gmx_constr_t init_constraints(FILE *fplog,
gmx_mtop_t *mtop, t_inputrec *ir,
gmx_edsam_t ed, t_state *state,
t_commrec *cr)
{
int ncon, nset, nmol, settle_type, i, natoms, mt, nflexcon;
struct gmx_constr *constr;
char *env;
t_ilist *ilist;
gmx_mtop_ilistloop_t iloop;
ncon =
gmx_mtop_ftype_count(mtop, F_CONSTR) +
gmx_mtop_ftype_count(mtop, F_CONSTRNC);
nset = gmx_mtop_ftype_count(mtop, F_SETTLE);
if (ncon+nset == 0 && ir->ePull != epullCONSTRAINT && ed == NULL)
{
return NULL;
}
snew(constr, 1);
constr->ncon_tot = ncon;
constr->nflexcon = 0;
if (ncon > 0)
{
constr->n_at2con_mt = mtop->nmoltype;
snew(constr->at2con_mt, constr->n_at2con_mt);
for (mt = 0; mt < mtop->nmoltype; mt++)
{
constr->at2con_mt[mt] = make_at2con(0, mtop->moltype[mt].atoms.nr,
mtop->moltype[mt].ilist,
mtop->ffparams.iparams,
EI_DYNAMICS(ir->eI), &nflexcon);
for (i = 0; i < mtop->nmolblock; i++)
{
if (mtop->molblock[i].type == mt)
{
constr->nflexcon += mtop->molblock[i].nmol*nflexcon;
}
}
}
if (constr->nflexcon > 0)
{
if (fplog)
{
fprintf(fplog, "There are %d flexible constraints\n",
constr->nflexcon);
if (ir->fc_stepsize == 0)
{
fprintf(fplog, "\n"
"WARNING: step size for flexible constraining = 0\n"
" All flexible constraints will be rigid.\n"
" Will try to keep all flexible constraints at their original length,\n"
" but the lengths may exhibit some drift.\n\n");
constr->nflexcon = 0;
}
}
if (constr->nflexcon > 0)
{
please_cite(fplog, "Hess2002");
}
}
if (ir->eConstrAlg == econtLINCS)
{
constr->lincsd = init_lincs(fplog, mtop,
constr->nflexcon, constr->at2con_mt,
DOMAINDECOMP(cr) && cr->dd->bInterCGcons,
ir->nLincsIter, ir->nProjOrder);
}
if (ir->eConstrAlg == econtSHAKE)
{
if (DOMAINDECOMP(cr) && cr->dd->bInterCGcons)
{
gmx_fatal(FARGS, "SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS");
}
if (constr->nflexcon)
{
gmx_fatal(FARGS, "For this system also velocities and/or forces need to be constrained, this can not be done with SHAKE, you should select LINCS");
}
please_cite(fplog, "Ryckaert77a");
if (ir->bShakeSOR)
{
please_cite(fplog, "Barth95a");
}
constr->shaked = shake_init();
}
}
if (nset > 0)
{
please_cite(fplog, "Miyamoto92a");
constr->bInterCGsettles = inter_charge_group_settles(mtop);
/* Check that we have only one settle type */
settle_type = -1;
iloop = gmx_mtop_ilistloop_init(mtop);
while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
{
for (i = 0; i < ilist[F_SETTLE].nr; i += 4)
{
if (settle_type == -1)
{
settle_type = ilist[F_SETTLE].iatoms[i];
}
else if (ilist[F_SETTLE].iatoms[i] != settle_type)
{
gmx_fatal(FARGS,
"The [molecules] section of your topology specifies more than one block of\n"
