static void
nb_listed_warning_rlimit(const rvec *x, int ai, int aj, int * global_atom_index, real r, real rlimit)
{
gmx_warning("Listed nonbonded interaction between particles %d and %d\n"
"at distance %.3f which is larger than the table limit %.3f nm.\n\n"
"This is likely either a 1,4 interaction, or a listed interaction inside\n"
"a smaller molecule you are decoupling during a free energy calculation.\n"
"Since interactions at distances beyond the table cannot be computed,\n"
"they are skipped until they are inside the table limit again. You will\n"
"only see this message once, even if it occurs for several interactions.\n\n"
"IMPORTANT: This should not happen in a stable simulation, so there is\n"
"probably something wrong with your system. Only change the table-extension\n"
"distance in the mdp file if you are really sure that is the reason.\n",
glatnr(global_atom_index, ai), glatnr(global_atom_index, aj), r, rlimit);
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), r);
}
}
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;
}