void dump_leaf (
tree_s *tree,
leaf_s *leaf,
unint indent)
{
rec_s *end = &leaf->l_rec[leaf->l_num];
rec_s *r;
char *c;
unsigned i;
//unsigned j;
//FN;
if (!leaf) return;
pr_indent(indent);
printf("leaf: num keys = %d end = %d total = %d current = %u\n",
leaf->l_num, leaf->l_end, leaf->l_total,
free_space(leaf));
fflush(stdout);
for (r = leaf->l_rec, i = 0; r < end; r++, i++) {
c = (char *)leaf + r->r_start;
pr_indent(indent);
printf("\t%4d. %16llx %4d:%4d ",
i, r->r_key, r->r_start, r->r_len);
dump_rec(tree, r->r_key, c, r->r_len);
printf("\n");
fflush(stdout);
}
fflush(stdout);
}
static void pr_cosine(FILE *fp,int indent,const char *title,t_cosines *cos,
gmx_bool bMDPformat)
{
int j;
if (bMDPformat) {
fprintf(fp,"%s = %d\n",title,cos->n);
}
else {
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
fprintf(fp,"n = %d\n",cos->n);
if (cos->n > 0) {
(void) pr_indent(fp,indent+2);
fprintf(fp,"a =");
for(j=0; (j<cos->n); j++)
fprintf(fp," %e",cos->a[j]);
fprintf(fp,"\n");
(void) pr_indent(fp,indent+2);
fprintf(fp,"phi =");
for(j=0; (j<cos->n); j++)
fprintf(fp," %e",cos->phi[j]);
fprintf(fp,"\n");
}
}
}
void pr_header(FILE *fp,int indent,char *title,t_tpxheader *sh)
{
if (available(fp,sh,title))
{
indent=pr_title(fp,indent,title);
pr_indent(fp,indent);
fprintf(fp,"bIr = %spresent\n",sh->bIr?"":"not ");
pr_indent(fp,indent);
fprintf(fp,"bBox = %spresent\n",sh->bBox?"":"not ");
pr_indent(fp,indent);
fprintf(fp,"bTop = %spresent\n",sh->bTop?"":"not ");
pr_indent(fp,indent);
fprintf(fp,"bX = %spresent\n",sh->bX?"":"not ");
pr_indent(fp,indent);
fprintf(fp,"bV = %spresent\n",sh->bV?"":"not ");
pr_indent(fp,indent);
fprintf(fp,"bF = %spresent\n",sh->bF?"":"not ");
pr_indent(fp,indent);
fprintf(fp,"natoms = %d\n",sh->natoms);
pr_indent(fp,indent);
fprintf(fp,"step = %d\n",sh->step);
pr_indent(fp,indent);
fprintf(fp,"t = %e\n",sh->t);
pr_indent(fp,indent);
fprintf(fp,"lambda = %e\n",sh->lambda);
}
}
static void pr_groups(FILE *fp,int indent,const char *title,
gmx_groups_t *groups,
gmx_bool bShowNumbers)
{
int grpnr[egcNR];
int nat_max,i,g;
pr_grps(fp,indent,"grp",groups->grps,groups->grpname,bShowNumbers);
pr_strings(fp,indent,"grpname",groups->grpname,groups->ngrpname,bShowNumbers);
(void) pr_indent(fp,indent);
fprintf(fp,"groups ");
for(g=0; g<egcNR; g++)
{
printf(" %5.5s",gtypes[g]);
}
printf("\n");
(void) pr_indent(fp,indent);
fprintf(fp,"allocated ");
nat_max = 0;
for(g=0; g<egcNR; g++)
{
printf(" %5d",groups->ngrpnr[g]);
nat_max = max(nat_max,groups->ngrpnr[g]);
}
printf("\n");
if (nat_max == 0)
{
(void) pr_indent(fp,indent);
fprintf(fp,"groupnr[%5s] =","*");
for(g=0; g<egcNR; g++)
{
fprintf(fp," %3d ",0);
}
fprintf(fp,"\n");
}
else
{
for(i=0; i<nat_max; i++)
{
(void) pr_indent(fp,indent);
fprintf(fp,"groupnr[%5d] =",i);
for(g=0; g<egcNR; g++)
{
fprintf(fp," %3d ",
groups->grpnr[g] ? groups->grpnr[g][i] : 0);
}
fprintf(fp,"\n");
