real
do_listed_vdw_q(int ftype,int nbonds,
const t_iatom iatoms[],const t_iparams iparams[],
const rvec x[],rvec f[],rvec fshift[],
const t_pbc *pbc,const t_graph *g,
real lambda,real *dvdlambda,
const t_mdatoms *md,
const t_forcerec *fr,gmx_grppairener_t *grppener,
int *global_atom_index)
{
static gmx_bool bWarn=FALSE;
real eps,r2,*tab,rtab2=0;
rvec dx,x14[2],f14[2];
int i,ai,aj,itype;
int typeA[2]={0,0},typeB[2]={0,1};
real chargeA[2]={0,0},chargeB[2];
int gid,shift_vir,shift_f;
int j_index[] = { 0, 1 };
int i0=0,i1=1,i2=2;
ivec dt;
int outeriter,inneriter;
int nthreads = 1;
int count;
real krf,crf,tabscale;
int ntype=0;
real *nbfp=NULL;
real *egnb=NULL,*egcoul=NULL;
t_nblist tmplist;
int icoul,ivdw;
gmx_bool bMolPBC,bFreeEnergy;
t_pf_global *pf_global;
#if GMX_THREAD_SHM_FDECOMP
pthread_mutex_t mtx;
#else
void * mtx = NULL;
#endif
#if GMX_THREAD_SHM_FDECOMP
pthread_mutex_initialize(&mtx);
#endif
bMolPBC = fr->bMolPBC;
pf_global = fr->pf_global;
switch (ftype) {
case F_LJ14:
case F_LJC14_Q:
eps = fr->epsfac*fr->fudgeQQ;
ntype = 1;
egnb = grppener->ener[egLJ14];
egcoul = grppener->ener[egCOUL14];
break;
case F_LJC_PAIRS_NB:
eps = fr->epsfac;
ntype = 1;
egnb = grppener->ener[egLJSR];
egcoul = grppener->ener[egCOULSR];
break;
default:
gmx_fatal(FARGS,"Unknown function type %d in do_nonbonded14",
ftype);
}
tab = fr->tab14.tab;
rtab2 = sqr(fr->tab14.r);
tabscale = fr->tab14.scale;
krf = fr->k_rf;
crf = fr->c_rf;
/* Determine the values for icoul/ivdw. */
if (fr->bEwald) {
icoul = 1;
}
else if(fr->bcoultab)
{
icoul = 3;
}
else if(fr->eeltype == eelRF_NEC)
{
icoul = 2;
}
else
{
icoul = 1;
}
if(fr->bvdwtab)
{
ivdw = 3;
}
else if(fr->bBHAM)
{
ivdw = 2;
}
else
{
ivdw = 1;
}
/* We don't do SSE or altivec here, due to large overhead for 4-fold
* unrolling on short lists
*/
bFreeEnergy = FALSE;
for(i=0; (i<nbonds); )
{
itype = iatoms[i++];
ai = iatoms[i++];
aj = iatoms[i++];
gid = GID(md->cENER[ai],md->cENER[aj],md->nenergrp);
switch (ftype) {
case F_LJ14:
bFreeEnergy =
(fr->efep != efepNO &&
((md->nPerturbed && (md->bPerturbed[ai] || md->bPerturbed[aj])) ||
iparams[itype].lj14.c6A != iparams[itype].lj14.c6B ||
iparams[itype].lj14.c12A != iparams[itype].lj14.c12B));
chargeA[0] = md->chargeA[ai];
chargeA[1] = md->chargeA[aj];
nbfp = (real *)&(iparams[itype].lj14.c6A);
break;
case F_LJC14_Q:
eps = fr->epsfac*iparams[itype].ljc14.fqq;
chargeA[0] = iparams[itype].ljc14.qi;
chargeA[1] = iparams[itype].ljc14.qj;
nbfp = (real *)&(iparams[itype].ljc14.c6);
break;
case F_LJC_PAIRS_NB:
chargeA[0] = iparams[itype].ljcnb.qi;
chargeA[1] = iparams[itype].ljcnb.qj;
nbfp = (real *)&(iparams[itype].ljcnb.c6);
break;
}
if (!bMolPBC)
{
/* This is a bonded interaction, atoms are in the same box */
shift_f = CENTRAL;
r2 = distance2(x[ai],x[aj]);
}
else
{
/* Apply full periodic boundary conditions */
shift_f = pbc_dx_aiuc(pbc,x[ai],x[aj],dx);
r2 = norm2(dx);
}
if (r2 >= rtab2)
{
if (!bWarn)
{
fprintf(stderr,"Warning: 1-4 interaction between %d and %d "
"at distance %.3f which is larger than the 1-4 table size %.3f nm\n",
glatnr(global_atom_index,ai),
glatnr(global_atom_index,aj),
sqrt(r2), sqrt(rtab2));
fprintf(stderr,"These are ignored for the rest of the simulation\n");
fprintf(stderr,"This usually means your system is exploding,\n"
"if not, you should increase table-extension in your mdp file\n"
"or with user tables increase the table size\n");
