void
nb_kernel310_ppc_altivec (int * p_nri,
int iinr[],
int jindex[],
int jjnr[],
int shift[],
float shiftvec[],
float fshift[],
int gid[],
float pos[],
float faction[],
float charge[],
float * p_facel,
float * p_krf,
float * p_crf,
float Vc[],
int type[],
int * p_ntype,
float vdwparam[],
float Vvdw[],
float * p_tabscale,
float VFtab[],
float invsqrta[],
float dvda[],
float * p_gbtabscale,
float GBtab[],
int * p_nthreads,
int * count,
void * mtx,
int * outeriter,
int * inneriter,
float * work)
{
vector float ix,iy,iz,shvec;
vector float vfacel,tsc,fs,fs2,nul;
vector float dx,dy,dz;
vector float Vvdwtot,vctot,qq,iq,c6,c12,VVc,FFc;
vector float fix,fiy,fiz;
vector float tmp1,tmp2,tmp3,tmp4;
vector float rinv,r,rinvsq,rsq,rinvsix,Vvdw6,Vvdw12;
int n,k,ii,is3,ii3,ntiA,nj0,nj1;
int jnra,jnrb,jnrc,jnrd;
int j3a,j3b,j3c,j3d;
int nri, ntype, nouter, ninner;
int tja,tjb,tjc,tjd;
#ifdef GMX_THREADS
int nn0, nn1;
#endif
nouter = 0;
ninner = 0;
nri = *p_nri;
ntype = *p_ntype;
nul=vec_zero();
vfacel=load_float_and_splat(p_facel);
tsc=load_float_and_splat(p_tabscale);
#ifdef GMX_THREADS
nthreads = *p_nthreads;
do {
gmx_thread_mutex_lock((gmx_thread_mutex_t *)mtx);
nn0 = *count;
nn1 = nn0+(nri-nn0)/(2*nthreads)+3;
*count = nn1;
gmx_thread_mutex_unlock((gmx_thread_mutex_t *)mtx);
if(nn1>nri) nn1=nri;
for(n=nn0; (n<nn1); n++) {
#if 0
} /* maintain correct indentation even with conditional left braces */
#endif
#else /* without gmx_threads */
for(n=0;n<nri;n++) {
#endif
is3 = 3*shift[n];
shvec = load_xyz(shiftvec+is3);
ii = iinr[n];
ii3 = 3*ii;
ix = load_xyz(pos+ii3);
Vvdwtot = nul;
vctot = nul;
fix = nul;
fiy = nul;
fiz = nul;
ix = vec_add(ix,shvec);
nj0 = jindex[n];
nj1 = jindex[n+1];
splat_xyz_to_vectors(ix,&ix,&iy,&iz);
ntiA = 2*ntype*type[ii];
iq = vec_madd(load_float_and_splat(charge+ii),vfacel,nul);
for(k=nj0; k<(nj1-3); k+=4) {
jnra = jjnr[k];
jnrb = jjnr[k+1];
jnrc = jjnr[k+2];
jnrd = jjnr[k+3];
j3a = 3*jnra;
j3b = 3*jnrb;
j3c = 3*jnrc;
j3d = 3*jnrd;
transpose_4_to_3(load_xyz(pos+j3a),
load_xyz(pos+j3b),
load_xyz(pos+j3c),
load_xyz(pos+j3d),&dx,&dy,&dz);
dx = vec_sub(ix,dx);
dy = vec_sub(iy,dy);
dz = vec_sub(iz,dz);