}
}
}
static void pr_branch(struct mtree *mt, struct branch *branch, int indent)
{
int i;
struct twig *twig = branch->twig;
pr_indent(indent);
printf("branch: blknum=%lld seqnum=%lld num_twigs=%d\n",
branch->blknum, branch->seqnum, branch->num_twigs);
for (i = 0; i < branch->num_twigs; i++, twig++) {
pr_indent(indent);
printf("%d. %8lld: %8lld\n", i, twig->blknum, twig->key);
pr_block(mt, twig->blknum, indent+1);
}
}
static int pr_blocka_title(FILE *fp,int indent,const char *title,t_blocka *block)
{
int i;
if (available(fp,block,indent,title))
{
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"nr=%d\n",block->nr);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"nra=%d\n",block->nra);
}
return indent;
}
static void pr_leaf(struct leaf *leaf, int indent)
{
int i;
struct record *rec = (struct record *)leaf->data;
pr_indent(indent);
printf("leaf: blknum=%lld seqnum=%lld num_recs=%d end=%d\n",
leaf->blknum, leaf->seqnum, leaf->num_recs, leaf->end);
for (i = 0; i < leaf->num_recs; i++, rec++) {
pr_indent(indent);
printf("%8lld: %*s\n", rec->key, rec->size,
(char *)(&leaf->data[rec->offset]));
}
}
void pr_symtab(FILE *fp,int indent,char *title,t_symtab *symtab)
{
int i,j,nr;
t_symbuf *symbuf;
if (available(fp,symtab,title))
{
indent=pr_title_n(fp,indent,title,symtab->nr);
i=0;
nr=symtab->nr;
symbuf=symtab->symbuf;
while (symbuf!=NULL)
{
for (j=0; (j < symbuf->bufsize) && (j < nr); j++)
{
if(fp)
{
pr_indent(fp,indent);
fprintf(fp,"%s[%d]=\"%s\"\n",title,i++,symbuf->buf[j]);
}
}
nr-=j;
symbuf=symbuf->next;
}
assert(nr==0);
}
}
void pr_int64(FILE *fp, int indent, const char *title, gmx_int64_t i)
{
char buf[STEPSTRSIZE];
pr_indent(fp, indent);
fprintf(fp, "%-30s = %s\n", title, gmx_step_str(i, buf));
}
void list_xtc(const char *fn)
{
t_fileio *xd;
int indent;
char buf[256];
rvec *x;
matrix box;
int nframe, natoms, step;
real prec, time;
gmx_bool bOK;
xd = open_xtc(fn, "r");
read_first_xtc(xd, &natoms, &step, &time, box, &x, &prec, &bOK);
nframe = 0;
do
{
sprintf(buf, "%s frame %d", fn, nframe);
indent = 0;
indent = pr_title(stdout, indent, buf);
pr_indent(stdout, indent);
fprintf(stdout, "natoms=%10d step=%10d time=%12.7e prec=%10g\n",
natoms, step, time, prec);
pr_rvecs(stdout, indent, "box", box, DIM);
pr_rvecs(stdout, indent, "x", x, natoms);
nframe++;
}
while (read_next_xtc(xd, natoms, &step, &time, box, x, &prec, &bOK));
if (!bOK)
{
fprintf(stderr, "\nWARNING: Incomplete frame at time %g\n", time);
}
sfree(x);
close_xtc(xd);
}
void pr_rvecs_of_dim(FILE *fp, int indent, const char *title, const rvec vec[], int n, int dim)
{
const char *fshort = "%12.5e";
const char *flong = "%15.8e";
const char *format;
int i, j;
if (getenv("GMX_PRINT_LONGFORMAT") != nullptr)
{
format = flong;
}
else
{
format = fshort;
}
if (available(fp, vec, indent, title))
{
indent = pr_title_nxn(fp, indent, title, n, dim);
for (i = 0; i < n; i++)
{
