void write_grid_file(void) {
/* The following subroutine saves the depth, reduced gravity of */
/* each interface, the potential density of each layer, and the */
/* Coriolis parameter. A variety of metric terms are written to a */
/* separate file. */
char filename[40]; /* The file name of the save file. */
char filepath[120]; /* The path (dir/file) to the file. */
int i, j, cdfid, timeid;
size_t err = 1;
struct varcdfinfo varinfo[10];
/* vardesc is a structure defined in HIM_io.h. The elements of */
/* this structure, in order, are: (1) the variable name for the NetCDF*/
/* file; (2) the variable's long name; (3) a character indicating the */
/* horizontal grid, which may be '1' (column), 'h', 'q', 'u', or 'v', */
/* for the corresponding C-grid variable; (4) a character indicating */
/* the vertical grid, which may be 'L' (layer), 'i' (interface), */
/* '2' (mixed-layers), or '1' (no vertical location); (5) a character */
/* indicating the time levels of the field, which may be 's' (snap- */
/* shot), 'a' (average between snapshots), 'm' (monthly average), or */
/* '1' (no time variation); (6) the variable's units; and (7) a */
/* character indicating the size in memory to write, which may be */
/* 'd' (8-byte) or 'f' (4-byte). */
vardesc vars[4] = {
{"D","Basin Depth",'h','1','1',"meter", 'd'},
{"g","Reduced gravity",'1','L','1',"meter second-2", 'd'},
{"R","Target Potential Density",'1','L','1',"kilogram meter-3", 'd'},
{"f","Coriolis Parameter",'q','1','1',"second-1", 'd'}
};
sprintf(filename,"D.%d.%d.%d",NXTOT,NYTOT,NZ);
strcpy(filepath, directory);
strcat(filepath, filename);
create_file(filepath, vars, 4, &cdfid, &timeid, varinfo);
err *= write_field(cdfid, vars[0], varinfo[0], 0, D[0]);
err *= write_field(cdfid, vars[1], varinfo[1], 0, g);
err *= write_field(cdfid, vars[2], varinfo[2], 0, Rlay);
err *= write_field(cdfid, vars[3], varinfo[3], 0, f[0]);
close_file(&cdfid);
if (err == 0)
printf("Problems saving general parameters.\n");
{
/* ### REVISIT THIS PART OF THE ROUTINE AFTER METRICS... ### */
double out[NYMEM][NXMEM]; /* An array for output. */
extern double hmask[NYMEM][NXMEM];
vardesc vars2[10]={
{"geolatb","latitude at q points",'q','1','1',"degree",'d'},
{"geolonb","longitude at q points",'q','1','1',"degree",'d'},
{"wet", "land or ocean?", 'h','1','1',"none",'d'},
{"geolat", "latitude at h points", 'h','1','1',"degree",'d'},
{"geolon","longitude at h points",'h','1','1',"degree",'d'},
{"dxh","Zonal grid spacing at h points",'h','1','1',"m",'d'},
{"dxq","Zonal grid spacing at q points",'q','1','1',"m",'d'},
{"dyh","Meridional grid spacing at h points",'h','1','1',"m",'d'},
{"dyq","Meridional grid spacing at q points",'q','1','1',"m",'d'},
{"Ah","Area of h cells",'h','1','1',"m2",'d'},
};
sprintf(filename,"grid.%d.%d",NXTOT,NYTOT);
strcpy(filepath, directory);
strcat(filepath, filename);
create_file(filepath, vars2, 10, &cdfid, &timeid, varinfo);
err *= write_field(cdfid, vars2[0], varinfo[0], 0, geolatq[0]);
err *= write_field(cdfid, vars2[1], varinfo[1], 0, geolonq[0]);
err *= write_field(cdfid, vars2[2], varinfo[2], 0, hmask[0]);
err *= write_field(cdfid, vars2[3], varinfo[3], 0, geolath[0]);
err *= write_field(cdfid, vars2[4], varinfo[4], 0, geolonh[0]);
for (j=0;j<NYMEM;j++) for (i=0;i<NXMEM;i++) out[j][i]=DXh(j,i);
err *= write_field(cdfid, vars2[5], varinfo[5], 0, out[0]);
for (j=0;j<NYMEM;j++) for (i=0;i<NXMEM;i++) out[j][i]=DXq(j,i);
err *= write_field(cdfid, vars2[6], varinfo[6], 0, out[0]);
for (j=0;j<NYMEM;j++) for (i=0;i<NXMEM;i++) out[j][i]=DYh(j,i);
err *= write_field(cdfid, vars2[7], varinfo[7], 0, out[0]);
for (j=0;j<NYMEM;j++) for (i=0;i<NXMEM;i++) out[j][i]=DYq(j,i);
err *= write_field(cdfid, vars2[8], varinfo[8], 0, out[0]);
for (j=0;j<NYMEM;j++) for (i=0;i<NXMEM;i++) out[j][i]=DXDYh(j,i);
err *= write_field(cdfid, vars2[9], varinfo[9], 0, out[0]);
close_file(&cdfid);
if (err == 0)
printf("Problems saving latitude and longitude and wet.\n");
}
}
void tracer(int itts)
{
/* This subroutine time steps the tracer concentration. */
/* A positive definite scheme is used. */
double minslope; /* The maximum concentration slope per */
/* grid point consistent with mono- */
/* tonicity, in conc. (nondim.). */
double ***hvol; /* The cell volume of an h-element */
double slope[NXMEM+NYMEM][NTR]; /* The concentration slope per grid */
/* point in units of concentration (nondim.). */
double fluxtr[NXMEM+NYMEM][NTR];/* The flux of tracer across a */
/* boundary, in m3 * conc. (nondim.). */
double ***uhr; /* The remaining zonal and meridional */
double ***vhr; /* thickness fluxes, in m3.*/
