blob: 0c8892fac695ea6d1a4ffb45e6c33ce70429e61a (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
|
// Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
#ifndef GLOBALS_H_INCLUDED
#define GLOBALS_H_INCLUDED
#define RCSID_GLOBALS_H "$Id$"
extern int debug_flags;
extern int Interrupted;
extern struct xyz Center;
extern struct xyz Bbox[2];
extern int Iteration;
extern char *CommandLine;
// definitions for command line args
extern int ToMinimize;
extern int IterPerFrame;
extern int NumFrames;
extern int DumpAsText;
extern int DumpIntermediateText;
extern int PrintFrameNums;
extern int OutputFormat;
extern int KeyRecordInterval;
extern int DirectEvaluate;
extern int QuadraticStretchPotential;
extern int PrintPotentialEnergy;
extern float ExcessiveEnergyLevel;
extern char *IDKey;
extern char *InputFileName;
extern char *OutputFileName;
extern char *TraceFileName;
extern char *BaseFileName;
extern char *GromacsOutputBaseName;
extern char *PathToCpp;
extern char *SystemParametersFileName;
extern char *AmberBondedParametersFileName;
extern char *AmberNonbondedParametersFileName;
extern char *AmberChargesFileName;
extern int QualityWarningLevel;
extern float SimpleMovieForceScale;
extern double MinimizeThresholdCutoverRMS;
extern double MinimizeThresholdCutoverMax;
extern double MinimizeThresholdEndRMS;
extern double MinimizeThresholdEndMax;
extern double VanDerWaalsCutoffRadius;
extern double VanDerWaalsCutoffFactor;
extern int EnableElectrostatic;
extern int NeighborSearching;
extern int TimeReversal;
extern double ThermostatGamma;
extern double ThermostatG1;
extern int UseAMBER;
extern int TypeFeedback;
extern int LoadedSystemParameters;
extern char *UserParametersFileName;
extern int LoadedUserParameters;
extern FILE *OutputFile;
extern FILE *TraceFile;
extern int Count;
// have we warned the user about too much energy in a dynamics run?
// Each warning location warns only if ExcessiveEnergyWarning is zero.
// If it warns, it increments ExcessiveEnergyWarningThisFrame. After
// each dynamics frame, ExcessiveEnergyWarning is set if
// ExcessiveEnergyWarningThisFrame is non-zero.
extern int ExcessiveEnergyWarning;
extern int ExcessiveEnergyWarningThisFrame;
// have we warned the user about using a generic/guessed force field parameter?
extern int ComputedParameterWarning;
extern int InterruptionWarning;
extern int _last_iteration;
/** constants: timestep (.1 femtosecond), scale of distance (picometers) */
extern double Dt;
extern double Dx;
extern double Dmass; // units of mass vs. kg
extern double Temperature; /* Kelvins */
extern const double Boltz; /* k, in J/K */
extern const double Pi;
extern const double COULOMB; // aJ pm e^-2
extern const double MinElectrostaticSensitivity; // aJ
extern const double DielectricConstant; // unitless
extern double totClipped; // internal thermostat for numerical stability
extern void reinit_globals(void);
extern void constrainGlobals(void);
extern void printGlobals(void);
#endif /* GLOBALS_H_INCLUDED */
|