bWarn = TRUE;
}
if (debug)
fprintf(debug,"%8f %8f %8f\n%8f %8f %8f\n1-4 (%d,%d) interaction not within cut-off! r=%g. Ignored\n",
x[ai][XX],x[ai][YY],x[ai][ZZ],
x[aj][XX],x[aj][YY],x[aj][ZZ],
glatnr(global_atom_index,ai),
glatnr(global_atom_index,aj),
sqrt(r2));
}
else
{
copy_rvec(x[ai],x14[0]);
copy_rvec(x[aj],x14[1]);
clear_rvec(f14[0]);
clear_rvec(f14[1]);
#ifdef DEBUG
fprintf(debug,"LJ14: grp-i=%2d, grp-j=%2d, ngrp=%2d, GID=%d\n",
md->cENER[ai],md->cENER[aj],md->nenergrp,gid);
#endif
outeriter = inneriter = count = 0;
if (bFreeEnergy)
{
chargeB[0] = md->chargeB[ai];
chargeB[1] = md->chargeB[aj];
/* We pass &(iparams[itype].lj14.c6A) as LJ parameter matrix
* to the innerloops.
* Here we use that the LJ-14 parameters are stored in iparams
* as c6A,c12A,c6B,c12B, which are referenced correctly
* in the innerloops if we assign type combinations 0-0 and 0-1
* to atom pair ai-aj in topologies A and B respectively.
*/
if(ivdw==2)
{
gmx_fatal(FARGS,"Cannot do free energy Buckingham interactions.");
}
count = 0;
gmx_nb_free_energy_kernel(icoul,
ivdw,
i1,
&i0,
j_index,
&i1,
&shift_f,
fr->shift_vec[0],
fshift[0],
&gid,
x14[0],
f14[0],
chargeA,
chargeB,
eps,
krf,
crf,
fr->ewaldcoeff,
egcoul,
typeA,
typeB,
ntype,
nbfp,
egnb,
tabscale,
tab,
lambda,
dvdlambda,
fr->sc_alpha,
fr->sc_power,
fr->sc_sigma6_def,
fr->sc_sigma6_min,
TRUE,
&outeriter,
&inneriter);
}
else
{
/* Not perturbed - call kernel 330 */
nb_kernel330
( &i1,
&i0,
j_index,
&i1,
&shift_f,
fr->shift_vec[0],
fshift[0],
&gid,
x14[0],
f14[0],
chargeA,
&eps,
&krf,
&crf,
egcoul,
typeA,
&ntype,
nbfp,
egnb,
&tabscale,
tab,
NULL,
NULL,
NULL,
NULL,
&nthreads,
&count,
(void *)&mtx,
&outeriter,
&inneriter,
NULL);
}
/* Add the forces */
rvec_inc(f[ai],f14[0]);
rvec_dec(f[aj],f14[0]);
if (pf_global->bInitialized)
pf_atom_add_bonded(pf_global, ai, aj, PF_INTER_NB14, f14[0]);
if (g)
{
/* Correct the shift forces using the graph */
ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
shift_vir = IVEC2IS(dt);
rvec_inc(fshift[shift_vir],f14[0]);
rvec_dec(fshift[CENTRAL],f14[0]);
}
/* flops: eNR_KERNEL_OUTER + eNR_KERNEL330 + 12 */
}
}
return 0.0;
}
void do_nonbonded(t_commrec *cr,t_forcerec *fr,
rvec x[],rvec f[],t_mdatoms *mdatoms,t_blocka *excl,
real egnb[],real egcoul[],real egpol[],rvec box_size,
t_nrnb *nrnb,real lambda,real *dvdlambda,
int nls,int eNL,int flags)
{
gmx_bool bLR,bDoForces,bForeignLambda;
t_nblist * nlist;
real * fshift;
int n,n0,n1,i,i0,i1,nrnb_ind,sz;
t_nblists *nblists;
gmx_bool bWater;
FILE * fp;
int fac=0;
int nthreads = 1;
int tabletype;
int outeriter,inneriter;
real * tabledata = NULL;
gmx_gbdata_t gbdata;
nb_kernel_t *kernelptr=NULL;
nb_adress_kernel_t *adresskernelptr=NULL;
gmx_bool bCG; /* for AdresS */
int k;/* for AdresS */
bLR = (flags & GMX_DONB_LR);
bDoForces = (flags & GMX_DONB_FORCES);
bForeignLambda = (flags & GMX_DONB_FOREIGNLAMBDA);
bCG = FALSE; /* for AdresS */
gbdata.gb_epsilon_solvent = fr->gb_epsilon_solvent;
gbdata.epsilon_r = fr->epsilon_r;
gbdata.gpol = egpol;
if (!fr->adress_type==eAdressOff && !bDoForces){
gmx_fatal(FARGS,"No force kernels not implemeted for adress");
}
if(fr->bAllvsAll)
{
if(fr->bGB)
{
#if (defined GMX_SSE2 || defined GMX_X86_64_SSE || defined GMX_X86_64_SSE2 || defined GMX_IA32_SSE || defined GMX_IA32_SSE2)
# ifdef GMX_DOUBLE
if(fr->UseOptimizedKernels)
{