double uhh[NXMEM]; /* uhh and vhh are the reduced fluxes */
double vhh[NYMEM]; /* during the current iteration, in m3.d */
double hup, hlos; /* hup is the upwind volume, hlos is the */
/* part of that volume that might be lost */
/* due to advection out the other side of */
/* the grid box, both in m3. */
double ts2;
double landvolfill; /* An arbitrary? nonzero cell volume, m3. */
double ***ear;
double ***ebr;
double ***wdh;
double bet[NXMEM]; /* bet and gam are variables used by the */
double gam[NZ][NXMEM]; /* tridiagonal solver. */
double hnew0[NXMEM]; /* The original topmost layer thickness, */
#if defined AGE2 || defined AGE3
// extern double hnew[NZ][NXMEM][NYMEM];
extern double ***hnew;
#else
double ***hnew;
#endif
double hlst1, Ihnew;
double hlst[NYMEM];
// double MLMIN = EPSILON; /* min depth for ML */
double MLMIN = 4.25;
double BLMIN = 0.20;
#ifdef ENTRAIN
double nts = dt/DT; /* number of timesteps (#day*86400/3600seconds) */
#endif
int i, j, k, m, ii, pstage;
int itt;
double fract1;
double fract2;
# ifdef WRTTS
double wrts;
# endif
hvol = alloc3d(NZ,NXMEM,NYMEM);
if(hvol == NULL) {
fprintf(stderr,"not enough memory for hvol!\n");
}
uhr = alloc3d(NZ,NXMEM,NYMEM);
if(uhr == NULL) {
fprintf(stderr,"not enough memory for uhr!\n");
}
vhr = alloc3d(NZ,NXMEM,NYMEM);
if(vhr == NULL) {
fprintf(stderr,"not enough memory for vhr!\n");
}
ear = alloc3d(NZ,NXMEM,NYMEM);
if(ear == NULL) {
fprintf(stderr,"not enough memory for ear!\n");
}
ebr = alloc3d(NZ,NXMEM,NYMEM);
if(ebr == NULL) {
fprintf(stderr,"not enough memory for ebr!\n");
}
wdh = alloc3d(NZ,NXMEM,NYMEM);
if(wdh == NULL) {
fprintf(stderr,"not enough memory for wdh!\n");
}
#if !defined AGE2 && !defined AGE3
hnew = alloc3d(NZ,NXMEM,NYMEM);
if(hnew == NULL) {
fprintf(stderr,"not enough memory for hnew!\n");
}
#endif
landvolfill = EPSILON*1000000.0; /* This is arbitrary. */
/* zonal re-entrance */
#pragma omp parallel
{
#pragma omp for private(j,k)
for (j=0;j<=NYMEM-1;j++) {
for (k=0;k<NZ;k++) {
uhtm[k][nx+1][j] = uhtm[k][2][j];
uhtm[k][nx+2][j] = uhtm[k][3][j];
uhtm[k][0][j] = uhtm[k][nx-1][j];
uhtm[k][1][j] = uhtm[k][nx][j];
vhtm[k][nx+1][j] = vhtm[k][2][j];
vhtm[k][nx+2][j] = vhtm[k][3][j];
vhtm[k][0][j] = vhtm[k][nx-1][j];
vhtm[k][1][j] = vhtm[k][nx][j];
}
for (k=0;k<NZ+1;k++) {
wd[k][nx+1][j] = wd[k][2][j];
wd[k][nx+2][j] = wd[k][3][j];
wd[k][0][j] = wd[k][nx-1][j];
wd[k][1][j] = wd[k][nx][j];
}
}
/* meridional re-entrance */
#pragma omp for private(i,k,ii)
for (i=2;i<=nx;i++) {
ii = 363 - i;
for (k=0;k<NZ;k++) {
uhtm[k][ii][ny+1] = (-1)*uhtm[k][i][ny];
uhtm[k][ii][ny+2] = (-1)*uhtm[k][i][ny-1];
vhtm[k][ii][ny+1] = (-1)*vhtm[k][i][ny];
vhtm[k][ii][ny+2] = (-1)*vhtm[k][i][ny-1];
}
for (k=0;k<NZ+1;k++) {
wd[k][ii][ny+1] = wd[k][i][ny];
wd[k][ii][ny+2] = wd[k][i][ny-1];
}
}
#pragma omp for private(i,j,k)
for (k=0;k<NZ;k++) {
/* Put the thickness fluxes into uhr and vhr. */
for (j=0;j<=ny+2;j++) {
for (i=0;i<=nx+2;i++) {
uhr[k][i][j] = uhtm[k][i][j]*dt;
vhr[k][i][j] = vhtm[k][i][j]*dt;
if (h[k][i][j] < EPSILON) {
h[k][i][j] = 1.0*EPSILON;
}
/* This line calculates the cell volume */
hvol[k][i][j] = DXDYh(i,j)*h[k][i][j];
hnew[k][i][j] = h[k][i][j];
}
}
}
/* calculate the diapycnal velocities at the interfaces */
/* if we read in the ea, eb and eaml variables */
/* Otherwise we read in wd directly */
#ifdef ENTRAIN
#pragma omp for private(i,j)
for (i=X0;i<=nx+1;i++)
for (j=Y0;j<=ny;j++)
wd[0][i][j] = nts*eaml[i][j];
#pragma omp for private(i,j,k)
for (k=1;k<NZ;k++) {
for (i=X0;i<=nx+1;i++)
for (j=Y0;j<=ny;j++)
wd[k][i][j] = nts*(ea[k][i][j] - eb[k-1][i][j]);
}
#endif
} // omp
#define STANDARD_ADVECTION
//#undef STANDARD_ADVECTION
#ifdef STANDARD_ADVECTION
/*
pstage=1;
print_tr(pstage);
*/
/* beginning of itt loop */
for (itt = 0; itt < NUM_ADV_ITER; itt++) {
/* big loop over k */
//ompfail
#pragma omp parallel
{
#pragma omp for private(i,j,k,m,minslope,slope,uhh,vhh,fluxtr,hup,hlos,ts2,hlst,hlst1,Ihnew)
for (k=0;k<NZ;k++)
{
/* To insure positive definiteness of the thickness at each */
/* iteration, the mass fluxes out of each layer are checked each */
/* time. This may not be very efficient, but it should be reliable. */
/* ============================================================ */
/* first advect zonally */
/* ============================================================ */
#ifndef ADV1D
for (j=Y1;j<=ny;j++) {
/* Calculate the i-direction profiles (slopes) of each tracer that */
/* is being advected. */
//#pragma omp for private(i,m,minslope)
for (i=X0;i<=nx+1;i++) {
for (m=0;m<NTR;m++) {
minslope = 4.0*((fabs(tr[m][k][i+1][j]-tr[m][k][i][j]) <
fabs(tr[m][k][i][j]-tr[m][k][i-1][j])) ?
