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// Copyright 2005 Nanorex, Inc. See LICENSE file for details.
/* factor for a unit vector given length squared -- rtned in uf, i is temp */
/** tables and setup function for same */
double uft1[UFTLEN], uft2[UFTLEN];
double uffunc(double uf) {
return 1.0/sqrt(uf);
}
from main() before setupPositionsArrays:
maktab(uft1, uft2, uffunc, UFSTART, UFTLEN, UFSCALE);
/** data for the 5-carbon test molecule */
struct xyz diam[5]=
{{0.0, 0.0, 0.0},
{176.7, 176.7, 0.0},
{176.7, 0.0, 176.7},
{0.0, 176.7, 176.7},
{88.33, 88.33, 88.33}};
int PartNo=0, DisplayStyle=1; /* 0 nothing, 1 ball/stick, 2 vdW surface */
int findbond(int btyp) {
int i;
if (btyp < 0)
btyp = -btyp;
for (i=0; i < BSTABSIZE; i++)
if (bstab[i].typ == btyp)
return i;
// fprintf(stderr, "Bond type %d not found\n",btyp);
return -1;
}
int findtorq(int btyp1, int btyp2) {
int i;
for (i=0; i < BENDATASIZE; i++) {
if (iabs(bendata[i].b1typ) == iabs(btyp1) &&
iabs(bendata[i].b2typ) == iabs(btyp2)) return i;
if (iabs(bendata[i].b1typ) == iabs(btyp2) &&
iabs(bendata[i].b2typ) == iabs(btyp1)) return i;
}
// fprintf(stderr, "Bend type %d-%d not found\n",btyp1,btyp2);
return 0; // the default bend type
}
// printers.c
// unused
static void pbontyp(FILE *f, struct bsdata *ab) {
fprintf(f, "Bond between %d / %d of order %d: type %d, length %f, stiffness %f\n table %d, start %f, scale %d\n",
ab->a1,ab->a2,ab->ord,ab->typ,ab->r0,ab->ks,
ab->table,ab->start,ab->scale);
}
//unused
static void bondump(FILE *f) { /* gather bond statistics */
int histo[50][23], totno[50], btyp, i, j, k, n;
double r, perc, means[50];
struct bondStretch *bt;
for (i=0; i<50; i++) {
totno[i] = 0;
means[i] = 0.0;
for (j=0; j<23; j++)
histo[i][j]=0;
}
for (i=0; i<Nexbon; i++) {
bt=bond[i].type;
// XXX btyp = bt-bstab;
totno[btyp]++;
r=vlen(vdif(Positions[bond[i].an1], Positions[bond[i].an2]));
means[btyp] += r;
perc = (r/bt->r0)*20.0 - 8.5;
k=(int)perc;
if (k<0) k=0;
if (k>22) k=22;
histo[btyp][k]++;
}
for (i=0; i<BSTABSIZE; i++) if (totno[i]) {
fprintf(f, "Bond type %s-%s, %d occurences, mean %.2f pm:\n",
periodicTable[bstab[i].a1].symbol, periodicTable[bstab[i].a2].symbol, totno[i],
means[i]/(double)totno[i]);
for (j=0; j<23; j++) {
if ((j-1)%10) fprintf(f, " |");
else fprintf(f, "-+");
n=(80*histo[i][j])/totno[i];
if (histo[i][j] && n==0) fprintf(f, ".");
for (k=0; k<n; k++) fprintf(f, "M");
fprintf(f, "\n");
}}
fprintf(f, "Iteration %d\n",Iteration);
}
// unused
static void pangben(FILE *f, struct angben *ab) {
fprintf(f, "Bend between %d / %d: kb=%.2f, th0=%.2f\n",
ab->b1typ,ab->b2typ,ab->kb,ab->theta0);
}
// unused
static void speedump(FILE *f) { /* gather bond statistics */
int histo[20], iv, i, j, k, n;
double v, eng, toteng=0.0;
for (i=0; i<21; i++) {
histo[i]=0;
}
for (i=0; i<Nexatom; i++) {
v=vlen(vdif(OldPositions[i],Positions[i]));
eng= atom[i].energ*v*v;
toteng += eng;
iv=(int)(eng*1e21);
if (iv>20) iv=20;
histo[iv]++;
}
fprintf(f, "Kinetic energies:\n");
for (j=0; j<21; j++) {
if (j%5) fprintf(f, " |");
else fprintf(f, "-+");
n=(70*histo[j])/Nexatom;
if (histo[j] && n==0) fprintf(f, ".");
for (k=0; k<n; k++) fprintf(f, "M");
fprintf(f, "\n");
}
