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);
}
}
void pr_top(FILE *fp,int indent,const char *title,t_topology *top, gmx_bool bShowNumbers)
{
if (available(fp,top,indent,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),bShowNumbers);
pr_atomtypes(fp,indent,"atomtypes",&(top->atomtypes),bShowNumbers);
pr_block(fp,indent,"cgs",&top->cgs, bShowNumbers);
pr_block(fp,indent,"mols",&top->mols, bShowNumbers);
pr_blocka(fp,indent,"excls",&top->excls, bShowNumbers);
pr_idef(fp,indent,"idef",&top->idef,bShowNumbers);
}
}
void pr_top(FILE *fp, int indent, const char *title, const t_topology *top, gmx_bool bShowNumbers)
{
if (available(fp, top, indent, title))
{
indent = pr_title(fp, indent, title);
pr_indent(fp, indent);
fprintf(fp, "name=\"%s\"\n", *(top->name));
pr_atoms(fp, indent, "atoms", &(top->atoms), bShowNumbers);
pr_atomtypes(fp, indent, "atomtypes", &(top->atomtypes), bShowNumbers);
pr_block(fp, indent, "cgs", &top->cgs, bShowNumbers);
pr_block(fp, indent, "mols", &top->mols, bShowNumbers);
pr_str(fp, indent, "bIntermolecularInteractions",
gmx::boolToString(top->bIntermolecularInteractions));
pr_blocka(fp, indent, "excls", &top->excls, bShowNumbers);
pr_idef(fp, indent, "idef", &top->idef, bShowNumbers);
}
}
static void make_shake_sblock_serial(struct gmx_constr *constr,
t_idef *idef, t_mdatoms *md)
{
int i, j, m, ncons;
int bstart, bnr;
t_blocka sblocks;
t_sortblock *sb;
t_iatom *iatom;
atom_id *inv_sblock;
/* Since we are processing the local topology,
* the F_CONSTRNC ilist has been concatenated to the F_CONSTR ilist.
*/
ncons = idef->il[F_CONSTR].nr/3;
init_blocka(&sblocks);
gen_sblocks(NULL, 0, md->homenr, idef, &sblocks, FALSE);
/*
bstart=(idef->nodeid > 0) ? blocks->multinr[idef->nodeid-1] : 0;
nblocks=blocks->multinr[idef->nodeid] - bstart;
*/
bstart = 0;
constr->nblocks = sblocks.nr;
if (debug)
{
fprintf(debug, "ncons: %d, bstart: %d, nblocks: %d\n",
ncons, bstart, constr->nblocks);
}
/* Calculate block number for each atom */
inv_sblock = make_invblocka(&sblocks, md->nr);
done_blocka(&sblocks);
/* Store the block number in temp array and
* sort the constraints in order of the sblock number
* and the atom numbers, really sorting a segment of the array!
*/
#ifdef DEBUGIDEF
pr_idef(fplog, 0, "Before Sort", idef);
#endif
iatom = idef->il[F_CONSTR].iatoms;
snew(sb, ncons);
for (i = 0; (i < ncons); i++, iatom += 3)
{
for (m = 0; (m < 3); m++)
{
sb[i].iatom[m] = iatom[m];
}
sb[i].blocknr = inv_sblock[iatom[1]];
}
/* Now sort the blocks */
if (debug)
{
pr_sortblock(debug, "Before sorting", ncons, sb);
fprintf(debug, "Going to sort constraints\n");
}
qsort(sb, ncons, (size_t)sizeof(*sb), pcomp);
if (debug)
{
pr_sortblock(debug, "After sorting", ncons, sb);
}
iatom = idef->il[F_CONSTR].iatoms;
