NOsh class

Class for parsing for fixed format input files. More...

Files
file	nosh.h
	Contains declarations for class NOsh.
Data Structures
struct	sNOsh
	Class for parsing fixed format input files. More...
struct	sNOsh_calc
	Calculation class for use when parsing fixed format input files. More...
Defines
#define	NOSH_MAXMOL   20
	Maximum number of molecules in a run.
#define	NOSH_MAXCALC   20
	Maximum number of calculations in a run.
#define	NOSH_MAXPRINT   20
	Maximum number of PRINT statements in a run.
#define	NOSH_MAXPOP   20
	Maximum number of operations in a PRINT statement.
Typedefs
typedef enum eNOsh_MolFormat	NOsh_MolFormat
	Declare NOsh_MolFormat type.
typedef enum eNOsh_CalcType	NOsh_CalcType
	Declare NOsh_CalcType type.
typedef enum eNOsh_ParmFormat	NOsh_ParmFormat
	Declare NOsh_ParmFormat type.
typedef enum eNOsh_PrintType	NOsh_PrintType
	Declare NOsh_PrintType type.
typedef sNOsh	NOsh
	Declaration of the NOsh class as the NOsh structure.
typedef sNOsh_calc	NOsh_calc
	Declaration of the NOsh_calc class as the NOsh_calc structure.
Enumerations
enum	eNOsh_MolFormat {   NMF_PQR = 0,   NMF_PDB = 1 }
	Molecule file format types. More...
enum	eNOsh_CalcType {   NCT_MG = 0,   NCT_FEM = 1 }
	NOsh calculation types. More...
enum	eNOsh_ParmFormat { NPF_FLAT = 0 }
	Parameter file format types. More...
enum	eNOsh_PrintType {   NPT_ENERGY = 0,   NPT_FORCE = 1 }
	NOsh print types. More...
Functions
char *	NOsh_getMolpath (NOsh *thee, int imol)
	Returns path to specified molecule.
char *	NOsh_getDielXpath (NOsh *thee, int imap)
	Returns path to specified x-shifted dielectric map.
char *	NOsh_getDielYpath (NOsh *thee, int imap)
	Returns path to specified y-shifted dielectric map.
char *	NOsh_getDielZpath (NOsh *thee, int imap)
	Returns path to specified z-shifted dielectric map.
char *	NOsh_getKappapath (NOsh *thee, int imap)
	Returns path to specified kappa map.
char *	NOsh_getChargepath (NOsh *thee, int imap)
	Returns path to specified charge distribution map.
NOsh_calc *	NOsh_getCalc (NOsh *thee, int icalc)
	Returns specified calculation object.
int	NOsh_getDielfmt (NOsh *thee, int imap)
	Returns format of specified dielectric map.
int	NOsh_getKappafmt (NOsh *thee, int imap)
	Returns format of specified kappa map.
int	NOsh_getChargefmt (NOsh *thee, int imap)
	Returns format of specified charge map.
NOsh_PrintType	NOsh_printWhat (NOsh *thee, int iprint)
	Return an integer ID of the observable to print (.
char *	NOsh_elecname (NOsh *thee, int ielec)
	Return an integer mapping of an ELEC statement to a calculation ID (.
int	NOsh_elec2calc (NOsh *thee, int icalc)
	Return the name of an elec statement.
int	NOsh_printNarg (NOsh *thee, int iprint)
	Return number of arguments to PRINT statement (.
int	NOsh_printOp (NOsh *thee, int iprint, int iarg)
	Return integer ID for specified operation (.
int	NOsh_printCalc (NOsh *thee, int iprint, int iarg)
	Return calculation ID for specified PRINT statement (.
NOsh *	NOsh_ctor (int rank, int size)
	Construct NOsh.
int	NOsh_ctor2 (NOsh *thee, int rank, int size)
	FORTRAN stub to construct NOsh.
void	NOsh_dtor (NOsh **thee)
	Object destructor.
void	NOsh_dtor2 (NOsh *thee)
	FORTRAN stub for object destructor.
int	NOsh_parse (NOsh *thee, Vio *sock)
	Parse an input file from a socket.
int	NOsh_parseFile (NOsh *thee, char *filename)
	Parse an input file only from a file.
int	NOsh_setupMGMANUAL (NOsh *thee, MGparm *mgparm, PBEparm *pbeparm)
	Setup NOsh, MGparm, and PBEparm objects for a MG-MANUAL ELEC calculation.
int	NOsh_setupMGAUTO (NOsh *thee, MGparm *mgparm, PBEparm *pbeparm)
	Setup NOsh, MGparm, and PBEparm objects for a MG-AUTO ELEC calculation.
int	NOsh_setupMGPARA (NOsh *thee, MGparm *mgparm, PBEparm *pbeparm)
	Setup NOsh, MGparm, and PBEparm objects for a MG-PARA ELEC calculation.

