void check_ir_old_tpx_versions(t_commrec *cr, FILE *fplog,
t_inputrec *ir, gmx_mtop_t *mtop)
{
/* Check required for old tpx files */
if (IR_TWINRANGE(*ir) && ir->nstlist > 1 &&
ir->nstcalcenergy % ir->nstlist != 0)
{
md_print_warn(cr, fplog, "Old tpr file with twin-range settings: modifying energy calculation and/or T/P-coupling frequencies\n");
if (gmx_mtop_ftype_count(mtop, F_CONSTR) +
gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0 &&
ir->eConstrAlg == econtSHAKE)
{
md_print_warn(cr, fplog, "With twin-range cut-off's and SHAKE the virial and pressure are incorrect\n");
if (ir->epc != epcNO)
{
gmx_fatal(FARGS, "Can not do pressure coupling with twin-range cut-off's and SHAKE");
}
}
check_nst_param(fplog, cr, "nstlist", ir->nstlist,
"nstcalcenergy", &ir->nstcalcenergy);
if (ir->epc != epcNO)
{
check_nst_param(fplog, cr, "nstlist", ir->nstlist,
"nstpcouple", &ir->nstpcouple);
}
check_nst_param(fplog, cr, "nstcalcenergy", ir->nstcalcenergy,
"nstenergy", &ir->nstenergy);
check_nst_param(fplog, cr, "nstcalcenergy", ir->nstcalcenergy,
"nstlog", &ir->nstlog);
if (ir->efep != efepNO)
{
check_nst_param(fplog, cr, "nstcalcenergy", ir->nstcalcenergy,
"nstdhdl", &ir->fepvals->nstdhdl);
}
}
if (EI_VV(ir->eI) && IR_TWINRANGE(*ir) && ir->nstlist > 1)
{
gmx_fatal(FARGS, "Twin-range multiple time stepping does not work with integrator %s.", ei_names[ir->eI]);
}
}
void global_stat(gmx_global_stat_t gs,
t_commrec *cr, gmx_enerdata_t *enerd,
tensor fvir, tensor svir, rvec mu_tot,
t_inputrec *inputrec,
gmx_ekindata_t *ekind, gmx_constr_t constr,
t_vcm *vcm,
int nsig, real *sig,
int *totalNumberOfBondedInteractions,
gmx_bool bSumEkinhOld, int flags)
/* instead of current system, gmx_booleans for summing virial, kinetic energy, and other terms */
{
t_bin *rb;
int *itc0, *itc1;
int ie = 0, ifv = 0, isv = 0, irmsd = 0, imu = 0;
int idedl = 0, idvdll = 0, idvdlnl = 0, iepl = 0, icm = 0, imass = 0, ica = 0, inb = 0;
int isig = -1;
int icj = -1, ici = -1, icx = -1;
int inn[egNR];
real copyenerd[F_NRE];
int nener, j;
real *rmsd_data = NULL;
double nb;
gmx_bool bVV, bTemp, bEner, bPres, bConstrVir, bEkinAveVel, bReadEkin;
bool checkNumberOfBondedInteractions = flags & CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
bVV = EI_VV(inputrec->eI);
bTemp = flags & CGLO_TEMPERATURE;
bEner = flags & CGLO_ENERGY;
bPres = (flags & CGLO_PRESSURE);
bConstrVir = (flags & CGLO_CONSTRAINT);
bEkinAveVel = (inputrec->eI == eiVV || (inputrec->eI == eiVVAK && bPres));
bReadEkin = (flags & CGLO_READEKIN);
rb = gs->rb;
itc0 = gs->itc0;
itc1 = gs->itc1;
reset_bin(rb);
/* This routine copies all the data to be summed to one big buffer
* using the t_bin struct.