pr_indent(fp, indent);
fprintf(fp, "%s[%5d]={", title, i);
for (j = 0; j < dim; j++)
{
if (j != 0)
{
fprintf(fp, ", ");
}
fprintf(fp, format, vec[i][j]);
}
fprintf(fp, "}\n");
}
}
}
void pr_rvecs(FILE *fp,int indent,const char *title,rvec vec[],int n)
{
const char *fshort = "%12.5e";
const char *flong = "%15.8e";
const char *format;
int i,j;
if (getenv("LONGFORMAT") != NULL)
format = flong;
else
format = fshort;
if (available(fp,vec,indent,title)) {
indent=pr_title_nxn(fp,indent,title,n,DIM);
for (i=0; i<n; i++) {
(void) pr_indent(fp,indent);
(void) fprintf(fp,"%s[%5d]={",title,i);
for (j=0; j<DIM; j++) {
if (j != 0)
(void) fprintf(fp,", ");
(void) fprintf(fp,format,vec[i][j]);
}
(void) fprintf(fp,"}\n");
}
}
}
/*! \brief Callback used by list_tng_for_gmx_dump. */
static void list_tng_inner(const char *fn,
gmx_bool bFirstFrame,
real *values,
gmx_int64_t step,
double frame_time,
gmx_int64_t n_values_per_frame,
gmx_int64_t n_atoms,
real prec,
gmx_int64_t nframe,
char *block_name)
{
char buf[256];
int indent = 0;
if (bFirstFrame)
{
sprintf(buf, "%s frame %" GMX_PRId64, fn, nframe);
indent = 0;
indent = pr_title(stdout, indent, buf);
pr_indent(stdout, indent);
fprintf(stdout, "natoms=%10" GMX_PRId64 " step=%10" GMX_PRId64 " time=%12.7e",
n_atoms, step, frame_time);
if (prec > 0)
{
fprintf(stdout, " prec=%10g", prec);
}
fprintf(stdout, "\n");
}
pr_reals_of_dim(stdout, indent, block_name, values, n_atoms, n_values_per_frame);
}
STATIC void node_dump(Linear_s *t, Blknum_t blknum, int indent)
{
Buf_s *buf;
Node_s *node;
Blknum_t overflow;
if (!blknum) return;
buf = t_get(t, blknum);
node = buf->d;
Hrec_s rec;
unint i;
if (Dump_buf) {
pr_buf(buf, indent);
}
pr_head(node, indent);
for (i = 0; i < node->numrecs; i++) {
rec = get_rec(node, i);
pr_indent(indent);
printf("%ld. ", i);
rec_dump(rec);
}
overflow = node->overflow;
buf_put(&buf);
if (overflow) {
node_dump(t, overflow, indent+1);
}
}
static void pr_gmx_large_int(FILE *fp,int indent,const char *title,gmx_large_int_t i)
{
char buf[STEPSTRSIZE];
pr_indent(fp,indent);
fprintf(fp,"%-20s = %s\n",title,gmx_step_str(i,buf));
}
void pr_block(FILE *fp,int indent,const char *title,t_block *block,gmx_bool bShowNumbers)
{
int i,j,ok,size,start,end;
if (available(fp,block,indent,title))
{
indent=pr_block_title(fp,indent,title,block);
start=0;
end=start;
if ((ok=(block->index[start]==0))==0)
(void) fprintf(fp,"block->index[%d] should be 0\n",start);
else
for (i=0; i<block->nr; i++)
{
end=block->index[i+1];
size=pr_indent(fp,indent);
if (end<=start)
size+=fprintf(fp,"%s[%d]={}\n",title,i);
else
size+=fprintf(fp,"%s[%d]={%d..%d}\n",
title,bShowNumbers?i:-1,
bShowNumbers?start:-1,bShowNumbers?end-1:-1);
start=end;
}
}
}
void pr_symtab(FILE *fp, int indent, const char *title, t_symtab *symtab)
{
int i, j, nr;
t_symbuf *symbuf;
if (available(fp, symtab, indent, title))
{
indent = pr_title_n(fp, indent, title, symtab->nr);