rsq = vec_madd(dx,dx,nul);
rsq = vec_madd(dy,dy,rsq);
rsq = vec_madd(dz,dz,rsq);
rinv = do_invsqrt(rsq);
rinvsq = vec_madd(rinv,rinv,nul);
r = vec_madd(rinv,rsq,nul);
rinvsix = vec_madd(rinvsq,rinvsq,nul);
rinvsix = vec_madd(rinvsix,rinvsq,nul);
tja = ntiA+2*type[jnra];
tjb = ntiA+2*type[jnrb];
tjc = ntiA+2*type[jnrc];
tjd = ntiA+2*type[jnrd];
qq = vec_madd(load_4_float(charge+jnra,charge+jnrb,
charge+jnrc,charge+jnrd),iq,nul);
load_4_pair(vdwparam+tja,vdwparam+tjb,vdwparam+tjc,vdwparam+tjd,&c6,&c12);
do_4_ctable_coul(VFtab,vec_madd(r,tsc,nul),&VVc,&FFc);
fs2 = vec_madd(qq,FFc,nul); /* fijC */
vctot = vec_madd(qq,VVc,vctot);
Vvdw6 = vec_madd(c6,rinvsix,nul);
Vvdw12 = vec_madd(c12,vec_madd(rinvsix,rinvsix,nul),
nul);
fs = vec_madd(vec_twelve(),Vvdw12,nul);
fs = vec_nmsub(vec_six(),Vvdw6,fs);
fs = vec_madd(fs,rinv,nul);
Vvdwtot = vec_add(Vvdwtot,Vvdw12);
fs = vec_nmsub(fs2,tsc,fs);
fs = vec_madd(fs,rinv,nul);
Vvdwtot = vec_sub(Vvdwtot,Vvdw6);
fix = vec_madd(fs,dx,fix); /* +=fx */
fiy = vec_madd(fs,dy,fiy); /* +=fy */
fiz = vec_madd(fs,dz,fiz); /* +=fz */
dx = vec_nmsub(dx,fs,nul); /* -fx */
dy = vec_nmsub(dy,fs,nul); /* -fy */
dz = vec_nmsub(dz,fs,nul); /* -fz */
transpose_3_to_4(dx,dy,dz,&tmp1,&tmp2,&tmp3,&tmp4);
add_xyz_to_mem(faction+j3a,tmp1);
add_xyz_to_mem(faction+j3b,tmp2);
add_xyz_to_mem(faction+j3c,tmp3);
add_xyz_to_mem(faction+j3d,tmp4);
}
if(k<(nj1-1)) {
jnra = jjnr[k];
jnrb = jjnr[k+1];
j3a = 3*jnra;
j3b = 3*jnrb;
transpose_2_to_3(load_xyz(pos+j3a),
load_xyz(pos+j3b),&dx,&dy,&dz);
dx = vec_sub(ix,dx);
dy = vec_sub(iy,dy);
dz = vec_sub(iz,dz);
rsq = vec_madd(dx,dx,nul);
rsq = vec_madd(dy,dy,rsq);
rsq = vec_madd(dz,dz,rsq);
zero_highest_2_elements_in_vector(&rsq);
rinv = do_invsqrt(rsq);
zero_highest_2_elements_in_vector(&rinv);
rinvsq = vec_madd(rinv,rinv,nul);
r = vec_madd(rinv,rsq,nul);
rinvsix = vec_madd(rinvsq,rinvsq,nul);
rinvsix = vec_madd(rinvsix,rinvsq,nul);
tja = ntiA+2*type[jnra];
tjb = ntiA+2*type[jnrb];
qq = vec_madd(load_2_float(charge+jnra,charge+jnrb),iq,nul);
load_2_pair(vdwparam+tja,vdwparam+tjb,&c6,&c12);
do_2_ctable_coul(VFtab,vec_madd(r,tsc,nul),&VVc,&FFc);
fs2 = vec_madd(qq,FFc,nul); /* fijC */