*/
/* First, we neeed to identify which enerd->term should be
communicated. Temperature and pressure terms should only be
communicated and summed when they need to be, to avoid repeating
the sums and overcounting. */
nener = filter_enerdterm(enerd->term, TRUE, copyenerd, bTemp, bPres, bEner);
/* First, the data that needs to be communicated with velocity verlet every time
This is just the constraint virial.*/
if (bConstrVir)
{
isv = add_binr(rb, DIM*DIM, svir[0]);
where();
}
/* We need the force virial and the kinetic energy for the first time through with velocity verlet */
if (bTemp || !bVV)
{
if (ekind)
{
for (j = 0; (j < inputrec->opts.ngtc); j++)
{
if (bSumEkinhOld)
{
itc0[j] = add_binr(rb, DIM*DIM, ekind->tcstat[j].ekinh_old[0]);
}
if (bEkinAveVel && !bReadEkin)
{
itc1[j] = add_binr(rb, DIM*DIM, ekind->tcstat[j].ekinf[0]);
}
else if (!bReadEkin)
{
itc1[j] = add_binr(rb, DIM*DIM, ekind->tcstat[j].ekinh[0]);
}
}
/* these probably need to be put into one of these categories */
where();
idedl = add_binr(rb, 1, &(ekind->dekindl));
where();
ica = add_binr(rb, 1, &(ekind->cosacc.mvcos));
where();
}
}
where();
if (bPres)
{
ifv = add_binr(rb, DIM*DIM, fvir[0]);
}
if (bEner)
{
where();
ie = add_binr(rb, nener, copyenerd);
where();
if (constr)
{
rmsd_data = constr_rmsd_data(constr);
if (rmsd_data)
{
irmsd = add_binr(rb, 2, rmsd_data);
}
}
if (!inputrecNeedMutot(inputrec))
{
imu = add_binr(rb, DIM, mu_tot);
where();
}
for (j = 0; (j < egNR); j++)
{
inn[j] = add_binr(rb, enerd->grpp.nener, enerd->grpp.ener[j]);
}
where();
if (inputrec->efep != efepNO)
{
idvdll = add_bind(rb, efptNR, enerd->dvdl_lin);
idvdlnl = add_bind(rb, efptNR, enerd->dvdl_nonlin);
if (enerd->n_lambda > 0)
{
iepl = add_bind(rb, enerd->n_lambda, enerd->enerpart_lambda);
}
}
}
if (vcm)
{
icm = add_binr(rb, DIM*vcm->nr, vcm->group_p[0]);
where();
imass = add_binr(rb, vcm->nr, vcm->group_mass);
where();
if (vcm->mode == ecmANGULAR)
{
icj = add_binr(rb, DIM*vcm->nr, vcm->group_j[0]);
where();
icx = add_binr(rb, DIM*vcm->nr, vcm->group_x[0]);
where();
ici = add_binr(rb, DIM*DIM*vcm->nr, vcm->group_i[0][0]);
where();
}
}
if (checkNumberOfBondedInteractions)
{
nb = cr->dd->nbonded_local;
inb = add_bind(rb, 1, &nb);
}
where();
if (nsig > 0)
{
isig = add_binr(rb, nsig, sig);
}
/* Global sum it all */
if (debug)
{
fprintf(debug, "Summing %d energies\n", rb->maxreal);
}
sum_bin(rb, cr);
where();
/* Extract all the data locally */
if (bConstrVir)
{
extract_binr(rb, isv, DIM*DIM, svir[0]);
}
/* We need the force virial and the kinetic energy for the first time through with velocity verlet */
if (bTemp || !bVV)
{
if (ekind)
{
for (j = 0; (j < inputrec->opts.ngtc); j++)
{
if (bSumEkinhOld)
{
extract_binr(rb, itc0[j], DIM*DIM, ekind->tcstat[j].ekinh_old[0]);
}
if (bEkinAveVel && !bReadEkin)
{
extract_binr(rb, itc1[j], DIM*DIM, ekind->tcstat[j].ekinf[0]);
}
else if (!bReadEkin)
{
extract_binr(rb, itc1[j], DIM*DIM, ekind->tcstat[j].ekinh[0]);
}
}
extract_binr(rb, idedl, 1, &(ekind->dekindl));
extract_binr(rb, ica, 1, &(ekind->cosacc.mvcos));
where();
}
}
if (bPres)
{
extract_binr(rb, ifv, DIM*DIM, fvir[0]);
}
if (bEner)
{
extract_binr(rb, ie, nener, copyenerd);
if (rmsd_data)
{
extract_binr(rb, irmsd, 2, rmsd_data);
}
