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;
}
real orires(int nfa,const t_iatom forceatoms[],const t_iparams ip[],
const rvec x[],rvec f[],rvec fshift[],
const t_pbc *pbc,const t_graph *g,
real lambda,real *dvdlambda,
const t_mdatoms *md,t_fcdata *fcd,
int *global_atom_index,int ftype,gmx_mc_move *mc_move)
{
atom_id ai,aj;
int fa,d,i,type,ex,power,ki=CENTRAL;
ivec dt;
real r2,invr,invr2,fc,smooth_fc,dev,devins,pfac;
rvec r,Sr,fij;
real vtot;
const t_oriresdata *od;
bool bTAV;
vtot = 0;
od = &(fcd->orires);
if (od->fc != 0)
{
bTAV = (od->edt != 0);
smooth_fc = od->fc;
if (bTAV)
{
/* Smoothly switch on the restraining when time averaging is used */
smooth_fc *= (1.0 - od->exp_min_t_tau);
}
d = 0;
for(fa=0; fa<nfa; fa+=3)
{
type = forceatoms[fa];
ai = forceatoms[fa+1];
aj = forceatoms[fa+2];
if (pbc)
{
ki = pbc_dx_aiuc(pbc,x[ai],x[aj],r);
}
else
{
rvec_sub(x[ai],x[aj],r);
}
r2 = norm2(r);
invr = invsqrt(r2);
invr2 = invr*invr;
ex = ip[type].orires.ex;
power = ip[type].orires.power;
fc = smooth_fc*ip[type].orires.kfac;
dev = od->otav[d] - ip[type].orires.obs;
/* NOTE:
* there is no real potential when time averaging is applied
*/
vtot += 0.5*fc*sqr(dev);
if (bTAV)
{
/* Calculate the force as the sqrt of tav times instantaneous */
devins = od->oins[d] - ip[type].orires.obs;
if (dev*devins <= 0)
{
dev = 0;
}
else
{
dev = sqrt(dev*devins);
if (devins < 0)
{
dev = -dev;
}
}
}
pfac = fc*ip[type].orires.c*invr2;
for(i=0; i<power; i++)
{
pfac *= invr;
}
mvmul(od->S[ex],r,Sr);
for(i=0; i<DIM; i++)
{
fij[i] =
-pfac*dev*(4*Sr[i] - 2*(2+power)*invr2*iprod(Sr,r)*r[i]);
}
if (g)
{
ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
ki=IVEC2IS(dt);
}
for(i=0; i<DIM; i++)
{
f[ai][i] += fij[i];
f[aj][i] -= fij[i];
fshift[ki][i] += fij[i];
fshift[CENTRAL][i] -= fij[i];
}
d++;
}
}
return vtot;
/* Approx. 80*nfa/3 flops */
}
real ta_disres(int nfa,const t_iatom forceatoms[],const t_iparams ip[],
const rvec x[],rvec f[],rvec fshift[],
const t_pbc *pbc,const t_graph *g,
real lambda,real *dvdlambda,
const t_mdatoms *md,t_fcdata *fcd,
int *global_atom_index)
{
const real sixth=1.0/6.0;
const real seven_three=7.0/3.0;
atom_id ai,aj;
int fa,res,npair,p,pair,ki=CENTRAL,m;
int type;
rvec dx;
real weight_rt_1;
real smooth_fc,Rt,Rtav,rt2,*Rtl_6,*Rt_6,*Rtav_6;
real k0,f_scal=0,fmax_scal,fk_scal,fij;
real tav_viol,instant_viol,mixed_viol,violtot,vtot;
real tav_viol_Rtav7,instant_viol_Rtav7;
real up1,up2,low;
gmx_bool bConservative,bMixed,bViolation;
ivec it,jt,dt;
t_disresdata *dd;
int dr_weighting;
gmx_bool dr_bMixed;
dd = &(fcd->disres);
dr_weighting = dd->dr_weighting;
dr_bMixed = dd->dr_bMixed;
Rtl_6 = dd->Rtl_6;
Rt_6 = dd->Rt_6;
Rtav_6 = dd->Rtav_6;
tav_viol=instant_viol=mixed_viol=tav_viol_Rtav7=instant_viol_Rtav7=0;
smooth_fc = dd->dr_fc;
if (dd->dr_tau != 0)
{
/* scaling factor to smoothly turn on the restraint forces *
* when using time averaging */
smooth_fc *= (1.0 - dd->exp_min_t_tau);
}
violtot = 0;
vtot = 0;
/* 'loop' over all atom pairs (pair_nr=fa/3) involved in restraints, *
* the total number of atoms pairs is nfa/3 */
