Grid::Grid(Grid *Orig){
int i;
domainname = strdup(Orig->domainname);
domainfile = Orig->domainfile;
totverts = Orig->totverts;
xcoords = dvector(0, totverts-1);
ycoords = dvector(0, totverts-1);
zcoords = dvector(0, totverts-1);
dcopy(totverts, Orig->xcoords, 1, xcoords, 1);
dcopy(totverts, Orig->ycoords, 1, ycoords, 1);
dcopy(totverts, Orig->zcoords, 1, zcoords, 1);
nel = Orig->nel;
nverts = ivector(0, nel-1);
icopy(nel, Orig->nverts, 1, nverts, 1);
vertids = imatrix(0, nel-1, 0, Max_Nverts-1);
icopy(nel*Max_Nverts, Orig->vertids[0], 1, vertids[0], 1);
elmtids = ivector(0, nel-1);
icopy(nel, Orig->elmtids, 1, elmtids, 1);
vertexmap = imatrix(0, nel-1, 0, Max_Nverts-1);
icopy(nel*Max_Nverts, Orig->vertexmap[0], 1, vertexmap[0], 1);
}
/*
count the number of nodal domains in grid
precondition: grid must be ny x nx
inputs:
grid - function values sampled at grid points
counted - array to store nodal domain numbers in. mask should be applied to this already
sizefile - file to write size of nodal domains to
output: return value - count of nodal domains
*/
int countNodalDomains(bit_array_t *signs, bit_array_t *counted, FILE *sizefile) {
int i, j;
int rc;
int nx, ny;
nx = signs->nx;
ny = signs->ny;
#ifdef DEBUG
bit_array2file(signs, "../data/signs.dat");
domain_numbers = imatrix(ny, nx);
#endif
int nd = 0; // count of nodal domains
int size; // area of last nodal domain (in pixels)
i = 0;
j = 0;
while (findNextUnseen(counted, &i, &j, ny, nx)) {
nd++;
size = findDomain(signs, counted, i, j, nd, ny, nx);
if (sizefile) {
fprintf(sizefile, "%d ", size);
}
}
#ifdef DEBUG
intArray2file(domain_numbers, ny, nx, "../data/counted.dat");
#endif
return nd;
}
int main(int argc, char* argv[])
{
FILE *in;
int **image;
double **image_i;
double **image_d;
int c;
int N;
int coeff_start = 5000, wm_length = 10000;
double wm_alpha = 0.2;
int width, height;
pgm_init(&argc, argv); wm_init2();
while ((c = getopt(argc, argv, "a:s:l:")) != EOF) {
switch (c) {
case 'a':
wm_alpha = atof(optarg);
break;
case 's':
coeff_start = atoi(optarg);
break;
case 'l':
wm_length = atoi(optarg);
break;
}
}
argc -= optind;
argv += optind;
in = stdin;
open_image(in, &width, &height);
image = imatrix(height, width);
load_image(image, in, width, height);
if (height == width)
N = height;
else {
fprintf(stderr, "Cannot Proccess non-square images!\n");
exit( -11);
}
image_i = dmatrix(height, width);
image_d = dmatrix(height, width);
if (image_d == NULL) {
fprintf(stderr, "Unable to allocate the double array\n");
exit(1);
}
matrix_i2d(image, image_i, N);
hartley(image_i, image_d, N);
read_watermark(image_d, N, coeff_start, wm_length, wm_alpha);
freematrix_d(image_i, height);
freematrix_d(image_d, height);
fclose(in);
exit(EXIT_SUCCESS);
}
/*
* ASSEMBLE_K - assemble global stiffness matrix from individual elements 23feb94
*/
void assemble_K(
double **K,
int DoF, int nE,
vec3 *xyz, float *r, double *L, double *Le,
int *N1, int *N2,
float *Ax, float *Asy, float *Asz,
float *Jx, float *Iy, float *Iz,
float *E, float *G, float *p,
int shear, int geom, double **Q, int debug
){
double **k; /* element stiffness matrix in global coord */
int **ind, /* member-structure DoF index table */
res=0,
i, j, ii, jj, l, ll;
char stiffness_fn[FILENMAX];
for (i=1; i<=DoF; i++) for (j=1; j<=DoF; j++) K[i][j] = 0.0;
k = dmatrix(1,12,1,12);
ind = imatrix(1,12,1,nE);
for ( i=1; i<= nE; i++ ) {
ind[1][i] = 6*N1[i] - 5; ind[7][i] = 6*N2[i] - 5;
ind[2][i] = ind[1][i] + 1; ind[8][i] = ind[7][i] + 1;
ind[3][i] = ind[1][i] + 2; ind[9][i] = ind[7][i] + 2;
ind[4][i] = ind[1][i] + 3; ind[10][i] = ind[7][i] + 3;
ind[5][i] = ind[1][i] + 4; ind[11][i] = ind[7][i] + 4;
ind[6][i] = ind[1][i] + 5; ind[12][i] = ind[7][i] + 5;
}
for ( i = 1; i <= nE; i++ ) {
elastic_K ( k, xyz, r, L[i], Le[i], N1[i], N2[i],
Ax[i],Asy[i],Asz[i], Jx[i],Iy[i],Iz[i], E[i],G[i], p[i], shear);
if (geom)
geometric_K( k, xyz, r, L[i], Le[i], N1[i], N2[i],
Ax[i], Asy[i],Asz[i],
Jx[i], Iy[i], Iz[i],
E[i],G[i], p[i], -Q[i][1], shear);
if (debug) {
res = sprintf(stiffness_fn,"k_%03d",i);
save_dmatrix(stiffness_fn,k,1,12,1,12,0, "w");
}
for ( l=1; l <= 12; l++ ) {
ii = ind[l][i];
for ( ll=1; ll <= 12; ll++ ) {
jj = ind[ll][i];
K[ii][jj] += k[l][ll];
}
}
}
free_dmatrix ( k,1,12,1,12);
free_imatrix(ind,1,12,1,nE);
return;
}
int main(int argc, char** argv) {
long nrh, nrl, nch, ncl;
byte** I;
byte** binary;
byte** droits;
int theta, roMax, ro;
int** tableRT;
I = LoadPGM_bmatrix("route0.pgm", &nrl, &nrh, &ncl, &nch);
binary = bmatrix(nrl, nrh, ncl, nch);
roMax = sqrt(nrh * nrh + nch * nch);
tableRT = imatrix(0, 179, 0, roMax);
droits = bmatrix(0, 179, 0, roMax);
int i, j;
for (i = nrl; i < nrh; i++) {
for (j = ncl; j < nch; j++) {
if (I[i][j] >= 180)
binary[i][j] = 255;
else
binary[i][j] = 0;
}
}
for (theta = 0; theta < 180; theta++) {
for (ro = 0; ro < roMax; ro++) {
tableRT[theta][ro] = 0;
}
}
for (theta = 0; theta < 180; theta++) {
for (i = nrl; i < nrh; i++) {
for (j = ncl; j < nch; j++) {
if (I[i][j] >= 180) {
ro = i * cos(rad(theta)) + j * sin(rad(theta));
tableRT[theta][abs(ro)]++;
}
}
}
}
int max = 0;
for (theta = 0; theta < 180; theta++) {
for (ro = 0; ro < roMax; ro++) {
if (tableRT[theta][ro] > max) {
max = tableRT[theta][ro];
}
}
}
SavePGM_bmatrix(binary, nrl, nrh, ncl, nch, "route_binary.pgm");
free_bmatrix(I, nrl, nrh, ncl, nch);
free_bmatrix(binary, nrl, nrh, ncl, nch);
return 0;
}
int main(int argc, char* argv[])
{
FILE *in;
int **image_i;
double *image_f = NULL;
int N;
int c;
int coeff_start = 5000, wm_length = 10000;
double wm_alpha = 0.2;
pgm_init(&argc, argv); wm_init2();
while ((c = getopt(argc, argv, "a:s:l:")) != EOF) {
switch (c) {
case 'a':
wm_alpha = atof(optarg);
break;
case 's':
coeff_start = atoi(optarg);
break;
case 'l':
wm_length = atoi(optarg);
break;
}
}
argc -= optind;
argv += optind;
in = stdin;
open_image(in, &width, &height);
image_i = imatrix(height, width);
load_image(image_i, in, width, height);
if (height == width)
N = height;
else {
fprintf(stderr, "Cannot Proccess non-square images!\n");
exit( -11);
}
initialize_constants();
image_f = (double *)calloc(N * N, sizeof(double));
if (image_f == NULL) {
printf("Unable to allocate the float array\n");
exit(1);
}
put_image_from_int_2_double(image_i, image_f, N);
fct2d(image_f, N, N);
read_watermark(image_f, N, coeff_start, wm_length, wm_alpha);
fclose(in);
freematrix(image_i, height);
free(image_f);
exit(EXIT_SUCCESS);
}
AffineTransform AffineTransform::inverse() const
{
double determinant = det();
if (determinant == 0.0)
return AffineTransform();
else {
double dinv = 1.0 / determinant;
AffineTransform imatrix((m_m22 * dinv), (-m_m12 * dinv),
(-m_m21 * dinv), (m_m11 * dinv),
((m_m21 * m_dy - m_m22 * m_dx) * dinv),
((m_m12 * m_dx - m_m11 * m_dy) * dinv));
return imatrix;
}
}
INTMATRIX *new_intmatrix(long nrh,long nch)
{
INTMATRIX *m;
m=(INTMATRIX *)malloc(sizeof(INTMATRIX));
if (!m) t_error("allocation failure in INTMATRIX()");
m->isdynamic=isDynamic;
m->nrl=NL;
m->nrh=nrh;
m->ncl=NL;
m->nch=nch;
m->co=imatrix(1,nrh,1,nch);
return m;
}
QWMatrix QWMatrix::invert( bool *invertible ) const
{
double det = _m11*_m22 - _m12*_m21;
if ( QABS(det) < 0.000001 ) { // very close to zero
if ( invertible ) // (whatever that means...)
*invertible = FALSE; // singular matrix
QWMatrix defaultMatrix;
return defaultMatrix;
}
else { // invertible matrix
if ( invertible )
*invertible = TRUE;
double dinv = 1.0/det;
QWMatrix imatrix( (float)(_m22*dinv), (float)(-_m12*dinv),
(float)(-_m21*dinv), (float)( _m11*dinv),
(float)((_m21*_dy - _m22*_dx)*dinv),
(float)((_m12*_dx - _m11*_dy)*dinv) );
return imatrix;
}
}
QWMatrix QWMatrix::invert( bool *invertible ) const
{
double det = _m11*_m22 - _m12*_m21;
if ( det == 0.0 ) {
if ( invertible )
*invertible = FALSE; // singular matrix
QWMatrix defaultMatrix;
return defaultMatrix;
}
else { // invertible matrix
if ( invertible )
*invertible = TRUE;
double dinv = 1.0/det;
QWMatrix imatrix( (_m22*dinv), (-_m12*dinv),
(-_m21*dinv), ( _m11*dinv),
((_m21*_dy - _m22*_dx)*dinv),
((_m12*_dx - _m11*_dy)*dinv) );
return imatrix;
}
}
int main(void)
{
int i,j,**nmbr;
float ccc,chisq,cramrv,df,prob;
char dummy[MAXSTR],fate[NDAT+1][16],mon[NMON+1][6],txt[16];
FILE *fp;
nmbr=imatrix(1,NDAT,1,NMON);
if ((fp = fopen("table1.dat","r")) == NULL)
nrerror("Data file table1.dat not found\n");
fgets(dummy,MAXSTR,fp);
fgets(dummy,MAXSTR,fp);
fscanf(fp,"%16c",txt);
txt[15]='\0';
for (i=1;i<=12;i++) fscanf(fp," %s",mon[i]);
fgets(dummy,MAXSTR,fp);
fgets(dummy,MAXSTR,fp);
for (i=1;i<=NDAT;i++) {
fscanf(fp,"%16[^0123456789]",fate[i]);
fate[i][15]='\0';
for (j=1;j<=12;j++)
fscanf(fp,"%d ",&nmbr[i][j]);
}
fclose(fp);
printf("\n%s",txt);
for (i=1;i<=12;i++) printf("%5s",mon[i]);
printf("\n\n");
for (i=1;i<=NDAT;i++) {
printf("%s",fate[i]);
for (j=1;j<=12;j++) printf("%5d",nmbr[i][j]);
printf("\n");
}
cntab1(nmbr,NDAT,NMON,&chisq,&df,&prob,&cramrv,&ccc);
printf("\n%15s chi-squared %20.2f\n"," ",chisq);
printf("%15s degrees of freedom%20.2f\n"," ",df);
printf("%15s probability %20.4f\n"," ",prob);
printf("%15s cramer-v %20.4f\n"," ",cramrv);
printf("%15s contingency coeff.%20.4f\n"," ",ccc);
free_imatrix(nmbr,1,NDAT,1,NMON);
return 0;
}
/*
* allocate memory for the matrices. placeholder can be an empty
* floorplan frame with only the names of the functional units
*/
block_model_t *alloc_block_model(thermal_config_t *config, flp_t *placeholder)
{
/* shortcuts */
int n = placeholder->n_units;
int m = NL*n+EXTRA;
block_model_t *model = (block_model_t *) calloc (1, sizeof(block_model_t));
if (!model)
fatal("memory allocation error\n");
model->config = *config;
model->n_units = model->base_n_units = n;
model->n_nodes = m;
model->border = imatrix(n, 4);
model->len = dmatrix(n, n); /* len[i][j] = length of shared edge bet. i & j */
model->g = dmatrix(m, m); /* g[i][j] = conductance bet. nodes i & j */
model->gx = dvector(n); /* lumped conductances in x direction */
model->gy = dvector(n); /* lumped conductances in y direction */
model->gx_int = dvector(n); /* lateral conductances in the interface layer */
model->gy_int = dvector(n);
model->gx_sp = dvector(n); /* lateral conductances in the spreader layer */
model->gy_sp = dvector(n);
model->gx_hs = dvector(n); /* lateral conductances in the heatsink layer */
model->gy_hs = dvector(n);
/* vertical conductances to ambient */
model->g_amb = dvector(n+EXTRA);
model->t_vector = dvector(m);/* scratch pad */
model->p = ivector(m); /* permutation vector for b's LUP decomposition */
model->a = dvector(m); /* vertical Cs - diagonal matrix stored as a 1-d vector */
model->inva = dvector(m); /* inverse of the above */
/* B, C and LU are (NL*n+EXTRA)x(NL*n+EXTRA) matrices */
model->b = dmatrix(m, m);
model->c = dmatrix(m, m);
model->lu = dmatrix(m, m);
model->flp = placeholder;
return model;
}
void trexR(int *threshold, // input, threshold count of rare variants
int *tablevec, // input, vector to fill 3x2 obsTable
double *chistatObs,
double *chi2sided,
double *chi1sided,
int *chistatSign,
double *fisher2sided,
double *fisher1sided,
int *fisherSign,
double *probExcluded)
{
// DECLARE OBJECTS FOR INPUT AND OUTPUT FROM PROGRAM
static int verbose=0;
// PREPARE DATA FOR TREX DRIVER
int nrow=3;
int ncol=2;
int **obsTable = imatrix(1,nrow, 1,ncol);
if(!obsTable)
errmsg("Memory allocation failure for obsTable\n");
fillTable(tablevec, obsTable, nrow, ncol);
// CALL TREX DRIVER