(tr[m][k][i+1][j]-tr[m][k][i][j]) :
(tr[m][k][i][j]-tr[m][k][i-1][j]));
slope[i][m] = umask[i][j]*umask[i-1][j] *
(((tr[m][k][i+1][j]-tr[m][k][i][j]) *
(tr[m][k][i][j]-tr[m][k][i-1][j]) < 0.0) ? 0.0 :
((fabs(tr[m][k][i+1][j]-tr[m][k][i-1][j])<fabs(minslope)) ?
0.5*(tr[m][k][i+1][j]-tr[m][k][i-1][j]) : 0.5*minslope));
}
}
//#pragma omp barrier
/* Calculate the i-direction fluxes of each tracer, using as much */
/* the minimum of the remaining mass flux (uhr) and the half the mass */
/* in the cell plus whatever part of its half of the mass flux that */
/* the flux through the other side does not require. */
//#pragma omp for private(i,m,hup,hlos,ts2)
for (i=X0;i<=nx;i++) {
if (uhr[k][i][j] == 0.0) {
uhh[i] = 0.0;
for (m=0;m<NTR;m++) fluxtr[i][m] = 0.0;
}
else if (uhr[k][i][j] < 0.0) {
if (k==0 || k==1 ) {
hup = (hvol[k][i+1][j]-DXDYh(i+1,j)*MLMIN);
} else {
hup = (hvol[k][i+1][j]-DXDYh(i+1,j)*EPSILON);
}
hlos = D_MAX(0.0,uhr[k][i+1][j]);
if (((hup + uhr[k][i][j] - hlos) < 0.0) &&
((0.5*hup + uhr[k][i][j]) < 0.0)) {
uhh[i] = D_MIN(-0.5*hup,-hup+hlos);
}
else uhh[i] = uhr[k][i][j];
ts2 = 0.5*(1.0 + uhh[i]/hvol[k][i+1][j]);
for (m=0;m<NTR;m++) {
fluxtr[i][m] = uhh[i]*(tr[m][k][i+1][j] - slope[i+1][m]*ts2);
}
}
else {
if (k==0 || k==1 ) {
hup = (hvol[k][i][j]-DXDYh(i,j)*MLMIN);
} else {
hup = (hvol[k][i][j]-DXDYh(i,j)*EPSILON);
}
hlos = D_MAX(0.0,-uhr[k][i-1][j]);
if (((hup - uhr[k][i][j] - hlos) < 0.0) &&
((0.5*hup - uhr[k][i][j]) < 0.0)) {
uhh[i] = D_MAX(0.5*hup,hup-hlos);
}
else uhh[i] = uhr[k][i][j];
ts2 = 0.5*(1.0 - uhh[i]/hvol[k][i][j]);
for (m=0;m<NTR;m++) {
fluxtr[i][m] = uhh[i]*(tr[m][k][i][j] + slope[i][m]*ts2);
}
}
}
//#pragma omp barrier
/* Calculate new tracer concentration in each cell after accounting */
/* for the i-direction fluxes. */
uhr[k][X0][j] -= uhh[X0];
// #pragma omp barrier
//#pragma omp for private(i,m,hlst1,Ihnew)
for (i=X1;i<=nx;i++) {
if ((uhh[i] != 0.0) || (uhh[i-1] != 0.0))
{
uhr[k][i][j] -= uhh[i];
hlst1 = hvol[k][i][j];
hvol[k][i][j] -= (uhh[i] - uhh[i-1]);
Ihnew = 1.0 / hvol[k][i][j];
for (m=0;m<NTR;m++) {
tr[m][k][i][j] *= hlst1;
tr[m][k][i][j] = (tr[m][k][i][j] -
(fluxtr[i][m]-fluxtr[i-1][m])) * Ihnew;
}
}
}
// #pragma omp barrier
} /* j loop */
#endif
/* ============================================================ */
/* now advect meridionally */
/* ============================================================ */
#ifndef ADV1D
for (i=X1;i<=nx;i++) {
/* Calculate the j-direction profiles (slopes) of each tracer that */
/* is being advected. */
//#pragma omp for private(j,m,minslope)
for (j=Y0;j<=ny+1;j++) {
for (m=0;m<NTR;m++) {
minslope = 4.0*((fabs(tr[m][k][i][j+1]-tr[m][k][i][j]) <
fabs(tr[m][k][i][j]-tr[m][k][i][j-1])) ?
(tr[m][k][i][j+1]-tr[m][k][i][j]) :
(tr[m][k][i][j]-tr[m][k][i][j-1]));
slope[j][m] = vmask[i][j] * vmask[i][j-1] *
(((tr[m][k][i][j+1]-tr[m][k][i][j]) *
(tr[m][k][i][j]-tr[m][k][i][j-1]) < 0.0) ? 0.0 :
((fabs(tr[m][k][i][j+1]-tr[m][k][i][j-1])<fabs(minslope)) ?