nb_kernel_allvsallgb_sse2_double(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,egpol,
&outeriter,&inneriter,&fr->AllvsAll_work);
}
else
{
nb_kernel_allvsallgb(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,egpol,
&outeriter,&inneriter,&fr->AllvsAll_work);
}
# else /* not double */
if(fr->UseOptimizedKernels)
{
nb_kernel_allvsallgb_sse2_single(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,egpol,
&outeriter,&inneriter,&fr->AllvsAll_work);
}
else
{
nb_kernel_allvsallgb(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,egpol,
&outeriter,&inneriter,&fr->AllvsAll_work);
}
# endif /* double/single alt. */
#else /* no SSE support compiled in */
nb_kernel_allvsallgb(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,egpol,
&outeriter,&inneriter,&fr->AllvsAll_work);
#endif
inc_nrnb(nrnb,eNR_NBKERNEL_ALLVSALLGB,inneriter);
}
else
{
#if (defined GMX_SSE2 || defined GMX_X86_64_SSE || defined GMX_X86_64_SSE2 || defined GMX_IA32_SSE || defined GMX_IA32_SSE2)
# ifdef GMX_DOUBLE
if(fr->UseOptimizedKernels)
{
nb_kernel_allvsall_sse2_double(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,
&outeriter,&inneriter,&fr->AllvsAll_work);
}
else
{
nb_kernel_allvsall(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,
&outeriter,&inneriter,&fr->AllvsAll_work);
}
# else /* not double */
if(fr->UseOptimizedKernels)
{
nb_kernel_allvsall_sse2_single(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,
&outeriter,&inneriter,&fr->AllvsAll_work);
}
else
{
nb_kernel_allvsall(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,
&outeriter,&inneriter,&fr->AllvsAll_work);
}
# endif /* double/single check */
#else /* No SSE2 support compiled in */
nb_kernel_allvsall(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,
&outeriter,&inneriter,&fr->AllvsAll_work);
#endif
inc_nrnb(nrnb,eNR_NBKERNEL_ALLVSALL,inneriter);
}
inc_nrnb(nrnb,eNR_NBKERNEL_OUTER,outeriter);
return;
}
if (eNL >= 0)
{
i0 = eNL;
i1 = i0+1;
}
else
{
i0 = 0;
i1 = eNL_NR;
}
if (nls >= 0)
{
n0 = nls;
n1 = nls+1;
}
else
{
n0 = 0;
n1 = fr->nnblists;
}
if(nb_kernel_list == NULL)
{
gmx_fatal(FARGS,"gmx_setup_kernels has not been called");
}
fshift = fr->fshift[0];
for(n=n0; (n<n1); n++)
{
nblists = &fr->nblists[n];
for(i=i0; (i<i1); i++)
{
outeriter = inneriter = 0;
if (bLR)
{
nlist = &(nblists->nlist_lr[i]);
}
else
{
nlist = &(nblists->nlist_sr[i]);
}
if (nlist->nri > 0)
{
nrnb_ind = nlist->il_code;
if(nrnb_ind==eNR_NBKERNEL_FREE_ENERGY)
{
/* generic free energy, use combined table */
tabledata = nblists->tab.tab;
}
else
{
if (bForeignLambda)
{
/* We don't need the non-perturbed interactions */
continue;
}
tabletype = nb_kernel_table[nrnb_ind];
/* normal kernels, not free energy */
if (!bDoForces)
{
nrnb_ind += eNR_NBKERNEL_NR/2;
}
if(tabletype == TABLE_COMBINED)
{
tabledata = nblists->tab.tab;
}
else if(tabletype == TABLE_COUL)
{
tabledata = nblists->coultab;
}
else if(tabletype == TABLE_VDW)
{
tabledata = nblists->vdwtab;
}
else
{
tabledata = NULL;
}
}
nlist->count = 0;
if(nlist->free_energy)
{
if(nlist->ivdw==2)
{
gmx_fatal(FARGS,"Cannot do free energy Buckingham interactions.");
}
gmx_nb_free_energy_kernel(nlist->icoul,
nlist->ivdw,
nlist->nri,
nlist->iinr,
nlist->jindex,
nlist->jjnr,
nlist->shift,
fr->shift_vec[0],
fshift,
nlist->gid,
x[0],
f[0],
mdatoms->chargeA,
mdatoms->chargeB,
fr->epsfac,
fr->k_rf,
fr->c_rf,
fr->ewaldcoeff,
egcoul,
mdatoms->typeA,
mdatoms->typeB,