res = 0;
fa = 0;
while (fa < nfa)
{
type = forceatoms[fa];
/* Take action depending on restraint, calculate scalar force */
npair = ip[type].disres.npair;
up1 = ip[type].disres.up1;
up2 = ip[type].disres.up2;
low = ip[type].disres.low;
k0 = smooth_fc*ip[type].disres.kfac;
/* save some flops when there is only one pair */
if (ip[type].disres.type != 2)
{
bConservative = (dr_weighting == edrwConservative) && (npair > 1);
bMixed = dr_bMixed;
Rt = pow(Rt_6[res],-sixth);
Rtav = pow(Rtav_6[res],-sixth);
}
else
{
/* When rtype=2 use instantaneous not ensemble avereged distance */
bConservative = (npair > 1);
bMixed = FALSE;
Rt = pow(Rtl_6[res],-sixth);
Rtav = Rt;
}
if (Rtav > up1)
{
bViolation = TRUE;
tav_viol = Rtav - up1;
}
else if (Rtav < low)
{
bViolation = TRUE;
tav_viol = Rtav - low;
}
else
{
bViolation = FALSE;
}
if (bViolation)
{
/* NOTE:
* there is no real potential when time averaging is applied
*/
vtot += 0.5*k0*sqr(tav_viol);
if (1/vtot == 0)
{
printf("vtot is inf: %f\n",vtot);
}
if (!bMixed)
{
f_scal = -k0*tav_viol;
violtot += fabs(tav_viol);
}
else
{
if (Rt > up1)
{
if (tav_viol > 0)
{
instant_viol = Rt - up1;
}
else
{
bViolation = FALSE;
}
}
else if (Rt < low)
{
if (tav_viol < 0)
{
instant_viol = Rt - low;
}
else
{
bViolation = FALSE;
}
}
else
{
bViolation = FALSE;
}
if (bViolation)
{
mixed_viol = sqrt(tav_viol*instant_viol);
f_scal = -k0*mixed_viol;
violtot += mixed_viol;
}
}
}
if (bViolation)
{
fmax_scal = -k0*(up2-up1);
/* Correct the force for the number of restraints */
if (bConservative)
{
f_scal = max(f_scal,fmax_scal);
if (!bMixed)
{
f_scal *= Rtav/Rtav_6[res];
}
else
{
f_scal /= 2*mixed_viol;
tav_viol_Rtav7 = tav_viol*Rtav/Rtav_6[res];
instant_viol_Rtav7 = instant_viol*Rt/Rt_6[res];
}
}
else
{
f_scal /= (real)npair;
f_scal = max(f_scal,fmax_scal);
}
/* Exert the force ... */
/* Loop over the atom pairs of 'this' restraint */
for(p=0; p<npair; p++)
{
pair = fa/3;
ai = forceatoms[fa+1];
aj = forceatoms[fa+2];
if (pbc)
{
ki = pbc_dx_aiuc(pbc,x[ai],x[aj],dx);
}
else
{
rvec_sub(x[ai],x[aj],dx);
}
rt2 = iprod(dx,dx);
weight_rt_1 = gmx_invsqrt(rt2);
if (bConservative)
{
if (!dr_bMixed)
{
weight_rt_1 *= pow(dd->rm3tav[pair],seven_three);
}
else
{
weight_rt_1 *= tav_viol_Rtav7*pow(dd->rm3tav[pair],seven_three)+
instant_viol_Rtav7*pow(dd->rt[pair],-7);
}
}
fk_scal = f_scal*weight_rt_1;
if (g)
{
ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
ki=IVEC2IS(dt);
}
for(m=0; m<DIM; m++)
{
fij = fk_scal*dx[m];
f[ai][m] += fij;
f[aj][m] -= fij;
fshift[ki][m] += fij;
fshift[CENTRAL][m] -= fij;
}
fa += 3;
}
}
else
{
/* No violation so force and potential contributions */
fa += 3*npair;
}
res++;
}
dd->sumviol = violtot;
/* Return energy */
return vtot;
}
real RF_excl_correction(FILE *log,
const t_forcerec *fr,t_graph *g,
const t_mdatoms *mdatoms,const t_blocka *excl,
rvec x[],rvec f[],rvec *fshift,const t_pbc *pbc,
real lambda,real *dvdlambda)
{
/* Calculate the reaction-field energy correction for this node:
* epsfac q_i q_j (k_rf r_ij^2 - c_rf)
* and force correction for all excluded pairs, including self pairs.