vctot = vec_madd(qq,VVc,vctot);
Vvdw6 = vec_madd(c6,rinvsix,nul);
Vvdw12 = vec_madd(c12,vec_madd(rinvsix,rinvsix,nul),
nul);
fs = vec_madd(vec_twelve(),Vvdw12,nul);
fs = vec_nmsub(vec_six(),Vvdw6,fs);
Vvdwtot = vec_add(Vvdwtot,Vvdw12);
fs = vec_madd(fs,rinv,nul);
fs = vec_nmsub(fs2,tsc,fs);
fs = vec_madd(fs,rinv,nul);
Vvdwtot = vec_sub(Vvdwtot,Vvdw6);
fix = vec_madd(fs,dx,fix); /* +=fx */
fiy = vec_madd(fs,dy,fiy); /* +=fy */
fiz = vec_madd(fs,dz,fiz); /* +=fz */
dx = vec_nmsub(dx,fs,nul); /* -fx */
dy = vec_nmsub(dy,fs,nul); /* -fy */
dz = vec_nmsub(dz,fs,nul); /* -fz */
transpose_3_to_2(dx,dy,dz,&tmp1,&tmp2);
add_xyz_to_mem(faction+j3a,tmp1);
add_xyz_to_mem(faction+j3b,tmp2);
k += 2;
}
if((nj1-nj0) & 0x1) {
jnra = jjnr[k];
j3a = 3*jnra;
transpose_1_to_3(load_xyz(pos+j3a),&dx,&dy,&dz);
dx = vec_sub(ix,dx);
dy = vec_sub(iy,dy);
dz = vec_sub(iz,dz);
rsq = vec_madd(dx,dx,nul);
rsq = vec_madd(dy,dy,rsq);
rsq = vec_madd(dz,dz,rsq);
zero_highest_3_elements_in_vector(&rsq);
rinv = do_invsqrt(rsq);
zero_highest_3_elements_in_vector(&rinv);
rinvsq = vec_madd(rinv,rinv,nul);
r = vec_madd(rinv,rsq,nul);
rinvsix = vec_madd(rinvsq,rinvsq,nul);
rinvsix = vec_madd(rinvsix,rinvsq,nul);
tja = ntiA+2*type[jnra];
qq = vec_madd(load_1_float(charge+jnra),iq,nul);
load_1_pair(vdwparam+tja,&c6,&c12);
do_1_ctable_coul(VFtab,vec_madd(r,tsc,nul),&VVc,&FFc);
fs2 = vec_madd(qq,FFc,nul); /* fijC */
vctot = vec_madd(qq,VVc,vctot);
Vvdw6 = vec_madd(c6,rinvsix,nul);
Vvdw12 = vec_madd(c12,vec_madd(rinvsix,rinvsix,nul),
nul);
fs = vec_madd(vec_twelve(),Vvdw12,nul);
fs = vec_nmsub(vec_six(),Vvdw6,fs);
fs = vec_madd(fs,rinv,nul);
Vvdwtot = vec_add(Vvdwtot,Vvdw12);
fs = vec_nmsub(fs2,tsc,fs);
fs = vec_madd(fs,rinv,nul);
Vvdwtot = vec_sub(Vvdwtot,Vvdw6);
fix = vec_madd(fs,dx,fix); /* +=fx */
fiy = vec_madd(fs,dy,fiy); /* +=fy */
fiz = vec_madd(fs,dz,fiz); /* +=fz */
dx = vec_nmsub(dx,fs,nul); /* -fx */
dy = vec_nmsub(dy,fs,nul); /* -fy */
dz = vec_nmsub(dz,fs,nul); /* -fz */
transpose_3_to_1(dx,dy,dz,&tmp1);
add_xyz_to_mem(faction+j3a,tmp1);
}
/* update outer data */
transpose_3_to_4(fix,fiy,fiz,&tmp1,&tmp2,&tmp3,&tmp4);
tmp1 = vec_add(tmp1,tmp3);
