GromacsTopFile.C File Reference

#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.

Defines

#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


Define Documentation

#define ANGLES   7

Definition at line 38 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define ANGLETYPES   9

Definition at line 40 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define ANGSTROMS_PER_NM   10

Definition at line 13 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define ATOMS   1

Definition at line 32 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define ATOMTYPES   8

Definition at line 39 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define BONDS   5

Definition at line 36 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define BONDTYPES   6

Definition at line 37 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define CODE_REDUNDANT   0

Definition at line 48 of file GromacsTopFile.C.

#define DEFAULTS   12

Definition at line 43 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define DIHEDRALS   10

Definition at line 41 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define DIHEDRALTYPES   11

Definition at line 42 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define EXCLUSIONS   15

Definition at line 46 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define JOULES_PER_CALORIE   4.184

Definition at line 12 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define LINESIZE   200

Definition at line 28 of file GromacsTopFile.C.

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

#define MIN_DEBUG_LEVEL   3

Definition at line 51 of file GromacsTopFile.C.

#define MOLECULES   3

Definition at line 34 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define MOLECULETYPE   2

Definition at line 33 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define NONBOND   13

Definition at line 44 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define PAIRS   14

Definition at line 45 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define SYSTEM   4

Definition at line 35 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

#define UNKNOWN   0

Definition at line 31 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().


Variable Documentation

bool bool_negative_number_warning_flag = false

Definition at line 61 of file GromacsTopFile.C.

Referenced by GromacsTopFile::GromacsTopFile().

ResizeArray<int> exclusions_atom_i

Definition at line 56 of file GromacsTopFile.C.

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

ResizeArray<int> exclusions_atom_j

Definition at line 57 of file GromacsTopFile.C.

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

int numExclusion = 0

Definition at line 58 of file GromacsTopFile.C.

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

int numGaussPair = 0

Definition at line 60 of file GromacsTopFile.C.

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

int numLJPair = 0

Definition at line 59 of file GromacsTopFile.C.

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


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