"a [moleculetype] with a [settles] block. Only one such is allowed. If you\n"
"are trying to partition your solvent into different *groups* (e.g. for\n"
"freezing, T-coupling, etc.) then you are using the wrong approach. Index\n"
"files specify groups. Otherwise, you may wish to change the least-used\n"
"block of molecules with SETTLE constraints into 3 normal constraints.");
}
}
}
constr->n_at2settle_mt = mtop->nmoltype;
snew(constr->at2settle_mt, constr->n_at2settle_mt);
for (mt = 0; mt < mtop->nmoltype; mt++)
{
constr->at2settle_mt[mt] =
make_at2settle(mtop->moltype[mt].atoms.nr,
&mtop->moltype[mt].ilist[F_SETTLE]);
}
}
constr->maxwarn = 999;
env = getenv("GMX_MAXCONSTRWARN");
if (env)
{
constr->maxwarn = 0;
sscanf(env, "%d", &constr->maxwarn);
if (fplog)
{
fprintf(fplog,
"Setting the maximum number of constraint warnings to %d\n",
constr->maxwarn);
}
if (MASTER(cr))
{
fprintf(stderr,
"Setting the maximum number of constraint warnings to %d\n",
constr->maxwarn);
}
}
if (constr->maxwarn < 0 && fplog)
{
fprintf(fplog, "maxwarn < 0, will not stop on constraint errors\n");
}
constr->warncount_lincs = 0;
constr->warncount_settle = 0;
/* Initialize the essential dynamics sampling.
* Put the pointer to the ED struct in constr */
constr->ed = ed;
if (ed != NULL || state->edsamstate.nED > 0)
{
init_edsam(mtop, ir, cr, ed, state->x, state->box, &state->edsamstate);
}
constr->warn_mtop = mtop;
return constr;
}
static bool constrain_lincs(FILE *log,t_topology *top,t_inputrec *ir,
int step,t_mdatoms *md,int start,int homenr,
int *nbl,int **sbl,
rvec *x,rvec *xprime,rvec *min_proj,matrix box,
real lambda,real *dvdlambda,bool bCoordinates,
bool bInit,t_nrnb *nrnb,bool bDumpOnError)
{
static int *bla1,*bla2,*blnr,*blbnb,nrtot=0;
static rvec *r;
static real *bllen,*blc,*blcc,*blm,*tmp1,*tmp2,*tmp3,*lincslam,
*bllen0,*ddist;
static int nc;
static bool bItEqOrder;
char buf[STRLEN];
int b,i,j,nit,warn,p_imax,error;
real wang,p_max,p_rms;
real dt,dt_2;
bool bOK;
bOK = TRUE;
if (bInit) {
nc = top->idef.il[F_SHAKE].nr/3;
init_lincs(stdlog,top,ir,md,start,homenr,
&nrtot,
&r,&bla1,&bla2,&blnr,&blbnb,
&bllen,&blc,&blcc,&blm,&tmp1,&tmp2,&tmp3,&lincslam,
&bllen0,&ddist);
#ifdef SPEC_CPU
bItEqOrder = FALSE;
#else
bItEqOrder = (getenv("GMX_ACCURATE_LINCS") != NULL);
#endif
}
else if (nc != 0) {
/* If there are any constraints */
if (bCoordinates) {
dt = ir->delta_t;
dt_2 = 1.0/(dt*dt);
if (ir->efep != efepNO)
for(i=0;i<nc;i++)
bllen[i]=bllen0[i]+lambda*ddist[i];
/* Set the zero lengths to the old lengths */
for(b=0; b<nc; b++)
if (bllen0[b]<GMX_REAL_MIN) {