for (i = 0; (i < ncons); i++, iatom += 3)
{
for (m = 0; (m < 3); m++)
{
iatom[m] = sb[i].iatom[m];
}
}
#ifdef DEBUGIDEF
pr_idef(fplog, 0, "After Sort", idef);
#endif
j = 0;
snew(constr->sblock, constr->nblocks+1);
bnr = -2;
for (i = 0; (i < ncons); i++)
{
if (sb[i].blocknr != bnr)
{
bnr = sb[i].blocknr;
constr->sblock[j++] = 3*i;
}
}
/* Last block... */
constr->sblock[j++] = 3*ncons;
if (j != (constr->nblocks+1))
{
fprintf(stderr, "bstart: %d\n", bstart);
fprintf(stderr, "j: %d, nblocks: %d, ncons: %d\n",
j, constr->nblocks, ncons);
for (i = 0; (i < ncons); i++)
{
fprintf(stderr, "i: %5d sb[i].blocknr: %5u\n", i, sb[i].blocknr);
}
for (j = 0; (j <= constr->nblocks); j++)
{
fprintf(stderr, "sblock[%3d]=%5d\n", j, (int)constr->sblock[j]);
}
gmx_fatal(FARGS, "DEATH HORROR: "
"sblocks does not match idef->il[F_CONSTR]");
}
sfree(sb);
sfree(inv_sblock);
}
static bool low_constrain(FILE *log,t_topology *top,t_inputrec *ir,
int step,t_mdatoms *md,int start,int homenr,
rvec *x,rvec *xprime,rvec *min_proj,matrix box,
real lambda,real *dvdlambda,t_nrnb *nrnb,
bool bCoordinates,bool bInit)
{
static int nblocks=0;
static int *sblock=NULL;
static int nsettle,settle_type;
static int *owptr;
static bool bDumpOnError = TRUE;
char buf[STRLEN];
bool bOK;
t_sortblock *sb;
t_block *blocks=&(top->blocks[ebSBLOCKS]);
t_idef *idef=&(top->idef);
t_iatom *iatom;
atom_id *inv_sblock;
int i,j,m,bnr;
int ncons,bstart,error;
bOK = TRUE;
if (bInit) {
/* Output variables, initiate them right away */
if ((ir->etc==etcBERENDSEN) || (ir->epc==epcBERENDSEN))
please_cite(log,"Berendsen84a");
#ifdef SPEC_CPU
bDumpOnError = TRUE;
#else
bDumpOnError = (getenv("NO_SHAKE_ERROR") == NULL);
#endif
/* Put the oxygen atoms in the owptr array */
nsettle=idef->il[F_SETTLE].nr/2;
if (nsettle > 0) {
snew(owptr,nsettle);
settle_type=idef->il[F_SETTLE].iatoms[0];
for (j=0; (j<idef->il[F_SETTLE].nr); j+=2) {
if (idef->il[F_SETTLE].iatoms[j] != settle_type)
fatal_error(0,"More than one settle type (%d and %d)",
settle_type,idef->il[F_SETTLE].iatoms[j]);
owptr[j/2]=idef->il[F_SETTLE].iatoms[j+1];
#ifdef DEBUG
fprintf(log,"owptr[%d]=%d\n",j/2,owptr[j/2]);
#endif
}
/* We used to free this memory, but ED sampling needs it later on
* sfree(idef->il[F_SETTLE].iatoms);
*/
please_cite(log,"Miyamoto92a");
}
ncons=idef->il[F_SHAKE].nr/3;
if (ncons > 0)
{
bstart=(idef->nodeid > 0) ? blocks->multinr[idef->nodeid-1] : 0;
nblocks=blocks->multinr[idef->nodeid] - bstart;
if (debug)
fprintf(debug,"ncons: %d, bstart: %d, nblocks: %d\n",
ncons,bstart,nblocks);
/* Calculate block number for each atom */
inv_sblock=make_invblock(blocks,md->nr);
/* Store the block number in temp array and
* sort the constraints in order of the sblock number
* and the atom numbers, really sorting a segment of the array!