if (!inputrecNeedMutot(inputrec))
{
extract_binr(rb, imu, DIM, mu_tot);
}
for (j = 0; (j < egNR); j++)
{
extract_binr(rb, inn[j], enerd->grpp.nener, enerd->grpp.ener[j]);
}
if (inputrec->efep != efepNO)
{
extract_bind(rb, idvdll, efptNR, enerd->dvdl_lin);
extract_bind(rb, idvdlnl, efptNR, enerd->dvdl_nonlin);
if (enerd->n_lambda > 0)
{
extract_bind(rb, iepl, enerd->n_lambda, enerd->enerpart_lambda);
}
}
where();
filter_enerdterm(copyenerd, FALSE, enerd->term, bTemp, bPres, bEner);
}
if (vcm)
{
extract_binr(rb, icm, DIM*vcm->nr, vcm->group_p[0]);
where();
extract_binr(rb, imass, vcm->nr, vcm->group_mass);
where();
if (vcm->mode == ecmANGULAR)
{
extract_binr(rb, icj, DIM*vcm->nr, vcm->group_j[0]);
where();
extract_binr(rb, icx, DIM*vcm->nr, vcm->group_x[0]);
where();
extract_binr(rb, ici, DIM*DIM*vcm->nr, vcm->group_i[0][0]);
where();
}
}
if (checkNumberOfBondedInteractions)
{
extract_bind(rb, inb, 1, &nb);
*totalNumberOfBondedInteractions = static_cast<int>(nb+0.5);
}
if (nsig > 0)
{
extract_binr(rb, isig, nsig, sig);
}
where();
}
gmx_bool constrain(FILE *fplog, gmx_bool bLog, gmx_bool bEner,
struct gmx_constr *constr,
t_idef *idef, t_inputrec *ir, gmx_ekindata_t *ekind,
t_commrec *cr,
gmx_int64_t step, int delta_step,
t_mdatoms *md,
rvec *x, rvec *xprime, rvec *min_proj,
gmx_bool bMolPBC, matrix box,
real lambda, real *dvdlambda,
rvec *v, tensor *vir,
t_nrnb *nrnb, int econq, gmx_bool bPscal,
real veta, real vetanew)
{
gmx_bool bOK, bDump;
int start, homenr, nrend;
int i, j, d;
int ncons, settle_error;
tensor vir_r_m_dr;
rvec *vstor;
real invdt, vir_fac, t;
t_ilist *settle;
int nsettle;
t_pbc pbc, *pbc_null;
char buf[22];
t_vetavars vetavar;
int nth, th;
if (econq == econqForceDispl && !EI_ENERGY_MINIMIZATION(ir->eI))
{
gmx_incons("constrain called for forces displacements while not doing energy minimization, can not do this while the LINCS and SETTLE constraint connection matrices are mass weighted");
}
bOK = TRUE;
bDump = FALSE;
start = 0;
homenr = md->homenr;
nrend = start+homenr;
/* set constants for pressure control integration */
init_vetavars(&vetavar, econq != econqCoord,
veta, vetanew, ir, ekind, bPscal);
if (ir->delta_t == 0)
{
invdt = 0;
}
else
{
invdt = 1/ir->delta_t;
}
if (ir->efep != efepNO && EI_DYNAMICS(ir->eI))
{
/* Set the constraint lengths for the step at which this configuration
* is meant to be. The invmasses should not be changed.
*/
lambda += delta_step*ir->fepvals->delta_lambda;
}
if (vir != NULL)
{
clear_mat(vir_r_m_dr);
}
where();
settle = &idef->il[F_SETTLE];
nsettle = settle->nr/(1+NRAL(F_SETTLE));
if (nsettle > 0)
{
nth = gmx_omp_nthreads_get(emntSETTLE);
}
else
{
nth = 1;
}
if (nth > 1 && constr->vir_r_m_dr_th == NULL)
{
snew(constr->vir_r_m_dr_th, nth);
snew(constr->settle_error, nth);
}
settle_error = -1;
/* We do not need full pbc when constraints do not cross charge groups,
* i.e. when dd->constraint_comm==NULL.
* Note that PBC for constraints is different from PBC for bondeds.
* For constraints there is both forward and backward communication.
*/
if (ir->ePBC != epbcNONE &&
(cr->dd || bMolPBC) && !(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;
}
/* Communicate the coordinates required for the non-local constraints
* for LINCS and/or SETTLE.