i = bla1[b];
j = bla2[b];
bllen[b] = sqrt(sqr(x[i][XX]-x[j][XX])+
sqr(x[i][YY]-x[j][YY])+
sqr(x[i][ZZ]-x[j][ZZ]));
}
wang=ir->LincsWarnAngle;
if (do_per_step(step,ir->nstlog) || step<0)
cconerr(&p_max,&p_rms,&p_imax,xprime,nc,bla1,bla2,bllen);
if ((ir->eI == eiSteep) || (ir->eI == eiCG) || bItEqOrder)
/* Use more iterations when doing energy minimization, *
* because we need very accurate positions and forces. */
nit = ir->nProjOrder;
else
nit = 1;
#ifdef USE_FORTRAN
#ifdef DOUBLE
F77_FUNC(flincsd,FLINCSD)(x[0],xprime[0],&nc,bla1,bla2,blnr,blbnb,
bllen,blc,blcc,blm,&nit,&ir->nProjOrder,
md->invmass,r[0],tmp1,tmp2,tmp3,&wang,&warn,
lincslam);
#else
F77_FUNC(flincs,FLINCS)(x[0],xprime[0],&nc,bla1,bla2,blnr,blbnb,
bllen,blc,blcc,blm,&nit,&ir->nProjOrder,
md->invmass,r[0],tmp1,tmp2,tmp3,&wang,&warn,
lincslam);
#endif
#else
clincs(x,xprime,nc,bla1,bla2,blnr,blbnb,
bllen,blc,blcc,blm,nit,ir->nProjOrder,
md->invmass,r,tmp1,tmp2,tmp3,wang,&warn,lincslam);
#endif
if (ir->efep != efepNO) {
real dvdl=0;
for(i=0; (i<nc); i++)
dvdl+=lincslam[i]*dt_2*ddist[i];
*dvdlambda+=dvdl;
}
if(stdlog)
{
if (do_per_step(step,ir->nstlog) || (step<0))
{
fprintf(stdlog," Rel. Constraint Deviation: Max between atoms RMS\n");
fprintf(stdlog," Before LINCS %.6f %6d %6d %.6f\n",
p_max,bla1[p_imax]+1,bla2[p_imax]+1,p_rms);
cconerr(&p_max,&p_rms,&p_imax,xprime,nc,bla1,bla2,bllen);
fprintf(stdlog," After LINCS %.6f %6d %6d %.6f\n\n",
p_max,bla1[p_imax]+1,bla2[p_imax]+1,p_rms);
}
}
if (warn > 0)
{
if (bDumpOnError && stdlog)
{
cconerr(&p_max,&p_rms,&p_imax,xprime,nc,bla1,bla2,bllen);
sprintf(buf,"\nStep %d, time %g (ps) LINCS WARNING\n"
"relative constraint deviation after LINCS:\n"
"max %.6f (between atoms %d and %d) rms %.6f\n",
step,ir->init_t+step*ir->delta_t,
p_max,bla1[p_imax]+1,bla2[p_imax]+1,p_rms);
fprintf(stdlog,"%s",buf);
fprintf(stderr,"%s",buf);
lincs_warning(x,xprime,nc,bla1,bla2,bllen,wang);
}
bOK = (p_max < 0.5);
}
for(b=0; (b<nc); b++)
if (bllen0[b] < GMX_REAL_MIN)
bllen[b] = 0;
}
else
{
#ifdef USE_FORTRAN
#ifdef DOUBLE
F77_FUNC(flincspd,FLINCSPD)(x[0],xprime[0],min_proj[0],&nc,bla1,bla2,blnr,blbnb,
blc,blcc,blm,&ir->nProjOrder,
md->invmass,r[0],tmp1,tmp2,tmp3);
#else
F77_FUNC(flincsp,FLINCSP)(x[0],xprime[0],min_proj[0],&nc,bla1,bla2,blnr,blbnb,
blc,blcc,blm,&ir->nProjOrder,
md->invmass,r[0],tmp1,tmp2,tmp3);
#endif
#else
clincsp(x,xprime,min_proj,nc,bla1,bla2,blnr,blbnb,
blc,blcc,blm,ir->nProjOrder,
md->invmass,r,tmp1,tmp2,tmp3);
#endif
}
/* count assuming nit=1 */
inc_nrnb(nrnb,eNR_LINCS,nc);
inc_nrnb(nrnb,eNR_LINCSMAT,(2+ir->nProjOrder)*nrtot);
}
return bOK;
}
