static void do_my_pme(FILE *fp,real tm,gmx_bool bVerbose,t_inputrec *ir,
rvec x[],rvec xbuf[],rvec f[],
real charge[],real qbuf[],real qqbuf[],
matrix box,gmx_bool bSort,
t_commrec *cr,t_nsborder *nsb,t_nrnb *nrnb,
t_block *excl,real qtot,
t_forcerec *fr,int index[],FILE *fp_xvg,
int ngroups,unsigned short cENER[])
{
real ener,vcorr,q,xx,dvdl=0,vdip,vcharge;
tensor vir,vir_corr,vir_tot;
rvec mu_tot[2];
int i,m,ii,ig,jg;
real **epme,*qptr;
/* Initiate local variables */
fr->f_el_recip = f;
clear_mat(vir);
clear_mat(vir_corr);
if (ngroups > 1) {
fprintf(fp,"There are %d energy groups\n",ngroups);
snew(epme,ngroups);
for(i=0; (i<ngroups); i++)
snew(epme[i],ngroups);
}
/* Put x is in the box, this part needs to be parallellized properly */
/*put_atoms_in_box(box,nsb->natoms,x);*/
/* Here sorting of X (and q) is done.
* Alternatively, one could just put the atoms in one of the
* cr->nnodes slabs. That is much cheaper than sorting.
*/
for(i=0; (i<nsb->natoms); i++)
index[i] = i;
if (bSort) {
xptr = x;
qsort(index,nsb->natoms,sizeof(index[0]),comp_xptr);
xptr = NULL; /* To trap unintentional use of the ptr */
}
/* After sorting we only need the part that is to be computed on
* this processor. We also compute the mu_tot here (system dipole)
*/
clear_rvec(mu_tot[0]);
for(i=START(nsb); (i<START(nsb)+HOMENR(nsb)); i++) {
ii = index[i];
q = charge[ii];
qbuf[i] = q;
for(m=0; (m<DIM); m++) {
xx = x[ii][m];
xbuf[i][m] = xx;
mu_tot[0][m] += q*xx;
}
clear_rvec(f[ii]);
}
copy_rvec(mu_tot[0],mu_tot[1]);
if (debug) {
pr_rvec(debug,0,"qbuf",qbuf,nsb->natoms,TRUE);
pr_rvecs(debug,0,"xbuf",xbuf,nsb->natoms);
pr_rvecs(debug,0,"box",box,DIM);
}
for(ig=0; (ig<ngroups); ig++) {
for(jg=ig; (jg<ngroups); jg++) {
if (ngroups > 1) {
for(i=START(nsb); (i<START(nsb)+HOMENR(nsb)); i++) {
if ((cENER[i] == ig) || (cENER[i] == jg))
qqbuf[i] = qbuf[i];
else
qqbuf[i] = 0;
}
qptr = qqbuf;
}
else
qptr = qbuf;
ener = do_pme(fp,bVerbose,ir,xbuf,f,qptr,qptr,box,cr,
nsb,nrnb,vir,fr->ewaldcoeff,FALSE,0,&dvdl,FALSE);
vcorr = ewald_LRcorrection(fp,nsb,cr,fr,qptr,qptr,excl,xbuf,box,mu_tot,
ir->ewald_geometry,ir->epsilon_surface,
0,&dvdl,&vdip,&vcharge);
gmx_sum(1,&ener,cr);
gmx_sum(1,&vcorr,cr);
if (ngroups > 1)
epme[ig][jg] = ener+vcorr;
}
}
if (ngroups > 1) {
if (fp_xvg)
fprintf(fp_xvg,"%10.3f",tm);
for(ig=0; (ig<ngroups); ig++) {
for(jg=ig; (jg<ngroups); jg++) {
if (ig != jg)
epme[ig][jg] -= epme[ig][ig]+epme[jg][jg];
if (fp_xvg)
fprintf(fp_xvg," %12.5e",epme[ig][jg]);
}
}
if (fp_xvg)
fprintf(fp_xvg,"\n");
}
else {
fprintf(fp,"Time: %10.3f Energy: %12.5e Correction: %12.5e Total: %12.5e\n",
tm,ener,vcorr,ener+vcorr);
if (fp_xvg)
fprintf(fp_xvg,"%10.3f %12.5e %12.5e %12.5e\n",tm,ener+vcorr,vdip,vcharge);
if (bVerbose) {
m_add(vir,vir_corr,vir_tot);
gmx_sum(9,vir_tot[0],cr);
pr_rvecs(fp,0,"virial",vir_tot,DIM);
}
fflush(fp);
}
}
void force(FILE *fp, int step,
t_forcerec *fr, t_inputrec *ir,
t_idef *idef, t_nsborder *nsb,
t_commrec *cr, t_commrec *mcr,
t_nrnb *nrnb,
t_groups *grps, t_mdatoms *md,
int ngener, t_grpopts *opts,
rvec x[], rvec f[],
real epot[], t_fcdata *fcd,
bool bVerbose, matrix box,
real lambda, t_graph *graph,
t_block *excl, bool bNBFonly,
matrix lr_vir, rvec mu_tot,
real qsum, bool bGatherOnly)
{
int i,nit;
bool bDoEpot;
rvec box_size;
real Vlr,Vcorr=0;
/* Reset box */
for(i=0; (i<DIM); i++)
box_size[i]=box[i][i];
bDoEpot=((fr->nmol > 0) && (fr->nstcalc > 0) && (mod(step,fr->nstcalc)==0));
/* Reset epot... */
if (bDoEpot)
for(i=0; (i<fr->nmol); i++)
fr->mol_epot[i]=0.0;
debug_gmx();
/* Call the short range functions all in one go. */
do_fnbf(fp,cr,fr,x,f,md,
fr->bBHAM ? grps->estat.ee[egBHAM] : grps->estat.ee[egLJ],
grps->estat.ee[egCOUL],box_size,nrnb,
lambda,&epot[F_DVDL],FALSE,-1);
debug_gmx();
if (debug)
pr_rvecs(debug,0,"fshift after SR",fr->fshift,SHIFTS);
/* Shift the coordinates. Must be done before bonded forces and PPPM,
* but is also necessary for SHAKE and update, therefore it can NOT
* go when no bonded forces have to be evaluated.