trexDriver(*threshold, obsTable,
chistatObs, chi2sided, chi1sided, chistatSign,
fisher2sided, fisher1sided, fisherSign,
probExcluded, verbose);
// CLEAN MEMORY AND RETURN
free_imatrix(obsTable, 1, nrow, 1, ncol);
return;
}
double calc_misfit(float **sectiondata, float **section, int ntr, int ns, int LNORM, float L2, int itest, int sws, int swstestshot,int ntr_glob, int **recpos_loc, int nsrc_glob, int ishot){
/* declaration of variables */
extern float DT;
extern int MYID;
extern int TRKILL;
extern char TRKILL_FILE[STRING_SIZE];
float intseis, intseis_data, intseis_synthetics, abs_synthetics, abs_data;
int i,j;
float l2;
float L2_dummy;
int umax=0, h;
/* declaration of variables for trace killing */
int ** kill_tmp, *kill_vector;
char trace_kill_file[STRING_SIZE];
FILE *ftracekill;
if(TRKILL){
kill_tmp = imatrix(1,ntr_glob,1,nsrc_glob);
kill_vector = ivector(1,ntr);
ftracekill=fopen(TRKILL_FILE,"r");
if (ftracekill==NULL) err(" Trace kill file could not be opened!");
for(i=1;i<=ntr_glob;i++){
for(j=1;j<=nsrc_glob;j++){
fscanf(ftracekill,"%d",&kill_tmp[i][j]);
}
}
fclose(ftracekill);
h=1;
for(i=1;i<=ntr;i++){
kill_vector[h] = kill_tmp[recpos_loc[3][i]][ishot];
h++;
}
} /* end if(TRKILL)*/
/* calculate misfit */
for(i=1;i<=ntr;i++){
if((TRKILL==1)&&(kill_vector[i]==1))
continue;
intseis = 0.0;
intseis_data = 0.0;
intseis_synthetics = 0.0;
abs_data = 0.0;
abs_synthetics = 0.0;
L2_dummy=0.0;
for(j=1;j<=ns;j++){
/*printf("%d \t %d \t %e \t %e \n",i,j,sectionpdata[i][j],sectionp[i][j]);*/
/* calculate L2 residuals */
if((LNORM==2) ||(LNORM==6)){
intseis += section[i][j]-sectiondata[i][j];}
if(LNORM==5){
intseis_data += sectiondata[i][j]*DT;
intseis_synthetics += section[i][j]*DT;
abs_data += intseis_data*intseis_data;
abs_synthetics += intseis_synthetics*intseis_synthetics;
L2_dummy+=(intseis_data*intseis_synthetics);}
/* calculate norm */
/*if((sws==1)&&(swstestshot==1)){*/
if(((LNORM==2) ||(LNORM==6)) &&(swstestshot==1)){
/*L2+=sectiondiff[i][invtime]*sectiondiff[i][invtime];*/
L2+=intseis*intseis*DT*DT;
}
}
if(LNORM==5){
L2 -= L2_dummy/(sqrt(abs_data)*sqrt(abs_synthetics));}
}
l2=L2;
return l2;
/* free memory for trace killing */
if(TRKILL){
free_imatrix(kill_tmp,1,ntr_glob,1,nsrc_glob);
free_ivector(kill_vector,1,ntr);
}
}
int main(int argn, char** args){
if (argn !=2 ) {
printf("When running the simulation, please give a valid scenario file name!\n");
return 1;
}
//set the scenario
char *filename = NULL;
filename = args[1];
//initialize variables
double t = 0; /*time start*/
int it, n = 0; /*iteration and time step counter*/
double res; /*residual for SOR*/
/*arrays*/
double **U, **V, **P;
double **RS, **F, **G;
int **Flag; //additional data structure for arbitrary geometry
/*those to be read in from the input file*/
double Re, UI, VI, PI, GX, GY, t_end, xlength, ylength, dt, dx, dy, alpha, omg, tau, eps, dt_value;
int imax, jmax, itermax;
double presLeft, presRight, presDelta; //for pressure stuff
int wl, wr, wt, wb;
char problem[32];
double vel; //in case of a given inflow or wall velocity
//read the parameters, using problem.dat, including wl, wr, wt, wb
read_parameters(filename, &Re, &UI, &VI, &PI, &GX, &GY, &t_end, &xlength, &ylength, &dt, &dx, &dy, &imax,
&jmax, &alpha, &omg, &tau, &itermax, &eps, &dt_value, &wl, &wr, &wt, &wb, problem, &presLeft, &presRight, &presDelta, &vel);
int pics = dt_value/dt; //just a helping variable for outputing vtk
//allocate memory, including Flag
U = matrix(0, imax+1, 0, jmax+1);
V = matrix(0, imax+1, 0, jmax+1);
P = matrix(0, imax+1, 0, jmax+1);
RS = matrix(1, imax, 1, jmax);
F = matrix(0, imax, 1, jmax);
G = matrix(1, imax, 0, jmax);
Flag = imatrix(0, imax+1, 0, jmax+1); // or Flag = imatrix(1, imax, 1, jmax);
int kmax = 20; //test no slip boundary value function
double ***U3d = (double ***) malloc((size_t)((imax+1)*(jmax+1)*(kmax+1) * sizeof(double*)) ); //test no slip boundary value function
double ***V3d = (double ***) malloc((size_t)((imax+1)*(jmax+1)*(kmax+1) * sizeof(double*)) ); //test no slip boundary value function
double ***W3d = (double ***) malloc((size_t)((imax+1)*(jmax+1)*(kmax+1) * sizeof(double*)) ); //test no slip boundary value function
int ***Flag3d = (int ***) malloc((size_t)((imax+1)*(jmax+1)*(kmax+1) * sizeof(int*)) ); //test no slip boundary value function
//initialisation, including **Flag
init_flag(problem, imax, jmax, presDelta, Flag);
init_uvp(UI, VI, PI, imax, jmax, U, V, P, problem);
//going through all time steps
while(t < t_end){
//adaptive time stepping
calculate_dt(Re, tau, &dt, dx, dy, imax, jmax, U, V);
//setting bound.values
boundaryvalues(imax, jmax, U, V, P, wl, wr, wt, wb, F, G, problem, Flag, vel); //including P, wl, wr, wt, wb, F, G, problem
//test no slip boundary value function
for(int i=1; i<=imax; i++){
for(int j=1; j<=jmax; j++){
for(int k=1; k<=kmax; k++){
boundaryvalues_no_slip(i, j, k, U3d, V3d, W3d, Flag3d); //test no slip boundary value function
}
}
}
//computing F, G and right hand side of pressue eq.
calculate_fg(Re, GX, GY, alpha, dt, dx, dy, imax, jmax, U, V, F, G, Flag);
calculate_rs(dt, dx, dy, imax, jmax, F, G, RS);
//iteration counter
it = 0;
do{
//
//perform SOR iteration, at same time set bound.values for P and new residual value
sor(omg, dx, dy, imax, jmax, P, RS, &res, Flag, presLeft, presRight);
it++;
}while(it<itermax && res>eps);
/* if (it == itermax) {
printf("Warning: sor while loop exits because it reaches the itermax. res = %f, time =%f\n", res, t);
}
*/ //calculate U and V of this time step
calculate_uv(dt, dx, dy, imax, jmax, U, V, F, G, P, Flag);
//indent time and number of time steps
n++;
t += dt;
//output of pics for animation
if (n%pics==0 ){
write_vtkFile(filename, n, xlength, ylength, imax, jmax, dx, dy, U, V, P);
}
}
//output of U, V, P at the end for visualization
//write_vtkFile("DrivenCavity", n, xlength, ylength, imax, jmax, dx, dy, U, V, P);
//free memory
free_matrix(U, 0, imax+1, 0, jmax+1);
free_matrix(V, 0, imax+1, 0, jmax+1);
free_matrix(P, 0, imax+1, 0, jmax+1);
free_matrix(RS, 1, imax, 1, jmax);
free_matrix(F, 0, imax, 1, jmax);
free_matrix(G, 1, imax, 0, jmax);
free_imatrix(Flag, 0, imax+1, 0, jmax+1);
free(U3d);
free(V3d);
free(W3d);
free(Flag3d);
return -1;
}
void Load_HO_Surface(char *name)
{
register int i,j;
int np,nface,ntot,info;
FILE *infile;
char buf[BUFSIZ],*p;
double *Rpts, *Spts;
if(Loaded_Surf_File)
return; // allow for multiple calls
// check for .hsf file first
sprintf(buf,"%s.hsf",strtok(name,"."));
if(!(infile = fopen(buf,"r")))
{
fprintf(stderr,"unable to open file %s or %s\n"
"Run homesh on the .fro file to generate "
"high order surface file \n",name,buf);
exit(1);
}
// read header
fgets(buf,BUFSIZ,infile);
p = strchr(buf,'=');
sscanf(++p,"%d",&np);
p = strchr(p,'=');
sscanf(++p,"%d",&nface);
Snp = np;
Snface = nface;
ntot = np*(np+1)/2;
Rpts = dvector(0,ntot-1);
Spts = dvector(0,ntot-1);
// read in point distribution in standard region
fgets(buf,BUFSIZ,infile);
fscanf(infile,"# %lf",Rpts);
for(i = 1; i < ntot; ++i)
fscanf(infile,"%lf",Rpts+i);
fgets(buf,BUFSIZ,infile);
fscanf(infile,"# %lf",Spts);
for(i = 1; i < ntot; ++i)
fscanf(infile,"%lf",Spts+i);
fgets(buf,BUFSIZ,infile);
fgets(buf,BUFSIZ,infile);
SurXpts = dmatrix(0,nface-1,0,ntot-1);
SurYpts = dmatrix(0,nface-1,0,ntot-1);
SurZpts = dmatrix(0,nface-1,0,ntot-1);
// read surface points
for(i = 0; i < nface; ++i)
{
fgets(buf,BUFSIZ,infile);
for(j = 0; j < ntot; ++j)
{
fgets(buf,BUFSIZ,infile);
sscanf(buf,"%lf%lf%lf",SurXpts[i]+j,SurYpts[i]+j,SurZpts[i]+j);
}
// read input connectivity data
for(j = 0; j < (np-1)*(np-1); ++j)
fgets(buf,BUFSIZ,infile);
}
fgets(buf,BUFSIZ,infile);
// read Vertids to match with .rea file
surfids = imatrix(0,nface,0,4);
for(i = 0; i < nface; ++i)
{
fgets(buf,BUFSIZ,infile);
sscanf(buf,"# %*d%d%d%d",surfids[i],surfids[i]+1,surfids[i]+2);
surfids[i][0]--;
surfids[i][1]--;
surfids[i][2]--;
surfids[i][3] = surfids[i][0] + surfids[i][1] + surfids[i][2];
}
Tri T;
T.qa = Snp+1;
T.qb = Snp;
T.lmax = Snp;
Basis *B = Tri_addbase(Snp,Snp+1,Snp,Snp);
double av,bv,*hr,*hs,v1,v2;
hr = dvector(0,Snp);
hs = dvector(0,Snp);
// setup collocation interpolation matrix
CollMat = dmatrix(0,ntot-1,0,ntot-1);
for(i = 0; i < ntot; ++i)
{
av = (fabs(1.0-Spts[i]) > FPTOL)? 2*(1+Rpts[i])/(1-Spts[i])-1: 0;
bv = Spts[i];
Tri_get_point_shape(&T,av,bv,hr,hs);
for(j =0; j < ntot; ++j)
{
v1 = ddot(Snp+1,hr,1,B->vert[j].a,1);
v2 = ddot(Snp,hs,1,B->vert[j].b,1);
CollMat[i][j] = v1*v2;
}
}
Tri_reset_basis(B);
CollMatIpiv = ivector(0,ntot-1);
// invert matrix
dgetrf(ntot,ntot,*CollMat,ntot,CollMatIpiv,info);
if(info)
fprintf(stderr,"Trouble factoring collocation matrix\n");
Loaded_Surf_File = 1;
free(hr);
free(hs);
free(Rpts);
free(Spts);
}
void laplace_fourier_res(float **sectionvy_obs, float **sectionvy, float **sectiondiff, int ntr, int ntr_glob, int ns, int ishot, int nshots, int iter, int **recpos, int **recpos_loc, float **srcpos){
/* declaration of global variables */
extern float DT, DH, OFFSETC;
extern int SEIS_FORMAT, MYID, NT, TIMEWIN;
extern char SEIS_FILE_VY[STRING_SIZE], PARA[STRING_SIZE], DATA_DIR[STRING_SIZE];
extern int TRKILL, OFFSET_MUTE, GRAD_FORM;
extern char TRKILL_FILE[STRING_SIZE];
/* declaration of variables for trace killing */
int ** kill_tmp, *kill_vector, h, j, i, Npad;
char trace_kill_file[STRING_SIZE];
FILE *ftracekill;
/* declaration of variables for offset-muting */
float offset, xr, yr, xs, ys;
/* complex variables for source wavelet estimation */
fftw_complex *D_ss, *D_ss_fd;
/* parameters for STA/LTA first arrival picking */
float *picked_times=NULL;
/* variables for data integration */
int invtime;
float **integrated_section=NULL, **integrated_sectiondata=NULL;
float EPS_NORM;
integrated_section = matrix(1,ntr,1,ns);
integrated_sectiondata = matrix(1,ntr,1,ns);
Npad = 2.0 * ns;
Npad = (int)(pow(2.0, ceil(log((double)(Npad))/log(2.0))+2.0) );
EPS_NORM=1e0;
/* Allocate memory */
D_ss = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) * Npad);
D_ss_fd = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) * Npad);
/* reverse time direction integrate data if GRAD_FORM=1 */
for(i=1;i<=ntr;i++){
invtime = ns;
for(j=1;j<=ns;j++){
if(GRAD_FORM==1){
integrated_section[i][invtime] += DT*sectionvy[i][j];
integrated_sectiondata[i][invtime] += DT*sectionvy_obs[i][j];
}
if(GRAD_FORM==2){
integrated_section[i][invtime] = sectionvy[i][j];
integrated_sectiondata[i][invtime] = sectionvy_obs[i][j];
}
invtime--;
}
}
/* pick first arrivals in the synthetic data with STA/LTA-picker and apply time window to field data before stf inversion */
/*if(TIMEWIN==3){
picked_times = vector(1,ntr);
stalta(sectionvy, ntr, ns, picked_times, ishot);
time_window_stf(sectionvy_obs, iter, ntr, ns, ishot);
}*/
TIMEWIN=2;
/* apply time damping to field and model data */
picked_times = vector(1,ntr);
time_window(integrated_sectiondata,picked_times,iter,ntr_glob,recpos_loc,ntr,ns,ishot);
time_window(integrated_section,picked_times,iter,ntr_glob,recpos_loc,ntr,ns,ishot);
/* TRKILL==1 - trace killing is applied */
if(TRKILL){
kill_tmp = imatrix(1,nshots,1,ntr);
kill_vector = ivector(1,ntr);
ftracekill=fopen(TRKILL_FILE,"r");
if (ftracekill==NULL) err(" Trace kill file could not be opened!");
for(i=1;i<=nshots;i++){
for(j=1;j<=ntr;j++){
fscanf(ftracekill,"%d",&kill_tmp[i][j]);
}
}
fclose(ftracekill);
for(i=1;i<=ntr;i++){
kill_vector[i] = kill_tmp[ishot][i];
}
