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;
}
gmx_bool constrain_lincs(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
t_inputrec *ir,
gmx_large_int_t step,
struct gmx_lincsdata *lincsd,t_mdatoms *md,
t_commrec *cr,
rvec *x,rvec *xprime,rvec *min_proj,matrix box,
real lambda,real *dvdlambda,
real invdt,rvec *v,
gmx_bool bCalcVir,tensor rmdr,
int econq,
t_nrnb *nrnb,
int maxwarn,int *warncount)
{
char buf[STRLEN],buf2[22],buf3[STRLEN];
int i,warn,p_imax,error;
real ncons_loc,p_ssd,p_max;
t_pbc pbc,*pbc_null;
rvec dx;
gmx_bool bOK;
bOK = TRUE;
if (lincsd->nc == 0 && cr->dd == NULL)
{
if (bLog || bEner)
{
lincsd->rmsd_data[0] = 0;
if (ir->eI == eiSD2 && v == NULL)
{
i = 2;
}
else
{
i = 1;
}
lincsd->rmsd_data[i] = 0;
}
return bOK;
}
/* We do not need full pbc when constraints do not cross charge groups,
* i.e. when dd->constraint_comm==NULL
*/
if ((cr->dd || ir->bPeriodicMols) && !(cr->dd && cr->dd->constraint_comm==NULL))
{
/* With pbc=screw the screw has been changed to a shift
* by the constraint coordinate communication routine,
* so that here we can use normal pbc.
*/
pbc_null = set_pbc_dd(&pbc,ir->ePBC,cr->dd,FALSE,box);
}
else
{
pbc_null = NULL;
}
if (cr->dd)
{
/* Communicate the coordinates required for the non-local constraints */
dd_move_x_constraints(cr->dd,box,x,xprime);
/* dump_conf(dd,lincsd,NULL,"con",TRUE,xprime,box); */
}
else if (PARTDECOMP(cr))
{
pd_move_x_constraints(cr,x,xprime);
}
if (econq == econqCoord)
{
if (ir->efep != efepNO)
{
if (md->nMassPerturbed && lincsd->matlam != md->lambda)
{
set_lincs_matrix(lincsd,md->invmass,md->lambda);
}
for(i=0; i<lincsd->nc; i++)
{
lincsd->bllen[i] = lincsd->bllen0[i] + lambda*lincsd->ddist[i];
}
}
if (lincsd->ncg_flex)
{
/* Set the flexible constraint lengths to the old lengths */
if (pbc_null)
{
for(i=0; i<lincsd->nc; i++)
{
if (lincsd->bllen[i] == 0) {
pbc_dx_aiuc(pbc_null,x[lincsd->bla[2*i]],x[lincsd->bla[2*i+1]],dx);
lincsd->bllen[i] = norm(dx);
}
}
}
else
{
for(i=0; i<lincsd->nc; i++)
{
if (lincsd->bllen[i] == 0)
{
lincsd->bllen[i] =
sqrt(distance2(x[lincsd->bla[2*i]],
x[lincsd->bla[2*i+1]]));
}
}
}
}
if (bLog && fplog)
{
cconerr(cr->dd,lincsd->nc,lincsd->bla,lincsd->bllen,xprime,pbc_null,
&ncons_loc,&p_ssd,&p_max,&p_imax);
}
do_lincs(x,xprime,box,pbc_null,lincsd,md->invmass,cr,
ir->LincsWarnAngle,&warn,
invdt,v,bCalcVir,rmdr);
if (ir->efep != efepNO)
{
real dt_2,dvdl=0;
dt_2 = 1.0/(ir->delta_t*ir->delta_t);
for(i=0; (i<lincsd->nc); i++)
{
dvdl += lincsd->lambda[i]*dt_2*lincsd->ddist[i];
}
*dvdlambda += dvdl;
}
if (bLog && fplog && lincsd->nc > 0)
{
fprintf(fplog," Rel. Constraint Deviation: RMS MAX between atoms\n");
fprintf(fplog," Before LINCS %.6f %.6f %6d %6d\n",
sqrt(p_ssd/ncons_loc),p_max,
ddglatnr(cr->dd,lincsd->bla[2*p_imax]),
ddglatnr(cr->dd,lincsd->bla[2*p_imax+1]));
}
if (bLog || bEner)
{
cconerr(cr->dd,lincsd->nc,lincsd->bla,lincsd->bllen,xprime,pbc_null,
&ncons_loc,&p_ssd,&p_max,&p_imax);
/* Check if we are doing the second part of SD */
if (ir->eI == eiSD2 && v == NULL)
{
i = 2;
}
else
{
i = 1;
}
lincsd->rmsd_data[0] = ncons_loc;
lincsd->rmsd_data[i] = p_ssd;
}
else
{
lincsd->rmsd_data[0] = 0;
lincsd->rmsd_data[1] = 0;
lincsd->rmsd_data[2] = 0;
}