i = 0;
nr = symtab->nr;
symbuf = symtab->symbuf;
while (symbuf != NULL)
{
for (j = 0; (j < symbuf->bufsize) && (j < nr); j++)
{
pr_indent(fp, indent);
(void) fprintf(fp, "%s[%d]=\"%s\"\n", title, i++, symbuf->buf[j]);
}
nr -= j;
symbuf = symbuf->next;
}
if (nr != 0)
{
gmx_incons("Printing symbol table (symtab) structure");
}
}
}
static void pr_rec (Rec_s r, int indent)
{
pr_indent(indent);
pr_lump(r.key);
printf(": ");
pr_lump(r.val);
printf("\n");
}
STATIC void pr_head(Node_s *node, int indent)
{
pr_indent(indent);
printf("blknum %lld overflow %lld",
(u64)node->blknum,
(u64)node->overflow);
printf(" numrecs %d free %d end %d\n",
node->numrecs, node->free, node->end);
}
int available(FILE *fp,void *p,int indent,const char *title)
{
if (!p) {
if (indent > 0)
pr_indent(fp,indent);
(void) fprintf(fp,"%s: not available\n",title);
}
return (p!=NULL);
}
void pr_commrec(FILE *fp,int indent,t_commrec *cr)
{
pr_indent(fp,indent);
fprintf(fp,"commrec:\n");
indent+=2;
pr_indent(fp,indent);
fprintf(fp,"nodeid = %d\n",cr->nodeid);
pr_indent(fp,indent);
fprintf(fp,"nnodes = %d\n",cr->nnodes);
pr_indent(fp,indent);
fprintf(fp,"npmenodes = %d\n",cr->npmenodes);
/*
pr_indent(fp,indent);
fprintf(fp,"threadid = %d\n",cr->threadid);
pr_indent(fp,indent);
fprintf(fp,"nthreads = %d\n",cr->nthreads);
*/
}
static void pr_leaf (BtNode_s *leaf, int indent)
{
int i;
for (i = 0; i < leaf->num; i++) {
pr_indent(indent);
printf("%llu\n", leaf->key[i]);
}
}
static int pr_block_title(FILE *fp,int indent,char *title,t_block *block)
{
int i;
if (available(fp,block,title))
{
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
fprintf(fp,"multinr[division over processors]:");
for (i=0; (i<MAXNODES); i++)
(void) fprintf(fp," %d",block->multinr[i]);
fprintf(fp,"\n");
(void) pr_indent(fp,indent);
(void) fprintf(fp,"nr=%d\n",block->nr);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"nra=%d\n",block->nra);
}
return indent;
}
void pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block,gmx_bool bShowNumbers)
{
int i,j,ok,size,start,end;
if (available(fp,block,indent,title))
{
indent=pr_blocka_title(fp,indent,title,block);
start=0;
end=start;
if ((ok=(block->index[start]==0))==0)
(void) fprintf(fp,"block->index[%d] should be 0\n",start);
else
for (i=0; i<block->nr; i++)
{
end=block->index[i+1];
size=pr_indent(fp,indent);
if (end<=start)
size+=fprintf(fp,"%s[%d]={",title,i);
else
size+=fprintf(fp,"%s[%d][%d..%d]={",
title,bShowNumbers?i:-1,
bShowNumbers?start:-1,bShowNumbers?end-1:-1);
for (j=start; j<end; j++)
{
if (j>start) size+=fprintf(fp,", ");
if ((size)>(USE_WIDTH))
{
(void) fprintf(fp,"\n");
size=pr_indent(fp,indent+INDENT);
}
size+=fprintf(fp,"%u",block->a[j]);
}
(void) fprintf(fp,"}\n");
start=end;
}
if ((end!=block->nra)||(!ok))
{
(void) pr_indent(fp,indent);
(void) fprintf(fp,"tables inconsistent, dumping complete tables:\n");