0.5*(tr[m][k][i][j+1]-tr[m][k][i][j-1]) : 0.5*minslope));
}
}
// #pragma omp barrier
/* Calculate the j-direction fluxes of each tracer, using as much */
/* the minimum of the remaining mass flux (vhr) and the half the mass */
/* in the cell plus whatever part of its half of the mass flux that */
/* the flux through the other side does not require. */
//#pragma omp for private(j,m,hup,hlos,ts2)
for (j=Y0;j<=ny;j++) {
if (vhr[k][i][j] == 0.0) {
vhh[j] = 0.0;
for (m=0;m<NTR;m++) fluxtr[j][m] = 0.0;
}
else if (vhr[k][i][j] < 0.0) {
if (k==0 || k==1 ) {
hup = (hvol[k][i][j+1]-DXDYh(i,j+1)*MLMIN);
} else {
hup = (hvol[k][i][j+1]-DXDYh(i,j+1)*EPSILON);
}
hlos = D_MAX(0.0,vhr[k][i][j+1]);
if (((hup + vhr[k][i][j] - hlos) < 0.0) &&
((0.5*hup + vhr[k][i][j]) < 0.0)) {
vhh[j] = D_MIN(-0.5*hup,-hup+hlos);
}
else vhh[j] = vhr[k][i][j];
ts2 = 0.5*(1.0 + vhh[j]/(hvol[k][i][j+1]));
for (m=0;m<NTR;m++) {
fluxtr[j][m] = vhh[j]*(tr[m][k][i][j+1] - slope[j+1][m]*ts2);
}
}
else {
if (k==0 || k==1 ) {
hup = (hvol[k][i][j]-DXDYh(i,j)*MLMIN);
} else {
hup = (hvol[k][i][j]-DXDYh(i,j)*EPSILON);
}
hlos = D_MAX(0.0,-vhr[k][i][j-1]);
if (((hup - vhr[k][i][j] - hlos) < 0.0)
&& ((0.5*hup - vhr[k][i][j]) < 0.0)) {
vhh[j] = D_MAX(0.5*hup,hup-hlos);
}
else vhh[j] = vhr[k][i][j];
ts2 = 0.5*(1.0 - vhh[j] / (hvol[k][i][j]));
for (m=0;m<NTR;m++) {
fluxtr[j][m] = vhh[j]*(tr[m][k][i][j] + slope[j][m]*ts2);
}
}
}
// #pragma omp barrier
/* Calculate new tracer concentration in each cell after accounting */
/* for the j-direction fluxes. */
vhr[k][i][Y0] -= vhh[Y0];
// #pragma omp barrier
//#pragma omp for private(j,m,Ihnew)
for (j=Y1;j<=ny;j++) {
if ((vhh[j] != 0.0) || (vhh[j-1] != 0.0)) {
hlst[j] = hvol[k][i][j];
hvol[k][i][j] -= (vhh[j] - vhh[j-1]);
Ihnew = 1.0 / hvol[k][i][j];
vhr[k][i][j] -= vhh[j];
for (m=0;m<NTR;m++) {
tr[m][k][i][j] *= hlst[j];
tr[m][k][i][j] = (tr[m][k][i][j] -
fluxtr[j][m] + fluxtr[j-1][m]) * Ihnew;
}
}
}
// #pragma omp barrier
} /* i loop */
#endif
} /* end of big loop over k */
/* calculate new thickness field - to be used for vertical */
/* tracer advection from updated volumes (vol + fluxes) */
#pragma omp for private(i,j,k)
for (k=0; k<=NZ-1; k++) {
for (i=X1; i<=nx; i++) {
for (j=Y1; j<=ny; j++) {
hnew[k][i][j] = hvol[k][i][j]/DXDYh(i,j);
if (hnew[k][i][j] < EPSILON) {
hnew[k][i][j] = EPSILON;
}
}
}
}
/* ============================================================ */
/* now advect vertically */
/* ============================================================ */
#pragma omp for private(i,j,hup,hlos)
for (j=Y1; j<=ny; j++) {
for (i=X1; i<=nx; i++) {
/* work from top to bottom - by interfaces - interface k is the */
/* interface between layer k and layer k-1. net flux at this */
/* interface is wd[[k][i][j]= ea[k][i][j] and eb[k-1][i][j] */
/* k=0 */
if (wd[0][i][j] == 0.0) {
wdh[0][i][j] = 0.0;
}
else if (wd[0][i][j] < 0.0) {
hup = hnew[0][i][j] - MLMIN;
hlos = D_MAX(0.0, wd[1][i][j]);
if (((hup + wd[0][i][j] - hlos) < 0.0) &&
((0.5*hup + wd[0][i][j]) < 0.0)) {
wdh[0][i][j] = D_MIN(-0.5*hup,-hup+hlos);
}
else wdh[0][i][j] = wd[0][i][j];
}
else {
wdh[0][i][j] = wd[0][i][j];
}
}
}
#pragma omp for private(i,j,hup,hlos)
for (j=Y1; j<=ny; j++) {
for (i=X1; i<=nx; i++) {
/* k=1 */
if (wd[1][i][j] == 0.0) {
wdh[1][i][j] = 0.0;
}
else if (wd[1][i][j] > 0.0) {
hup = hnew[0][i][j] - MLMIN;
hlos = D_MAX(0.0, -wd[0][i][j]);
if (((hup - wd[1][i][j] - hlos) < 0.0) &&
((0.5*hup - wd[1][i][j]) < 0.0)) {
wdh[1][i][j] = D_MAX(0.5*hup,hup-hlos);
}