if (bLog && fplog && lincsd->nc > 0)
{
fprintf(fplog,
" After LINCS %.6f %.6f %6d %6d\n\n",
sqrt(p_ssd/ncons_loc),p_max,
ddglatnr(cr->dd,lincsd->bla[2*p_imax]),
ddglatnr(cr->dd,lincsd->bla[2*p_imax+1]));
}
if (warn > 0)
{
if (maxwarn >= 0)
{
cconerr(cr->dd,lincsd->nc,lincsd->bla,lincsd->bllen,xprime,pbc_null,
&ncons_loc,&p_ssd,&p_max,&p_imax);
if (MULTISIM(cr))
{
sprintf(buf3," in simulation %d", cr->ms->sim);
}
else
{
buf3[0] = 0;
}
sprintf(buf,"\nStep %s, time %g (ps) LINCS WARNING%s\n"
"relative constraint deviation after LINCS:\n"
"rms %.6f, max %.6f (between atoms %d and %d)\n",
gmx_step_str(step,buf2),ir->init_t+step*ir->delta_t,
buf3,
sqrt(p_ssd/ncons_loc),p_max,
ddglatnr(cr->dd,lincsd->bla[2*p_imax]),
ddglatnr(cr->dd,lincsd->bla[2*p_imax+1]));
if (fplog)
{
fprintf(fplog,"%s",buf);
}
fprintf(stderr,"%s",buf);
lincs_warning(fplog,cr->dd,x,xprime,pbc_null,
lincsd->nc,lincsd->bla,lincsd->bllen,
ir->LincsWarnAngle,maxwarn,warncount);
}
bOK = (p_max < 0.5);
}
if (lincsd->ncg_flex) {
for(i=0; (i<lincsd->nc); i++)
if (lincsd->bllen0[i] == 0 && lincsd->ddist[i] == 0)
lincsd->bllen[i] = 0;
}
}
else
{
do_lincsp(x,xprime,min_proj,pbc_null,lincsd,md->invmass,econq,dvdlambda,
bCalcVir,rmdr);
}
/* count assuming nit=1 */
inc_nrnb(nrnb,eNR_LINCS,lincsd->nc);
inc_nrnb(nrnb,eNR_LINCSMAT,(2+lincsd->nOrder)*lincsd->ncc);
if (lincsd->ntriangle > 0)
{
inc_nrnb(nrnb,eNR_LINCSMAT,lincsd->nOrder*lincsd->ncc_triangle);
}
if (v)
{
inc_nrnb(nrnb,eNR_CONSTR_V,lincsd->nc*2);
}
if (bCalcVir)
{
inc_nrnb(nrnb,eNR_CONSTR_VIR,lincsd->nc);
}
return bOK;
}
gmx_bool constrain_lincs(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
t_inputrec *ir,
gmx_large_int_t step,
struct gmx_lincsdata *lincsd,t_mdatoms *md,
t_commrec *cr,
rvec *x,rvec *xprime,rvec *min_proj,
matrix box,t_pbc *pbc,
real lambda,real *dvdlambda,
real invdt,rvec *v,
gmx_bool bCalcVir,tensor vir_r_m_dr,
int econq,
t_nrnb *nrnb,
int maxwarn,int *warncount)
{
char buf[STRLEN],buf2[22],buf3[STRLEN];
int i,warn,p_imax,error;
real ncons_loc,p_ssd,p_max=0;
rvec dx;
gmx_bool bOK;
bOK = TRUE;
if (lincsd->nc == 0 && cr->dd == NULL)
{
if (bLog || bEner)
{
lincsd->rmsd_data[0] = 0;
if (ir->eI == eiSD2 && v == NULL)
{
i = 2;
}
else
{
i = 1;
}
lincsd->rmsd_data[i] = 0;
}
return bOK;
}
if (econq == econqCoord)
{
if (ir->efep != efepNO)
{
if (md->nMassPerturbed && lincsd->matlam != md->lambda)
{
set_lincs_matrix(lincsd,md->invmass,md->lambda);
}
for(i=0; i<lincsd->nc; i++)
{
lincsd->bllen[i] = lincsd->bllen0[i] + lambda*lincsd->ddist[i];
}
}
if (lincsd->ncg_flex)
{
/* Set the flexible constraint lengths to the old lengths */
if (pbc != NULL)
{
for(i=0; i<lincsd->nc; i++)
{
if (lincsd->bllen[i] == 0) {
pbc_dx_aiuc(pbc,x[lincsd->bla[2*i]],x[lincsd->bla[2*i+1]],dx);
lincsd->bllen[i] = norm(dx);
}
}
}
else
{
for(i=0; i<lincsd->nc; i++)
{
if (lincsd->bllen[i] == 0)
{
lincsd->bllen[i] =
sqrt(distance2(x[lincsd->bla[2*i]],
x[lincsd->bla[2*i+1]]));
}
}
}
}
if (bLog && fplog)
{
cconerr(cr->dd,lincsd->nc,lincsd->bla,lincsd->bllen,xprime,pbc,
&ncons_loc,&p_ssd,&p_max,&p_imax);
}
/* This warn var can be updated by multiple threads
* at the same time. But as we only need to detect
* if a warning occured or not, this is not an issue.