fr->ntype,
fr->nbfp,
egnb,
nblists->tab.scale,
tabledata,
lambda,
dvdlambda,
fr->sc_alpha,
fr->sc_power,
fr->sc_sigma6_def,
fr->sc_sigma6_min,
bDoForces,
&outeriter,
&inneriter);
}
else if (nlist->enlist == enlistCG_CG)
{
if (fr->adress_type==eAdressOff){
/* Call the charge group based inner loop */
gmx_nb_generic_cg_kernel(nlist,
fr,
mdatoms,
x[0],
f[0],
fshift,
egcoul,
egnb,
nblists->tab.scale,
tabledata,
&outeriter,
&inneriter);
}
else
{
/*gmx_nb_generic_adress_kernel(nlist,
fr,
mdatoms,
x[0],
f[0],
fshift,
egcoul,
egnb,
nblists->tab.scale,
tabledata,
&outeriter,
&inneriter);*/
gmx_fatal(FARGS,"Death & horror! Adress cgcg kernel not implemented anymore.\n");
}
}
else
{
/* AdresS*/
/* for adress we need to determine for each energy group wether it is explicit or coarse-grained */
if (!fr->adress_type == eAdressOff) {
bCG = FALSE;
if ( !fr->adress_group_explicit[ mdatoms->cENER[nlist->iinr[0]] ] ){
bCG=TRUE;
}
/* If this processor has only explicit atoms (w=1)
skip the coarse grained force calculation. Same for
only coarsegrained atoms and explicit interactions.
Last condition is to make sure that generic kernel is not
skipped*/
if (mdatoms->pureex && bCG && nb_kernel_list[nrnb_ind] != NULL) continue;
if (mdatoms->purecg && !bCG && nb_kernel_list[nrnb_ind] != NULL) continue;
}
if (fr->adress_type == eAdressOff ||
mdatoms->pureex ||
mdatoms->purecg){
/* if we only have to calculate pure cg/ex interactions
we can use the faster standard gromacs kernels*/
kernelptr = nb_kernel_list[nrnb_ind];
}else{
/* This processor has hybrid interactions which means
* we have to
* use our own kernels. We have two kernel types: one that
* calculates the forces with the explicit prefactor w1*w2
* and one for coarse-grained with (1-w1*w2)
* explicit kernels are the second part of the kernel
* list */
if (!bCG) nrnb_ind += eNR_NBKERNEL_NR/2;
adresskernelptr = nb_kernel_list_adress[nrnb_ind];
}
if (kernelptr == NULL && adresskernelptr == NULL)
{
/* Call a generic nonbonded kernel */
/* If you want to hack/test your own interactions,
* do it in this routine and make sure it is called
* by setting the environment variable GMX_NB_GENERIC.
*/
if (fr->adress_type==eAdressOff){
gmx_nb_generic_kernel(nlist,
fr,
mdatoms,
x[0],
f[0],
fshift,
egcoul,
egnb,
nblists->tab.scale,
tabledata,
&outeriter,
&inneriter);
}else /* do generic AdResS kernels (slow)*/
{
gmx_nb_generic_adress_kernel(nlist,
fr,
mdatoms,
x[0],
f[0],
fshift,
egcoul,
egnb,
nblists->tab.scale,
tabledata,
&outeriter,
&inneriter,
bCG);
}
}
else
{
/* Call nonbonded kernel from function pointer */
if (kernelptr!=NULL){
(*kernelptr)( &(nlist->nri),
nlist->iinr,
nlist->jindex,
nlist->jjnr,
nlist->shift,
fr->shift_vec[0],
fshift,
nlist->gid,
x[0],
f[0],
mdatoms->chargeA,
&(fr->epsfac),
&(fr->k_rf),
&(fr->c_rf),
egcoul,
mdatoms->typeA,
&(fr->ntype),
fr->nbfp,
egnb,
&(nblists->tab.scale),
tabledata,
fr->invsqrta,
fr->dvda,
&(fr->gbtabscale),
fr->gbtab.tab,
&nthreads,
&(nlist->count),
nlist->mtx,
&outeriter,
&inneriter,
(real *)&gbdata);
}else if (adresskernelptr != NULL)
{ /* Adress kernels */
(*adresskernelptr)( &(nlist->nri),
nlist->iinr,
nlist->jindex,
nlist->jjnr,
nlist->shift,
fr->shift_vec[0],
fshift,
nlist->gid,
x[0],
f[0],
mdatoms->chargeA,
&(fr->epsfac),
&(fr->k_rf),
&(fr->c_rf),
egcoul,
mdatoms->typeA,
&(fr->ntype),
fr->nbfp,
egnb,
&(nblists->tab.scale),