*/
int top,i,j,j1,j2,k,ki;
double q2sumA,q2sumB,ener;
const real *chargeA,*chargeB;
real ek,ec,L1,qiA,qiB,qqA,qqB,qqL,v;
rvec dx,df;
atom_id *AA;
ivec dt;
int start = mdatoms->start;
int end = mdatoms->homenr+start;
int niat;
gmx_bool bMolPBC = fr->bMolPBC;
if (fr->n_tpi)
/* For test particle insertion we only correct for the test molecule */
start = mdatoms->nr - fr->n_tpi;
ek = fr->epsfac*fr->k_rf;
ec = fr->epsfac*fr->c_rf;
chargeA = mdatoms->chargeA;
chargeB = mdatoms->chargeB;
AA = excl->a;
ki = CENTRAL;
if (fr->bDomDec)
niat = excl->nr;
else
niat = end;
q2sumA = 0;
q2sumB = 0;
ener = 0;
if (mdatoms->nChargePerturbed == 0) {
for(i=start; i<niat; i++) {
qiA = chargeA[i];
if (i < end)
q2sumA += qiA*qiA;
/* Do the exclusions */
j1 = excl->index[i];
j2 = excl->index[i+1];
for(j=j1; j<j2; j++) {
k = AA[j];
if (k > i) {
qqA = qiA*chargeA[k];
if (qqA != 0) {
if (g) {
rvec_sub(x[i],x[k],dx);
ivec_sub(SHIFT_IVEC(g,i),SHIFT_IVEC(g,k),dt);
ki=IVEC2IS(dt);
} else if (bMolPBC) {
ki = pbc_dx_aiuc(pbc,x[i],x[k],dx);
} else
rvec_sub(x[i],x[k],dx);
ener += qqA*(ek*norm2(dx) - ec);
svmul(-2*qqA*ek,dx,df);
rvec_inc(f[i],df);
rvec_dec(f[k],df);
rvec_inc(fshift[ki],df);
rvec_dec(fshift[CENTRAL],df);
}
}
}
}
ener += -0.5*ec*q2sumA;
} else {
L1 = 1.0 - lambda;
for(i=start; i<niat; i++) {
qiA = chargeA[i];
qiB = chargeB[i];
if (i < end) {
q2sumA += qiA*qiA;
q2sumB += qiB*qiB;
}
/* Do the exclusions */
j1 = excl->index[i];
j2 = excl->index[i+1];
for(j=j1; j<j2; j++) {
k = AA[j];
if (k > i) {
qqA = qiA*chargeA[k];
qqB = qiB*chargeB[k];
if (qqA != 0 || qqB != 0) {
qqL = L1*qqA + lambda*qqB;
if (g) {
rvec_sub(x[i],x[k],dx);
ivec_sub(SHIFT_IVEC(g,i),SHIFT_IVEC(g,k),dt);
ki=IVEC2IS(dt);
} else if (bMolPBC) {
ki = pbc_dx_aiuc(pbc,x[i],x[k],dx);
} else
rvec_sub(x[i],x[k],dx);
v = ek*norm2(dx) - ec;
ener += qqL*v;
svmul(-2*qqL*ek,dx,df);
rvec_inc(f[i],df);
rvec_dec(f[k],df);
rvec_inc(fshift[ki],df);
rvec_dec(fshift[CENTRAL],df);
*dvdlambda += (qqB - qqA)*v;
}
}
}
}
ener += -0.5*ec*(L1*q2sumA + lambda*q2sumB);
*dvdlambda += -0.5*ec*(q2sumB - q2sumA);
}
if (debug)
fprintf(debug,"RF exclusion energy: %g\n",ener);
return ener;
}
real
do_nonbonded_listed(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 *dvdl,
const t_mdatoms *md,
const t_forcerec *fr, gmx_grppairener_t *grppener,
int *global_atom_index)
{
int ielec, ivdw;
real qq, c6, c12;
rvec dx;
ivec dt;
int i, j, itype, ai, aj, gid;
int fshift_index;
real r2, rinv;
real fscal, velec, vvdw;
