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common.h 4.01 KiB
/**
*** Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by
*** The Board of Trustees of the University of Illinois.
*** All rights reserved.
**/
/*
common definitions for namd.
*/
#ifndef COMMON_H
#define COMMON_H
#include <sys/stat.h>
#if !defined(WIN32) || defined(__CYGWIN__)
#include <unistd.h>
#endif
#include <stdio.h>
#include <limits.h>
#if ( INT_MAX == 2147483647L )
typedef int int32;
#elif ( SHRT_MAX == 2147483647L )
typedef short int32;
#endif
#ifdef _MSC_VER
typedef __int64 int64;
#else
#if ( INT_MAX == 9223372036854775807LL )
typedef int int64;
#elif ( LONG_MAX == 9223372036854775807LL )
typedef long int64;
#else
typedef long long int64;
#endif
#endif
#if defined(PLACEMENT_NEW)
void * ::operator new (size_t, void *p) { return p; }
#elif defined(PLACEMENT_NEW_GLOBAL)
void * operator new (size_t, void *p) { return p; }
#endif
#define COLOUMB 332.0636f
#define BOLTZMAN 0.001987191f
#define TIMEFACTOR 48.88821f
#define PRESSUREFACTOR 6.95E4f
#define PDBVELFACTOR 20.45482706f
#define PDBVELINVFACTOR (1.0f/PDBVELFACTOR)
#define PNPERKCALMOL 69.479f
#ifndef PI
#define PI 3.141592653589793f
#endif
#ifndef TWOPI
#define TWOPI 2.0f * PI
#endif
#ifndef ONE
#define ONE 1.000000000000000f
#endif
#ifndef ZERO
#define ZERO 0.000000000000000f
#endif
#ifndef SMALLRAD#define SMALLRAD 0.0005f
#endif
#ifndef SMALLRAD2
#define SMALLRAD2 SMALLRAD*SMALLRAD
#endif
/* Define the size for Real and BigReal. Real is usually mapped to float */
/* and BigReal to double. To get BigReal mapped to float, use the */
/* -DSHORTREALS compile time option */
typedef float Real;
#ifdef SHORTREALS
typedef float BigReal;
#else
typedef float BigReal;
#endif
#ifndef FALSE
#define FALSE 0
#define TRUE 1
#endif
#ifndef NO
#define NO 0
#define YES 1
#endif
#ifndef STRINGNULL
#define STRINGNULL '\0'
#endif
#define MAX_NEIGHBORS 27
typedef int Bool;
class Communicate;
// global functions
void NAMD_quit(const char *);
void NAMD_die(const char *);
void NAMD_err(const char *); // also prints strerror(errno)
void NAMD_bug(const char *);
void NAMD_backup_file(const char *filename, const char *extension = 0);
// void NAMD_write(int fd, const void *buf, size_t count); // NAMD_die on error
char *NAMD_stringdup(const char *);
FILE *Fopen(const char *filename, const char *mode);
int Fclose(FILE *fout);
/*int stat(const char* fn, struct stat* buf)
{
return stat((char*)fn, buf);
}*/
// message tags
#define SIMPARAMSTAG 100 // Tag for SimParameters class
#define STATICPARAMSTAG 101 // Tag for Parameters class
#define MOLECULETAG 102 // Tag for Molecule class
#define FULLTAG 104
#define FULLFORCETAG 105
#define DPMTATAG 106
#define CYCLE_BARRIER 0
#define PME_BARRIER 0
#define STEP_BARRIER 0
#define USE_BARRIER (CYCLE_BARRIER || PME_BARRIER || STEP_BARRIER)
// DMK - Atom Separation (water vs. non-water)
// Setting this define to a non-zero value will cause the
// HomePatches to separate the hydrogen groups in their
// HomePatch::atom lists (all water molecules first, in arbitrary
// order, followed by all non-waters, in arbitrary order).
#define NAMD_SeparateWaters 0
// DMK - Atom Sort
// Setting this define to a non-zero value will cause the nonbonded compute
// objects (pairs, not selfs) to sort the atoms along a line connecting the
// center of masses of the two patches. This is only done during timesteps
// where the pairlists are being generated. As the pairlist is being
// generated, once an atom that is far enough away along the line is found,
// the remaining atoms are automatically skipped (avoiding a distance
// calculation/check for them).
// NOTE: The "less branches" flag toggles between two versions of merge sort.
// When it is non-zero, a version that has fewer branches (but more integer
// math) is used. This version may or may not be faster or some architectures.
#define NAMD_ComputeNonbonded_SortAtoms 0
#define NAMD_ComputeNonbonded_SortAtoms_LessBranches 1
// plf -- alternate water models
#define WAT_TIP3 0
#define WAT_TIP4 1
#endif