tabledata,
fr->invsqrta,
fr->dvda,
&(fr->gbtabscale),
fr->gbtab.tab,
&nthreads,
&(nlist->count),
nlist->mtx,
&outeriter,
&inneriter,
fr->adress_ex_forcecap,
mdatoms->wf);
}
}
}
/* Update flop accounting */
/* Outer loop in kernel */
switch (nlist->enlist) {
case enlistATOM_ATOM: fac = 1; break;
case enlistSPC_ATOM: fac = 3; break;
case enlistSPC_SPC: fac = 9; break;
case enlistTIP4P_ATOM: fac = 4; break;
case enlistTIP4P_TIP4P: fac = 16; break;
case enlistCG_CG: fac = 1; break;
}
inc_nrnb(nrnb,eNR_NBKERNEL_OUTER,fac*outeriter);
/* inner loop in kernel */
inc_nrnb(nrnb,nrnb_ind,inneriter);
}
}
}
}
void do_nonbonded(t_commrec *cr,t_forcerec *fr,
rvec x[],rvec f[],t_mdatoms *mdatoms,t_blocka *excl,
real egnb[],real egcoul[],real egpol[],rvec box_size,
t_nrnb *nrnb,real lambda,real *dvdlambda,
int nls,int eNL,int flags)
{
gmx_bool bLR,bDoForces,bForeignLambda;
t_nblist * nlist;
real * fshift;
int n,n0,n1,i,i0,i1,nrnb_ind,sz;
t_nblists *nblists;
gmx_bool bWater;
nb_kernel_t * kernelptr;
pf_nb_kernel_t *pf_kernelptr;
FILE * fp;
int fac=0;
int nthreads = 1;
int tabletype;
int outeriter,inneriter;
real * tabledata = NULL;
gmx_gbdata_t gbdata;
bLR = (flags & GMX_DONB_LR);
bDoForces = (flags & GMX_DONB_FORCES);
bForeignLambda = (flags & GMX_DONB_FOREIGNLAMBDA);
gbdata.gb_epsilon_solvent = fr->gb_epsilon_solvent;
gbdata.epsilon_r = fr->epsilon_r;
gbdata.gpol = egpol;
if(fr->bAllvsAll)
{
if(fr->bGB)
{
#if (defined GMX_SSE2 || defined GMX_X86_64_SSE || defined GMX_X86_64_SSE2 || defined GMX_IA32_SSE || defined GMX_IA32_SSE2)
# ifdef GMX_DOUBLE
if(fr->UseOptimizedKernels)
{
nb_kernel_allvsallgb_sse2_double(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,egpol,
&outeriter,&inneriter,&fr->AllvsAll_work);
}
else
{
nb_kernel_allvsallgb(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,egpol,
&outeriter,&inneriter,&fr->AllvsAll_work);
}
# else /* not double */
if(fr->UseOptimizedKernels)
{
nb_kernel_allvsallgb_sse2_single(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,egpol,
&outeriter,&inneriter,&fr->AllvsAll_work);
}
else
{
nb_kernel_allvsallgb(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,egpol,
&outeriter,&inneriter,&fr->AllvsAll_work);
}
# endif /* double/single alt. */
#else /* no SSE support compiled in */
nb_kernel_allvsallgb(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,egpol,
&outeriter,&inneriter,&fr->AllvsAll_work);
#endif
inc_nrnb(nrnb,eNR_NBKERNEL_ALLVSALLGB,inneriter);
}
else
{
#if (defined GMX_SSE2 || defined GMX_X86_64_SSE || defined GMX_X86_64_SSE2 || defined GMX_IA32_SSE || defined GMX_IA32_SSE2)
# ifdef GMX_DOUBLE
if(fr->UseOptimizedKernels)
{
nb_kernel_allvsall_sse2_double(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,
&outeriter,&inneriter,&fr->AllvsAll_work);
}
else
{
nb_kernel_allvsall(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,
&outeriter,&inneriter,&fr->AllvsAll_work);
}
# else /* not double */
if(fr->UseOptimizedKernels)
{
nb_kernel_allvsall_sse2_single(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,
&outeriter,&inneriter,&fr->AllvsAll_work);
}
else
{
nb_kernel_allvsall(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,
&outeriter,&inneriter,&fr->AllvsAll_work);
}
# endif /* double/single check */
#else /* No SSE2 support compiled in */
nb_kernel_allvsall(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,
&outeriter,&inneriter,&fr->AllvsAll_work);