real * energygrp_elec;
real * energygrp_vdw;
static gmx_bool warned_rlimit = FALSE;
/* Free energy stuff */
gmx_bool bFreeEnergy;
real LFC[2], LFV[2], DLF[2], lfac_coul[2], lfac_vdw[2], dlfac_coul[2], dlfac_vdw[2];
real qqB, c6B, c12B, sigma2_def, sigma2_min;
switch (ftype)
{
case F_LJ14:
case F_LJC14_Q:
energygrp_elec = grppener->ener[egCOUL14];
energygrp_vdw = grppener->ener[egLJ14];
break;
case F_LJC_PAIRS_NB:
energygrp_elec = grppener->ener[egCOULSR];
energygrp_vdw = grppener->ener[egLJSR];
break;
default:
energygrp_elec = NULL; /* Keep compiler happy */
energygrp_vdw = NULL; /* Keep compiler happy */
gmx_fatal(FARGS, "Unknown function type %d in do_nonbonded14", ftype);
break;
}
if (fr->efep != efepNO)
{
/* Lambda factor for state A=1-lambda and B=lambda */
LFC[0] = 1.0 - lambda[efptCOUL];
LFV[0] = 1.0 - lambda[efptVDW];
LFC[1] = lambda[efptCOUL];
LFV[1] = lambda[efptVDW];
/*derivative of the lambda factor for state A and B */
DLF[0] = -1;
DLF[1] = 1;
/* precalculate */
sigma2_def = pow(fr->sc_sigma6_def, 1.0/3.0);
sigma2_min = pow(fr->sc_sigma6_min, 1.0/3.0);
for (i = 0; i < 2; i++)
{
lfac_coul[i] = (fr->sc_power == 2 ? (1-LFC[i])*(1-LFC[i]) : (1-LFC[i]));
dlfac_coul[i] = DLF[i]*fr->sc_power/fr->sc_r_power*(fr->sc_power == 2 ? (1-LFC[i]) : 1);
lfac_vdw[i] = (fr->sc_power == 2 ? (1-LFV[i])*(1-LFV[i]) : (1-LFV[i]));
dlfac_vdw[i] = DLF[i]*fr->sc_power/fr->sc_r_power*(fr->sc_power == 2 ? (1-LFV[i]) : 1);
}
}
else
{
sigma2_min = sigma2_def = 0;
}
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);
/* Get parameters */
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));
qq = md->chargeA[ai]*md->chargeA[aj]*fr->epsfac*fr->fudgeQQ;
c6 = iparams[itype].lj14.c6A;
c12 = iparams[itype].lj14.c12A;
break;
case F_LJC14_Q:
qq = iparams[itype].ljc14.qi*iparams[itype].ljc14.qj*fr->epsfac*iparams[itype].ljc14.fqq;
c6 = iparams[itype].ljc14.c6;
c12 = iparams[itype].ljc14.c12;
break;
case F_LJC_PAIRS_NB:
qq = iparams[itype].ljcnb.qi*iparams[itype].ljcnb.qj*fr->epsfac;
c6 = iparams[itype].ljcnb.c6;
c12 = iparams[itype].ljcnb.c12;
break;
default:
/* Cannot happen since we called gmx_fatal() above in this case */
qq = c6 = c12 = 0; /* Keep compiler happy */
break;
}
/* To save flops in the optimized kernels, c6/c12 have 6.0/12.0 derivative prefactors
* included in the general nfbp array now. This means the tables are scaled down by the
* same factor, so when we use the original c6/c12 parameters from iparams[] they must
* be scaled up.