for(i=1;i<=ntr;i++){
if(kill_vector[i]==1){
for(j=1;j<=ns;j++){
integrated_section[i][j]=0.0;
integrated_sectiondata[i][j]=0.0;
}
}
}
}
/* trace killing ends here */
/* apply offset mute */
if(OFFSET_MUTE){
/*printf("OFFSETC = %f \n",OFFSETC);
printf("OFFSET_MUTE = %d \n",OFFSET_MUTE); */
for (i=1;i<=ntr;i++){
/* calculate source and receiver positions */
xr = recpos[1][recpos_loc[3][i]]*DH;
xs = srcpos[1][ishot];
yr = recpos[2][recpos_loc[3][i]]*DH;
ys = srcpos[2][ishot];
/* calculate absolute offset */
offset = sqrt(((xs-xr)*(xs-xr))+((ys-yr)*(ys-yr)));
/* mute far-offset data*/
if((OFFSET_MUTE==1)&&(offset>=OFFSETC)){
for(j=1;j<=ns;j++){
integrated_section[i][j]=0.0;
integrated_sectiondata[i][j]=0.0;
}
}
/* mute near-offset data*/
if((OFFSET_MUTE==2)&&(offset<=OFFSETC)){
for(j=1;j<=ns;j++){
integrated_section[i][j]=0.0;
integrated_sectiondata[i][j]=0.0;
}
}
}
} /* end of OFFSET_MUTE */
/* FFT of each data and model trace and calculation of nominator and denominator of Wiener deconvolution */
for(i=1;i<=ntr;i++){
/* allocate memory for complex variables */
fftw_complex *in_data, *out_data, *in_model, *out_model, *res_td, *res;
fftw_plan p_data,p_model;
in_data = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) * Npad);
out_data = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) * Npad);
in_model = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) * Npad);
out_model = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) * Npad);
res_td = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) * Npad);
res = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) * Npad);
/* define real and imaginary parts of data vectors and apply zero-padding */
for(j=0;j<Npad;j++){
if(j<ns){
in_model[j] = (integrated_section[i][j+1]) + 0.0*I;
in_data[j] = (integrated_sectiondata[i][j+1]) + 0.0*I;
}
else{
in_model[j] = 0.0 + 0.0*I;
in_data[j] = 0.0 + 0.0*I;
}
}
/* apply FFTW */
p_data = fftw_plan_dft_1d(Npad, in_data, out_data, 1, FFTW_ESTIMATE);
p_model = fftw_plan_dft_1d(Npad, in_model, out_model, 1, FFTW_ESTIMATE);
fftw_execute(p_data);
fftw_execute(p_model);
/* calculate data residuals in the Laplace-Fourier domain (Jun etal., 2014)*/
for(j=0;j<Npad;j++){
/* real parts of the nominator and denominator */
res[j] = (1.0/out_model[j]+EPS_NORM)*conj(log(out_model[j]+EPS_NORM)-log(out_data[j]+EPS_NORM));
}
/* inverse FFTW of data residuals */
fftw_plan p_stf;
p_stf = fftw_plan_dft_1d(Npad, res, res_td, -1, FFTW_ESTIMATE);
fftw_execute(p_stf);
/* extract real part and write data to sectiondiff */
/*h=1;
for(j=Npad;j>Npad-ns;j--){
sectiondiff[i][h]=creal(res_td[h])/Npad;
h=h+1;
}*/
for(j=1;j<=ns;j++){
sectiondiff[i][j] = integrated_section[i][j] - integrated_sectiondata[i][j];
}
fftw_destroy_plan(p_data);
fftw_free(in_data);
fftw_free(out_data);
fftw_destroy_plan(p_model);
fftw_destroy_plan(p_stf);
fftw_free(in_model);
fftw_free(out_model);
fftw_free(res);
fftw_free(res_td);
}
/* free memory for trace killing and FFTW */
if(TRKILL){
free_imatrix(kill_tmp,1,nshots,1,ntr);
free_ivector(kill_vector,1,ntr);
}
fftw_free(D_ss);
fftw_free(D_ss_fd);
free_vector(picked_times,1,ntr);
free_matrix(integrated_section,1,ntr,1,ns);
free_matrix(integrated_sectiondata,1,ntr,1,ns);
}
void create_RC_matrices(flp_t *flp, int omit_lateral)
{
int i, j, k = 0, n = flp->n_units;
int **border;
double **len, *gx, *gy, **g, *c_ver, **t, *gx_sp, *gy_sp;
double r_sp1, r_sp2, r_hs; /* lateral resistances to spreader and heatsink */
/* NOTE: *_mid - the vertical R/C from CENTER nodes of spreader
* and heatsink. *_per - the vertical R/C from PERIPHERAL (n,s,e,w) nodes
*/
double r_sp_per, r_hs_mid, r_hs_per, c_sp_per, c_hs_mid, c_hs_per;
double gn_sp=0, gs_sp=0, ge_sp=0, gw_sp=0;
double w_chip = get_total_width (flp); /* x-axis */
double l_chip = get_total_height (flp); /* y-axis */
border = imatrix(n, 4);
len = matrix(n, n); /* len[i][j] = length of shared edge bet. i & j */
gx = vector(n); /* lumped conductances in x direction */
gy = vector(n); /* lumped conductances in y direction */
gx_sp = vector(n); /* lateral conductances in the spreader layer */
gy_sp = vector(n);
g = matrix(NL*n+EXTRA, NL*n+EXTRA); /* g[i][j] = conductance bet. nodes i & j */
c_ver = vector(NL*n+EXTRA); /* vertical capacitance */
b = matrix(NL*n+EXTRA, NL*n+EXTRA); /* B, C, INVA and INVB are (NL*n+EXTRA)x(NL*n+EXTRA) matrices */
c = matrix(NL*n+EXTRA, NL*n+EXTRA);
inva = matrix(NL*n+EXTRA, NL*n+EXTRA);
invb = matrix(NL*n+EXTRA, NL*n+EXTRA);
t = matrix (NL*n+EXTRA, NL*n+EXTRA); /* copy of B */
/* compute the silicon fitting factor - see pg 10 of the UVA CS tech report - CS-TR-2003-08 */
factor_chip = C_FACTOR * ((SPEC_HEAT_INT / SPEC_HEAT_SI) * (w_chip + 0.88 * t_interface) \
* (l_chip + 0.88 * t_interface) * t_interface / ( w_chip * l_chip * t_chip) + 1);
/* fitting factor for interface - same rationale as above */
factor_int = C_FACTOR * ((SPEC_HEAT_CU / SPEC_HEAT_INT) * (w_chip + 0.88 * t_spreader) \
* (l_chip + 0.88 * t_spreader) * t_spreader / ( w_chip * l_chip * t_interface) + 1);
/*printf("fitting factors : %lf, %lf\n", factor_chip, factor_int); */
/* gx's and gy's of blocks */
for (i = 0; i < n; i++) {
/* at the silicon layer */
if (omit_lateral) {
gx[i] = gy[i] = 0;
}
else {
gx[i] = 1.0/getr(K_SI, flp->units[i].height, flp->units[i].width, l_chip, t_chip);
gy[i] = 1.0/getr(K_SI, flp->units[i].width, flp->units[i].height, w_chip, t_chip);
}
/* at the spreader layer */
gx_sp[i] = 1.0/getr(K_CU, flp->units[i].height, flp->units[i].width, l_chip, t_spreader);
gy_sp[i] = 1.0/getr(K_CU, flp->units[i].width, flp->units[i].height, w_chip, t_spreader);
}
/* shared lengths between blocks */
for (i = 0; i < n; i++)
for (j = i; j < n; j++)
len[i][j] = len[j][i] = get_shared_len(flp, i, j);
/* lateral R's of spreader and sink */
r_sp1 = getr(K_CU, (s_spreader+3*w_chip)/4.0, (s_spreader-w_chip)/4.0, w_chip, t_spreader);
r_sp2 = getr(K_CU, (3*s_spreader+w_chip)/4.0, (s_spreader-w_chip)/4.0, (s_spreader+3*w_chip)/4.0, t_spreader);
r_hs = getr(K_CU, (s_sink+3*s_spreader)/4.0, (s_sink-s_spreader)/4.0, s_spreader, t_sink);
/* vertical R's and C's of spreader and sink */
r_sp_per = RHO_CU * t_spreader * 4.0 / (s_spreader * s_spreader - w_chip*l_chip);
c_sp_per = factor_pack * SPEC_HEAT_CU * t_spreader * (s_spreader * s_spreader - w_chip*l_chip) / 4.0;
r_hs_mid = RHO_CU * t_sink / (s_spreader*s_spreader);
c_hs_mid = factor_pack * SPEC_HEAT_CU * t_sink * (s_spreader * s_spreader);
r_hs_per = RHO_CU * t_sink * 4.0 / (s_sink * s_sink - s_spreader*s_spreader);
c_hs_per = factor_pack * SPEC_HEAT_CU * t_sink * (s_sink * s_sink - s_spreader*s_spreader) / 4.0;
/* short the R's from block centers to a particular chip edge */
for (i = 0; i < n; i++) {
if (eq(flp->units[i].bottomy + flp->units[i].height, l_chip)) {
gn_sp += gy_sp[i];
border[i][2] = 1; /* block is on northern border */
}
if (eq(flp->units[i].bottomy, 0)) {
gs_sp += gy_sp[i];
border[i][3] = 1; /* block is on southern border */
}
if (eq(flp->units[i].leftx + flp->units[i].width, w_chip)) {
ge_sp += gx_sp[i];
border[i][1] = 1; /* block is on eastern border */
}
if (eq(flp->units[i].leftx, 0)) {
gw_sp += gx_sp[i];
border[i][0] = 1; /* block is on western border */
}
}
/* overall R and C between nodes */
for (i = 0; i < n; i++) {
double area = (flp->units[i].height * flp->units[i].width);
/*
* amongst functional units in the various layers
* resistances in the interface layer are assumed
* to be infinite
*/
for (j = 0; j < n; j++) {
double part = 0, part_sp = 0;
if (is_horiz_adj(flp, i, j)) {
part = gx[i] / flp->units[i].height;
part_sp = gx_sp[i] / flp->units[i].height;
}
else if (is_vert_adj(flp, i,j)) {
part = gy[i] / flp->units[i].width;
part_sp = gy_sp[i] / flp->units[i].width;
}
g[i][j] = part * len[i][j];
g[HSP*n+i][HSP*n+j] = part_sp * len[i][j];
}
/* vertical g's in the silicon layer */
g[i][IFACE*n+i]=g[IFACE*n+i][i]=2.0/(RHO_SI * t_chip / area);
/* vertical g's in the interface layer */
g[IFACE*n+i][HSP*n+i]=g[HSP*n+i][IFACE*n+i]=2.0/(RHO_INT * t_interface / area);
/* vertical g's in the spreader layer */
g[HSP*n+i][NL*n+SP_B]=g[NL*n+SP_B][HSP*n+i]=2.0/(RHO_CU * t_spreader / area);
/* C's from functional units to ground */
c_ver[i] = factor_chip * SPEC_HEAT_SI * t_chip * area;
/* C's from interface portion of the functional units to ground */
c_ver[IFACE*n+i] = factor_int * SPEC_HEAT_INT * t_interface * area;
/* C's from spreader portion of the functional units to ground */
c_ver[HSP*n+i] = factor_pack * SPEC_HEAT_CU * t_spreader * area;
/* lateral g's from block center (spreader layer) to peripheral (n,s,e,w) spreader nodes */
g[HSP*n+i][NL*n+SP_N]=g[NL*n+SP_N][HSP*n+i]=2.0*border[i][2]/((1.0/gy_sp[i])+r_sp1*gn_sp/gy_sp[i]);
g[HSP*n+i][NL*n+SP_S]=g[NL*n+SP_S][HSP*n+i]=2.0*border[i][3]/((1.0/gy_sp[i])+r_sp1*gs_sp/gy_sp[i]);
g[HSP*n+i][NL*n+SP_E]=g[NL*n+SP_E][HSP*n+i]=2.0*border[i][1]/((1.0/gx_sp[i])+r_sp1*ge_sp/gx_sp[i]);
g[HSP*n+i][NL*n+SP_W]=g[NL*n+SP_W][HSP*n+i]=2.0*border[i][0]/((1.0/gx_sp[i])+r_sp1*gw_sp/gx_sp[i]);
}
/* max slope (max_power * max_vertical_R / vertical RC time constant) for silicon */
max_slope = MAX_PD / (factor_chip * t_chip * SPEC_HEAT_SI);
/* vertical g's and C's between central nodes */
/* between spreader bottom and sink bottom */
g[NL*n+SINK_B][NL*n+SP_B]=g[NL*n+SP_B][NL*n+SINK_B]=2.0/r_hs_mid;
/* from spreader bottom to ground */
c_ver[NL*n+SP_B]=c_hs_mid;
/* from sink bottom to ground */
c_ver[NL*n+SINK_B] = factor_pack * c_convec;
/* g's and C's from peripheral(n,s,e,w) nodes */
for (i = 1; i <= 4; i++) {
/* vertical g's between peripheral spreader nodes and spreader bottom */
g[NL*n+SP_B-i][NL*n+SP_B]=g[NL*n+SP_B][NL*n+SP_B-i]=2.0/r_sp_per;
/* lateral g's between peripheral spreader nodes and peripheral sink nodes */
g[NL*n+SP_B-i][NL*n+SINK_B-i]=g[NL*n+SINK_B-i][NL*n+SP_B-i]=2.0/(r_hs + r_sp2);
/* vertical g's between peripheral sink nodes and sink bottom */
g[NL*n+SINK_B-i][NL*n+SINK_B]=g[NL*n+SINK_B][NL*n+SINK_B-i]=2.0/r_hs_per;
/* from peripheral spreader nodes to ground */
c_ver[NL*n+SP_B-i]=c_sp_per;
/* from peripheral sink nodes to ground */
c_ver[NL*n+SINK_B-i]=c_hs_per;
}
/* calculate matrices A, B such that A(dT) + BT = POWER */
for (i = 0; i < NL*n+EXTRA; i++) {
for (j = 0; j < NL*n+EXTRA; j++) {
if (i==j) {
inva[i][j] = 1.0/c_ver[i];
if (i == NL*n+SINK_B) /* sink bottom */
b[i][j] += 1.0 / r_convec;
for (k = 0; k < NL*n+EXTRA; k++) {
if ((g[i][k]==0.0)||(g[k][i])==0.0)
continue;
else
/* here is why the 2.0 factor comes when calculating g[][] */
b[i][j] += 1.0/((1.0/g[i][k])+(1.0/g[k][i]));
}
} else {
inva[i][j]=0.0;
if ((g[i][j]==0.0)||(g[j][i])==0.0)
b[i][j]=0.0;
else
b[i][j]=-1.0/((1.0/g[i][j])+(1.0/g[j][i]));
}
}
}
/* we are always going to use the eqn dT + A^-1 * B T = A^-1 * POWER. so, store C = A^-1 * B */
matmult(c, inva, b, NL*n+EXTRA);
/* we will also be needing INVB so store it too */
copy_matrix(t, b, NL*n+EXTRA, NL*n+EXTRA);
matinv(invb, t, NL*n+EXTRA);
/* dump_vector(c_ver, NL*n+EXTRA); */
/* dump_matrix(g, NL*n+EXTRA, NL*n+EXTRA); */
/* dump_matrix(c, NL*n+EXTRA, NL*n+EXTRA); */
/* cleanup */
free_matrix(t, NL*n+EXTRA);
free_matrix(g, NL*n+EXTRA);
free_matrix(len, n);
free_imatrix(border, n);
free_vector(c_ver);
free_vector(gx);
free_vector(gy);
free_vector(gx_sp);
free_vector(gy_sp);
}
static Gdinfo *ReadGridFile(FileList *f) {
register int i,j,k;
char buf[BUFSIZ];
int nel,npt,nbnd,vid,vid1,eid,eid1,**bndpts,trip;