#endif
inc_nrnb(nrnb,eNR_NBKERNEL_ALLVSALL,inneriter);
}
inc_nrnb(nrnb,eNR_NBKERNEL_OUTER,outeriter);
return;
}
if (eNL >= 0)
{
i0 = eNL;
i1 = i0+1;
}
else
{
i0 = 0;
i1 = eNL_NR;
}
if (nls >= 0)
{
n0 = nls;
n1 = nls+1;
}
else
{
n0 = 0;
n1 = fr->nnblists;
}
if(nb_kernel_list == NULL)
{
gmx_fatal(FARGS,"gmx_setup_kernels has not been called");
}
fshift = fr->fshift[0];
for(n=n0; (n<n1); n++)
{
nblists = &fr->nblists[n];
for(i=i0; (i<i1); i++)
{
outeriter = inneriter = 0;
if (bLR)
{
nlist = &(nblists->nlist_lr[i]);
}
else
{
nlist = &(nblists->nlist_sr[i]);
}
if (nlist->nri > 0)
{
nrnb_ind = nlist->il_code;
if(nrnb_ind==eNR_NBKERNEL_FREE_ENERGY)
{
/* generic free energy, use combined table */
tabledata = nblists->tab.tab;
}
else
{
if (bForeignLambda)
{
/* We don't need the non-perturbed interactions */
continue;
}
tabletype = nb_kernel_table[nrnb_ind];
/* normal kernels, not free energy */
if (!bDoForces)
{
nrnb_ind += eNR_NBKERNEL_NR/2;
}
if(tabletype == TABLE_COMBINED)
{
tabledata = nblists->tab.tab;
}
else if(tabletype == TABLE_COUL)
{
tabledata = nblists->coultab;
}
else if(tabletype == TABLE_VDW)
{
tabledata = nblists->vdwtab;
}
else
{
tabledata = NULL;
}
}
nlist->count = 0;
if(nlist->free_energy)
{
if(nlist->ivdw==2)
{
gmx_fatal(FARGS,"Cannot do free energy Buckingham interactions.");
}
gmx_nb_free_energy_kernel(nlist->icoul,
nlist->ivdw,
nlist->nri,
nlist->iinr,
nlist->jindex,
nlist->jjnr,
nlist->shift,
fr->shift_vec[0],
fshift,
nlist->gid,
x[0],
f[0],
mdatoms->chargeA,
mdatoms->chargeB,
fr->epsfac,
fr->k_rf,
fr->c_rf,
fr->ewaldcoeff,
egcoul,
mdatoms->typeA,
mdatoms->typeB,
fr->ntype,
fr->nbfp,
egnb,
nblists->tab.scale,
tabledata,
lambda,
dvdlambda,
fr->sc_alpha,
fr->sc_power,
fr->sc_sigma6_def,
fr->sc_sigma6_min,
bDoForces,
&outeriter,
&inneriter);
}
else if (nlist->enlist == enlistCG_CG)
{
/* Call the charge group based inner loop */
gmx_nb_generic_cg_kernel(nlist,
fr,
mdatoms,
x[0],
f[0],
fshift,
egcoul,
egnb,
nblists->tab.scale,
tabledata,
&outeriter,
&inneriter);
}
else
{
/* Not free energy */
/* Pairwise forces between solute and solvent don't bring much information, as the molecules of solvent
* move around. For this reason, only pairwise forces between solute atoms are calculated.
* This allows the normal (non-pairwise force) kernels to be used for solute-solvent and solvent-solvent
* interactions; the main reason is performance, as the normal kernels are not slowed down by the
* checking whether atom is involved in an interesting interaction.
*/
if ((fr->pf_global) && (nlist->enlist == enlistATOM_ATOM))
{
pf_kernelptr = pf_nb_kernel_list[nrnb_ind];
(*pf_kernelptr)( &(nlist->nri),
nlist->iinr,
nlist->jindex,
nlist->jjnr,
nlist->shift,
fr->shift_vec[0],
fshift,
nlist->gid,
x[0],
f[0],
mdatoms->chargeA,
&(fr->epsfac),
&(fr->k_rf),
&(fr->c_rf),
egcoul,
mdatoms->typeA,
&(fr->ntype),
fr->nbfp,
egnb,
&(nblists->tab.scale),
tabledata,
fr->invsqrta,
fr->dvda,
&(fr->gbtabscale),
fr->gbtab.tab,
&nthreads,
&(nlist->count),
nlist->mtx,
&outeriter,
&inneriter,
(real *)&gbdata,
fr->pf_global);
}
else {
/* non pairwise force kernel */
kernelptr = nb_kernel_list[nrnb_ind];
if (kernelptr == NULL)
{
/* Call a generic nonbonded kernel */
/* If you want to hack/test your own interactions,
* do it in this routine and make sure it is called
* by setting the environment variable GMX_NB_GENERIC.