else wdh[1][i][j] = wd[1][i][j];
}
else {
hup = hnew[1][i][j] - MLMIN;
hlos = D_MAX(0.0,wd[2][i][j]);
if (((hup + wd[1][i][j] - hlos) < 0.0) &&
((0.5*hup + wd[1][i][j]) < 0.0)) {
wdh[1][i][j] = D_MIN(-0.5*hup,-hup+hlos);
}
else wdh[1][i][j] = wd[1][i][j];
}
}
}
#pragma omp for private(i,j,hup,hlos)
for (j=Y1; j<=ny; j++) {
for (i=X1; i<=nx; i++) {
/* k=2 */
if (wd[2][i][j] == 0.0) {
wdh[2][i][j] = 0.0;
}
else if (wd[2][i][j] > 0.0) {
hup = hnew[1][i][j] - MLMIN;
hlos = D_MAX(0.0, -wd[1][i][j]);
if (((hup - wd[2][i][j] - hlos) < 0.0) &&
((0.5*hup - wd[2][i][j]) < 0.0)) {
wdh[2][i][j] = D_MAX(0.5*hup,hup-hlos);
}
else wdh[2][i][j] = wd[2][i][j];
}
else {
hup = hnew[2][i][j] - EPSILON;
hlos = D_MAX(0.0,wd[3][i][j]);
if (((hup + wd[2][i][j] - hlos) < 0.0) &&
((0.5*hup + wd[2][i][j]) < 0.0)) {
wdh[2][i][j] = D_MIN(-0.5*hup,-hup+hlos);
}
else wdh[2][i][j] = wd[2][i][j];
}
}
}
/* k=3 --> NZ-1 */
#pragma omp for private(i,j,k,hup,hlos)
for (k=3; k<=NZ-1; k++) {
for (j=Y1; j<=ny; j++) {
for (i=X1; i<=nx; i++) {
if (wd[k][i][j] == 0.0) {
wdh[k][i][j] = 0.0;
}
else if (wd[k][i][j] > 0.0) {
hup = hnew[k-1][i][j] - EPSILON;
hlos = D_MAX(0.0, -wd[k-1][i][j]);
if (((hup - wd[k][i][j] - hlos) < 0.0) &&
((0.5*hup - wd[k][i][j]) < 0.0)) {
wdh[k][i][j] = D_MAX(0.5*hup,hup-hlos);
}
else wdh[k][i][j] = wd[k][i][j];
}
else {
hup = hnew[k][i][j] - EPSILON;
if (k != NZ-1) {
hlos = D_MAX(0.0,wd[k+1][i][j]);
} else {
hlos = 0.0;
}
if (((hup + wd[k][i][j] - hlos) < 0.0) &&
((0.5*hup + wd[k][i][j]) < 0.0)) {
wdh[k][i][j] = D_MIN(-0.5*hup,-hup+hlos);
}
else wdh[k][i][j] = wd[k][i][j];
}
} /* k */
} /* j */
} /* i */
#pragma omp for private(i,j)
for (i=X1; i<=nx; i++)
for (j=Y1; j<=ny; j++) {
ear[0][i][j] = wdh[0][i][j];
/* added by Curtis - bottom ebr wasn't set anywhere else */
ebr[NZ-1][i][j] = 0;
}
#pragma omp for private(i,j,k)
for (k=1;k<=NZ-1;k++) {
for (i=X1; i<=nx; i++) {
for (j=Y1; j<=ny; j++) {
ear[k][i][j] = 0.5 * (fabs(wdh[k][i][j]) + wdh[k][i][j]);
ebr[k-1][i][j] = 0.5 * (fabs(wdh[k][i][j]) - wdh[k][i][j]);
}
}
}
#pragma omp for private(i,j,k,m,hnew0,bet,gam)
for (j=Y1; j<=ny; j++) {
for (i=X1; i<=nx; i++) {
hnew0[i] = hnew[0][i][j];
bet[i]=1.0/(hnew[0][i][j] + ebr[0][i][j] + wdh[0][i][j]);
for (m=0;m<NTR;m++)
tr[m][0][i][j] = bet[i]*(hnew0[i]*tr[m][0][i][j]);
}
for (k=1;k<=NZ-1;k++) {
for (i=X1;i<=nx;i++) {
gam[k][i] = ebr[k-1][i][j] * bet[i];
bet[i]=1.0/(hnew[k][i][j] + ebr[k][i][j] +
(1.0-gam[k][i])*ear[k][i][j]);
for (m=0;m<NTR;m++)
tr[m][k][i][j] = bet[i] * (hnew[k][i][j]*tr[m][k][i][j] +
ear[k][i][j]*(tr[m][k-1][i][j]) );
}
}
for (m=0;m<NTR;m++)
for (k=NZ-2;k>=0;k--) {
for (i=X1;i<=nx;i++) {
tr[m][k][i][j] += gam[k+1][i]*tr[m][k+1][i][j];
}
}
} /*j*/
/* update hvol with diapycnal fluxes */
#pragma omp for private(i,j,k)
for (k=0;k<NZ-1;k++) {
for (i=X1; i<=nx; i++)
for (j=Y1; j<=ny; j++)
hnew[k][i][j] += (wdh[k][i][j] - wdh[k+1][i][j]);
}
#pragma omp for private(i,j)
for (i=X1; i<=nx; i++)
for (j=Y1; j<=ny; j++)
hnew[NZ-1][i][j] += wdh[NZ-1][i][j];
#pragma omp for private(i,j,k)
for (k=0;k<=NZ-1;k++)
for (i=X1; i<=nx; i++)
for (j=Y1; j<=ny; j++) {
if (hnew[k][i][j] < EPSILON) hnew[k][i][j] = EPSILON;
hvol[k][i][j] = DXDYh(i,j)*hnew[k][i][j];
if ( wd[k][i][j] > 0.0 && ( wdh[k][i][j] > wd[k][i][j] ))
printf("case 1 wdh[k]\n");
else if ( wd[k][i][j] < 0.0 && ( wdh[k][i][j] < wd[k][i][j] ))
printf("case 2 wdh[k]\n");
wd[k][i][j] -= wdh[k][i][j];
}
#else /* STANDARD_ADVECTION */
/* big loop over k */