Gdinfo *ginfo = (Gdinfo *)malloc(sizeof(Gdinfo));
Cinfo *con,*c,*c1;
FILE *fp = f->in.fp;
/* read boundary condition file */
if(f->mesh.name) ReadBcond(f->mesh.fp,ginfo);
fgets(buf,BUFSIZ,fp);
fgets(buf,BUFSIZ,fp);
sscanf(buf,"%d%d%d%*d",&nel,&npt,&nbnd);
ginfo->nel = nel;
ginfo->npt = npt;
ginfo->nbnd = nbnd;
ginfo->elmtpts = imatrix(0,nel-1,0,2);
ginfo->x = dvector(0,npt-1);
ginfo->y = dvector(0,npt-1);
bndpts = imatrix(0,nel-1,0,2);
ginfo->elmtcon = (Cinfo**)malloc(nel*sizeof(Cinfo *));
ginfo->elmtcon[0] = (Cinfo *)calloc(3*nel,sizeof(Cinfo) );
for(k = 1; k < nel; ++k) ginfo->elmtcon[k] = ginfo->elmtcon[k-1]+3;
con = (Cinfo *)calloc(npt,sizeof(Cinfo));
/* read element vertex co-ordinate indices */
fgets(buf,BUFSIZ,fp);
for(k = 0; k < nel; ++k) {
fgets (buf,BUFSIZ,fp);
sscanf(buf,"%*d%d%d%d",ginfo->elmtpts[k],
ginfo->elmtpts[k]+1,ginfo->elmtpts[k]+2);
}
/* read co-ordinates */
fgets(buf,BUFSIZ,fp);
for(k = 0; k < npt; ++k) {
fgets (buf,BUFSIZ,fp);
sscanf(buf,"%*d%lf%lf",ginfo->x+k,ginfo->y+k);
}
/* read boundary info */
fgets(buf,BUFSIZ,fp);
for(k = 0; k < nbnd; ++k) {
fgets (buf,BUFSIZ,fp);
sscanf(buf,"%d%d%*d%d",bndpts[k],bndpts[k]+1,bndpts[k]+2);
}
/* sort out connectivity */
/* get list of all elements at a vertex */
for(k = 0; k < nel; ++k)
for(i = 0; i < 3; ++i)
addcon(con+ginfo->elmtpts[k][i]-1,k+1,i);
/* search through element list and fill out element connectivity */
for(i = 0; i < npt; ++i) {
for(c = con[i].next; c; c = c->next) {
vid = (c->vsid+1)%3;
eid = c->elmtid;
for(c1 = con[i].next; c1; c1 = c1->next) {
vid1 = (c1->vsid+2)%3;
eid1 = c1->elmtid;
if(ginfo->elmtpts[eid-1][vid] == ginfo->elmtpts[eid1-1][vid1]) {
ginfo->elmtcon[eid -1][c->vsid].type = 'E';
ginfo->elmtcon[eid -1][c->vsid].elmtid = eid1;
ginfo->elmtcon[eid -1][c->vsid].vsid = vid1;
ginfo->elmtcon[eid1-1][vid1 ].type = 'E';
ginfo->elmtcon[eid1-1][vid1 ].elmtid = eid;
ginfo->elmtcon[eid1-1][vid1 ].vsid = c->vsid;
}
}
}
}
/* check through list and match any missing element with boundary values */
for(k = 0; k < nel; ++k)
for(i = 0; i < 3; ++i)
if(!ginfo->elmtcon[k][i].elmtid) {
vid = ginfo->elmtpts[k][i];
vid1 = ginfo->elmtpts[k][(i+1)%3];
/* check to see that this side is a boundary */
for(j = 0,trip=1; j < nbnd; ++j)
if(vid == bndpts[j][0] && vid1 == bndpts[j][1]) {
/* set boundary condition from given values if present */
if(f->mesh.name) {
register int i1;
Bndinfo *b;
Curinfo *c;
for(b=ginfo->bnd; b; b = b->next)
if(b->region == bndpts[j][2]) {
ginfo->elmtcon[k][i].type = b->type;
switch(b->type) {
case 'W':
case 'O':
case 'S':
case 'B':
case 'M':
case 'I':
case 'Z':
break;
case 'V':
case 'F':
dcopy(b->nbcs,b->data.val,1,ginfo->elmtcon[k][i].f,1);
break;
case 'v':
case 'f':
case 'm':
for(i1=0; i1 < b->nbcs; ++i1)
ginfo->elmtcon[k][i].str[i1] = b->data.str[i1];
break;
}
}
for(c=ginfo->curve; c; c = c->next) {
if(c->region == bndpts[j][2]) {
/* reset co-ordinates */
switch(c->type) {
case 'C': /* arc */
{
double theta;
theta = atan2(ginfo->y[vid-1]-c->info.arc.yc,
ginfo->x[vid-1]-c->info.arc.xc);
ginfo->x[vid-1] = fabs(c->info.arc.radius)*cos(theta)
+ c->info.arc.xc;
ginfo->y[vid-1] = fabs(c->info.arc.radius)*sin(theta)
+ c->info.arc.yc;
theta = atan2(ginfo->y[vid1-1]-c->info.arc.yc,
ginfo->x[vid1-1]-c->info.arc.xc);
ginfo->x[vid1-1] = fabs(c->info.arc.radius)*cos(theta)
+ c->info.arc.xc;
ginfo->y[vid1-1] = fabs(c->info.arc.radius)*sin(theta)
+ c->info.arc.yc;
break;
}
}
/* add curved information about element to ginfo */
addcurve(ginfo,k+1,i,c->idtype);
}
}
}
else
ginfo->elmtcon[k][i].type = 'W';
trip=0;
}
if(trip)
fprintf(stderr,"side %d of element %d using coordinate indices"
" (%d,%d) is not a boundary\n",i+1,k+1,vid,vid1);
}
/* free the con list */
for(k = 0; k < npt; ++k) {
c = con[k].next;
while(c) {
c1 = c->next;
free(c);
c = c1;
}
}
free(con);
free_imatrix(bndpts,0,0);
return ginfo;
}
Grid::Grid(char *fname){
register int i,j;
char buf[BUFSIZ];
if(option("REAFILE")){
register int k,l;
int dim;
double **xloc, **yloc, **zloc;
int **locvid;
sprintf(buf, "%s.rea",strtok(fname,"\n"));
domainname = strdup(buf);
domainfile = fopen(domainname,"r");
if(!findSection("MESH",buf,domainfile))
{fputs("Grid_rea: Section not found\n", stderr); exit(-1);}
get_next_line(domainfile, buf);
sscanf(buf,"%d%d",&nel,&dim);
if(dim != 3){ fputs("Grid_rea: Mesh is not 3D\n",stderr); exit(-1);}
xloc = dmatrix(0,nel-1,0,Max_Nverts-1);
yloc = dmatrix(0,nel-1,0,Max_Nverts-1);
zloc = dmatrix(0,nel-1,0,Max_Nverts-1);
nverts = ivector(0, nel-1);
/* read local mesh */
for(k = 0; k < nel; k++) {
get_next_line(domainfile, buf); /* element header */
if(strstr(buf,"Hex") || strstr(buf,"hex")){
fscanf(domainfile,"%lf%lf%lf%lf%lf%lf%lf%lf",
xloc[k],xloc[k]+1,xloc[k]+2,xloc[k]+3,xloc[k]+4,
xloc[k]+5,xloc[k]+6,xloc[k]+7);
fscanf(domainfile,"%lf%lf%lf%lf%lf%lf%lf%lf",
yloc[k],yloc[k]+1,yloc[k]+2,yloc[k]+3,yloc[k]+4,
yloc[k]+5,yloc[k]+6,yloc[k]+7);
fscanf(domainfile,"%lf%lf%lf%lf%lf%lf%lf%lf",
zloc[k],zloc[k]+1,zloc[k]+2,zloc[k]+3,zloc[k]+4,
zloc[k]+5,zloc[k]+6,zloc[k]+7);
get_next_line(domainfile, buf); /* get remainder of line */
nverts[k] = 8;
}
else if(strstr(buf,"Prism") || strstr(buf,"prism")){
fscanf(domainfile,"%lf%lf%lf%lf%lf%lf",
xloc[k],xloc[k]+1,xloc[k]+2,xloc[k]+3,xloc[k]+4,xloc[k]+5);
fscanf(domainfile,"%lf%lf%lf%lf%lf%lf",
yloc[k],yloc[k]+1,yloc[k]+2,yloc[k]+3,yloc[k]+4,yloc[k]+5);
fscanf(domainfile,"%lf%lf%lf%lf%lf%lf",
zloc[k],zloc[k]+1,zloc[k]+2,zloc[k]+3,zloc[k]+4,zloc[k]+5);
get_next_line(domainfile, buf); /* get remainder of line */
nverts[k] = 6;
}
else if(strstr(buf,"Pyr") || strstr(buf,"pyr")){
fscanf(domainfile,"%lf%lf%lf%lf%lf",
xloc[k],xloc[k]+1,xloc[k]+2,xloc[k]+3,xloc[k]+4);
fscanf(domainfile,"%lf%lf%lf%lf%lf",
yloc[k],yloc[k]+1,yloc[k]+2,yloc[k]+3,yloc[k]+4);
fscanf(domainfile,"%lf%lf%lf%lf%lf",
zloc[k],zloc[k]+1,zloc[k]+2,zloc[k]+3,zloc[k]+4);
get_next_line(domainfile, buf); /* get remainder of line */
nverts[k] = 5;
}
else{ /* assume it is a tet */
fscanf(domainfile,"%lf%lf%lf%lf",xloc[k],xloc[k]+1,xloc[k]+2,xloc[k]+3);
fscanf(domainfile,"%lf%lf%lf%lf",yloc[k],yloc[k]+1,yloc[k]+2,yloc[k]+3);
fscanf(domainfile,"%lf%lf%lf%lf",zloc[k],zloc[k]+1,zloc[k]+2,zloc[k]+3);
get_next_line(domainfile, buf); /* get remainder of line */
nverts[k] = 4;
}
}
/* search through elements and search for similar elements */
vertids = imatrix(0,nel-1,0,Max_Nverts-1);
ifill(nel*Max_Nverts,-1,vertids[0],1);
totverts=0;
for(k = 0; k < nel; ++k)
for(i= 0; i < nverts[k]; ++i)
if(vertids[k][i] == -1){
vertids[k][i] = totverts++;
for(l = k+1; l < nel; ++l)
for(j = 0; j < nverts[l]; ++j)
if(vertids[l][j] == -1){
if(same(xloc[l][j],xloc[k][i]) && same(yloc[l][j],yloc[k][i])
&& same(zloc[l][j],zloc[k][i]))
vertids[l][j] = vertids[k][i];
}
}
xcoords = dvector(0, totverts-1);
ycoords = dvector(0, totverts-1);
zcoords = dvector(0, totverts-1);
for(k = 0; k < nel; ++k)
for(i= 0; i < nverts[k]; ++i){
xcoords[vertids[k][i]] = xloc[k][i];
ycoords[vertids[k][i]] = yloc[k][i];
zcoords[vertids[k][i]] = zloc[k][i];
}
free_dmatrix(xloc,0,0);
free_dmatrix(yloc,0,0);
free_dmatrix(zloc,0,0);
}
else{
char language;
sprintf(buf, strtok(fname, "\n"));
domainname = strdup(buf);
domainfile = fopen(domainname, "r");
get_next_line(domainfile, buf);
sscanf(buf, "%c", &language);
get_next_line(domainfile, buf);
sscanf(buf, "%d", &totverts);
xcoords = dvector(0, totverts-1);
ycoords = dvector(0, totverts-1);
zcoords = dvector(0, totverts-1);
for(i=0;i<totverts;++i){
get_next_line(domainfile, buf);
sscanf(buf, "%lf %lf %lf", xcoords+i, ycoords+i, zcoords+i);
}
get_next_line(domainfile, buf);
sscanf(buf, "%d", &nel);
nverts = ivector(0, nel-1);
vertids = imatrix(0, nel-1, 0, Max_Nverts-1);
ifill(nel*Max_Nverts, -1, vertids[0], 1);
for(i=0;i<nel;++i){
get_next_line(domainfile, buf);
sscanf(buf, "%d", nverts+i);
switch(nverts[i]){
case 4:
sscanf(buf, "%*d %d %d %d %d",
vertids[i], vertids[i]+1, vertids[i]+2, vertids[i]+3);
break;
case 5:
sscanf(buf, "%*d %d %d %d %d %d",
vertids[i], vertids[i]+1, vertids[i]+2, vertids[i]+3,
vertids[i]+4);
break;
case 6:
sscanf(buf, "%*d %d %d %d %d %d %d",
vertids[i], vertids[i]+1, vertids[i]+2, vertids[i]+3,
vertids[i]+4, vertids[i]+5);
break;
case 8:
sscanf(buf, "%*d %d %d %d %d %d %d %d %d",
vertids[i], vertids[i]+1, vertids[i]+2, vertids[i]+3,
vertids[i]+4, vertids[i]+5, vertids[i]+6, vertids[i]+7);
break;
}
if(language == 'F'){
for(j=0;j<nverts[i];++j)
vertids[i][j] -=1;
}
}
}
elmtids = ivector(0, nel-1);
for(i=0;i<nel;++i)
elmtids[i] = i;
vertexmap = imatrix(0, nel-1, 0, Max_Nverts-1);
ifill(nel*Max_Nverts, -1, vertexmap[0], 1);
for(i=0;i<nel;++i)
for(j=0;j<nverts[i];++j)
vertexmap[i][j] = j;
}
/*
* Function to be called from Python
*/
static PyObject* py_smith_waterman_context(PyObject* self, PyObject* args)
{
char *seq1 = NULL;
char *seq2 = NULL;
char retstr[100] = {'\0'};
int len1, len2;
int i, j;
int gap_opening, gap_extension;
static int ** similarity = NULL;
PyArg_ParseTuple(args, "s#s#ii", &seq1, &len1, &seq2, &len2, &gap_opening, &gap_extension);
if (!seq1 || !seq2) {
sprintf (retstr, "no seq in py_smith_waterman_context");
return Py_BuildValue("s", retstr);
}
/* passing a matrix this way is all to painful, so we'll elegantyly hardcode it: */
if ( !similarity) {
similarity = imatrix(ASCII_SIZE, ASCII_SIZE);
if (!similarity) {
sprintf (retstr, "error alloc matrix space");
return Py_BuildValue("s", retstr);
}
load_sim_matrix (similarity);
}
/**********************************************************************************/
//int gap_opening = -5; // used in 15_make_maps
//int gap_extension = -3;
//char gap_character = '-'
//int gap_opening = -3; // used in 25_db_migration/06_make_alignments
//int gap_extension = 0;
char gap_character = '#';
int endgap = 0;
int use_endgap = 0;
int far_away = -1;
int max_i = len1;
int max_j = len2;
// allocation, initialization
int **F = NULL;
char **direction = NULL;
int *map_i2j = NULL;
int *map_j2i = NULL;
if ( ! (F= imatrix (max_i+1, max_j+1)) ) {
sprintf (retstr, "error alloc matrix space");
return Py_BuildValue("s", retstr);
}
if ( ! (direction = cmatrix (max_i+1, max_j+1)) ) {
sprintf (retstr, "error alloc matrix space");
return Py_BuildValue("s", retstr);
}
if (! (map_i2j = emalloc( (max_i+1)*sizeof(int))) ) {
sprintf (retstr, "error alloc matrix space");
return Py_BuildValue("s", retstr);
}
if (! (map_j2i = emalloc( (max_j+1)*sizeof(int))) ) {
sprintf (retstr, "error alloc matrix space");
return Py_BuildValue("s", retstr);
}
for (i=0; i<=max_i; i++) map_i2j[i]=far_away;
for (j=0; j<=max_j; j++) map_j2i[j]=far_away;
int F_max = far_away;
int F_max_i = 0;
int F_max_j = 0;
int penalty = 0;
int i_sim, j_sim, diag_sim, max_sim;
int i_between_exons = 1;
int j_between_exons = 1;
//
for (i=0; i<=max_i; i++) {
if (i > 0) {
if (seq1[i-1] == 'B') {
i_between_exons = 0;
} else if ( seq1[i-1] == 'Z'){
i_between_exons = 1;
}
}
for (j=0; j<=max_j; j++) {
if (j > 0) {
if (seq2[j-1] == 'B') {
j_between_exons = 0;
} else if (seq2[j-1] == 'Z') {
j_between_exons = 1;
}
}
if ( !i && !j ){
F[0][0] = 0;
direction[i][j] = 'd';
continue;
}
if ( i && j ){
/**********************************/
penalty = 0;
if ( direction[i-1][j] == 'i' ) {
// gap extension
if (j_between_exons) {
penalty = 0;
} else {
if (use_endgap && j==max_j){
penalty = endgap;
} else {
penalty = gap_extension;
}
}
} else {
// gap opening */
if (j_between_exons) {
penalty = 0;
} else {