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Detailed Description

Class for parsing for fixed format input files.

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Enumeration Type Documentation

enum eNOsh_CalcType

NOsh calculation types. Enumeration values: NCT_MG  Multigrid NCT_FEM  Finite element

enum eNOsh_MolFormat

Molecule file format types. Enumeration values: NMF_PQR  PQR format NMF_PDB  PDB format

enum eNOsh_ParmFormat

Parameter file format types. Enumeration values: NPF_FLAT  Flat-file format

enum eNOsh_PrintType

NOsh print types. Enumeration values: NPT_ENERGY  Energy NPT_FORCE  Force

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Function Documentation

NOsh* NOsh_ctor (  int  rank, int  size )

Construct NOsh. Author: Nathan Baker Parameters: rank  Rank of current processor in parallel calculation (0 if not parallel) size  Number of processors in parallel calculation (1 if not parallel) Returns: Newly allocated and initialized NOsh object

int NOsh_ctor2 (  NOsh *  thee, int  rank, int  size )

FORTRAN stub to construct NOsh. Author: Nathan Baker Parameters: thee  Space for NOsh objet rank  Rank of current processor in parallel calculation (0 if not parallel) size  Number of processors in parallel calculation (1 if not parallel) Returns: 1 if successful, 0 otherwise

void NOsh_dtor (  NOsh **  thee  )

Object destructor. Author: Nathan Baker Parameters: thee  Pointer to memory location of NOsh object

void NOsh_dtor2 (  NOsh *  thee  )

FORTRAN stub for object destructor. Author: Nathan Baker Parameters: thee  Pointer to NOsh object

int NOsh_elec2calc (  NOsh *  thee, int  icalc )

Return the name of an elec statement. Author: Todd Dolinsky Parameters: thee  NOsh object to use icalc  ID of CALC statement Returns: The name (if present) of an ELEC statement

char* NOsh_elecname (  NOsh *  thee, int  ielec )

Return an integer mapping of an ELEC statement to a calculation ID (. See also: elec2calc) Author: Nathan Baker Parameters: thee  NOsh object to use ielec  ID of ELEC statement Returns: An integer mapping of an ELEC statement to a calculation ID ( See also: elec2calc)

NOsh_calc* NOsh_getCalc (  NOsh *  thee, int  icalc )

Returns specified calculation object. Author: Nathan Baker Parameters: thee  Pointer to NOsh object icalc  Calculation ID of interest Returns: Pointer to specified calculation object

int NOsh_getChargefmt (  NOsh *  thee, int  imap )

Returns format of specified charge map. Author: Nathan Baker Parameters: thee  Pointer to NOsh object imap  Calculation ID of interest Returns: Format of charge map

char* NOsh_getChargepath (  NOsh *  thee, int  imap )

Returns path to specified charge distribution map. Author: Nathan Baker Parameters: thee  Pointer to NOsh object imap  Map ID of interest Returns: Path string

int NOsh_getDielfmt (  NOsh *  thee, int  imap )

Returns format of specified dielectric map. Author: Nathan Baker Parameters: thee  Pointer to NOsh object imap  Calculation ID of interest Returns: Format of dielectric map

char* NOsh_getDielXpath (  NOsh *  thee, int  imap )

Returns path to specified x-shifted dielectric map. Author: Nathan Baker Parameters: thee  Pointer to NOsh object imap  Map ID of interest Returns: Path string

char* NOsh_getDielYpath (  NOsh *  thee, int  imap )

Returns path to specified y-shifted dielectric map. Author: Nathan Baker Parameters: thee  Pointer to NOsh object imap  Map ID of interest Returns: Path string

char* NOsh_getDielZpath (  NOsh *  thee, int  imap )

Returns path to specified z-shifted dielectric map. Author: Nathan Baker Parameters: thee  Pointer to NOsh object imap  Map ID of interest Returns: Path string

int NOsh_getKappafmt (  NOsh *  thee, int  imap )