*/
if (cr->dd)
{
dd_move_x_constraints(cr->dd, box, x, xprime, econq == econqCoord);
}
if (constr->lincsd != NULL)
{
bOK = constrain_lincs(fplog, bLog, bEner, ir, step, constr->lincsd, md, cr,
x, xprime, min_proj,
box, pbc_null, lambda, dvdlambda,
invdt, v, vir != NULL, vir_r_m_dr,
econq, nrnb,
constr->maxwarn, &constr->warncount_lincs);
if (!bOK && constr->maxwarn >= 0)
{
if (fplog != NULL)
{
fprintf(fplog, "Constraint error in algorithm %s at step %s\n",
econstr_names[econtLINCS], gmx_step_str(step, buf));
}
bDump = TRUE;
}
}
if (constr->nblocks > 0)
{
switch (econq)
{
case (econqCoord):
bOK = bshakef(fplog, constr->shaked,
md->invmass, constr->nblocks, constr->sblock,
idef, ir, x, xprime, nrnb,
constr->lagr, lambda, dvdlambda,
invdt, v, vir != NULL, vir_r_m_dr,
constr->maxwarn >= 0, econq, &vetavar);
break;
case (econqVeloc):
bOK = bshakef(fplog, constr->shaked,
md->invmass, constr->nblocks, constr->sblock,
idef, ir, x, min_proj, nrnb,
constr->lagr, lambda, dvdlambda,
invdt, NULL, vir != NULL, vir_r_m_dr,
constr->maxwarn >= 0, econq, &vetavar);
break;
default:
gmx_fatal(FARGS, "Internal error, SHAKE called for constraining something else than coordinates");
break;
}
if (!bOK && constr->maxwarn >= 0)
{
if (fplog != NULL)
{
fprintf(fplog, "Constraint error in algorithm %s at step %s\n",
econstr_names[econtSHAKE], gmx_step_str(step, buf));
}
bDump = TRUE;
}
}
if (nsettle > 0)
{
int calcvir_atom_end;
if (vir == NULL)
{
calcvir_atom_end = 0;
}
else
{
calcvir_atom_end = md->homenr;
}
switch (econq)
{
case econqCoord:
#pragma omp parallel for num_threads(nth) schedule(static)
for (th = 0; th < nth; th++)
{
int start_th, end_th;
if (th > 0)
{
clear_mat(constr->vir_r_m_dr_th[th]);
}
start_th = (nsettle* th )/nth;
end_th = (nsettle*(th+1))/nth;
if (start_th >= 0 && end_th - start_th > 0)
{
csettle(constr->settled,
end_th-start_th,
settle->iatoms+start_th*(1+NRAL(F_SETTLE)),
pbc_null,
x[0], xprime[0],
invdt, v ? v[0] : NULL, calcvir_atom_end,
th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
th == 0 ? &settle_error : &constr->settle_error[th],
&vetavar);
}
}
inc_nrnb(nrnb, eNR_SETTLE, nsettle);
if (v != NULL)
{
inc_nrnb(nrnb, eNR_CONSTR_V, nsettle*3);
}
if (vir != NULL)
{
inc_nrnb(nrnb, eNR_CONSTR_VIR, nsettle*3);
}
break;
case econqVeloc:
case econqDeriv:
case econqForce:
case econqForceDispl:
#pragma omp parallel for num_threads(nth) schedule(static)
for (th = 0; th < nth; th++)
{
int start_th, end_th;
if (th > 0)
{
clear_mat(constr->vir_r_m_dr_th[th]);
}
start_th = (nsettle* th )/nth;
end_th = (nsettle*(th+1))/nth;
if (start_th >= 0 && end_th - start_th > 0)
{
settle_proj(constr->settled, econq,
end_th-start_th,
settle->iatoms+start_th*(1+NRAL(F_SETTLE)),
pbc_null,
x,
xprime, min_proj, calcvir_atom_end,
th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
&vetavar);
}
}
/* This is an overestimate */
inc_nrnb(nrnb, eNR_SETTLE, nsettle);
break;
case econqDeriv_FlexCon:
/* Nothing to do, since the are no flexible constraints in settles */
break;
default:
gmx_incons("Unknown constraint quantity for settle");
}
}
if (settle->nr > 0)
