common.h

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00001 
00007 /*
00008    common definitions for namd.
00009 */
00010 
00011 #ifndef COMMON_H
00012 #define COMMON_H
00013 
00014 #if !defined(WIN32) || defined(__CYGWIN__)
00015 #include <unistd.h>
00016 #endif
00017 #include <stdio.h>
00018 #include <limits.h>
00019 
00020 #if ( INT_MAX == 2147483647L )
00021 typedef int     int32;
00022 #elif ( SHRT_MAX == 2147483647L )
00023 typedef short   int32;
00024 #endif
00025 
00026 #ifdef _MSC_VER
00027 typedef __int64 int64;
00028 #else
00029 #if ( INT_MAX == 9223372036854775807LL )
00030 typedef int int64;
00031 #elif ( LONG_MAX == 9223372036854775807LL )
00032 typedef long int64;
00033 #else
00034 typedef long long int64;
00035 #endif
00036 #endif
00037 
00038 #if defined(PLACEMENT_NEW)
00039 void * ::operator new (size_t, void *p) { return p; }
00040 #elif defined(PLACEMENT_NEW_GLOBAL)
00041 void * operator new (size_t, void *p) { return p; }
00042 #endif
00043 
00044 #define COULOMB 332.0636
00045 #define BOLTZMANN 0.001987191
00046 #define TIMEFACTOR 48.88821
00047 #define PRESSUREFACTOR 6.95E4
00048 #define PDBVELFACTOR 20.45482706
00049 #define PDBVELINVFACTOR (1.0/PDBVELFACTOR)
00050 #define PNPERKCALMOL 69.479
00051 
00052 /* Some plagtforms don't have nearbyint or round, so we'll define one */
00053 /* that works everywhere */
00054 #ifdef POWERPC_TANINT
00055 extern "builtin" double __tanint(double); //IEEE round
00056 #define mynearbyint(x)  __tanint(x)
00057 #else
00058 #define mynearbyint(x)  floor((x)+0.5)
00059 #endif
00060 
00061 #ifndef PI
00062 #define PI      3.141592653589793
00063 #endif
00064 
00065 #ifndef TWOPI
00066 #define TWOPI   2.0 * PI
00067 #endif
00068 
00069 #ifndef ONE
00070 #define ONE     1.000000000000000
00071 #endif
00072 
00073 #ifndef ZERO
00074 #define ZERO    0.000000000000000
00075 #endif
00076 
00077 #ifndef SMALLRAD
00078 #define SMALLRAD      0.0005
00079 #endif
00080 
00081 #ifndef SMALLRAD2
00082 #define SMALLRAD2     SMALLRAD*SMALLRAD
00083 #endif
00084 
00085 /* Define the size for Real and BigReal.  Real is usually mapped to float */
00086 /* and BigReal to double.  To get BigReal mapped to float, use the        */
00087 /* -DSHORTREALS compile time option                                       */
00088 typedef float   Real;
00089 
00090 #ifdef SHORTREALS
00091 typedef float   BigReal;
00092 #else
00093 typedef double  BigReal;
00094 #endif
00095 
00096 #ifndef FALSE
00097 #define FALSE 0
00098 #define TRUE 1
00099 #endif
00100 
00101 #ifndef NO
00102 #define NO 0
00103 #define YES 1
00104 #endif
00105 
00106 #ifndef STRINGNULL
00107 #define STRINGNULL '\0'
00108 #endif
00109 
00110 #define MAX_NEIGHBORS 27
00111 
00112 typedef int Bool;
00113 
00114 class Communicate;
00115 
00116 // global functions
00117 void NAMD_quit(const char *);
00118 void NAMD_die(const char *);
00119 void NAMD_err(const char *);  // also prints strerror(errno)
00120 void NAMD_bug(const char *);
00121 int NAMD_file_exists(const char *filename);
00122 void NAMD_backup_file(const char *filename, const char *extension = 0);
00123 int NAMD_open_text(const char *fname, int append=0);
00124 void NAMD_write(int fd, const char *buf, size_t count, const char *fname = "in NAMD_write()"); // NAMD_die on error
00125 void NAMD_close(int fd, const char *fname);
00126 char *NAMD_stringdup(const char *);
00127 FILE *Fopen(const char *filename, const char *mode);
00128 int  Fclose(FILE *fout);
00129 
00130 // message tags
00131 #define SIMPARAMSTAG    100     //  Tag for SimParameters class
00132 #define STATICPARAMSTAG 101     //  Tag for Parameters class
00133 #define MOLECULETAG     102     //  Tag for Molecule class
00134 #define FULLTAG 104
00135 #define FULLFORCETAG 105
00136 #define DPMTATAG 106
00137 #define GRIDFORCEGRIDTAG 107
00138 #define COMPUTEMAPTAG 108
00139 
00140 #define CYCLE_BARRIER   0
00141 #define PME_BARRIER     0
00142 #define STEP_BARRIER    0
00143 
00144 #define USE_BARRIER   (CYCLE_BARRIER || PME_BARRIER || STEP_BARRIER)
00145 
00146 
00147 // DMK - Atom Separation (water vs. non-water)
00148 //   Setting this define to a non-zero value will cause the
00149 //   HomePatches to separate the hydrogen groups in their
00150 //   HomePatch::atom lists (all water molecules first, in arbitrary
00151 //   order, followed by all non-waters, in arbitrary order).
00152 #define NAMD_SeparateWaters    0
00153 
00154 // DMK - Atom Sort
00155 //   Setting this define to a non-zero value will cause the nonbonded compute
00156 //   objects (pairs, not selfs) to sort the atoms along a line connecting the
00157 //   center of masses of the two patches.  This is only done during timesteps
00158 //   where the pairlists are being generated.  As the pairlist is being
00159 //   generated, once an atom that is far enough away along the line is found,
00160 //   the remaining atoms are automatically skipped (avoiding a distance
00161 //   calculation/check for them).
00162 // NOTE: The "less branches" flag toggles between two versions of merge sort.
00163 //   When it is non-zero, a version that has fewer branches (but more integer
00164 //   math) is used.  This version may or may not be faster or some architectures.
00165 #define NAMD_ComputeNonbonded_SortAtoms                   1
00166   #define NAMD_ComputeNonbonded_SortAtoms_LessBranches    1
00167 
00168 // plf -- alternate water models
00169 #define WAT_TIP3 0
00170 #define WAT_TIP4 1
00171 #define WAT_SWM4 2  /* Drude model (5 charge sites) */
00172 
00173 
00174 #include "converse.h"
00175 
00176 #endif
00177 

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