*/
#ifdef DEBUGIDEF
pr_idef(stdlog,0,"Before Sort",idef);
#endif
iatom=idef->il[F_SHAKE].iatoms;
snew(sb,ncons);
for(i=0; (i<ncons); i++,iatom+=3) {
for(m=0; (m<3); m++)
sb[i].iatom[m]=iatom[m];
sb[i].blocknr=inv_sblock[iatom[1]];
}
/* Now sort the blocks */
if (debug) {
pr_sortblock(debug,"Before sorting",ncons,sb);
fprintf(debug,"Going to sort constraints\n");
}
qsort(sb,ncons,(size_t)sizeof(*sb),pcomp);
if (debug) {
fprintf(debug,"I used %d calls to pcomp\n",pcount);
pr_sortblock(debug,"After sorting",ncons,sb);
}
iatom=idef->il[F_SHAKE].iatoms;
for(i=0; (i<ncons); i++,iatom+=3)
for(m=0; (m<DIM); m++)
iatom[m]=sb[i].iatom[m];
#ifdef DEBUGIDEF
pr_idef(stdlog,0,"After Sort",idef);
#endif
j=0;
snew(sblock,nblocks+1);
bnr=-2;
for(i=0; (i<ncons); i++) {
if (sb[i].blocknr != bnr) {
bnr=sb[i].blocknr;
sblock[j++]=3*i;
}
}
/* Last block... */
sblock[j++]=3*ncons;
if (j != (nblocks+1) && log) {
fprintf(log,"bstart: %d\n",bstart);
fprintf(log,"j: %d, nblocks: %d, ncons: %d\n",
j,nblocks,ncons);
for(i=0; (i<ncons); i++)
fprintf(log,"i: %5d sb[i].blocknr: %5u\n",i,sb[i].blocknr);
for(j=0; (j<=nblocks); j++)
fprintf(log,"sblock[%3d]=%5d\n",j,(int) sblock[j]);
fatal_error(0,"DEATH HORROR: "
"top->blocks[ebSBLOCKS] does not match idef->il[F_SHAKE]");
}
sfree(sb);
sfree(inv_sblock);
}
if (idef->il[F_SHAKE].nr) {
if (ir->eConstrAlg == estLINCS || !bCoordinates) {
please_cite(stdlog,"Hess97a");
bOK = constrain_lincs(stdlog,top,ir,0,md,start,homenr,&nblocks,&sblock,
NULL,NULL,NULL,NULL,0,NULL,bCoordinates,TRUE,nrnb,
bDumpOnError);
}
else
please_cite(stdlog,"Ryckaert77a");
}
}
else {
/* !bInit */
if (nblocks > 0) {
where();
if (ir->eConstrAlg == estSHAKE)
bOK = bshakef(stdlog,homenr,md->invmass,nblocks,sblock,idef,
ir,box,x,xprime,nrnb,lambda,dvdlambda,bDumpOnError);
else if (ir->eConstrAlg == estLINCS)
bOK = constrain_lincs(stdlog,top,ir,step,md,
start,homenr,&nblocks,&sblock,
x,xprime,min_proj,box,lambda,dvdlambda,
bCoordinates,FALSE,nrnb,bDumpOnError);
if (!bOK && bDumpOnError && stdlog)
fprintf(stdlog,"Constraint error in algorithm %s at step %d\n",
eshake_names[ir->eConstrAlg],step);
}
if (nsettle > 0) {
int ow1;
real mO,mH,dOH,dHH;
ow1 = owptr[0];
mO = md->massA[ow1];
mH = md->massA[ow1+1];
dOH = top->idef.iparams[settle_type].settle.doh;
dHH = top->idef.iparams[settle_type].settle.dhh;
#ifdef USE_FORTRAN
#ifdef DOUBLE
F77_FUNC(fsettled,FSETTLED)(&nsettle,owptr,x[0],xprime[0],
&dOH,&dHH,&mO,&mH,&error);
#else
F77_FUNC(fsettle,FSETTLE)(&nsettle,owptr,x[0],xprime[0],
&dOH,&dHH,&mO,&mH,&error);
#endif
#else
csettle(stdlog,nsettle,owptr,x[0],xprime[0],dOH,dHH,mO,mH,&error);
#endif
inc_nrnb(nrnb,eNR_SETTLE,nsettle);
bOK = (error < 0);
if (!bOK && bDumpOnError && stdlog)
fprintf(stdlog,"\nt = %.3f ps: Water molecule starting at atom %d can not be "
"settled.\nCheck for bad contacts and/or reduce the timestep.",
ir->init_t+step*ir->delta_t,owptr[error]+1);
}
if (!bOK && bDumpOnError)
dump_confs(step,&(top->atoms),x,xprime,box);
}
return bOK;
}