if (use_endgap && j==max_j){
penalty = endgap;
} else{
penalty = gap_opening;
}
}
}
i_sim = F[i-1][j] + penalty;
/**********************************/
penalty = 0;
if ( direction[i][j-1] == 'j' ) {
// gap extension
if (i_between_exons) {
penalty = 0;
} else {
if (use_endgap && i==max_i){
penalty = endgap;
} else{
penalty = gap_extension;
}
}
} else {
// gap opening */
if (i_between_exons) {
penalty = 0;
} else {
if (use_endgap && i==max_i){
penalty = endgap;
} else {
penalty = gap_opening;
}
}
}
j_sim = F[i][j-1] + penalty;
/**********************************/
diag_sim = F[i-1][j-1] + similarity [seq1[i-1]][seq2[j-1]];
/**********************************/
max_sim = diag_sim;
direction[i][j] = 'd';
if ( i_sim > max_sim ){
max_sim = i_sim;
direction[i][j] = 'i';
}
if ( j_sim > max_sim ) {
max_sim = j_sim;
direction[i][j] = 'j';
}
} else if (j) {
penalty = 0;
if (j_between_exons) {
penalty = 0;
} else {
if (use_endgap) {
penalty = endgap;
} else {
if ( direction[i][j-1] =='j' ) {
penalty = gap_extension;
} else {
penalty = gap_opening;
}
}
}
j_sim = F[i][j-1] + penalty;
max_sim = j_sim;
direction[i][j] = 'j';
} else if (i) {
penalty = 0;
if (i_between_exons) {
penalty = 0;
} else {
if ( use_endgap) {
penalty = endgap;
} else {
if ( direction[i-1][j] == 'i' ) {
penalty = gap_extension;
} else {
penalty = gap_opening;
}
}
}
i_sim = F[i-1][j] + penalty;
max_sim = i_sim;
direction[i][j] = 'i';
}
if (max_sim < 0.0 ) max_sim = 0.0;
F[i][j] = max_sim;
if ( F_max < max_sim ) {
// TODO{ tie break here */
F_max = max_sim;
F_max_i = i;
F_max_j = j;
}
}
}
i = F_max_i;
j = F_max_j;
// aln_score = F[i][j] ;
while ( i>0 || j >0 ){
if ( i<0 || j<0 ){
sprintf (retstr, "Retracing error");
return Py_BuildValue("s", retstr);
}
if (direction[i][j] == 'd'){
map_i2j [i-1] = j-1;
map_j2i [j-1] = i-1;
i-= 1;
j-= 1;
} else if (direction[i][j] == 'i') {
map_i2j [i-1] = far_away;
i-= 1 ;
} else if (direction[i][j] == 'j') {
map_j2i [j-1] = far_away;
j-= 1 ;
} else{
sprintf (retstr, "Retracing error");
return Py_BuildValue("s", retstr);
}
}
char * aligned_seq_1 = NULL;
char * aligned_seq_2 = NULL;
/* (lets hope it gets properly freed in the main program */
if (! (aligned_seq_1 = emalloc( (len1+len2)*sizeof(char))) ) {
sprintf (retstr, "error alloc array space");
return Py_BuildValue("s", retstr);
}
if (! (aligned_seq_2 = emalloc( (len1+len2)*sizeof(char))) ) {
sprintf (retstr, "error alloc array space");
return Py_BuildValue("s", retstr);
}
i = 0;
j = 0;
int done = 0;
int pos = 0;
while (!done) {
if (j>=max_j && i>=max_i){
done = 1;
} else if (j<max_j && i<max_i){
if (map_i2j[i] == j){
aligned_seq_1[pos] = seq1[i];
aligned_seq_2[pos] = seq2[j];
i += 1;
j += 1;
} else if (map_i2j[i] < 0){
aligned_seq_1[pos] = seq1[i];
aligned_seq_2[pos] = gap_character;
i += 1;
} else if (map_j2i[j] < 0){
aligned_seq_1[pos] = gap_character;
aligned_seq_2[pos] = seq2[j];
j += 1;
}
} else if (j<max_j){
aligned_seq_1[pos] = gap_character;
aligned_seq_2[pos] = seq2[j];
j += 1;
} else {
aligned_seq_1[pos] = seq1[i];
aligned_seq_2[pos] = gap_character;
i += 1;
}
pos ++;
}
free_imatrix(F);
free_cmatrix(direction);
free(map_i2j);
free(map_j2i);
return Py_BuildValue("ss", aligned_seq_1, aligned_seq_2 );
}
/* "buildhessian" constructs a block Hessian and associated projection matrix
by application of the ANM. Atomic coordinates and block definitions are
provided in 'coords' and 'blocks'; ANM parameters are provided in 'cutoff'
and 'gamma'. On successful termination, the block Hessian is stored in
'hessian', and the projection matrix between block and all-atom spaces is
in 'projection'. */
static PyObject *buildhessian(PyObject *self, PyObject *args, PyObject *kwargs) {
PDB_File PDB;
dSparse_Matrix PP,HH;
PyArrayObject *coords, *blocks, *hessian, *projection;
double *XYZ,*hess,*proj;
long *BLK;
double **HB;
double cutoff = 15., gamma = 1., scl=1., mlo=1., mhi=-1.;
int natm, nblx, bmx;
int hsize,elm,bdim,i,j;
static char *kwlist[] = {"coords", "blocks", "hessian", "projection",
"natoms", "nblocks", "maxsize", "cutoff",
"gamma", "scale", "memlo", "memhi", NULL};
if (!PyArg_ParseTupleAndKeywords(args, kwargs, "OOOOiii|ddddd", kwlist,
&coords, &blocks, &hessian, &projection,
&natm, &nblx, &bmx, &cutoff, &gamma, &scl,
&mlo, &mhi))
return NULL;
XYZ = (double *) PyArray_DATA(coords);
BLK = (long *) PyArray_DATA(blocks);
hess = (double *) PyArray_DATA(hessian);
proj = (double *) PyArray_DATA(projection);
/* First allocate a PDB_File object to hold the coordinates and block
indices of the atoms. This wastes a bit of memory, but it prevents
the need to re-write all of the RTB functions that are used in
standalone C code. */
PDB.atom=malloc((size_t)((natm+2)*sizeof(Atom_Line)));
if(!PDB.atom) return PyErr_NoMemory();
for(i=1;i<=natm;i++){
PDB.atom[i].model=BLK[i-1];
for(j=0;j<3;j++)
PDB.atom[i].X[j]=XYZ[j*natm+i-1];
}
/* Find the projection matrix */
hsize = 18*bmx*nblx > 12*natm ? 12*natm : 18*bmx*nblx;
HH.IDX=imatrix(1,hsize,1,2);
HH.X=dvector(1,hsize);
elm=dblock_projections2(&HH,&PDB,natm,nblx,bmx);
PP.IDX=imatrix(1,elm,1,2);
PP.X=dvector(1,elm);
for(i=1;i<=elm;i++){
PP.IDX[i][1]=HH.IDX[i][1];
PP.IDX[i][2]=HH.IDX[i][2];
PP.X[i]=HH.X[i];
}
free_imatrix(HH.IDX,1,hsize,1,2);
free_dvector(HH.X,1,hsize);
dsort_PP2(&PP,elm,1);
/* Calculate the block Hessian */
HB=dmatrix(1,6*nblx,1,6*nblx);
bdim=calc_blessian_mem(&PDB,&PP,natm,nblx,elm,HB,cutoff,gamma,scl,mlo,mhi);
/* Cast the block Hessian and projection matrix into 1D arrays. */
copy_prj_ofst(&PP,proj,elm,bdim);
for(i=1;i<=bdim;i++)
for(j=1;j<=bdim;j++)
hess[bdim*(i-1)+j-1]=HB[i][j];
free(PDB.atom);
free_imatrix(PP.IDX,1,elm,1,2);
free_dvector(PP.X,1,elm);
free_dmatrix(HB,1,6*nblx,1,6*nblx);
Py_RETURN_NONE;
}
int main(int argc, char** args){
double Re, UI, VI, PI, GX, GY, t_end, xlength, ylength, dt, dx, dy, alpha, omg, tau, eps, dt_value, t, res, dp, nu;
double **U, **V, **P, **F, **G, **RS;
double **K, **E; /* turbulent kinetic energy k, dissipation rate epsilon*/
double Fu, Fv; /* force integration variables */
double KI, EI, cn, ce, c1, c2; /* K and E: Initial values for k and epsilon */
int n, it, imax, jmax, itermax, pb, boundaries[4];
int fluid_cells; /* Number of fluid cells in our geometry */
int **Flag; /* Flagflield matrix */
char vtkname[200];
char pgm[200];
char problem[10]; /* Problem name */
char fname[200];
if(argc<2){
printf("No parameter file specified. Terminating...\n");
exit(1);
}
sprintf(fname, "%s%s", CONFIGS_FOLDER, args[1]);
printf("%s\n",fname);
read_parameters(fname, &Re, &UI, &VI, &PI, &GX, &GY, &t_end, &xlength, &ylength, &dt, &dx, &dy, &imax, &jmax, &alpha, &omg, &itermax, &eps, boundaries, &dp, &pb, &KI, &EI, &cn, &ce, &c1, &c2, pgm, &nu, problem);
/* Allocate Flag matrix */
Flag = imatrix( 0, imax+1, 0, jmax+1 );
U = matrix ( 0 , imax+1 , 0 , jmax+1 );
V = matrix ( 0 , imax+1 , 0 , jmax+1 );
P = matrix ( 0 , imax+1 , 0 , jmax+1 );
F = matrix ( 0 , imax , 0 , jmax );
G = matrix ( 0 , imax , 0 , jmax );
RS = matrix ( 0 , imax , 0 , jmax );
K = matrix ( 0 , imax+1 , 0 , jmax+1 );
E = matrix ( 0 , imax+1 , 0 , jmax+1 );
/* Initialize values to the Flag, u, v and p */
init_flag(CONFIGS_FOLDER,pgm, imax, jmax, &fluid_cells, Flag );
init_uvp(UI, VI, PI, KI, EI, imax, jmax, U, V, P, K, E, Flag, problem );
printf("Problem: %s\n", problem );
printf( "xlength = %f, ylength = %f\n", xlength, ylength );
printf( "imax = %d, jmax = %d\n", imax, jmax );
printf( "dt = %f, dx = %f, dy = %f\n", dt, dx, dy);
printf( "Number of fluid cells = %d\n", fluid_cells );
printf( "Reynolds number: %f\n\n", Re);
t=.0;
n=0;
while( t <= t_end ){
boundaryvalues( imax, jmax, U, V, K, E, boundaries, Flag );
/* special inflow boundaries, including k and eps */
spec_boundary_val( problem, imax, jmax, U, V, K, E, Re, dp, cn, ylength);
/* calculate new values for k and eps */
comp_KAEP(Re, nu, cn, ce, c1, c2, alpha, dt, dx, dy, imax, jmax, U, V, K, E, GX, GY, Flag);
/* calculate new values for F and G */
calculate_fg( Re, GX, GY, alpha, dt, dx, dy, imax, jmax, U, V, F, G, K, E, nu, cn, Flag );
/* calculate right hand side */
calculate_rs( dt, dx, dy, imax, jmax, F, G, RS, Flag );
it = 0;
res = 10000.0;
while( it < itermax && fabs(res) > eps ){
sor( omg, dx, dy, imax, jmax, fluid_cells, P, RS, Flag, &res, problem, dp );
it++;
}
printf("[%5d: %f] dt: %f, sor iterations: %4d \n", n, t, dt, it);
/* calculate new values for u and v */
calculate_uv( dt, dx, dy, imax, jmax, U, V, F, G, P, Flag );
t += dt;
n++;
}
sprintf(vtkname, "%s%s", VISUA_FOLDER, args[1]);
write_vtkFile( vtkname, 1, xlength, ylength, imax, jmax, dx, dy, U, V, P, K, E, Flag);
comp_surface_force( Re, dx, dy, imax, jmax, U, V, P, Flag, &Fu, &Fv);
printf( "\nProblem: %s\n", problem );
printf( "xlength = %f, ylength = %f\n", xlength, ylength );
printf( "imax = %d, jmax = %d\n", imax, jmax );
printf( "dt = %f, dx = %f, dy = %f\n", dt, dx, dy);
printf( "Number of fluid cells = %d\n", fluid_cells );
printf( "Reynolds number: %f\n", Re);
printf( "Drag force = %f Lift force = %f\n", Fu, Fv);
/* free memory */
free_matrix(U,0,imax+1,0,jmax+1);
free_matrix(V,0,imax+1,0,jmax+1);
free_matrix(P,0,imax+1,0,jmax+1);
free_matrix(K,0,imax+1,0,jmax+1);
free_matrix(E,0,imax+1,0,jmax+1);
free_matrix(F,0,imax,0,jmax);
free_matrix(G,0,imax,0,jmax);
free_matrix(RS,0,imax,0,jmax);
free_imatrix(Flag,0,imax+1,0,jmax+1);
return 0;
}
main (int argc, char *argv[]){
int i,j,k;
manager_init();
parse_util_args(argc, argv);
iparam_set("LQUAD",3);
iparam_set("MQUAD",3);
iparam_set("NQUAD",3);
iparam_set("MODES",iparam("LQUAD")-1);
char *buf = (char*) calloc(BUFSIZ, sizeof(char));
char *fname = (char*) calloc(BUFSIZ, sizeof(char));
get_string("Enter name of input file", buf);
sprintf(fname, strtok(buf, "\n"));
Grid *grid = new Grid(fname);
Grid *grida = new Grid(grid);
grida->RenumberPrisms();
grida->FixPrismOrientation();
grid->ImportPrismOrientation(grida);
grida->RemovePrisms();
grida->RemoveHexes();
grida->FixTetOrientation();
grid->ImportTetOrientation(grida);
Element_List *U = grid->gen_aux_field();
int nel = U->nel;
get_string("Enter name of output file", buf);
sprintf(fname, strtok(buf, "\n"));
FILE *fout = fopen(fname, "w");
int Nfields, Nbdry;
get_int ("Enter number of fields", &Nfields);
get_int ("Enter number of boundaries (including default)", &Nbdry);
char **eqn = (char**) calloc(Nfields, sizeof(char*));
for(i=0;i<Nfields;++i){
eqn[i] = (char*)calloc(BUFSIZ, sizeof(char));
}
Bndry *Bc;
Bndry **Vbc = (Bndry**) calloc(Nfields, sizeof(Bndry*));
char *bndryeqn = (char*) calloc(BUFSIZ, sizeof(char));
int **bcmatrix = imatrix(0, U->nel-1, 0, Max_Nfaces-1);
izero(U->nel*Max_Nfaces, bcmatrix[0], 1);
int nb;
char type;
char curved, curvetype;
Curve *cur;
int curveid = 0;
for(nb=0;nb<Nbdry;++nb){
if(nb != Nbdry-1){
fprintf(stderr, "#\nBoundary: %d\n#\n", nb+1);
get_string("Enter function which has roots at boundary", bndryeqn);
fprintf(stderr, "#\n");
}
else{
fprintf(stderr, "#\nDefault Boundary:\n#\n");
}
get_char("Enter character type\n(v=velocity)\n"
"(W=wall)\n(O=outflow)\n(s=flux (Compressible only))\n",
&type);
fprintf(stderr, "#\n");
switch(type){
case 'W': case 'O':
break;
case 'v': case 's':
for(i=0;i<Nfields;++i){
get_string("Enter function definition", eqn[i]);
fprintf(stderr, "\n");
}
}
get_char("Is this boundary curved (y/n)?", &curved);
if(curved == 'y'){
++curveid;
get_char("Enter curve type\n(S=sphere)\n(C=cylinder)\n(T=taurus)\n",