// printf("phos(%d,%d,%d)=%g,uhtm=%g\n",0,190,26,tr[mPHOSPHATE][0][190][26],
// uhtm[0][190][26]);
// exit(1);
//yanxu: note these are null cycles, so I comment them out
//yanxu for (k=0;k<NZ;k++) {
// first advect zonally
//yanxu for (j=Y1;j<=ny;j++) {
//yanxu for (i=X0;i<=nx+1;i++) {
//yanxu for (m=0;m<NTR;m++) {
// fluxtr[i][m] = uhtm[i]*(tr[m][k][i][j]);
//yanxu }
//yanxu }
//yanxu }
// now advect meridionally
// null cycles again, yanxu
//yanxu for (i=X1;i<=nx;i++) {
//yanxu }
//yanxu } /* end of big loop over k */
/* calculate new thickness field - to be used for vertical */
/* tracer advection from updated volumes (vol + fluxes) */
#pragma omp for private(i,j,k)
for (k=0; k<=NZ-1; k++)
for (i=X1; i<=nx; i++)
for (j=Y1; j<=ny; j++) {
hnew[k][i][j] = hvol[k][i][j]/DXDYh(i,j);
if (hnew[k][i][j] < EPSILON) hnew[k][i][j] = EPSILON;
}
// now advect vertically
//yanxu: null cycles
//yanxu for (j=Y1; j<=ny; j++) {
//yanxu for (i=X1; i<=nx; i++) {
//yanxu
//yanxu }
//yanxu }
#endif /* STANDARD_ADVECTION */
/* zonal re-entrance */
#pragma omp for private(j,k,m)
for (j=0;j<NYMEM;j++) {
for (k=0;k<NZ;k++) {
uhr[k][nx+1][j] = uhr[k][2][j];
uhr[k][nx+2][j] = uhr[k][3][j];
uhr[k][0][j] = uhr[k][nx-1][j];
uhr[k][1][j] = uhr[k][nx][j];
vhr[k][nx+1][j] = vhr[k][2][j];
vhr[k][nx+2][j] = vhr[k][3][j];
vhr[k][0][j] = vhr[k][nx-1][j];
vhr[k][1][j] = vhr[k][nx][j];
hvol[k][nx+1][j] = hvol[k][2][j];
hvol[k][nx+2][j] = hvol[k][3][j];
hvol[k][0][j] = hvol[k][nx-1][j];
hvol[k][1][j] = hvol[k][nx][j];
for (m=0;m<NTR;m++) {
tr[m][k][nx+1][j] = tr[m][k][2][j];
tr[m][k][nx+2][j] = tr[m][k][3][j];
tr[m][k][0][j] = tr[m][k][nx-1][j];
tr[m][k][1][j] = tr[m][k][nx][j];
}
}
}
/* meridional re-entrance */
/* meridional re-entrance */
#pragma omp for private(i,k,ii,m)
for (i=2;i<=nx;i++) {
ii = 363 - i;
for (k=0;k<NZ;k++) {
uhr[k][ii][ny+1] = (-1)*uhr[k][i][ny];
uhr[k][ii][ny+2] = (-1)*uhr[k][i][ny-1];
vhr[k][ii][ny+1] = (-1)*vhr[k][i][ny];
vhr[k][ii][ny+2] = (-1)*vhr[k][i][ny-1];
hvol[k][ii][ny+1] = hvol[k][i][ny];
hvol[k][ii][ny+2] = hvol[k][i][ny-1];
for (m=0;m<NTR;m++) {
tr[m][k][ii][ny+1] = tr[m][k][i][ny];
tr[m][k][ii][ny+2] = tr[m][k][i][ny-1];
}
}
}
} // omp
#ifdef STANDARD_ADVECTION
# ifdef WRTTS
printf("itt = %i\n",itt);
wrts = (double)(itts)+(double)(itt)/11.+0.0001;
write_ts(wrts);
# endif // WRTTS
//****************************************************************************************
} /* end of temp itt iteration loop */
//****************************************************************************************
#endif
fract1 = (double)(NTSTEP-itts) / (double)NTSTEP;
fract2 = 1.0 - fract1;
//#pragma omp parallel for private(i,j,k) schedule(dynamic)
for (k=0;k<=NZ-1;k++) {
for (i=X1; i<=nx; i++) {
for (j=Y1; j<=ny; j++) {
# ifdef USE_CALC_H
h[k][i][j] = hnew[k][i][j];
if (h[k][i][j] < 0.0)
printf("tracadv l 796 - h[%d][%d][%d] = %g\n", k,i,j,
h[k][i][j]);
# else
h[k][i][j] = fract1*hstart[k][i][j] + fract2*hend[k][i][j];
//BX h[k][i][j] = hend[k][i][j];
# endif
#ifdef HTEST
htest[k][i][j] = hnew[k][i][j];
printf("htest(%d,%d,%d)=%g,hend=%g\n",
k,i,j,
// htest[k][i][j] = h[k][i][j];
#endif
}
}
}
//HF
// zonal re-entrance
//#pragma omp parallel for private(j,k) schedule(dynamic)
for (k=0;k<NZ;k++) {
for (j=0;j<=NYMEM-1;j++) {
h[k][nx+1][j] = h[k][2][j];
h[k][nx+2][j] = h[k][3][j];
h[k][0][j] = h[k][nx-1][j];
h[k][1][j] = h[k][nx][j];
}
}
// meridional re-entrance
//#pragma omp parallel for private(i,k,ii) schedule(dynamic)
for (i=2;i<=nx;i++) {
ii = 363 - i;
for (k=0;k<NZ;k++) {