Returns format of specified kappa map. Author: Nathan Baker Parameters: thee  Pointer to NOsh object imap  Calculation ID of interest Returns: Format of kappa map

char* NOsh_getKappapath (  NOsh *  thee, int  imap )

Returns path to specified kappa map. Author: Nathan Baker Parameters: thee  Pointer to NOsh object imap  Map ID of interest Returns: Path string

char* NOsh_getMolpath (  NOsh *  thee, int  imol )

Returns path to specified molecule. Author: Nathan Baker Parameters: thee  Pointer to NOsh object imol  Molecule ID of interest Returns: Path string

int NOsh_parse (  NOsh *  thee, Vio *  sock )

Parse an input file from a socket. Author: Nathan Baker and Todd Dolinsky Parameters: thee  Pointer to NOsh object sock  Stream of tokens to parse Returns: 1 if successful, 0 otherwise

int NOsh_parseFile (  NOsh *  thee, char *  filename )

Parse an input file only from a file. Note: Included for SWIG wrapper compatibility Author: Nathan Baker and Todd Dolinsky Parameters: thee  Pointer to NOsh object filename  Name/path of readable file Returns: 1 if successful, 0 otherwise

int NOsh_printCalc (  NOsh *  thee, int  iprint, int  iarg )

Return calculation ID for specified PRINT statement (. See also: printcalc) Author: Nathan Baker Parameters: thee  NOsh object to use iprint  ID of PRINT statement iarg  ID of operation in PRINT statement Returns: Calculation ID for specified PRINT statement ( See also: printcalc)

int NOsh_printNarg (  NOsh *  thee, int  iprint )

Return number of arguments to PRINT statement (. See also: printnarg) Author: Nathan Baker Parameters: thee  NOsh object to use iprint  ID of PRINT statement Returns: Number of arguments to PRINT statement ( See also: printnarg)

int NOsh_printOp (  NOsh *  thee, int  iprint, int  iarg )

Return integer ID for specified operation (. See also: printop) Author: Nathan Baker Parameters: thee  NOsh object to use iprint  ID of PRINT statement iarg  ID of operation in PRINT statement Returns: Integer ID for specified operation ( See also: printop)

NOsh_PrintType NOsh_printWhat (  NOsh *  thee, int  iprint )

Return an integer ID of the observable to print (. See also: printwhat) Author: Nathan Baker Parameters: thee  NOsh object to use iprint  ID of PRINT statement Returns: An integer ID of the observable to print ( See also: printwhat)

int NOsh_setupMGAUTO (  NOsh *  thee, MGparm *  mgparm, PBEparm *  pbeparm )

Setup NOsh, MGparm, and PBEparm objects for a MG-AUTO ELEC calculation. Author: Nathan Baker Parameters: thee  Pointer to NOsh object mgparm  Pointer to base MGparm object containing parameters for the run; these will be used to construct the MGparm objects inside the NOsh object (for actual use by the code during calculations) pbeparm  Pointer to PBEparm object containing basic parameters for run; these will be supplemented and modified (for consistency, etc.) by this function Returns: 1 if successful, 0 otherwise

int NOsh_setupMGMANUAL (  NOsh *  thee, MGparm *  mgparm, PBEparm *  pbeparm )

Setup NOsh, MGparm, and PBEparm objects for a MG-MANUAL ELEC calculation. Author: Nathan Baker Parameters: thee  Pointer to NOsh object mgparm  Pointer to MGparm object containing basic parameters for run; these will be supplemented and modified (for consistency, etc.) by this function pbeparm  Pointer to PBEparm object containing basic parameters for run; these will be supplemented and modified (for consistency, etc.) by this function Returns: 1 if successful, 0 otherwise

int NOsh_setupMGPARA (  NOsh *  thee, MGparm *  mgparm, PBEparm *  pbeparm )

Setup NOsh, MGparm, and PBEparm objects for a MG-PARA ELEC calculation. Author: Nathan Baker Parameters: thee  Pointer to NOsh object mgparm  Pointer to base MGparm object containing parameters for the run; these will be used to construct the MGparm objects inside the NOsh object (for actual use by the code during calculations) pbeparm  Pointer to PBEparm object containing basic parameters for run; these will be supplemented and modified (for consistency, etc.) by this function Returns: 1 if successful, 0 otherwise

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