*/
gmx_nb_generic_kernel(nlist,
fr,
mdatoms,
x[0],
f[0],
fshift,
egcoul,
egnb,
nblists->tab.scale,
tabledata,
&outeriter,
&inneriter);
}
else
{
/* Call nonbonded kernel from function pointer */
(*kernelptr)( &(nlist->nri),
nlist->iinr,
nlist->jindex,
nlist->jjnr,
nlist->shift,
fr->shift_vec[0],
fshift,
nlist->gid,
x[0],
f[0],
mdatoms->chargeA,
&(fr->epsfac),
&(fr->k_rf),
&(fr->c_rf),
egcoul,
mdatoms->typeA,
&(fr->ntype),
fr->nbfp,
egnb,
&(nblists->tab.scale),
tabledata,
fr->invsqrta,
fr->dvda,
&(fr->gbtabscale),
fr->gbtab.tab,
&nthreads,
&(nlist->count),
nlist->mtx,
&outeriter,
&inneriter,
(real *)&gbdata);
}
/* end of non pairwise force kernel */
}
}
/* Update flop accounting */
/* Outer loop in kernel */
switch (nlist->enlist) {
case enlistATOM_ATOM: fac = 1; break;
case enlistSPC_ATOM: fac = 3; break;
case enlistSPC_SPC: fac = 9; break;
case enlistTIP4P_ATOM: fac = 4; break;
case enlistTIP4P_TIP4P: fac = 16; break;
case enlistCG_CG: fac = 1; break;
}
inc_nrnb(nrnb,eNR_NBKERNEL_OUTER,fac*outeriter);
/* inner loop in kernel */
inc_nrnb(nrnb,nrnb_ind,inneriter);
}
}
}
}
void do_nonbonded(t_commrec *cr,t_forcerec *fr,
rvec x[],rvec f[],t_mdatoms *mdatoms,
real egnb[],real egcoul[],real egpol[],rvec box_size,
t_nrnb *nrnb,real lambda,real *dvdlambda,
int nls,int eNL,int flags,gmx_mc_move *mc_move)
{
bool bLR,bDoForces,bForeignLambda;
t_nblist * nlist,*nlist2=NULL;
t_nblists * nlists;
real * fshift;
int n,n0,n1,i,i0,i1,nrnb_ind,sz;
t_nblists *nblists;
bool bWater;
nb_kernel_t * kernelptr;
FILE * fp;
int fac=0;
int nthreads = 1;
int tabletype;
int outeriter,inneriter;
int *jindex,nj1,nri,*iinr,*jjnr;
real * tabledata = NULL;
real * enerd = NULL;
gmx_gbdata_t gbdata;
bLR = (flags & GMX_DONB_LR);
bDoForces = (flags & GMX_DONB_FORCES);
bForeignLambda = (flags & GMX_DONB_FOREIGNLAMBDA);
gbdata.gb_epsilon_solvent = fr->gb_epsilon_solvent;
gbdata.gpol = egpol;
if (eNL >= 0)
{
i0 = eNL;
i1 = i0+1;
}
else
{
i0 = 0;
i1 = eNL_NR;
}
if (nls >= 0)
{
n0 = nls;
n1 = nls+1;
}
else
{
n0 = 0;
n1 = fr->nnblists;
}
if(nb_kernel_list == NULL)
{
gmx_fatal(FARGS,"gmx_setup_kernels has not been called");
}
fshift = fr->fshift[0];
for(n=n0; (n<n1); n++)
{
nblists = &fr->nblists[n];
for(i=i0; (i<i1); i++)
{
outeriter = inneriter = 0;
if (bLR)
{
nlist = &(nblists->nlist_lr[i]);
}
else
{
nlist = &(nblists->nlist_sr[i]);
}
if (nlist->nri > 0)
{
nrnb_ind = nlist->il_code;
if(nrnb_ind==eNR_NBKERNEL_FREE_ENERGY)
{
/* generic free energy, use combined table */
tabledata = nblists->tab.tab;
}
else
{
if (bForeignLambda)
{
/* We don't need the non-perturbed interactions */
continue;
}
tabletype = nb_kernel_table[nrnb_ind];
/* normal kernels, not free energy */
if (!bDoForces)
{
nrnb_ind += eNR_NBKERNEL_NR/2;
}
if(tabletype == TABLE_COMBINED)
{
tabledata = nblists->tab.tab;
}
else if(tabletype == TABLE_COUL)
{
tabledata = nblists->coultab;
}
else if(tabletype == TABLE_VDW)
{
tabledata = nblists->vdwtab;
}
else
{
tabledata = NULL;
}
}
nlist->count = 0;
if(nlist->free_energy)