tmp2 = vec_add(tmp2,tmp4);
tmp1 = vec_add(tmp1,tmp2);
add_xyz_to_mem(faction+ii3,tmp1);
add_xyz_to_mem(fshift+is3,tmp1);
add_vector_to_float(Vc+gid[n],vctot);
add_vector_to_float(Vvdw+gid[n],Vvdwtot);
ninner += nj1 - nj0;
}
#ifdef GMX_THREADS
nouter += nn1 - nn0;
} while (nn1<nri);
#else
nouter = nri;
#endif
*outeriter = nouter;
*inneriter = ninner;
}
void
nb_kernel133nf_ppc_altivec(int * p_nri,
int iinr[],
int jindex[],
int jjnr[],
int shift[],
float shiftvec[],
float fshift[],
int gid[],
float pos[],
float faction[],
float charge[],
float * p_facel,
float * p_krf,
float * p_crf,
float Vc[],
int type[],
int * p_ntype,
float vdwparam[],
float Vvdw[],
float * p_tabscale,
float VFtab[],
float invsqrta[],
float dvda[],
float * p_gbtabscale,
float GBtab[],
int * p_nthreads,
int * count,
void * mtx,
int * outeriter,
int * inneriter,
float * work)
{
vector float iOx,iOy,iOz,iH1x,iH1y,iH1z,iH2x,iH2y,iH2z,iMx,iMy,iMz;
vector float dOx,dOy,dOz,dH1x,dH1y,dH1z,dH2x,dH2y,dH2z,dMx,dMy,dMz;
vector float Vvdwtot,c6,c12,VVd,VVr,tsc,r;
vector float vfacel,nul;
vector float vctot,qqM,qqH,iqM,iqH,jq;
vector float rinvO,rinvH1,rinvH2,rinvM,rsqO,rsqH1,rsqH2,rsqM;
int n,k,ii,is3,ii3,ntiA,nj0,nj1;
int jnra,jnrb,jnrc,jnrd;
int j3a,j3b,j3c,j3d;
int nri, ntype, nouter, ninner;
int tja,tjb,tjc,tjd;
#ifdef GMX_THREADS
int nn0, nn1;
#endif
nouter = 0;
ninner = 0;
nri = *p_nri;
ntype = *p_ntype;
nul=vec_zero();
tsc=load_float_and_splat(p_tabscale);
vfacel=load_float_and_splat(p_facel);
ii = iinr[0];
iqH = vec_madd(load_float_and_splat(charge+ii+1),vfacel,nul);
iqM = vec_madd(load_float_and_splat(charge+ii+3),vfacel,nul);
ntiA = 2*ntype*type[ii];
#ifdef GMX_THREADS
nthreads = *p_nthreads;
do {
gmx_thread_mutex_lock((gmx_thread_mutex_t *)mtx);
nn0 = *count;
nn1 = nn0+(nri-nn0)/(2*nthreads)+3;
*count = nn1;
gmx_thread_mutex_unlock((gmx_thread_mutex_t *)mtx);
if(nn1>nri) nn1=nri;
for(n=nn0; (n<nn1); n++) {
#if 0
} /* maintain correct indentation even with conditional left braces */
#endif
#else /* without gmx_threads */
for(n=0;n<nri;n++) {
#endif
is3 = 3*shift[n];
ii = iinr[n];
ii3 = 3*ii;
load_1_4atoms_shift_and_splat(pos+ii3,shiftvec+is3,&iOx,&iOy,&iOz,
