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// Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
#ifndef NEWTABLES_H_INCLUDED
#define NEWTABLES_H_INCLUDED
#define RCSID_NEWTABLES_H "$Id$"
/** table length for bond stretch/bending functions */
#define TABLEN 150
#define QUALITY_INTERPOLATED 4
#define QUALITY_GUESSED 3
#define QUALITY_INACCURATE 0
struct interpolationTable {
double start;
double scale;
// y = ax^3 + bx^2 + cx + d or...
// y = ((ax + b)x + c)x + d
// y' = 3ax^2 + 2bx + c or...
// y' = (3ax + 2b)x + c
double a[TABLEN];
double b[TABLEN];
double c[TABLEN];
double d[TABLEN];
};
struct bondStretch
{
char *bondName;
/** bond type, atom types & order */
//int typ, ord, a1, a2;
double ks; // stiffness in N/m
double r0; // base radius in pm, or 1e-12 m
double de; // aJ, or 1e-18 J
double beta; // sqrt(ks/2 de), 1e12 m^-1, for Morse
double inflectionR; // r value in pm where d^2(Lippincott(r)) / dr^2 == 0
// These are the indices into the interpolation tables where the
// potential exceeds ExcessiveEnergyLevel. If a dynamics run
// references table entries outside these bounds, a warning will be
// emitted.
int maxPhysicalTableIndex;
int minPhysicalTableIndex;
// For minimize, the potential function extends as a cubic
// polynomial beyond the end of the interpolation table:
// potential = potentialExtensionA
// + potentialExtensionB * r
// + potentialExtensionC * r^2
// + potentialExtensionD * r^3
double potentialExtensionA;
double potentialExtensionB;
double potentialExtensionC;
double potentialExtensionD;
int parameterQuality; // how sure are we of these parameters
// Non-zero if this stretch should be pure quadratic, instead of
// Lippincott-Morse. Set to 1 if GROMACS should consider this
// stretch to be a chemical bond (for purposes of excluding
// non-bonded interactions), or 6 for a quadratic potential without
// the bond.
int quadratic;
int warned; // set to non-zero if a warning about using this entry has been printed
struct interpolationTable LippincottMorse;
};
struct vanDerWaalsParameters
{
char *vdwName;
double rvdW; // in pm (1e-12 m)
double evdW; // in zJ (1e-21 J)
// Transition interval for smooth cutoff. Normal function is used
// for 0<r<cutoffRadiusStart. For
// cutoffRadiusStart<r<cutoffRadiusEnd the function is multiplied by
// a smooth transition function. For cutoffRadiusEnd<r, the value
// is identically zero. See smoothCutoff() in interpolate.c. If
// cutoffRadiusEnd<=cutoffRadiusStart, no transition function is
// used, instead, the potential is translated by vInfinity, so it
// reaches zero at cutoffRadiusEnd.
double cutoffRadiusStart; // in pm (1e-12 m)
double cutoffRadiusEnd; // in pm (1e-12 m)
// If no transition function is used, we subtract vInfinity from the
// potential, so it reaches zero at the end of the interpolation
// table, rather than have a step there.
// XXX This changes the depth of the potential well, which may be a problem.
double vInfinity; // potential at "infinity", the end of the interpolation table
// Index into the interpolation tables where the potential exceeds
// ExcessiveEnergyLevel. If a dynamics run references a table entry
// at less than this index, a warning will be emitted.
int minPhysicalTableIndex;
struct interpolationTable Buckingham;
};
struct electrostaticParameters
{
char *electrostaticName;
double k; // in aJ pm (1e-30 J m), potential is k/r, gradient is -k/r^2
double vInfinity; // potential at "infinity", the end of the interpolation table
double cutoffRadiusStart; // in pm (1e-12 m)
double cutoffRadiusEnd; // in pm (1e-12 m)
// Index into the interpolation tables where the potential exceeds
// ExcessiveEnergyLevel. If a dynamics run references a table entry
// at less than this index, a warning will be emitted.
int minPhysicalTableIndex;
struct interpolationTable Coulomb;
};
struct deTableEntry
{
double de;
};
struct bendData
{
char *bendName;
double kb; // stiffness in yJ / rad^2 (1e-24 J/rad^2)
double theta0;
double cosTheta0;
int parameterQuality; // how sure are we of these parameters
int warned; // set to non-zero if a warning about using this entry has been printed
};
#define MAX_ELEMENT 109
struct atomType
{
int protons;
int group;
int period;
char *symbol;
char *name;
double mass; // yg, or yoctograms, or 1e-24 g
double vanDerWaalsRadius; // Angstroms, or 1e-10 m
double e_vanDerWaals; // zJ, or zeptoJoules, or 1e-21 J
int n_bonds;
double covalentRadius; // pm, or 1e-12 m
double charge; // multiple of proton charge
int refCount;
int isVirtual; // type for a gromacs virtual interaction site
struct atomType *parent;
};
struct patternParameter
{
double value;
double angleUnits;
char *stringValue;
};
extern int numStruts;
extern struct atomType *getAtomTypeByIndex(int atomTypeIndex);
extern int isAtomTypeValid(int atomTypeIndex);
extern struct bondStretch *newBondStretch(char *bondName,
double ks,
double r0,
double de,
double beta,
double inflectionR,
int quality,
int quadratic);
extern struct bendData *newBendData(char *bendName, double kb, double theta0, int quality);
extern struct atomType *getAtomTypeByName(char *symbol);
extern struct patternParameter *getPatternParameter(char *name);
extern void initializeBondTable(void);
extern void destroyBondTable(void);
extern void reInitializeBondTable(void);
extern double getBondEquilibriumDistance(int element1, int element2, char bondOrder);
extern struct bondStretch *getBondStretch(int element1, int element2, char bondOrder);
extern struct bendData *getBendData(int element_center,
enum hybridization centerHybridization,
int element1,
char bondOrder1,
int element2,
char bondOrder2);
extern struct vanDerWaalsParameters *getVanDerWaalsTable(int element1, int element2);
extern struct electrostaticParameters *getElectrostaticParameters(int element1, int element2);
#endif
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