{
/* Combine virial and error info of the other threads */
for (i = 1; i < nth; i++)
{
m_add(vir_r_m_dr, constr->vir_r_m_dr_th[i], vir_r_m_dr);
settle_error = constr->settle_error[i];
}
if (econq == econqCoord && settle_error >= 0)
{
bOK = FALSE;
if (constr->maxwarn >= 0)
{
char buf[256];
sprintf(buf,
"\nstep " "%"GMX_PRId64 ": Water molecule starting at atom %d can not be "
"settled.\nCheck for bad contacts and/or reduce the timestep if appropriate.\n",
step, ddglatnr(cr->dd, settle->iatoms[settle_error*(1+NRAL(F_SETTLE))+1]));
if (fplog)
{
fprintf(fplog, "%s", buf);
}
fprintf(stderr, "%s", buf);
constr->warncount_settle++;
if (constr->warncount_settle > constr->maxwarn)
{
too_many_constraint_warnings(-1, constr->warncount_settle);
}
bDump = TRUE;
}
}
}
free_vetavars(&vetavar);
if (vir != NULL)
{
switch (econq)
{
case econqCoord:
vir_fac = 0.5/(ir->delta_t*ir->delta_t);
break;
case econqVeloc:
vir_fac = 0.5/ir->delta_t;
break;
case econqForce:
case econqForceDispl:
vir_fac = 0.5;
break;
default:
vir_fac = 0;
gmx_incons("Unsupported constraint quantity for virial");
}
if (EI_VV(ir->eI))
{
vir_fac *= 2; /* only constraining over half the distance here */
}
for (i = 0; i < DIM; i++)
{
for (j = 0; j < DIM; j++)
{
(*vir)[i][j] = vir_fac*vir_r_m_dr[i][j];
}
}
}
if (bDump)
{
dump_confs(fplog, step, constr->warn_mtop, start, homenr, cr, x, xprime, box);
}
if (econq == econqCoord)
{
if (ir->ePull == epullCONSTRAINT)
{
if (EI_DYNAMICS(ir->eI))
{
t = ir->init_t + (step + delta_step)*ir->delta_t;
}
else
{
t = ir->init_t;
}
set_pbc(&pbc, ir->ePBC, box);
pull_constraint(ir->pull, md, &pbc, cr, ir->delta_t, t, x, xprime, v, *vir);
}
if (constr->ed && delta_step > 0)
{
/* apply the essential dynamcs constraints here */
do_edsam(ir, step, cr, xprime, v, box, constr->ed);
}
}
return bOK;
}
gmx_bool constrain(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
struct gmx_constr *constr,
t_idef *idef,t_inputrec *ir,gmx_ekindata_t *ekind,
t_commrec *cr,
gmx_large_int_t step,int delta_step,
t_mdatoms *md,
rvec *x,rvec *xprime,rvec *min_proj,matrix box,
real lambda,real *dvdlambda,
rvec *v,tensor *vir,
t_nrnb *nrnb,int econq,gmx_bool bPscal,real veta, real vetanew)
{
gmx_bool bOK,bDump;
int start,homenr,nrend;
int i,j,d;
int ncons,error;
tensor rmdr;
rvec *vstor;
real invdt,vir_fac,t;
t_ilist *settle;
int nsettle;
t_pbc pbc;
char buf[22];
t_vetavars *vetavar;
if (econq == econqForceDispl && !EI_ENERGY_MINIMIZATION(ir->eI))
{
gmx_incons("constrain called for forces displacements while not doing energy minimization, can not do this while the LINCS and SETTLE constraint connection matrices are mass weighted");
}
bOK = TRUE;
bDump = FALSE;
start = md->start;
homenr = md->homenr;
nrend = start+homenr;
/* set constants for pressure control integration */
vetavar = init_vetavars(veta,vetanew,ir,ekind,bPscal);
if (ir->delta_t == 0)
{
invdt = 0;
}
else
{
invdt = 1/ir->delta_t;
}
if (ir->efep != efepNO && EI_DYNAMICS(ir->eI))
{
/* Set the constraint lengths for the step at which this configuration
* is meant to be. The invmasses should not be changed.