&iH1x,&iH1y,&iH1z,&iH2x,&iH2y,&iH2z,
&iMx,&iMy,&iMz);
vctot = nul;
Vvdwtot = nul;
nj0 = jindex[n];
nj1 = jindex[n+1];
for(k=nj0; k<(nj1-3); k+=4) {
jnra = jjnr[k];
jnrb = jjnr[k+1];
jnrc = jjnr[k+2];
jnrd = jjnr[k+3];
j3a = 3*jnra;
j3b = 3*jnrb;
j3c = 3*jnrc;
j3d = 3*jnrd;
transpose_4_to_3(load_xyz(pos+j3a),
load_xyz(pos+j3b),
load_xyz(pos+j3c),
load_xyz(pos+j3d),&dMx,&dMy,&dMz);
dOx = vec_sub(iOx,dMx);
dOy = vec_sub(iOy,dMy);
dOz = vec_sub(iOz,dMz);
dH1x = vec_sub(iH1x,dMx);
dH1y = vec_sub(iH1y,dMy);
dH1z = vec_sub(iH1z,dMz);
dH2x = vec_sub(iH2x,dMx);
dH2y = vec_sub(iH2y,dMy);
dH2z = vec_sub(iH2z,dMz);
dMx = vec_sub(iMx,dMx);
dMy = vec_sub(iMy,dMy);
dMz = vec_sub(iMz,dMz);
rsqO = vec_madd(dOx,dOx,nul);
rsqH1 = vec_madd(dH1x,dH1x,nul);
rsqH2 = vec_madd(dH2x,dH2x,nul);
rsqM = vec_madd(dMx,dMx,nul);
rsqO = vec_madd(dOy,dOy,rsqO);
rsqH1 = vec_madd(dH1y,dH1y,rsqH1);
rsqH2 = vec_madd(dH2y,dH2y,rsqH2);
rsqM = vec_madd(dMy,dMy,rsqM);
rsqO = vec_madd(dOz,dOz,rsqO);
rsqH1 = vec_madd(dH1z,dH1z,rsqH1);
rsqH2 = vec_madd(dH2z,dH2z,rsqH2);
rsqM = vec_madd(dMz,dMz,rsqM);
rinvO = do_invsqrt(rsqO);
do_3_invsqrt(rsqM,rsqH1,rsqH2,&rinvM,&rinvH1,&rinvH2);
r = vec_madd(rsqO,rinvO,nul);
tja = ntiA+2*type[jnra];
tjb = ntiA+2*type[jnrb];
tjc = ntiA+2*type[jnrc];
tjd = ntiA+2*type[jnrd];
/* load 4 j charges and multiply by iq */
jq=load_4_float(charge+jnra,charge+jnrb,
charge+jnrc,charge+jnrd);
load_4_pair(vdwparam+tja,vdwparam+tjb,vdwparam+tjc,vdwparam+tjd,&c6,&c12);
do_vonly_4_ljtable_lj(VFtab,vec_madd(r,tsc,nul),&VVd,&VVr);
Vvdwtot = vec_madd(c6,VVd,Vvdwtot);
Vvdwtot = vec_madd(c12,VVr,Vvdwtot);
qqH = vec_madd(iqH,jq,nul);
qqM = vec_madd(iqM,jq,nul);
vctot = vec_madd(qqM,rinvM,vctot);
vctot = vec_madd(qqH,rinvH1,vctot);
vctot = vec_madd(qqH,rinvH2,vctot);
}
if(k<(nj1-2))
{
jnra = jjnr[k];
jnrb = jjnr[k+1];
jnrc = jjnr[k+2];
j3a = 3*jnra;
j3b = 3*jnrb;
j3c = 3*jnrc;
transpose_4_to_3(load_xyz(pos+j3a),
load_xyz(pos+j3b),
load_xyz(pos+j3c),nul,&dMx,&dMy,&dMz);
dOx = vec_sub(iOx,dMx);
dOy = vec_sub(iOy,dMy);
dOz = vec_sub(iOz,dMz);
dH1x = vec_sub(iH1x,dMx);
dH1y = vec_sub(iH1y,dMy);
dH1z = vec_sub(iH1z,dMz);
dH2x = vec_sub(iH2x,dMx);