low_pr_blocka(fp,indent,title,block,bShowNumbers);
}
}
}
static void pr_cosine(FILE *fp,int indent,char *title,t_cosines *cos)
{
int j;
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
fprintf(fp,"n = %d\n",cos->n);
if (cos->n > 0) {
(void) pr_indent(fp,indent+2);
fprintf(fp,"a =");
for(j=0; (j<cos->n); j++)
fprintf(fp," %e",cos->a[j]);
fprintf(fp,"\n");
(void) pr_indent(fp,indent+2);
fprintf(fp,"phi =");
for(j=0; (j<cos->n); j++)
fprintf(fp," %e",cos->phi[j]);
fprintf(fp,"\n");
}
}
static void pr_branch (BtNode_s *branch, int indent)
{
int i;
pr_node(branch->first, indent + 1);
for (i = 0; i < branch->num; i++) {
pr_indent(indent);
printf("%llu\n", branch->twig[i].key);
pr_node(branch->twig[i].node, indent + 1);
}
}
void pr_ffparams(FILE *fp,int indent,const char *title,
gmx_ffparams_t *ffparams,
bool bShowNumbers)
{
int i,j;
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"atnr=%d\n",ffparams->atnr);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"ntypes=%d\n",ffparams->ntypes);
for (i=0; i<ffparams->ntypes; i++) {
(void) pr_indent(fp,indent+INDENT);
(void) fprintf(fp,"functype[%d]=%s, ",
bShowNumbers?i:-1,
interaction_function[ffparams->functype[i]].name);
pr_iparams(fp,ffparams->functype[i],&ffparams->iparams[i]);
}
(void) pr_real(fp,indent,"fudgeQQ",ffparams->fudgeQQ);
}
static void pr_node (BtNode_s *node, int indent)
{
if (!node) return;
pr_indent(indent);
printf("%p %s %d\n", node, pr_is_leaf(node), node->num);
if (node->is_leaf) {
pr_leaf(node, indent + 1);
} else {
pr_branch(node, indent + 1);
}
}
void pr_top(FILE *fp,int indent,char *title,t_topology *top)
{
if (available(fp,top,title)) {
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"name=\"%s\"\n",*(top->name));
pr_atoms(fp,indent,"atoms",&(top->atoms));
pr_blocks(fp,indent,"blocks",top->blocks,ebNR,eblock_names);
pr_idef(fp,indent,"idef",&top->idef);
}
}
static void pr_ilist(FILE *fp,int indent,char *title,
t_idef *idef,t_ilist *ilist)
{
int i,j,k,type,ftype;
t_iatom *iatoms;
if (available(fp,ilist,title))
{
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
fprintf(fp,"nr: %d\n",ilist->nr);
if (ilist->nr > 0) {
(void) pr_indent(fp,indent);
fprintf(fp,"multinr[division over processors]:");
for (i=0; (i<MAXNODES) && (ilist->multinr[i] > 0); i++)
(void) fprintf(fp," %d",ilist->multinr[i]);
fprintf(fp,"\n");
(void) pr_indent(fp,indent);
fprintf(fp,"iatoms:\n");
iatoms=ilist->iatoms;
for (i=j=0; i<ilist->nr;) {
#ifndef DEBUG
(void) pr_indent(fp,indent+INDENT);
type=*(iatoms++);
ftype=idef->functype[type];
(void) fprintf(fp,"%d type=%d (%s)",
bShowNumbers?j:-1,bShowNumbers?type:-1,
interaction_function[ftype].name);
j++;
for (k=0; k<interaction_function[ftype].nratoms; k++)
(void) fprintf(fp," %u",*(iatoms++));
(void) fprintf(fp,"\n");
i+=1+interaction_function[ftype].nratoms;
#else
fprintf(fp,"%5d%5d\n",i,iatoms[i]);
i++;
#endif
}
}
}
}
