NAMD: GromacsTopFile.C File Reference

NAMD

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <algorithm>
#include "common.h"
#include "ResizeArray.h"
#include "InfoStream.h"
#include "GromacsTopFile.h"
#include "Debug.h"

Go to the source code of this file.

Macros
#define	JOULES_PER_CALORIE 4.184

#define	ANGSTROMS_PER_NM 10

#define	LINESIZE 200

#define	UNKNOWN 0

#define	ATOMS 1

#define	MOLECULETYPE 2

#define	MOLECULES 3

#define	SYSTEM 4

#define	BONDS 5

#define	BONDTYPES 6

#define	ANGLES 7

#define	ATOMTYPES 8

#define	ANGLETYPES 9

#define	DIHEDRALS 10

#define	DIHEDRALTYPES 11

#define	DEFAULTS 12

#define	NONBOND 13

#define	PAIRS 14

#define	EXCLUSIONS 15

#define	CODE_REDUNDANT 0

#define	MIN_DEBUG_LEVEL 3

Variables
ResizeArray< int >	exclusions_atom_i

ResizeArray< int >	exclusions_atom_j

int	numExclusion = 0

int	numLJPair = 0

int	numGaussPair = 0

bool	bool_negative_number_warning_flag = false

Macro Definition Documentation

◆ ANGLES

#define ANGLES 7

Definition at line 38 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ ANGLETYPES

#define ANGLETYPES 9

Definition at line 40 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ ANGSTROMS_PER_NM

#define ANGSTROMS_PER_NM 10

Definition at line 13 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ ATOMS

#define ATOMS 1

Definition at line 32 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ ATOMTYPES

#define ATOMTYPES 8

Definition at line 39 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ BONDS

#define BONDS 5

Definition at line 36 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ BONDTYPES

#define BONDTYPES 6

Definition at line 37 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ CODE_REDUNDANT

#define CODE_REDUNDANT 0

Definition at line 48 of file GromacsTopFile.C.

◆ DEFAULTS

#define DEFAULTS 12

Definition at line 43 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ DIHEDRALS

#define DIHEDRALS 10

Definition at line 41 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ DIHEDRALTYPES

#define DIHEDRALTYPES 11

Definition at line 42 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ EXCLUSIONS

#define EXCLUSIONS 15

Definition at line 46 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ JOULES_PER_CALORIE

#define JOULES_PER_CALORIE 4.184

Definition at line 12 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ LINESIZE

#define LINESIZE 200

Definition at line 28 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ MIN_DEBUG_LEVEL

#define MIN_DEBUG_LEVEL 3

Definition at line 51 of file GromacsTopFile.C.

◆ MOLECULES

#define MOLECULES 3

Definition at line 34 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ MOLECULETYPE

#define MOLECULETYPE 2

Definition at line 33 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ NONBOND

#define NONBOND 13

Definition at line 44 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ PAIRS

#define PAIRS 14

Definition at line 45 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ SYSTEM

#define SYSTEM 4

Definition at line 35 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ UNKNOWN

#define UNKNOWN 0

Definition at line 31 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

Variable Documentation

◆ bool_negative_number_warning_flag

bool bool_negative_number_warning_flag = false

Definition at line 61 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

◆ exclusions_atom_i

ResizeArray<int> exclusions_atom_i

Definition at line 56 of file GromacsTopFile.C.

Referenced by GromacsTopFile::getExclusions(), and GromacsTopFile::GromacsTopFile().

◆ exclusions_atom_j

ResizeArray<int> exclusions_atom_j

Definition at line 57 of file GromacsTopFile.C.

Referenced by GromacsTopFile::getExclusions(), and GromacsTopFile::GromacsTopFile().

◆ numExclusion

int numExclusion = 0

Definition at line 58 of file GromacsTopFile.C.

Referenced by GromacsTopFile::getNumExclusions(), and GromacsTopFile::GromacsTopFile().

◆ numGaussPair

int numGaussPair = 0

Definition at line 60 of file GromacsTopFile.C.

Referenced by PairTable::addPairGaussType2(), GromacsTopFile::getNumGaussPair(), GromacsTopFile::getNumPair(), PairTable::getPairGaussArrays2(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

◆ numLJPair

int numLJPair = 0

Definition at line 59 of file GromacsTopFile.C.

Referenced by PairTable::addPairLJType2(), GromacsTopFile::getNumLJPair(), GromacsTopFile::getNumPair(), PairTable::getPairLJArrays2(), Molecule::receive_Molecule(), and Molecule::send_Molecule().