fprintf(f, "Iteration %d, KE %e --> %e\n",Iteration,TotalKE,FoundKE);
}
// simulator.h
/* indexed by element number */
struct atomtype {
/** in 1e-27 kg */
double mass;
/** in Angstroms */
double rvdw;
/** in zJ */
double evdw;
/** number of bonds */
int nbonds;
/** covalent radius */
double rcovalent;
/** element's symbol on periodic table */
char *symbol;
};
/* data for a stretch bond type */
struct bsdata {
/** bond type, atom types & order */
int typ, ord, a1, a2;
/** stiffness N/m */
double ks;
/** base radius pm */
double r0;
/** Morse/Lippincott PE parameters */
double de,beta;
/** interpolation table stuff */
double start;
struct dtab *table;
int scale;
};
/* bond angle bending data */
struct angben {
/** bondtypes, negative if bond's a2 is common */
int b1typ, b2typ;
/** kb in N/m */
double kb;
/** in radians */
double theta0;
};
/*
#define benrec(a1,o1,ac,o2,a2,kb,th) {bontyp(o1,ac,a1),bontyp(o2,ac,a2),\
kb*6.36e-2, th, 0.0, NULL, NULL, 0}
*/
// convert Ktheta from zJ to yJ, see
#define benrec(a1,ac,a2,kb,th) {bontyp(1,ac,a1),bontyp(1,ac,a2),\
kb*1000.0, th}
struct dtab { /* two interpolation tables */
double t1[TABLEN], t2[TABLEN];
};
/* mol.c */
extern struct vdWbuf vanderRoot;
extern double uft1[200];
extern double uft2[200];
extern double uffunc(double uf);
//extern struct xyz f;
extern struct xyz diam[5];
// extern char *elname[37];
#if 0
extern int findbond(int btyp);
extern int findtorq(int btyp1, int btyp2);
#endif
extern void makbon0(int a, int b, int ord);
extern void makbon1(int n);
extern void makvander0(int a1, int a2);
extern void makvander1(struct vdWbuf *buf, int n);
extern void calcloop(int iters);
extern void minimize(int NumFrames);
extern void keyboard(unsigned char key, int x, int y);
extern int main(int argc, char **argv);
/* display.c */
extern void display(void);
extern void init(void);
extern void display_init(int *argc, char *argv[]);
extern void display_mainloop(void);
// interpolate.c
void testInterpolateBondStretch(int ord, int a1, int a2)
{
int i;
double start;
double scale;
double *t1, *t2;
double rSquared;
double lowR, highR;
double lowRSquare;
double highRSquare;
double epsilon;
int steps;
int k;
double fac;
double func;
i = findbond(bontyp(ord, a1, a2));
R0 = bstab[i].r0;
Ks = bstab[i].ks;
De = bstab[i].de;
Beta = bstab[i].beta;
printf("# R0: %e Ks: %e De: %e Beta: %e\n", R0, Ks, De, Beta);
/* table setup for stretch, to be moved out of loop */
start=bstab[i].start;
scale=bstab[i].scale;
t1=bstab[i].table->t1;
t2=bstab[i].table->t2;
printf("# start: %e scale: %e\n", start, scale);
lowR = R0 * 0.496;
highR = R0 * 1.5;
steps = 10000;
lowRSquare = lowR * lowR;
highRSquare = highR * highR;
//highRSquare = TABLEN * scale * 1.5 + start;
epsilon = (highRSquare - lowRSquare) / steps ;
for (rSquared=lowRSquare; rSquared<highRSquare; rSquared += epsilon) {
k=(int)(rSquared-start)/scale;
if (k<0) {
fac=t1[0]+rSquared*t2[0];
} else if (k>=TABLEN) {
fac = t1[TABLEN-1]+((TABLEN-1)*scale+start)*t2[TABLEN-1];
} else {
fac=t1[k]+rSquared*t2[k];
}
// table lookup equivalent to: fac=lippmor(rSquared)
func = lippmor(rSquared);
printf("%e %e %e\n", sqrt(rSquared), fac, func);
}
exit(0);
}
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