h[k][ii][ny+1] = h[k][i][ny];
h[k][ii][ny+2] = h[k][i][ny-1];
}
}
//HF-e
# ifdef WRTTS
printf("End of tracadv\n");
wrts = (double)(itts)+(double)(itt)/11.+0.0005;
write_ts(wrts);
# endif // WRTTS
#ifdef DIFFUSE_TRACER
if ((KD>0.0) || (KDML>0.0)) {
diffuse_tracer();
}
#endif
pstage=4;
print_tr(pstage);
if ((KHTR>0.0)) {
tracer_hordiff();
}
pstage=5;
print_tr(pstage);
free3d(hvol, NZ);
free3d(uhr, NZ);
free3d(vhr, NZ);
free3d(ear, NZ);
free3d(ebr, NZ);
free3d(wdh, NZ);
#if !defined AGE2 && !defined AGE3
free3d(hnew, NZ);
#endif
}
void set_metrics(void)
{
int i,j;
extern double areagr[NXMEM][NYMEM];
double Iareagr[NXMEM][NYMEM];
/* Calculate the values of the metric terms that might be used */
/* and save them in arrays. */
#ifdef CARTESIAN
/* On a cartesian grid, the various DX... and DY... macros all */
/* point to the same scalars. */
i = 0; j = 0;
DXh(i,j) = RE * LENLON * M_PI / (180.0 * NXTOT);
DYh(i,j) = RE * LENLAT * M_PI / (180.0 * NYTOT);
IDXh(i,j) = 1.0 / DXh(i,j);
IDYh(i,j) = 1.0 / DYh(i,j);
DXDYh(i,j) = DXh(i,j) * DYh(i,j);
IDXDYh(i,j) = IDXh(i,j) * IDYh(i,j);
for (j=Y0-1;j<=ny+2;j++)
latq[j] = LOWLAT + LENLAT*(double)(j-Y0+Y0abs)/(double)NYTOT;
for (j=Y0;j<=ny;j++)
lath[j] = LOWLAT + LENLAT*((double)(j-Y0+Y0abs)-0.5)/(double)NYTOT;
for (i=X0-1;i<=nx+2;i++)
lonq[i] = WESTLON + LENLON*(double)(i-X0+X0abs)/(double)NXTOT;
for (i=X0;i<=nx;i++)
lonh[i] = WESTLON + LENLON*((double)(i-X0+X0abs)-0.5)/(double)NXTOT;
# if defined(PARALLEL_Y) && !defined(PARALLEL_IO) && defined(NETCDF_OUTPUT)
for (j=Y0;j<=NYTOT+Y0;j++)
latq_tot[j] = LOWLAT + LENLAT*(double)(j-Y0)/(double)NYTOT;
for (j=Y0;j<=NYTOT+Y0;j++)
lath_tot[j] = LOWLAT + LENLAT*((double)(j-Y0)-0.5)/(double)NYTOT;
# endif
# if defined(PARALLEL_X) && !defined(PARALLEL_IO) && defined(NETCDF_OUTPUT)
for (i=X0;i<=NXTOT+X0;i++)
lonq_tot[i] = WESTLON + LENLON*(double)(i-X0)/(double)NXTOT;
for (i=X0;i<=NXTOT+X0;i++)
lonh_tot[i] = WESTLON + LENLON*((double)(i-X0)-0.5)/(double)NXTOT;
# endif
#else
/* All of the metric terms should be defined over the domain from */
/* X0-1 to nx+2. Outside of the physical domain, both the metrics */
/* and their inverses may be set to zero. */
/* Any points that are outside of the computational domain should */
/* have their values set to zero _BEFORE_ setting the other metric */
/* terms, because these macros may or may not expand to 2-dimensional */
/* arrays. */
/* The metric terms within the computational domain are set here. */
# ifdef ISOTROPIC
{
double C0, I_C0, yq, yh, jd;
double fnRef, yRef; /* fnRef is the value of the integral of */
/* 1/(dx*cos(lat)) from the equator to a */
/* reference latitude, while yRef is the */
/* j-index of that reference latitude. */
int itt1, itt2;
C0 = M_PI*((double) LENLON / (double) (180*NXTOT)); I_C0 = 1.0 / C0;
/* With an isotropic grid, the north-south extent of the domain, */
/* the east-west extent, and the number of grid points in each */
/* direction are _not_ independent. Here the north-south extent */
/* will be determined to fit the east-west extent and the number of */
/* grid points. The grid is perfectly isotropic. */
# ifdef NORTHREFERENCE
/* The following 2 lines fixes the refererence latitude at the */
/* northern edge of the domain, LOWLAT+LENLAT at j=NYTOT+Y0. */
yRef = Y0abs - Y0 - NYTOT;
fnRef = I_C0 * INTSECY(((LOWLAT+LENLAT)*M_PI/180.0));
# else
/* The following line sets the refererence latitude LOWLAT at j=Y0. */
yRef = Y0abs - Y0; fnRef = I_C0 * INTSECY((LOWLAT*M_PI/180.0));