*/
if (debug && 0)
p_graph(debug,"DeBUGGGG",graph);
/* Check whether we need to do bondeds */
if (!bNBFonly) {
shift_self(graph,box,x);
if (debug && 0) {
fprintf(debug,"BBBBBBBBBBBBBBBB\n");
fprintf(debug,"%5d\n",graph->nnodes);
for(i=graph->start; (i<=graph->end); i++)
fprintf(debug,"%5d%5s%5s%5d%8.3f%8.3f%8.3f\n",
i,"A","B",i,x[i][XX],x[i][YY],x[i][ZZ]);
fprintf(debug,"%10.5f%10.5f%10.5f\n",
box[XX][XX],box[YY][YY],box[ZZ][ZZ]);
}
if (TRICLINIC(box))
inc_nrnb(nrnb,eNR_SHIFTX,2*graph->nnodes);
else
inc_nrnb(nrnb,eNR_SHIFTX,graph->nnodes);
debug_gmx();
}
if (EEL_LR(fr->eeltype)) {
switch (fr->eeltype) {
case eelPPPM:
Vlr = do_pppm(fp,FALSE,x,fr->f_pme,md->chargeT,
box_size,fr->phi,cr,nsb,nrnb);
break;
case eelPOISSON:
Vlr = do_poisson(fp,FALSE,ir,md->nr,x,fr->f_pme,md->chargeT,
box_size,fr->phi,cr,nrnb,&nit,TRUE);
break;
case eelPME:
Vlr = do_pme(fp,FALSE,ir,x,fr->f_pme,md->chargeT,
box,cr,nsb,nrnb,lr_vir,fr->ewaldcoeff,bGatherOnly);
break;
case eelEWALD:
Vlr = do_ewald(fp,FALSE,ir,x,fr->f_pme,md->chargeT,
box_size,cr,nsb,lr_vir,fr->ewaldcoeff);
break;
default:
Vlr = 0;
fatal_error(0,"No such electrostatics method implemented %s",
eel_names[fr->eeltype]);
}
if(fr->bEwald)
Vcorr =
ewald_LRcorrection(fp,nsb,cr,fr,md->chargeT,excl,x,box,mu_tot,qsum,
ir->ewald_geometry,ir->epsilon_surface,lr_vir);
else
Vcorr = shift_LRcorrection(fp,nsb,cr,fr,md->chargeT,excl,x,TRUE,box,lr_vir);
epot[F_LR] = Vlr + Vcorr;
if (debug)
fprintf(debug,"Vlr = %g, Vcorr = %g, Vlr_corr = %g\n",
Vlr,Vcorr,epot[F_LR]);
if (debug) {
pr_rvecs(debug,0,"lr_vir after corr",lr_vir,DIM);
pr_rvecs(debug,0,"fshift after LR Corrections",fr->fshift,SHIFTS);
}
}
debug_gmx();
if (debug)
print_nrnb(debug,nrnb);
debug_gmx();
if (!bNBFonly) {
calc_bonds(fp,cr,mcr,
idef,x,f,fr,graph,epot,nrnb,box,lambda,md,
opts->ngener,grps->estat.ee[egLJ14],grps->estat.ee[egCOUL14],
fcd,step,fr->bSepDVDL && do_per_step(step,ir->nstlog));
debug_gmx();
}
if (debug)
pr_rvecs(debug,0,"fshift after bondeds",fr->fshift,SHIFTS);
for(i=0; (i<F_EPOT); i++)
if (i != F_DISRES)
epot[F_EPOT]+=epot[i];
}