{
if(nlist->ivdw==2)
{
gmx_fatal(FARGS,"Cannot do free energy Buckingham interactions.");
}
gmx_nb_free_energy_kernel(nlist->icoul,
nlist->ivdw,
nlist->nri,
nlist->iinr,
nlist->jindex,
nlist->jjnr,
nlist->shift,
fr->shift_vec[0],
fshift,
nlist->gid,
x[0],
f[0],
mdatoms->chargeA,
mdatoms->chargeB,
fr->epsfac,
fr->k_rf,
fr->c_rf,
fr->ewaldcoeff,
egcoul,
mdatoms->typeA,
mdatoms->typeB,
fr->ntype,
fr->nbfp,
egnb,
nblists->tab.scale,
tabledata,
lambda,
dvdlambda,
fr->sc_alpha,
fr->sc_power,
fr->sc_sigma6,
bDoForces,
&outeriter,
&inneriter);
}
else if (nlist->enlist == enlistCG_CG)
{
/* Call the charge group based inner loop */
gmx_nb_generic_cg_kernel(nlist,
fr,
mdatoms,
x[0],
f[0],
fshift,
egcoul,
egnb,
nblists->tab.scale,
tabledata,
&outeriter,
&inneriter);
}
else
{
/* Not free energy */
kernelptr = nb_kernel_list[nrnb_ind];
if (kernelptr == NULL)
{
/* Call a generic nonbonded kernel */
/* If you want to hack/test your own interactions,
* do it in this routine and make sure it is called
* by setting the environment variable GMX_NB_GENERIC.
*/
gmx_nb_generic_kernel(nlist,
fr,
mdatoms,
x[0],
f[0],
fshift,
egcoul,
egnb,
nblists->tab.scale,
tabledata,
&outeriter,
&inneriter);
}
else
{
/* Call nonbonded kernel from function pointer */
/*if(mc_move)
{
if(mc_move->bNS[mc_move->cgs])
{
do_mclist(mc_move,nlist,fr->nblists_mc,n,i,bLR);
}
else if (1 == 2)
{
nlists = &fr->nblists_mc[mc_move->cgs][n];
if(bLR)
{
nlist2 = &nlists->nlist_lr[i];
}
else
{
nlist2 = &nlists->nlist_sr[i];
}
}
}*/
//mc_move=NULL;
//printf("nrnb %d %d %d\n",nrnb_ind,mc_move->start,mc_move->end);
(*kernelptr)( mc_move && nlist2 ? &(nlist2->nri) : &(nlist->nri),
mc_move && nlist2 ? nlist2->iinr : nlist->iinr,
mc_move && nlist2 ? nlist2->jindex : nlist->jindex,
mc_move && nlist2 ? nlist2->jjnr : nlist->jjnr,
mc_move && nlist2 ? nlist2->shift : nlist->shift,
fr->shift_vec[0],
fshift,
mc_move && nlist2 ? nlist2->gid : nlist->gid,
x[0],
f[0],
mdatoms->chargeA,
&(fr->epsfac),
&(fr->k_rf),
&(fr->c_rf),
egcoul,
mdatoms->typeA,
&(fr->ntype),
fr->nbfp,
egnb,
&(nblists->tab.scale),
tabledata,
mc_move ? mc_move->enerd[F_COUL_SR] : NULL,
mc_move ? mc_move->enerd[F_LJ] : NULL,
(mc_move) ? mc_move->enerd_prev[F_COUL_SR] : NULL,
(mc_move) ? mc_move->enerd_prev[F_LJ] : NULL,
(mc_move) ? mc_move->cgindex : NULL,
(mc_move) ? &mc_move->end : NULL,
(mc_move) ? &mc_move->homenr : NULL,
(mc_move) ? mc_move->sum_index : NULL,
fr->invsqrta,
fr->dvda,
&(fr->gbtabscale),
fr->gbtab.tab,
&nthreads,
&(nlist->count),
nlist->mtx,
&outeriter,
&inneriter,
(real *)&gbdata);
}
}
/* Update flop accounting */
/* Outer loop in kernel */
switch (nlist->enlist) {
case enlistATOM_ATOM: fac = 1; break;
case enlistSPC_ATOM: fac = 3; break;
case enlistSPC_SPC: fac = 9; break;
case enlistTIP4P_ATOM: fac = 4; break;
case enlistTIP4P_TIP4P: fac = 16; break;
case enlistCG_CG: fac = 1; break;
}
inc_nrnb(nrnb,eNR_NBKERNEL_OUTER,fac*outeriter);
/* inner loop in kernel */
inc_nrnb(nrnb,nrnb_ind,inneriter);
}
}
}
}