&curvetype);
switch(curvetype){
case 'S':{
double cx, cy, cz, cr;
get_double("Enter center x-coord", &cx);
get_double("Enter center y-coord", &cy);
get_double("Enter center z-coord", &cz);
get_double("Enter radius", &cr);
cur = (Curve*) calloc(1, sizeof(Curve));
cur->type = T_Sphere;
cur->info.sph.xc = cx;
cur->info.sph.yc = cy;
cur->info.sph.zc = cz;
cur->info.sph.radius = cr;
cur->id = curveid;
break;
}
case 'C':{
double cx, cy, cz, cr;
double ax, ay, az;
get_double("Enter point on axis x-coord", &cx);
get_double("Enter point on axis y-coord", &cy);
get_double("Enter point on axis z-coord", &cz);
get_double("Enter axis vector x-coord", &ax);
get_double("Enter axis vector y-coord", &ay);
get_double("Enter axis vector z-coord", &az);
get_double("Enter radius", &cr);
cur = (Curve*) calloc(1, sizeof(Curve));
cur->type = T_Cylinder;
cur->info.cyl.xc = cx;
cur->info.cyl.yc = cy;
cur->info.cyl.zc = cz;
cur->info.cyl.ax = ax;
cur->info.cyl.ay = ay;
cur->info.cyl.az = az;
cur->info.cyl.radius = cr;
cur->id = curveid;
break;
}
}
}
if(nb == Nbdry-1)
break;
double res;
Element *E;
for(E=U->fhead;E;E=E->next){
for(i=0;i<E->Nfaces;++i){
for(j=0;j<E->Nfverts(i);++j){
vector_def("x y z",bndryeqn);
vector_set(1,
&(E->vert[E->fnum(i,j)].x),
&(E->vert[E->fnum(i,j)].y),
&(E->vert[E->fnum(i,j)].z),
&res);
if(fabs(res)> TOL)
break;
}
if(j==E->Nfverts(i)){
if(curved == 'y'){
E->curve = (Curve*) calloc(1, sizeof(Curve));
memcpy(E->curve, cur, sizeof(Curve));
E->curve->face = i;
}
switch(type){
case 'W': case 'O':
for(j=0;j<Nfields;++j){
Bc = E->gen_bndry(type, i, 0.);
Bc->type = type;
add_bc(&Vbc[j], Bc);
}
bcmatrix[E->id][i] = 1;
break;
case 'v': case 's':
for(j=0;j<Nfields;++j){
Bc = E->gen_bndry(type, i, eqn[j]);
Bc->type = type;
add_bc(&Vbc[j], Bc);
}
bcmatrix[E->id][i] = 1;
break;
}
}
}
}
}
char is_periodic;
get_char("Is there periodicity in the x-direction (y/n)?", &is_periodic);
if(is_periodic == 'y')
get_double("Enter periodic length",&XPERIOD);
get_char("Is there periodicity in the y-direction (y/n)?", &is_periodic);
if(is_periodic == 'y')
get_double("Enter periodic length",&YPERIOD);
get_char("Is there periodicity in the z-direction (y/n)?", &is_periodic);
if(is_periodic == 'y')
get_double("Enter periodic length",&ZPERIOD);
// Do remaining connections
Element *E, *F;
for(E=U->fhead;E;E=E->next)
for(i=0;i<E->Nfaces;++i)
if(!bcmatrix[E->id][i])
for(F=E;F;F=F->next)
for(j=0;j<F->Nfaces;++j)
if(!bcmatrix[F->id][j])
if(neighbourtest(E,i,F,j) && !(E->id == F->id && i==j)){
bcmatrix[E->id][i] = 2;
bcmatrix[F->id][j] = 2;
set_link(E,i,F,j);
break;
}
// if the default bc is curved the make default bndries curved
if(curved == 'y'){
for(E=U->fhead;E;E=E->next)
for(i=0;i<E->Nfaces;++i)
if(!bcmatrix[E->id][i]){
E->curve = (Curve*) calloc(1, sizeof(Curve));
memcpy(E->curve, cur, sizeof(Curve));
E->curve->face = i;
}
}
fprintf(fout, "****** PARAMETERS *****\n");
fprintf(fout, " SolidMes \n");
fprintf(fout, " 3 DIMENSIONAL RUN\n");
fprintf(fout, " 0 PARAMETERS FOLLOW\n");
fprintf(fout, "0 Lines of passive scalar data follows2 CONDUCT; 2RHOCP\n");
fprintf(fout, " 0 LOGICAL SWITCHES FOLLOW\n");
fprintf(fout, "Dummy line from old nekton file\n");
fprintf(fout, "**MESH DATA** x,y,z, values of vertices 1,2,3,4.\n");
fprintf(fout, "%d 3 1 NEL NDIM NLEVEL\n", U->nel);
for(E=U->fhead;E;E=E->next){
switch(E->identify()){
case Nek_Tet:
fprintf(fout, "Element %d Tet\n", E->id+1);
break;
case Nek_Pyr:
fprintf(fout, "Element %d Pyr\n", E->id+1);
break;
case Nek_Prism:
fprintf(fout, "Element %d Prism\n", E->id+1);
break;
case Nek_Hex:
fprintf(fout, "Element %d Hex\n", E->id+1);
break;
}
for(i=0;i<E->Nverts;++i)
fprintf(fout, "%lf ", E->vert[i].x);
fprintf(fout, "\n");
for(i=0;i<E->Nverts;++i)
fprintf(fout, "%lf ", E->vert[i].y);
fprintf(fout, "\n");
for(i=0;i<E->Nverts;++i)
fprintf(fout, "%lf ", E->vert[i].z);
fprintf(fout, "\n");
}
fprintf(fout, "***** CURVED SIDE DATA ***** \n");
fprintf(fout, "%d Number of curve types\n", curveid);
for(i=0;i<curveid;++i){
int flag = 0;
for(E=U->fhead;!flag && E;E=E->next){
if(E->curve && E->curve->type != T_Straight){
if(E->curve->id == i+1){
switch(E->curve->type){
case T_Sphere:
fprintf(fout, "Sphere\n");
fprintf(fout, "%lf %lf %lf %lf %c\n",
E->curve->info.sph.xc,
E->curve->info.sph.yc,
E->curve->info.sph.zc,
E->curve->info.sph.radius,
'a'+i+1);
flag = 1;
break;
case T_Cylinder:
fprintf(fout, "Cylinder\n");
fprintf(fout, "%lf %lf %lf %lf %lf %lf %lf %c\n",
E->curve->info.cyl.xc,
E->curve->info.cyl.yc,
E->curve->info.cyl.zc,
E->curve->info.cyl.ax,
E->curve->info.cyl.ay,
E->curve->info.cyl.az,
E->curve->info.cyl.radius,
'a'+i+1);
flag = 1;
break;
}
}
}
}
}
int ncurvedsides = 0;
for(E=U->fhead;E;E=E->next){
if(E->curve && E->curve->type != T_Straight)
++ncurvedsides;
}
fprintf(fout, "%d Curved sides follow\n", ncurvedsides);
for(E=U->fhead;E;E=E->next)
if(E->curve && E->curve->type != T_Straight)
fprintf(fout, "%d %d %c\n", E->curve->face+1, E->id+1, 'a'+E->curve->id);
fprintf(fout, "***** BOUNDARY CONDITIONS ***** \n");
fprintf(fout, "***** FLUID BOUNDARY CONDITIONS ***** \n");
for(E=U->fhead;E;E=E->next){
for(j=0;j<E->Nfaces;++j){
if(bcmatrix[E->id][j] == 2){
fprintf(fout, "E %d %d %d %d\n", E->id+1, j+1,
E->face[j].link->eid+1, E->face[j].link->id+1);
}
else if(bcmatrix[E->id][j] == 1){
for(i=0;i<Nfields;++i)
for(Bc=Vbc[i];Bc;Bc=Bc->next){
if(Bc->elmt == E && Bc->face == j){
if(i==0)
switch(Bc->type){
case 'W':
fprintf(fout, "W %d %d 0. 0. 0.\n", E->id+1, j+1);
break;
case 'O':
fprintf(fout, "O %d %d 0. 0. 0.\n", E->id+1, j+1);
break;
case 'v':
fprintf(fout, "v %d %d 0. 0. 0.\n", E->id+1, j+1);
break;
case 's':
fprintf(fout, "s %d %d 0. 0. 0.\n", E->id+1, j+1);
break;
}
if(Bc->type == 's' || Bc->type == 'v')
fprintf(fout, "%c=%s\n", 'u'+i,Bc->bstring);
break;
}
}
}
else{
switch(type){
case 'W':
fprintf(fout, "W %d %d 0. 0. 0.\n", E->id+1, j+1);
break;
case 'O':
fprintf(fout, "O %d %d 0. 0. 0.\n", E->id+1, j+1);
break;
case 'v':
fprintf(fout, "v %d %d 0. 0. 0.\n", E->id+1, j+1);
break;
case 's':
fprintf(fout, "s %d %d 0. 0. 0.\n", E->id+1, j+1);
break;
}
if(type == 's' || type == 'v')
for(i=0;i<Nfields;++i)
fprintf(fout, "%c=%s\n", 'u'+i,eqn[i]);
}
}
}
char bufa[BUFSIZ];
fprintf(fout, "***** NO THERMAL BOUNDARY CONDITIONS *****\n");
get_char("Are you using a field file restart (y/n)?", &type);
if(type == 'y'){
fprintf(fout, "%d INITIAL CONDITIONS *****\n",1);
get_string("Enter name of restart file:", buf);
fprintf(fout, "Restart\n");
fprintf(fout, "%s\n", buf);
}
else{
fprintf(fout, "%d INITIAL CONDITIONS *****\n",1+Nfields);
fprintf(fout, "Given\n");
for(i=0;i<Nfields;++i){
sprintf(bufa, "Field %d ", i+1);
get_string(bufa, buf);
fprintf(fout, "%s\n", buf);
}
}
fprintf(fout, "***** DRIVE FORCE DATA ***** PRESSURE GRAD, FLOW, Q\n");
get_char("Are you using a forcing function (y/n)?", &type);
if(type == 'y'){
fprintf(fout, "%d Lines of Drive force data follow\n",
Nfields);
for(i=0;i<Nfields;++i){
sprintf(bufa, "FF%c = ", 'X'+i);
get_string(bufa,buf);
fprintf(fout, "FF%c = %s\n",'X'+i, buf);
}
}
else{
fprintf(fout, "0 Lines of Drive force data follow\n");
}
fprintf(fout, "***** Variable Property Data ***** Overrrides Parameter data.\n");
fprintf(fout, " 1 Lines follow.\n");
fprintf(fout, " 0 PACKETS OF DATA FOLLOW\n");
fprintf(fout, "***** HISTORY AND INTEGRAL DATA *****\n");
get_char("Are you using history points (y/n)?", &type);
if(type == 'y'){
int npoints;
get_int ("Enter number of points", &npoints);
fprintf(fout, " %d POINTS. Hcode, I,J,H,IEL\n", npoints);
for(i=0;i<npoints;++i){
sprintf(bufa, "Enter element number for point %d", i+1);
get_int(bufa,&j);
sprintf(bufa, "Enter vertex number for point %d", i+1);
get_int(bufa, &k);
fprintf(fout, "UVWP H %d 1 1 %d\n", k, j);
}
}
else{
fprintf(fout, " 0 POINTS. Hcode, I,J,H,IEL\n");
}
fprintf(fout, " ***** OUTPUT FIELD SPECIFICATION *****\n");
fprintf(fout, " 0 SPECIFICATIONS FOLLOW\n");
return 0;
}
int main(int argn, char** args){
double **U, **V, **P, **F, **G, **RS;
const char *szFileName = "dam_break.dat";
double Re, UI, VI, PI, GX, GY, t_end, xlength, ylength, dt, dx, dy, alpha, omg, tau, eps, dt_value;
double res = 0, t = 0, n = 0;
int imax, jmax, itermax, it;
/* Additional data structures for VOF */
double **fluidFraction;
double **fluidFraction_alt;
int **flagField;
double **dFdx, **dFdy;
int **pic;
char output_dirname[60];
double epsilon = 1e-10;
/* Read the program configuration file using read_parameters() */
read_parameters(szFileName, &Re, &UI, &VI, &PI, &GX, &GY, &t_end, &xlength, &ylength, &dt, &dx, &dy, &imax, &jmax, &alpha, &omg, &tau, &itermax, &eps, &dt_value);
/* Set up the matrices (arrays) needed using the matrix() command */
U = matrix(0, imax , 0, jmax+1);
V = matrix(0, imax+1, 0, jmax );
P = matrix(0, imax+1, 0, jmax+1);
F = matrix(0, imax , 0, jmax+1);
G = matrix(0, imax+1, 0, jmax );
RS= matrix(0, imax+1, 0, jmax+1);
flagField = imatrix(0, imax+1, 0, jmax+1);
fluidFraction = matrix(0, imax+1, 0, jmax+1);
fluidFraction_alt = matrix(0, imax+1, 0, jmax+1);
dFdx = matrix(0, imax+1, 0, jmax+1);
dFdy = matrix(0, imax+1, 0, jmax+1);
/*create a directory*/
strcpy(output_dirname, "dam_break/dam_break");
mkdir("dam_break", 0777);
/* Read pgm file with domain and initial setting */
pic = read_pgm("dam_break.pgm");
init_fluidFraction(pic, fluidFraction,fluidFraction_alt, imax, jmax);
/* Assign initial values to u, v, p */
init_uvp(UI, VI, PI, imax, jmax, U, V, P);
/* Set valid values for the fluid fraction */
adjust_fluidFraction(fluidFraction, flagField, epsilon, imax, jmax);
while(t <= t_end){
/*Select δt*/
calculate_dt(Re, tau, &dt, dx, dy, imax, jmax, U, V);
/* Set boundary values for u and v */
/* boundaryvalues(imax, jmax, U, V, flagField, dx, dy);
*/
/* Compute F(n) and G(n) */
calculate_fg(Re, GX, GY, alpha, dt, dx, dy, imax, jmax, U, V, F, G, flagField);
/* Compute the right-hand side rs of the pressure equation */
calculate_rs(dt, dx, dy, imax, jmax, F, G, RS, flagField);
/* Determine the orientation of the free surfaces */
calculate_freeSurfaceOrientation(fluidFraction, flagField, dFdx, dFdy, dx, dy, imax, jmax);
/* Perform SOR iterations */
it=0;
res = 1e6;
while(it < itermax && res > eps){
sor(omg, dx, dy, imax, jmax, P, RS, fluidFraction, flagField, dFdx, dFdy, &res);
it++;
}
/* Compute u(n+1) and v(n+1) */
calculate_uv(dt, dx, dy, imax, jmax, U, V, F, G, P, flagField);
boundaryvalues(imax, jmax, U, V, flagField, dx, dy);
/* Compute fluidFraction(n+1) */
calculate_fluidFraction(fluidFraction,fluidFraction_alt, flagField, U, V, dFdx, dFdy, imax, jmax, dx, dy, dt);
boundaryvalues(imax, jmax, U, V, flagField, dx, dy);
/* Set valid values for the fluid fraction */
adjust_fluidFraction(fluidFraction, flagField, epsilon, imax, jmax);
boundaryvalues(imax, jmax, U, V, flagField, dx, dy);
if((int)n % 10 == 0) {
write_vtkFile(output_dirname, n, xlength, ylength, imax, jmax, dx, dy, U, V, P, fluidFraction, flagField);
}
/* Print out simulation time and whether SOR converged */
printf("Time: %.4f", t);
if(res > eps) {printf("\t*** Did not converge (res=%f, eps=%f)", res, eps);return -1;}
printf("\n");
t = t + dt;
n++;
}
free_matrix(U , 0, imax , 0, jmax+1);
free_matrix(V , 0, imax+1, 0, jmax );
free_matrix(P , 0, imax+1, 0, jmax+1);
free_matrix(F , 0, imax , 0, jmax+1);
free_matrix(G , 0, imax+1, 0, jmax );
free_matrix(RS, 0, imax+1, 0, jmax+1);
return -1;
}
int main(int argc,char *argv[])