*/
c6 *= 6.0;
c12 *= 12.0;
/* Do we need to apply full periodic boundary conditions? */
if (fr->bMolPBC == TRUE)
{
fshift_index = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
}
else
{
fshift_index = CENTRAL;
rvec_sub(x[ai], x[aj], dx);
}
r2 = norm2(dx);
if (r2 >= fr->tab14.r*fr->tab14.r)
{
if (warned_rlimit == FALSE)
{
nb_listed_warning_rlimit(x, ai, aj, global_atom_index, sqrt(r2), fr->tab14.r);
warned_rlimit = TRUE;
}
continue;
}
if (bFreeEnergy)
{
/* Currently free energy is only supported for F_LJ14, so no need to check for that if we got here */
qqB = md->chargeB[ai]*md->chargeB[aj]*fr->epsfac*fr->fudgeQQ;
c6B = iparams[itype].lj14.c6B*6.0;
c12B = iparams[itype].lj14.c12B*12.0;
fscal = nb_free_energy_evaluate_single(r2, fr->sc_r_power, fr->sc_alphacoul, fr->sc_alphavdw,
fr->tab14.scale, fr->tab14.data, qq, c6, c12, qqB, c6B, c12B,
LFC, LFV, DLF, lfac_coul, lfac_vdw, dlfac_coul, dlfac_vdw,
fr->sc_sigma6_def, fr->sc_sigma6_min, sigma2_def, sigma2_min, &velec, &vvdw, dvdl);
}
else
{
/* Evaluate tabulated interaction without free energy */
fscal = nb_evaluate_single(r2, fr->tab14.scale, fr->tab14.data, qq, c6, c12, &velec, &vvdw);
}
energygrp_elec[gid] += velec;
energygrp_vdw[gid] += vvdw;
svmul(fscal, dx, dx);
/* Add the forces */
rvec_inc(f[ai], dx);
rvec_dec(f[aj], dx);
if (g)
{
/* Correct the shift forces using the graph */
ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
fshift_index = IVEC2IS(dt);
}
if (fshift_index != CENTRAL)
{
rvec_inc(fshift[fshift_index], dx);
rvec_dec(fshift[CENTRAL], dx);
}
}
return 0.0;
}
real orires(int nfa,t_iatom forceatoms[],t_iparams ip[],
rvec x[],rvec f[],t_forcerec *fr,t_graph *g,
matrix box,real lambda,real *dvdlambda,
t_mdatoms *md,int ngrp,real egnb[],real egcoul[],
t_fcdata *fcd)
{
atom_id ai,aj;
int fa,d,i,type,ex,power,ki;
ivec dt;
real r2,invr,invr2,fc,smooth_fc,dev,devins,pfac;
rvec r,Sr,fij;
real vtot;
t_oriresdata *od;
bool bTAV;
vtot = 0;
od = &(fcd->orires);
if (fabs(od->fc) > GMX_REAL_MIN) {
bTAV = (fabs(od->edt) > GMX_REAL_MIN);
/* Smoothly switch on the restraining when time averaging is used */
smooth_fc = od->fc*(1.0 - od->exp_min_t_tau);
d = 0;
for(fa=0; fa<nfa; fa+=3) {
type = forceatoms[fa];
ai = forceatoms[fa+1];
aj = forceatoms[fa+2];
rvec_sub(x[ai],x[aj],r);
r2 = norm2(r);
invr = invsqrt(r2);
invr2 = invr*invr;
ex = ip[type].orires.ex;
power = ip[type].orires.pow;
fc = smooth_fc*ip[type].orires.kfac;
dev = od->otav[d] - ip[type].orires.obs;
/* NOTE: there is no real potential when time averaging is applied */
vtot += 0.5*fc*sqr(dev);
if (bTAV) {
/* Calculate the force as the sqrt of tav times instantaneous */
devins = od->oins[d] - ip[type].orires.obs;
if (dev*devins <= 0)
dev = 0;
else {
dev = sqrt(dev*devins);
if (devins < 0)
dev = -dev;
}
}
pfac = fc*ip[type].orires.c*invr2;
for(i=0; i<power; i++)
pfac *= invr;
mvmul(od->S[ex],r,Sr);
for(i=0; i<DIM; i++)
fij[i] = -pfac*dev*(4*Sr[i] - 2*(2+power)*invr2*iprod(Sr,r)*r[i]);
ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
ki=IVEC2IS(dt);
for(i=0; i<DIM; i++) {
f[ai][i] += fij[i];
f[aj][i] -= fij[i];
fr->fshift[ki][i] += fij[i];
fr->fshift[CENTRAL][i] -= fij[i];
}
d++;
}
}
return vtot;
/* Approx. 80*nfa/3 flops */
}