void test_pppm(FILE *log, bool bVerbose,
bool bGenerGhat, char *ghatfn,
t_atoms *atoms, t_inputrec *ir,
rvec x[], rvec f[],
real charge[], rvec box,
real phi[], real phi_s[],
int nmol, t_commrec *cr,
bool bOld, t_block *cgs)
{
char buf[256];
real ener;
int i;
t_nrnb nrnb;
t_nsborder nsb;
init_nrnb(&nrnb);
calc_nsb(cgs,1,&nsb,0);
/* First time only setup is done! */
init_pppm(log,cr,&nsb,bVerbose,bOld,box,ghatfn,ir);
ener = do_pppm(log,bVerbose,x,f,charge,box,phi,cr,&nsb,&nrnb);
fprintf(log,"Vpppm = %g\n",ener);
sprintf(buf,"PPPM-%d.pdb",ir->nkx);
write_pqr(buf,atoms,x,phi,0);
pr_f("pppm-force",atoms->nr,f);
calc_ener(log,buf,FALSE,nmol,atoms->nr,phi,charge,&atoms->excl);
for(i=0; (i<atoms->nr); i++)
phi[i]+=phi_s[i];
sprintf(buf,"PPPM-%d+SR",ir->nkx);
calc_ener(log,buf,FALSE,nmol,atoms->nr,phi,charge,&atoms->excl);
strcat(buf,".pdb");
write_pqr(buf,atoms,x,phi,0);
}
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];
}