{
Centroid *SYS,*ENV;
Sprngmtx *Gamma;
char *sysfile,*envfile,*massfile,*ctfile,*spgfile;
double **GG;
double *CUT,**HS,**HE,**HX,**PH,*P;
double dd,x,y;
int **CT,**PIX,nss,nen,nn,ntp,nse,r1,c1,r2,c2,i,j,k;
int ptmd,rprm,pprm;
/* Formalities */
read_command_line(argc,argv,&pprm,&rprm,&ptmd,&MSCL);
/* Read coordinate and mass data */
sysfile=get_param(argv[pprm],"syscoords");
envfile=get_param(argv[pprm],"envcoords");
massfile=get_param(argv[pprm],"massfile");
SYS=read_centroids1(sysfile,massfile,&nss);
ENV=read_centroids1(envfile,massfile,&nen);
nn=nss+nen;
fprintf(stderr,"System read from %s: %d centroids\n",sysfile,nss);
fprintf(stderr,"Environment read from %s: %d centroids\n",envfile,nen);
fprintf(stderr,"Masses read from %s\n",massfile);
CT=imatrix(1,nn,1,nn);
/* Find extent of membrane */
membounds(ENV,nen,&MHI,&MLO);
/* Print masses, if called for */
if(ptmd==2){
for(i=1;i<=nss;i++)
for(j=-2;j<=0;j++){
k=3*i+j;
printf("%8d%8d% 25.15e\n",k,k,SYS[i].mass);
}
for(i=1;i<=nen;i++)
for(j=-2;j<=0;j++){
k=3*nss+3*i+j;
printf("%8d%8d% 25.15e\n",k,k,ENV[i].mass);
}
return 0;
}
/* ---------------- Assign contacts... ----------------- */
/* From a contact file... */
if((ctfile=get_param(argv[pprm],"contactfile"))!=NULL){
read_contacts(ctfile,CT,nn);
fprintf(stderr,"Contacts read from %s\n",ctfile);
}
/* ...or from a cutoff file... */
else if((ctfile=get_param(argv[pprm],"cutfile"))!=NULL){
fprintf(stderr,"Cutoff values read from %s\n",ctfile);
CUT=read_cutfile2(ctfile,SYS,ENV,nss,nen);
radius_contact_sysenv(CT,SYS,ENV,nss,nen,CUT);
}
/* ...or from default values */
else{
CUT=dvector(1,nn);
for(i=1;i<=nn;i++) CUT[i]=DEFCUT;
fprintf(stderr,"All cutoff values set to %.3f\n",DEFCUT);
radius_contact_sysenv(CT,SYS,ENV,nss,nen,CUT);
}
fprintf(stderr,"%d clusters\n",num_clusters(CT,nn));
if(ptmd==1){
fprintf(stderr,"Printing contacts\n");
for(i=1;i<=nn;i++)
for(j=i+1;j<=nn;j++)
if(CT[i][j]!=0)
printf("%d\t%d\n",i,j);
return 0;
}
/* ------- Construct the matrix of force constants -------*/
GG=dmatrix(1,nn,1,nn);
/* Read force constants from file... */
if((spgfile=get_param(argv[pprm],"springfile"))!=NULL){
fprintf(stderr,"Reading spring constants from %s\n",spgfile);
Gamma=read_springfile_sysenv(spgfile,SYS,ENV,nss,nen,&ntp);
spring_constants_sysenv(SYS,ENV,GG,CT,Gamma,nss,nen,ntp);
}
/* ...or else assign the default value to all springs */
else
for(i=1;i<=nn;i++)
for(j=i;j<=nn;j++)
if(CT[i][j]!=0)
GG[i][j]=GG[j][i]=DEFGAM;
/* Construct the mass-weighted Hessian from
coordinates, masses, and potential matrix */
fprintf(stderr,"Calculating Hessian...\n");
HS=dmatrix(1,3*nss,1,3*nss);
HE=dmatrix(1,3*nen,1,3*nen);
HX=dmatrix(1,3*nss,1,3*nen);
mwhess_sysenv(HS,HE,HX,SYS,ENV,GG,nss,nen);
/* PRINT THE ENVIRONMENT-ENVIRONMENT SUB-HESSIAN IN SPARSE FORMAT */
if(ptmd==0 && rprm==-1){
fprintf(stderr,"\nPrinting env-env sub-hessian...\n\n");
for(i=1;i<=3*nen;i++)
for(j=i;j<=3*nen;j++)
if(fabs(HE[i][j])>1.0e-10)
printf("%8d%8d% 25.15e\n",i,j,HE[i][j]);
return 0;
}
/* PRINT THE FULL HESSIAN IN SPARSE FORMAT */
if(ptmd==3){
for(i=1;i<=3*nss;i++){
for(j=i;j<=3*nss;j++)
if(fabs(HS[i][j])>1.0e-10)
printf("%8d%8d% 20.10e\n",i,j,HS[i][j]);
for(j=1;j<=3*nen;j++)
if(fabs(HX[i][j])>1.0e-10)
printf("%8d%8d% 20.10e\n",i,j+3*nss,HX[i][j]);
}
for(i=1;i<=3*nen;i++)
for(j=i;j<=3*nen;j++)
if(fabs(HE[i][j])>1.0e-10)
printf("%8d%8d% 20.10e\n",i+3*nss,j+3*nss,HE[i][j]);
return 0;
}
/* READ INVERSE OF ENVIRONMENTAL HESSIAN, OR INVERT HE */
free_imatrix(CT,1,nn,1,nn);
free_dmatrix(GG,1,nn,1,nn);
if(rprm!=-1){
fprintf(stderr,"Reading matrix from %s...\n",argv[rprm]);
read_sparsemtx(argv[rprm],HE,3*nen,3*nen);
}
else{
fprintf(stderr,"\nWell...How did I get here?\n\n");
exit(1);}
/* ---------------- CALCULATE AND PRINT THE PSEUDOHESSIAN ---------------- */
/* COUNT THE NUMBER OF NON-ZERO TERMS IN THE PROJECTION MATRIX */
nse=0;
for(i=1;i<=3*nss;i++)
for(j=1;j<=3*nen;j++)
if(fabs(HX[i][j])>1.0e-9) nse++;
fprintf(stderr,"%d non-zero projection elements\n",nse);
P=dvector(1,nse);
PIX=imatrix(1,nse,1,2);
k=1;
for(i=1;i<=3*nss;i++)
for(j=1;j<=3*nen;j++)
if(fabs(HX[i][j])>1.0e-9){
PIX[k][1]=i;
PIX[k][2]=j;
P[k]=HX[i][j];
k++;
}
free_dmatrix(HX,1,3*nss,1,3*nen);
PH=dmatrix(1,3*nss,1,3*nss);
for(i=1;i<=3*nss;i++)
for(j=i;j<=3*nss;j++)
PH[i][j]=PH[j][i]=0.0;
for(i=1;i<=nse;i++){
r1=PIX[i][1];
c1=PIX[i][2];
x=P[i];
for(j=i;j<=nse;j++){
r2=PIX[j][1];
c2=PIX[j][2];
y=HE[c1][c2]*P[j]*x;
PH[r1][r2]+=y;
if(r1==r2 && c1!=c2)
PH[r1][r2]+=y;
}
}
for(i=1;i<=3*nss;i++)
for(j=i;j<=3*nss;j++){
dd=HS[i][j]-PH[i][j];
if(fabs(dd)>1.0e-10)
printf("%8d%8d% 25.15e\n",i,j,dd);
}
return 0;
}
/* "calc_blessian_mem" calculates the block Hessian. */
int calc_blessian_mem(PDB_File *PDB,dSparse_Matrix *PP1,int nres,int nblx,
int elm,double **HB,double cut,double gam,double scl,
double mlo,double mhi)
{
dSparse_Matrix *PP2;
double **HR,***HT;
int **CT,*BST1,*BST2;
int ii,i,j,k,p,q,q1,q2,ti,tj,bi,bj,sb,nc,out;
/* ------------------- INITIALIZE LOCAL VARIABLES ------------------- */
/* HR holde three rows (corresponding to 1 residue) of the full Hessian */
HR=zero_dmatrix(1,3*nres,1,3);
/* CT is an array of contacts between blocks */
CT=unit_imatrix(0,nblx);
/* Copy PP1 to PP2 and sort by second element */
PP2=(dSparse_Matrix *)malloc((size_t)sizeof(dSparse_Matrix));
PP2->IDX=imatrix(1,elm,1,2);
PP2->X=dvector(1,elm);
copy_dsparse(PP1,PP2,1,elm);
dsort_PP2(PP2,elm,2);
/* BST1: for all j: BST1[i]<=j<BST[i+1], PP1->IDX[j][1]=i */
/* BST2: for all j: BST2[i]<=j<BST2[i+1], PP2->IDX[j][2]=i */
BST1=ivector(1,3*nres+1);
BST2=ivector(1,6*nblx+1);
init_bst(BST1,PP1,elm,3*nres+1,1);
init_bst(BST2,PP2,elm,6*nblx+1,2);
/* ------------------- LOCAL VARIABLES INITIALIZED ------------------ */
/* ------------- FIND WHICH BLOCKS ARE IN CONTACT --------------- */
nc=find_contacts1(CT,PDB,nres,nblx,cut);
/* Allocate a tensor for the block Hessian */
HT=zero_d3tensor(1,nc,1,6,1,6);
/* Calculate each super-row of the full Hessian */
for(ii=1;ii<=nres;ii++){
if(PDB->atom[ii].model!=0){
/* ----------------- FIND SUPER-ROW OF FULL HESSIAN --------------- */
hess_superrow_mem(HR,CT,PDB,nres,ii,cut,gam,scl,mlo,mhi);
/* Update elements of block hessian */
q1=BST1[3*(ii-1)+2];
q2=BST1[3*(ii-1)+3];
/* Sum over elements of projection matrix corresponding to residue ii:
for each k in the following loop, PP1->IDX[k][1]==3*ii + 0,1,2 */
for(k=BST1[3*ii-2];k<BST1[3*ii+1];k++){
if(k<q1) q=1;
else if(k<q2) q=2;
else q=3;
i=PP1->IDX[k][2];
bi=(i-1)/6+1;
ti=i-6*(bi-1);
/* Sum over all elements of projection matrix with column j>=i */
for(p=BST2[i];p<=elm;p++){
j=PP2->IDX[p][2];
bj=(j-1)/6+1;
sb=CT[bi][bj];
if(i<=j && sb!=0){ /* the first condition should ALWAYS hold */
tj=j-6*(bj-1);
HT[sb][ti][tj]+=(PP1->X[k]*PP2->X[p]*HR[PP2->IDX[p][1]][q]);
}
}
}
}
}
/* Print the block Hessian in sparse format */
out=bless_from_tensor(HB,HT,CT,nblx);
/* Free up memory */
free_dmatrix(HR,1,3*nres,1,3);
free_d3tensor(HT,1,nc,1,6,1,6);
free_imatrix(CT,0,nblx,0,nblx);
free_ivector(BST1,1,3*nres+1);
free_ivector(BST2,1,6*nblx+1);
free_imatrix(PP2->IDX,1,elm,1,2);
free_dvector(PP2->X,1,elm);
return out;
}
static int compute_tree_adaboost(ETree *etree,int n,int d,double *x[],int y[],
int nmodels,int stumps, int minsize)
{
int i,b;
int *samples;
double **trx;
int *try;
double *prob;
double *prob_copy;
double sumalpha;
double eps;
int *pred;
double *margin;
double sumprob;
if(nmodels<1){
fprintf(stderr,"compute_tree_adaboost: nmodels must be greater than 0\n");
return 1;
}
if(stumps != 0 && stumps != 1){
fprintf(stderr,"compute_tree_bagging: parameter stumps must be 0 or 1\n");
return 1;
}
if(minsize < 0){
fprintf(stderr,"compute_tree_bagging: parameter minsize must be >= 0\n");
return 1;
}
etree->nclasses=iunique(y,n, &(etree->classes));
if(etree->nclasses<=0){
fprintf(stderr,"compute_tree_adaboost: iunique error\n");
return 1;
}
if(etree->nclasses==1){
fprintf(stderr,"compute_tree_adaboost: only 1 class recognized\n");
return 1;
}
if(etree->nclasses==2)
if(etree->classes[0] != -1 || etree->classes[1] != 1){
fprintf(stderr,"compute_tree_adaboost: for binary classification classes must be -1,1\n");
return 1;
}
if(etree->nclasses>2){
fprintf(stderr,"compute_tree_adaboost: multiclass classification not allowed\n");
return 1;
}
if(!(etree->tree=(Tree *)calloc(nmodels,sizeof(Tree)))){
fprintf(stderr,"compute_tree_adaboost: out of memory\n");
return 1;
}
if(!(etree->weights=dvector(nmodels))){
fprintf(stderr,"compute_tree_adaboost: out of memory\n");
return 1;
}
if(!(trx=(double **)calloc(n,sizeof(double*)))){
fprintf(stderr,"compute_tree_adaboost: out of memory\n");
return 1;
}
if(!(try=ivector(n))){
fprintf(stderr,"compute_tree_adaboost: out of memory\n");
return 1;
}
if(!(prob_copy=dvector(n))){
fprintf(stderr,"compute_tree_adaboost: out of memory\n");
return 1;
}
if(!(prob=dvector(n))){
fprintf(stderr,"compute_tree_adaboost: out of memory\n");
return 1;
}
if(!(pred=ivector(n))){
fprintf(stderr,"compute_tree_adaboost: out of memory\n");
return 1;
}
for(i =0;i<n;i++)
prob[i]=1.0/(double)n;
etree->nmodels=nmodels;
sumalpha=0.0;
for(b=0;b<nmodels;b++){
for(i =0;i<n;i++)
prob_copy[i]=prob[i];
if(sample(n, prob_copy, n, &samples, TRUE,b)!=0){
fprintf(stderr,"compute_tree_adaboost: sample error\n");
return 1;
}
for(i=0;i<n;i++){
trx[i] = x[samples[i]];
try[i] = y[samples[i]];
}
if(compute_tree(&(etree->tree[b]),n,d,trx,try,stumps,minsize)!=0){
fprintf(stderr,"compute_tree_adaboost: compute_tree error\n");
return 1;
}
free_ivector(samples);
eps=0.0;
for(i=0;i<n;i++){
pred[i]=predict_tree(&(etree->tree[b]),x[i],&margin);
if(pred[i] < -1 ){
fprintf(stderr,"compute_tree_adaboost: predict_tree error\n");
return 1;
}
if(pred[i]==0 || pred[i] != y[i])
eps += prob[i];
free_dvector(margin);
}
if(eps > 0.0 && eps < 0.5){
etree->weights[b]=0.5 *log((1.0-eps)/eps);
sumalpha+=etree->weights[b];
}else{
etree->nmodels=b;
break;
}
sumprob=0.0;
for(i=0;i<n;i++){
prob[i]=prob[i]*exp(-etree->weights[b]*y[i]*pred[i]);
sumprob+=prob[i];
}
if(sumprob <=0.0){
fprintf(stderr,"compute_tree_adaboost: sumprob = 0\n");
return 1;
}
for(i=0;i<n;i++)
prob[i] /= sumprob;
}
if(etree->nmodels<=0){
fprintf(stderr,"compute_tree_adaboost: no models produced\n");
return 1;
}
if(sumalpha <=0){
fprintf(stderr,"compute_tree_adaboost: sumalpha = 0\n");
return 1;
}
for(b=0;b<etree->nmodels;b++)
etree->weights[b] /= sumalpha;
free(trx);
free_ivector(try);
free_ivector(pred);
free_dvector(prob);
free_dvector(prob_copy);
return 0;
}
static void split_node(Node *node,Node *nodeL,Node *nodeR,int classes[],
int nclasses)
{
int **indx;
double *tmpvar;
int i,j,k;
int **npL , **npR;
double **prL , **prR;
int totL,totR;
double a,b;
double *decrease_in_inpurity;
double max_decrease=0;
int splitvar;
int splitvalue;
int morenumerous;
nodeL->priors=dvector(nclasses);
nodeR->priors=dvector(nclasses);
nodeL->npoints_for_class=ivector(nclasses);
nodeR->npoints_for_class=ivector(nclasses);
indx=imatrix(node->nvar,node->npoints);
tmpvar=dvector(node->npoints);
decrease_in_inpurity=dvector(node->npoints-1);
npL=imatrix(node->npoints,nclasses);
npR=imatrix(node->npoints,nclasses);
prL=dmatrix(node->npoints,nclasses);
prR=dmatrix(node->npoints,nclasses);
splitvar=0;
splitvalue=0;
max_decrease=0;
for(i=0;i<node->nvar;i++){
for(j=0;j<node->npoints;j++)
tmpvar[j]=node->data[j][i];
for(j=0;j<node->npoints;j++)
indx[i][j]=j;
dsort(tmpvar,indx[i],node->npoints,SORT_ASCENDING);