# endif
/* Everything else should pretty much work. */
yq = LOWLAT*M_PI/180.0;
/* If the model is in parallel in the Y-direction, do the same set of */
/* calculations which would occur on a single processor. */
for (j=Y0-1-Y0abs;j<Y0-1;j++) {
jd = fnRef + (double) (j + yRef) - 0.5;
yh = find_root(jd,yq,&itt1);
jd = fnRef + (double) (j + yRef);
yq = find_root(jd,yh,&itt2);
# if defined(PARALLEL_Y) && !defined(PARALLEL_IO) && defined(NETCDF_OUTPUT)
latq_tot[j+Y0abs] = yq*180.0/M_PI;
lath_tot[j+Y0abs] = yh*180.0/M_PI;
# endif
}
for (j=Y0-1;j<=ny+2;j++) {
jd = fnRef + (double) (j + yRef) - 0.5;
yh = find_root(jd,yq,&itt1);
jd = fnRef + (double) (j + yRef);
yq = find_root(jd,yh,&itt2);
latq[j] = yq*180.0/M_PI;
lath[j] = yh*180.0/M_PI;
# if defined(PARALLEL_Y) && !defined(PARALLEL_IO) && defined(NETCDF_OUTPUT)
latq_tot[j+Y0abs] = yq*180.0/M_PI;
lath_tot[j+Y0abs] = yh*180.0/M_PI;
# endif
for (i=X0-1;i<=nx+2;i++) {
DXq(i,j) = cos(yq) * (RE * C0);
DYq(i,j) = DXq(i,j);
DXv(i,j) = DXq(i,j);
DYv(i,j) = DYq(i,j);
DXh(i,j) = cos(yh) * (RE * C0);
DYh(i,j) = DXh(i,j);
DXu(i,j) = DXh(i,j);
DYu(i,j) = DYh(i,j);
}
}
# if defined(PARALLEL_Y) && !defined(PARALLEL_IO) && defined(NETCDF_OUTPUT)
for (j=ny+3;j<=NYTOT+Y0-Y0abs;j++) {
jd = fnRef + (double) (j + yRef) - 0.5;
yh = find_root(jd,yq,&itt1);
jd = fnRef + (double) (j + yRef);
yq = find_root(jd,yh,&itt2);
latq_tot[j+Y0abs] = yq*180.0/M_PI;
lath_tot[j+Y0abs] = yh*180.0/M_PI;
}
# endif
}
for (i=X0-1;i<=nx+2;i++)
lonq[i] = WESTLON + LENLON*(double)(i-X0+X0abs)/(double)NXTOT;
for (i=X0;i<=nx;i++)
lonh[i] = WESTLON + LENLON*((double)(i-X0+X0abs)-0.5)/(double)NXTOT;
# if defined(PARALLEL_X) && !defined(PARALLEL_IO) && defined(NETCDF_OUTPUT)
for (i=X0;i<=NXTOT+X0;i++)
lonq_tot[i] = WESTLON + LENLON*(double)(i-X0)/(double)NXTOT;
for (i=X0;i<=NXTOT+X0;i++)
lonh_tot[i] = WESTLON + LENLON*((double)(i-X0)-0.5)/(double)NXTOT;
# endif
# else /* ISOTROPIC */
/* This code implements latitude/longitude coordinates on a sphere. */
//BX-a
// for (j=0;j<=NYTOT-1;j++) {
//HF for (j=Y0-1;j<=ny+2;j++) {
for (j=2;j<NYTOT+2;j++) {
latq[j] = qlat[j];
lath[j] = hlat[j];
}
//BX-e
/* HF for (i=0;i<=NXTOT-1;i++) {
for (j=0;j<=NYTOT-1;j++) {
DXq(i+2,j+2) = dxq[j][i];
DYq(i+2,j+2) = dyq[j][i];
DXv(i+2,j+2) = dxv[j][i];
DYv(i+2,j+2) = dyv[j][i];
DXh(i+2,j+2) = dxh[j][i];
DYh(i+2,j+2) = dyh[j][i];
DXu(i+2,j+2) = dxu[j][i];
DYu(i+2,j+2) = dyu[j][i];
}
} */
//BX-a
for (i=X0-1;i<=nx+2;i++)
lonq[i] = WESTLON + LENLON*(double)(i-X0+X0abs)/(double)NXTOT;
for (i=X0;i<=nx;i++)
lonh[i] = WESTLON + LENLON*((double)(i-X0+X0abs)-0.5)/(double)NXTOT;
//BX-e
#endif
/* The remaining code should not be changed. */
for (i=X0-1;i<=nx+2;i++) {
for (j=Y0-1;j<=ny+2;j++) {
IDXh(i,j) = (DXh(i,j) > 0.0) ? (1.0 / DXh(i,j)) : 0.0;
IDXu(i,j) = (DXu(i,j) > 0.0) ? (1.0 / DXu(i,j)) : 0.0;
IDXv(i,j) = (DXv(i,j) > 0.0) ? (1.0 / DXv(i,j)) : 0.0;
IDXq(i,j) = (DXq(i,j) > 0.0) ? (1.0 / DXq(i,j)) : 0.0;
IDYh(i,j) = (DYh(i,j) > 0.0) ? (1.0 / DYh(i,j)) : 0.0;
IDYu(i,j) = (DYu(i,j) > 0.0) ? (1.0 / DYu(i,j)) : 0.0;
IDYv(i,j) = (DYv(i,j) > 0.0) ? (1.0 / DYv(i,j)) : 0.0;
IDYq(i,j) = (DYq(i,j) > 0.0) ? (1.0 / DYq(i,j)) : 0.0;
//HF alternate def: DXDYh(i,j) = DXh(i,j) * DYh(i,j);
//HF alternate def: IDXDYh(i,j) = IDXh(i,j) * IDYh(i,j);
DXDYq(i,j) = DXq(i,j) * DYq(i,j);
IDXDYq(i,j) = IDXq(i,j) * IDYq(i,j);
Iareagr[i][j] = (areagr[i][j] > 0.0) ? (1.0 / areagr[i][j]) : 0.0;
DXDYh(i,j) = areagr[i][j];
IDXDYh(i,j) = Iareagr[i][j];
}
}
#endif /* CARTESIAN */
}