*/
warn = -1;
/* The OpenMP parallel region of constrain_lincs for coords */
#pragma omp parallel num_threads(lincsd->nth)
{
int th=gmx_omp_get_thread_num();
clear_mat(lincsd->th[th].vir_r_m_dr);
do_lincs(x,xprime,box,pbc,lincsd,th,
md->invmass,cr,
bCalcVir || (ir->efep != efepNO),
ir->LincsWarnAngle,&warn,
invdt,v,bCalcVir,
th==0 ? vir_r_m_dr : lincsd->th[th].vir_r_m_dr);
}
if (ir->efep != efepNO)
{
real dt_2,dvdl=0;
dt_2 = 1.0/(ir->delta_t*ir->delta_t);
for(i=0; (i<lincsd->nc); i++)
{
dvdl -= lincsd->mlambda[i]*dt_2*lincsd->ddist[i];
}
*dvdlambda += dvdl;
}
if (bLog && fplog && lincsd->nc > 0)
{
fprintf(fplog," Rel. Constraint Deviation: RMS MAX between atoms\n");
fprintf(fplog," Before LINCS %.6f %.6f %6d %6d\n",
sqrt(p_ssd/ncons_loc),p_max,
ddglatnr(cr->dd,lincsd->bla[2*p_imax]),
ddglatnr(cr->dd,lincsd->bla[2*p_imax+1]));
}
if (bLog || bEner)
{
cconerr(cr->dd,lincsd->nc,lincsd->bla,lincsd->bllen,xprime,pbc,
&ncons_loc,&p_ssd,&p_max,&p_imax);
/* Check if we are doing the second part of SD */
if (ir->eI == eiSD2 && v == NULL)
{
i = 2;
}
else
{
i = 1;
}
lincsd->rmsd_data[0] = ncons_loc;
lincsd->rmsd_data[i] = p_ssd;
}
else
{
lincsd->rmsd_data[0] = 0;
lincsd->rmsd_data[1] = 0;
lincsd->rmsd_data[2] = 0;
}
if (bLog && fplog && lincsd->nc > 0)
{
fprintf(fplog,
" After LINCS %.6f %.6f %6d %6d\n\n",
sqrt(p_ssd/ncons_loc),p_max,
ddglatnr(cr->dd,lincsd->bla[2*p_imax]),
ddglatnr(cr->dd,lincsd->bla[2*p_imax+1]));
}
if (warn >= 0)
{
if (maxwarn >= 0)
{
cconerr(cr->dd,lincsd->nc,lincsd->bla,lincsd->bllen,xprime,pbc,
&ncons_loc,&p_ssd,&p_max,&p_imax);
if (MULTISIM(cr))
{
sprintf(buf3," in simulation %d", cr->ms->sim);
}
else
{
buf3[0] = 0;
}
sprintf(buf,"\nStep %s, time %g (ps) LINCS WARNING%s\n"
"relative constraint deviation after LINCS:\n"
"rms %.6f, max %.6f (between atoms %d and %d)\n",
gmx_step_str(step,buf2),ir->init_t+step*ir->delta_t,
buf3,
sqrt(p_ssd/ncons_loc),p_max,
ddglatnr(cr->dd,lincsd->bla[2*p_imax]),
ddglatnr(cr->dd,lincsd->bla[2*p_imax+1]));
if (fplog)
{
fprintf(fplog,"%s",buf);
}
fprintf(stderr,"%s",buf);
lincs_warning(fplog,cr->dd,x,xprime,pbc,
lincsd->nc,lincsd->bla,lincsd->bllen,
ir->LincsWarnAngle,maxwarn,warncount);
}
bOK = (p_max < 0.5);
}
if (lincsd->ncg_flex) {
for(i=0; (i<lincsd->nc); i++)
if (lincsd->bllen0[i] == 0 && lincsd->ddist[i] == 0)
lincsd->bllen[i] = 0;
}
}
else
{
/* The OpenMP parallel region of constrain_lincs for derivatives */
#pragma omp parallel num_threads(lincsd->nth)
{
int th=gmx_omp_get_thread_num();
do_lincsp(x,xprime,min_proj,pbc,lincsd,th,
md->invmass,econq,ir->efep != efepNO ? dvdlambda : NULL,
bCalcVir,th==0 ? vir_r_m_dr : lincsd->th[th].vir_r_m_dr);
}
}
if (bCalcVir && lincsd->nth > 1)
{
for(i=1; i<lincsd->nth; i++)
{
m_add(vir_r_m_dr,lincsd->th[i].vir_r_m_dr,vir_r_m_dr);
}
}
/* count assuming nit=1 */
inc_nrnb(nrnb,eNR_LINCS,lincsd->nc);
inc_nrnb(nrnb,eNR_LINCSMAT,(2+lincsd->nOrder)*lincsd->ncc);
if (lincsd->ntriangle > 0)
{
inc_nrnb(nrnb,eNR_LINCSMAT,lincsd->nOrder*lincsd->ncc_triangle);
}
if (v)
{
inc_nrnb(nrnb,eNR_CONSTR_V,lincsd->nc*2);
}
if (bCalcVir)
{
inc_nrnb(nrnb,eNR_CONSTR_VIR,lincsd->nc);
}
return bOK;
}