for(k=0;k<nclasses;k++)
if(node->classes[indx[i][0]]==classes[k]){
npL[0][k] = 1;
npR[0][k] = node->npoints_for_class[k]-npL[0][k];
} else{
npL[0][k] = 0;
npR[0][k] = node->npoints_for_class[k];
}
for(j=1;j<node->npoints-1;j++)
for(k=0;k<nclasses;k++)
if(node->classes[indx[i][j]]==classes[k]){
npL[j][k] = npL[j-1][k] +1;
npR[j][k] = node->npoints_for_class[k] - npL[j][k];
}
else {
npL[j][k] = npL[j-1][k];
npR[j][k] = node->npoints_for_class[k] - npL[j][k];
}
for(j=0;j<node->npoints-1;j++){
if(node->data[indx[i][j]][i] != node->data[indx[i][j+1]][i]){
totL = totR = 0;
for(k=0;k<nclasses;k++)
totL += npL[j][k];
for(k=0;k<nclasses;k++)
prL[j][k] = (double) npL[j][k] / (double) totL;
for(k=0;k<nclasses;k++)
totR += npR[j][k];
for(k=0;k<nclasses;k++)
prR[j][k] = (double) npR[j][k] /(double) totR;
a = (double) totL / (double) node->npoints;
b = (double) totR / (double) node->npoints ;
decrease_in_inpurity[j] = gini_index(node->priors,nclasses) -
a * gini_index(prL[j],nclasses) - b * gini_index(prR[j],nclasses);
}
}
for(j=0;j<node->npoints-1;j++)
if(decrease_in_inpurity[j] > max_decrease){
max_decrease = decrease_in_inpurity[j];
splitvar=i;
splitvalue=j;
for(k=0;k<nclasses;k++){
nodeL->priors[k]=prL[splitvalue][k];
nodeR->priors[k]=prR[splitvalue][k];
nodeL->npoints_for_class[k]=npL[splitvalue][k];
nodeR->npoints_for_class[k]=npR[splitvalue][k];
}
}
}
node->var=splitvar;
node->value=(node->data[indx[splitvar][splitvalue]][node->var]+
node->data[indx[splitvar][splitvalue+1]][node->var])/2.;
nodeL->nvar=node->nvar;
nodeL->nclasses=node->nclasses;
nodeL->npoints=splitvalue+1;
nodeL->terminal=TRUE;
if(gini_index(nodeL->priors,nclasses) >0)
nodeL->terminal=FALSE;
nodeL->data=(double **) calloc(nodeL->npoints,sizeof(double *));
nodeL->classes=ivector(nodeL->npoints);
for(i=0;i<nodeL->npoints;i++){
nodeL->data[i] = node->data[indx[splitvar][i]];
nodeL->classes[i] = node->classes[indx[splitvar][i]];
}
morenumerous=0;
for(k=0;k<nclasses;k++)
if(nodeL->npoints_for_class[k] > morenumerous){
morenumerous = nodeL->npoints_for_class[k];
nodeL->node_class=classes[k];
}
nodeR->nvar=node->nvar;
nodeR->nclasses=node->nclasses;
nodeR->npoints=node->npoints-nodeL->npoints;
nodeR->terminal=TRUE;
if(gini_index(nodeR->priors,nclasses) >0)
nodeR->terminal=FALSE;
nodeR->data=(double **) calloc(nodeR->npoints,sizeof(double *));
nodeR->classes=ivector(nodeR->npoints);
for(i=0;i<nodeR->npoints;i++){
nodeR->data[i] = node->data[indx[splitvar][nodeL->npoints+i]];
nodeR->classes[i] = node->classes[indx[splitvar][nodeL->npoints+i]];
}
morenumerous=0;
for(k=0;k<nclasses;k++)
if(nodeR->npoints_for_class[k] > morenumerous){
morenumerous = nodeR->npoints_for_class[k];
nodeR->node_class=classes[k];
}
free_imatrix(indx, node->nvar,node->npoints);
free_imatrix(npL, node->npoints,nclasses);
free_imatrix(npR, node->npoints,nclasses);
free_dmatrix(prL, node->npoints,nclasses);
free_dmatrix(prR, node->npoints,nclasses);
free_dvector(tmpvar);
free_dvector(decrease_in_inpurity);
}
void Comnode(phylo t1, phylo t2)
{
int i, j, xnode, depth, common, matches1, matches2, p, q;
int matchcode = 0;
int t1md = 0;
int t2md = 0;
int *active_n;
int *matched1;
int *matched2;
int **comlist1; // contents: node number of a term taxon (use to lookup name)
// indexed by node, and then an index 0...
int *comlist1n; // the number of items in *comlist
int **comlist2; // contents: node number of a term taxon (use to lookup name)
// indexed by node, and then an index 0...
int *comlist2n; // the number of items in *comlist
char tmp[50];
phylo Out[1];
strcpy(t1.phyname, "Tree1");
// t1.arenotes = 1;
// t1.notes = cmatrix(0, t1.nnodes-1, 0, 49);
strcpy(t2.phyname, "Tree2");
// t2.arenotes = 1;
// t2.notes = cmatrix(0, t2.nnodes-1, 0, 49);
comlist1 = imatrix(0, t1.nnodes-1, 0, t1.termtaxa);
comlist1n = ivector(0, t1.nnodes-1);
comlist2 = imatrix(0, t2.nnodes-1, 0, t2.termtaxa);
comlist2n = ivector(0, t2.nnodes-1);
matched1 = ivector(0, t1.termtaxa-1);
matched2 = ivector(0, t2.termtaxa-1);
// printf("t1: nnodes: %d taxa1: %s\n", t1.nnodes, t1.taxalist[0]);
// printf("t2: nnodes: %d taxa1: %s\n", t2.nnodes, t2.taxalist[0]);
// make a full list of term taxa from each node:
// tree1:
for (i = 0; i < t1.nnodes; i++)
{
if (t1.depth[i] > t1md) t1md = t1.depth[i];
// need to clear the node names - they could cause confusion
// when bladjing, beacause the default names are the same for both
// trees
if (t1.noat[i] > 0) strcpy(t1.taxon[i], ".");
// these will get unmaned: see fy2new
}
active_n = ivector(0, t1.nnodes-1);
for (i = 0; i < t1.nnodes; i++)
{
active_n[i] = 1;
comlist1n[i] = 0;
for (depth = t1.depth[i]; depth <= t1md; depth++)
{
for (xnode = 0; xnode < t1.nnodes; xnode++)
{
if ( (t1.depth[xnode] == depth) && (active_n[xnode] == 1) )
{
// first we check to see if we have reached a tip
if (t1.noat[xnode] == 0)
{
// test to see that it is a common spp to tree 2
common = 0;
for (j = 0; j < t2.termtaxa; j++)
{
if (strcmp(t1.taxon[xnode], t2.taxalist[j]) == 0)\
common = 1;
}
if (common ==1)
{
comlist1[i][comlist1n[i]] = xnode;
comlist1n[i]++;
//printf("1 dependent to node %d is %s\n",
// i, t1.taxon[comlist1[i][comlist1n[i]-1]]);
}
active_n[xnode] = 0;
}
else
{
for (j = 0; j < t1.noat[xnode]; j++)
{
active_n[t1.down[xnode][j]] = 1;
}
active_n[xnode] = 0;
}
}
}
}
}
// make a full list of term taxa from each node:
// tree2:
for (i = 0; i < t2.nnodes; i++)
{
if (t2.depth[i] > t2md) t2md = t2.depth[i];
// need to clear the node names - they could cause confusion
// when bladjing, beacause the default names are the same for both
// trees
if (t2.noat[i] > 0) strcpy(t2.taxon[i], ".");
// these will get unmaned: see fy2new
}
active_n = ivector(0, t2.nnodes-1);
for (i = 0; i < t2.nnodes; i++)
{
active_n[i] = 1;
comlist2n[i] = 0;
for (depth = t2.depth[i]; depth <= t2md; depth++)
{
for (xnode = 0; xnode < t2.nnodes; xnode++)
{
if ( (t2.depth[xnode] == depth) && (active_n[xnode] == 1) )
{
// first we check to see if we have reached a tip
if (t2.noat[xnode] == 0)
{
// test to see that it is a common spp to tree 2
common = 0;
for (j = 0; j < t1.termtaxa; j++)
{
if (strcmp(t2.taxon[xnode], t1.taxalist[j]) == 0)\
common = 1;
}
if (common ==1)
{
comlist2[i][comlist2n[i]] = xnode;
comlist2n[i]++;
//printf("2 dependent to node %d is %s\n",
// i, t2.taxon[comlist2[i][comlist2n[i]-1]]);
}
active_n[xnode] = 0;
}
else
{
for (j = 0; j < t2.noat[xnode]; j++)
{
active_n[t2.down[xnode][j]] = 1;
}
active_n[xnode] = 0;
}
}
}
}
}
// Now, compare the nodes (once only for each pair)
for (i = 0; i < t1.nnodes; i++)
{
for (j = 0; j < t2.nnodes; j++)
{
// initialize:
for (p = 0; p < comlist1n[i]; p++) matched1[p] = 0;
for (q = 0; q < comlist2n[j]; q++) matched2[q] = 0;
// here's the crux - each one must have the same sublist to be valid
for (p = 0; p < comlist1n[i]; p++)
{
for(q= 0; q < comlist2n[j]; q++)
{
if (strcmp(t1.taxon[comlist1[i][p]],
t2.taxon[comlist2[j][q]] ) ==0 )
{
matched1[p] = 1;
matched2[q] = 1;
}
}
}
// check matches
matches1 = 0;
matches2 = 0;
for (p = 0; p < comlist1n[i]; p++)
{
if (matched1[p] == 1) matches1++;
}
for (q = 0; q < comlist2n[j]; q++)
{
if (matched2[q] == 1) matches2++;
}
if ( (matches1 == comlist1n[i]) && (matches2 == comlist2n[j]) && \
(matches1 > 1) && (matches2 > 1))
{
sprintf(tmp, "match%d", matchcode++);
//printf("tree1node%d matches with tree2node%d\n", i, j);
// more correct, but need to just use nodenames for r8s:
// strcat(t1.notes[i], tmp); strcat(t1.notes[i], " ");
// strcat(t2.notes[j], tmp); strcat(t2.notes[j], " ");
// for bladj (note the last one overrides the previous - this
// will general be correct
strcpy(t1.taxon[i], tmp);
strcpy(t2.taxon[j], tmp);
}
}
}
// Unname the "." node names (a hack)
for (i = 0; i < t1.nnodes; i++)
{
if (!strcmp(t1.taxon[i], ".")) strcpy(t1.taxon[i], "");
}
for (i = 0; i < t2.nnodes; i++)
{
if (!strcmp(t2.taxon[i], ".")) strcpy(t2.taxon[i], "");
}
printf("#NEXUS\n\nBEGIN TREES;\nTREE tree1 = ");
Fy2newRec(t1);
printf("TREE tree2 = ");
Fy2newRec(t2);
printf("END;\n");
Out[0] = t1;
//WriteNexus(Out, 1, InS, 0 , InC, 0 );
Out[0] = t2;
//WriteNexus(Out, 1, InS, 0 , InC, 0 );
}
int main ( int argc, char * argv[]) {
char pdbname[150] = {'\0'};
char selection_file[150] = {'\0'};
Residue * sequence;
int no_res, res_ctr;
int * selected;
double cutoff_dist, score;
double **distmat;
int ** cluster;
int c;
char chain_id = '\0';
FILE * fclust = NULL;
if ( argc < 5 ) {
fprintf (stderr,
"Usage: %s <pdbfile> <chain id>|'-' <selection file> <cutoff dist> \n"
"where selection file is of the format (for example) \n"
"F 3 \n"
"K 48 \n"
"R 50 \n"
"D 59 \n"
"E 82 \n"
"G 91 \n"
"A 97 \n"
"C 100 \n"
"etc \n"
"and the cutoff distance is given in Angstroms\n",
argv[0]);
exit (1);
}
sprintf ( pdbname, "%s", argv[1]);
chain_id = argv[2][0]=='-' ? '\0' : argv[2][0];
sprintf ( selection_file, "%s", argv[3]);
cutoff_dist = atof ( argv[4]);
printf ("cutoff distance: %5.2lf Angstroms\n", cutoff_dist);
/* input the structure */
if ( read_pdb ( pdbname, &chain_id, &sequence, &no_res) ) exit (1);
printf ("there are %d residues in %s, chain %c.\n", no_res, pdbname, chain_id);
/* input selection */
selected = emalloc (no_res*sizeof(int));
if (! selected) {
fprintf (stderr, "error allocating selection array\n");
exit(1); // leaky, leaky
}
if ( read_selection (sequence, no_res, selection_file, selected) ) exit (1);
/* allocate space for dist matrix */
distmat = (double**) dmatrix (0, no_res-1, 0, no_res-1);
/* calculate dist */
if ( determine_dist_matrix(distmat, sequence, no_res) ) exit(1);
/* cluster counting ... */
int no_of_clusters, max_size, secnd_max_size;
int * cluster_count;
int ** neighbors;
int res1, res2;
cluster_count = (int *) emalloc ( (no_res+1)*sizeof(int));
cluster = imatrix (0, no_res, 0, no_res);
neighbors = imatrix (0, no_res-1, 0, no_res-1);
for (res1=0; res1 < no_res; res1++ ) {
neighbors [res1][res1] = 1;
for (res2= res1+1; res2 < no_res; res2++ ) {
neighbors[res1][res2] = ( distmat[res1][res2] < cutoff_dist);
neighbors[res2][res1] = neighbors[res1][res2];
}
}
cluster_counter (no_res, neighbors, selected, cluster_count, & no_of_clusters,
&max_size, &secnd_max_size , cluster);
clustering_z_score ( no_res, neighbors, selected, &score);
if (0) {
printf ("runnning simulation ...\n");
int cluster_score (int no_of_res, int *seq, int ** adj_matrix,double *score);
int i, n;
int no_selected = 0;
for (i=0; i<no_res; i++) no_selected += selected[i];
cluster_score (no_res, selected, neighbors, &score);
printf (" selected %4d original cluster score = %8.2e\n", no_selected, score);
double frac = (double)no_selected/no_res;
double score = 0;
for (n=0; n<100; n++) { // number of reps
memset (selected, 0, no_res*sizeof(int));
for (i=0; i<no_res; i++) {
if (drand48() < frac) selected[i] = 1;
}
cluster_score (no_res, selected, neighbors, &score);
no_selected = 0;
for (i=0; i<no_res; i++) no_selected += selected[i];
printf (" selected %4d random score = %8.2e\n", no_selected, score);
}
}
/* output */
fclust = stdout;
for ( c=0; c <= no_res; c++) {
if ( ! cluster[c][0] ) {
continue;
}
if ( !c ) {
fprintf ( fclust,"\t isolated:\n");
} else {
fprintf ( fclust,"\t cluster size: %3d \n", cluster[c][0]);
}
for ( res_ctr=1; res_ctr <= cluster[c][0]; res_ctr++) {
fprintf ( fclust, "%s \n", sequence[ cluster[c][res_ctr] ].pdb_id );
}
}
fprintf (fclust, "\nclustering z-score: %8.3f\n", score);
return 0;
}