*/
lambda += delta_step*ir->delta_lambda;
}
if (vir != NULL)
{
clear_mat(rmdr);
}
where();
if (constr->lincsd)
{
bOK = constrain_lincs(fplog,bLog,bEner,ir,step,constr->lincsd,md,cr,
x,xprime,min_proj,box,lambda,dvdlambda,
invdt,v,vir!=NULL,rmdr,
econq,nrnb,
constr->maxwarn,&constr->warncount_lincs);
if (!bOK && constr->maxwarn >= 0)
{
if (fplog != NULL)
{
fprintf(fplog,"Constraint error in algorithm %s at step %s\n",
econstr_names[econtLINCS],gmx_step_str(step,buf));
}
bDump = TRUE;
}
}
if (constr->nblocks > 0)
{
switch (econq) {
case (econqCoord):
bOK = bshakef(fplog,constr->shaked,
homenr,md->invmass,constr->nblocks,constr->sblock,
idef,ir,box,x,xprime,nrnb,
constr->lagr,lambda,dvdlambda,
invdt,v,vir!=NULL,rmdr,constr->maxwarn>=0,econq,vetavar);
break;
case (econqVeloc):
bOK = bshakef(fplog,constr->shaked,
homenr,md->invmass,constr->nblocks,constr->sblock,
idef,ir,box,x,min_proj,nrnb,
constr->lagr,lambda,dvdlambda,
invdt,NULL,vir!=NULL,rmdr,constr->maxwarn>=0,econq,vetavar);
break;
default:
gmx_fatal(FARGS,"Internal error, SHAKE called for constraining something else than coordinates");
break;
}
if (!bOK && constr->maxwarn >= 0)
{
if (fplog != NULL)
{
fprintf(fplog,"Constraint error in algorithm %s at step %s\n",
econstr_names[econtSHAKE],gmx_step_str(step,buf));
}
bDump = TRUE;
}
}
settle = &idef->il[F_SETTLE];
if (settle->nr > 0)
{
nsettle = settle->nr/2;
switch (econq)
{
case econqCoord:
csettle(constr->settled,
nsettle,settle->iatoms,x[0],xprime[0],
invdt,v[0],vir!=NULL,rmdr,&error,vetavar);
inc_nrnb(nrnb,eNR_SETTLE,nsettle);
if (v != NULL)
{
inc_nrnb(nrnb,eNR_CONSTR_V,nsettle*3);
}
if (vir != NULL)
{
inc_nrnb(nrnb,eNR_CONSTR_VIR,nsettle*3);
}
bOK = (error < 0);
if (!bOK && constr->maxwarn >= 0)
{
char buf[256];
sprintf(buf,
"\nstep " gmx_large_int_pfmt ": Water molecule starting at atom %d can not be "
"settled.\nCheck for bad contacts and/or reduce the timestep if appropriate.\n",
step,ddglatnr(cr->dd,settle->iatoms[error*2+1]));
if (fplog)
{
fprintf(fplog,"%s",buf);
}
fprintf(stderr,"%s",buf);
constr->warncount_settle++;
if (constr->warncount_settle > constr->maxwarn)
{
too_many_constraint_warnings(-1,constr->warncount_settle);
}
bDump = TRUE;
break;
case econqVeloc:
case econqDeriv:
case econqForce:
case econqForceDispl:
settle_proj(fplog,constr->settled,econq,
nsettle,settle->iatoms,x,
xprime,min_proj,vir!=NULL,rmdr,vetavar);
/* This is an overestimate */
inc_nrnb(nrnb,eNR_SETTLE,nsettle);
break;
case econqDeriv_FlexCon:
/* Nothing to do, since the are no flexible constraints in settles */
break;
default:
gmx_incons("Unknown constraint quantity for settle");
}
}
}
free_vetavars(vetavar);
if (vir != NULL)
{
switch (econq)
{
case econqCoord:
vir_fac = 0.5/(ir->delta_t*ir->delta_t);
break;
case econqVeloc:
vir_fac = 0.5/ir->delta_t;
break;
case econqForce:
case econqForceDispl:
vir_fac = 0.5;
break;
default:
vir_fac = 0;
gmx_incons("Unsupported constraint quantity for virial");
}
if (EI_VV(ir->eI))
{
vir_fac *= 2; /* only constraining over half the distance here */
}
for(i=0; i<DIM; i++)
{
for(j=0; j<DIM; j++)
{
(*vir)[i][j] = vir_fac*rmdr[i][j];
}
}
}
if (bDump)
{
dump_confs(fplog,step,constr->warn_mtop,start,homenr,cr,x,xprime,box);
}
if (econq == econqCoord)
{
if (ir->ePull == epullCONSTRAINT)
{
if (EI_DYNAMICS(ir->eI))
{
t = ir->init_t + (step + delta_step)*ir->delta_t;
}
else
{
t = ir->init_t;
}
set_pbc(&pbc,ir->ePBC,box);
pull_constraint(ir->pull,md,&pbc,cr,ir->delta_t,t,x,xprime,v,*vir);
}
if (constr->ed && delta_step > 0)
{
/* apply the essential dynamcs constraints here */
do_edsam(ir,step,md,cr,xprime,v,box,constr->ed);
}
}
return bOK;
}
