(), setCalNuc(), and writeHead().

bool MTKpp::dcParser::bPwd [protected]

do energy decomposition

Referenced by dcParser(), setPWD(), and writeHead().

bool MTKpp::dcParser::bPwdAtom [protected]

do energy decomposition at atomic level

Referenced by dcParser(), setPWDatom(), and writeHead().

bool MTKpp::dcParser::bPwdResidue [protected]

do energy decomposition at residue level

Referenced by dcParser(), setPWDresidue(), and writeHead().

bool MTKpp::dcParser::bPrtSub [protected]

print subsystem info

Referenced by dcParser(), and setPrtSub().

bool MTKpp::dcParser::bPrtVec [protected]

print eigenvector info

Referenced by dcParser(), and setPrtVec().

bool MTKpp::dcParser::bPrtCoords [protected]

print coordinates

Referenced by dcParser(), and setPrtCoords().

bool MTKpp::dcParser::bPrtPar [protected]

print parameter info

Referenced by dcParser(), and setPrtPar().

bool MTKpp::dcParser::bPrtVdw [protected]

print van der Waals info

Referenced by dcParser(), and setPrtVdw().

bool MTKpp::dcParser::bAddMM [protected]

add MM correction [default]

Referenced by dcParser(), and setAddMM().

bool MTKpp::dcParser::bNoMM [protected]

no MM correction

Referenced by dcParser(), and setNoMM().

bool MTKpp::dcParser::bFullSCF [protected]

Referenced by dcParser(), and setFullSCF().

bool MTKpp::dcParser::bMaxIt [protected]

Referenced by dcParser(), and setMaxIt().

int MTKpp::dcParser::maxIt [protected]

Referenced by dcParser(), and setMaxIt().

bool MTKpp::dcParser::bCutRepul [protected]

Referenced by dcParser(), and setCutRepul().

double MTKpp::dcParser::cutRepul [protected]

Referenced by dcParser(), and setCutRepul().

bool MTKpp::dcParser::bIntegrals [protected]

Referenced by dcParser(), setIntegrals(), and writeHead().

std::string MTKpp::dcParser::integrals [protected]

Referenced by dcParser(), setIntegrals(), and writeHead().

bool MTKpp::dcParser::bTempK [protected]

Referenced by dcParser(), and setTempK().

double MTKpp::dcParser::tempK [protected]

Referenced by dcParser(), and setTempK().

bool MTKpp::dcParser::bMaxTime [protected]

Referenced by dcParser(), and setMaxTime().

int MTKpp::dcParser::maxTime [protected]

Referenced by dcParser(), and setMaxTime().

bool MTKpp::dcParser::bMinR [protected]

Referenced by dcParser(), and setMinR().

double MTKpp::dcParser::minR [protected]

Referenced by dcParser(), and setMinR().

bool MTKpp::dcParser::bQMAlign [protected]

Referenced by dcParser(), setQMAlign(), and writeHead().

bool MTKpp::dcParser::bChkRes [protected]

Referenced by dcParser(), and setChkRes().

bool MTKpp::dcParser::bDOS [protected]

Referenced by dcParser(), and setDos().

bool MTKpp::dcParser::bIP [protected]

Referenced by dcParser(), and setIP().

bool MTKpp::dcParser::bHomoLumo [protected]

Referenced by dcParser(), and setHomoLumo().

bool MTKpp::dcParser::bZmake [protected]

Referenced by dcParser(), and setZMake().

int MTKpp::dcParser::imult [protected]

Referenced by dcParser(), setImult(), and writeHead().

bool MTKpp::dcParser::bUhf [protected]

Referenced by dcParser(), setUhf(), and writeHead().

bool MTKpp::dcParser::bExternal [protected]

Referenced by dcParser(), setExternal(), and writeHead().

std::ofstream MTKpp::baseParser::outputFileStream [protected, inherited]

Output File Stream.

Referenced by MTKpp::baseParser::OpenFile().

bool MTKpp::baseParser::bError [protected, inherited]
std::string MTKpp::baseParser::errorMessage [protected, inherited]
unsigned int MTKpp::baseParser::NUM_INDENTS_PER_SPACE [protected, inherited]

The documentation for this class was generated from the following files:

Generated on Fri Dec 23 2011 09:28:57 for MTK++ by Doxygen 1.7.5.1