dH2y = vec_sub(iH2y,dMy);
dH2z = vec_sub(iH2z,dMz);
dMx = vec_sub(iMx,dMx);
dMy = vec_sub(iMy,dMy);
dMz = vec_sub(iMz,dMz);
rsqO = vec_madd(dOx,dOx,nul);
rsqH1 = vec_madd(dH1x,dH1x,nul);
rsqH2 = vec_madd(dH2x,dH2x,nul);
rsqM = vec_madd(dMx,dMx,nul);
rsqO = vec_madd(dOy,dOy,rsqO);
rsqH1 = vec_madd(dH1y,dH1y,rsqH1);
rsqH2 = vec_madd(dH2y,dH2y,rsqH2);
rsqM = vec_madd(dMy,dMy,rsqM);
rsqO = vec_madd(dOz,dOz,rsqO);
rsqH1 = vec_madd(dH1z,dH1z,rsqH1);
rsqH2 = vec_madd(dH2z,dH2z,rsqH2);
rsqM = vec_madd(dMz,dMz,rsqM);
rinvO = do_invsqrt(rsqO);
do_3_invsqrt(rsqM,rsqH1,rsqH2,&rinvM,&rinvH1,&rinvH2);
zero_highest_element_in_vector(&rinvO);
zero_highest_element_in_vector(&rsqO);
zero_highest_element_in_3_vectors(&rinvH1,&rinvH2,&rinvM);
r = vec_madd(rsqO,rinvO,nul);
jq=load_3_float(charge+jnra,charge+jnrb,charge+jnrc);
tja = ntiA+2*type[jnra];
tjb = ntiA+2*type[jnrb];
tjc = ntiA+2*type[jnrc];
/* load 3 j charges and multiply by iq */
load_3_pair(vdwparam+tja,vdwparam+tjb,vdwparam+tjc,&c6,&c12);
do_vonly_3_ljtable_lj(VFtab,vec_madd(r,tsc,nul),&VVd,&VVr);
Vvdwtot = vec_madd(c6,VVd,Vvdwtot);
Vvdwtot = vec_madd(c12,VVr,Vvdwtot);
qqH = vec_madd(iqH,jq,nul);
qqM = vec_madd(iqM,jq,nul);
vctot = vec_madd(qqM,rinvM,vctot);
vctot = vec_madd(qqH,rinvH1,vctot);
vctot = vec_madd(qqH,rinvH2,vctot);
}
else if(k<(nj1-1))
{
jnra = jjnr[k];
jnrb = jjnr[k+1];
j3a = 3*jnra;
j3b = 3*jnrb;
transpose_2_to_3(load_xyz(pos+j3a),
load_xyz(pos+j3b),&dMx,&dMy,&dMz);
dOx = vec_sub(iOx,dMx);
dOy = vec_sub(iOy,dMy);
dOz = vec_sub(iOz,dMz);
dH1x = vec_sub(iH1x,dMx);
dH1y = vec_sub(iH1y,dMy);
dH1z = vec_sub(iH1z,dMz);
dH2x = vec_sub(iH2x,dMx);
dH2y = vec_sub(iH2y,dMy);
dH2z = vec_sub(iH2z,dMz);
dMx = vec_sub(iMx,dMx);
dMy = vec_sub(iMy,dMy);
dMz = vec_sub(iMz,dMz);
rsqO = vec_madd(dOx,dOx,nul);
rsqH1 = vec_madd(dH1x,dH1x,nul);
rsqH2 = vec_madd(dH2x,dH2x,nul);
rsqM = vec_madd(dMx,dMx,nul);
rsqO = vec_madd(dOy,dOy,rsqO);
rsqH1 = vec_madd(dH1y,dH1y,rsqH1);
rsqH2 = vec_madd(dH2y,dH2y,rsqH2);
rsqM = vec_madd(dMy,dMy,rsqM);
rsqO = vec_madd(dOz,dOz,rsqO);
rsqH1 = vec_madd(dH1z,dH1z,rsqH1);
rsqH2 = vec_madd(dH2z,dH2z,rsqH2);
rsqM = vec_madd(dMz,dMz,rsqM);
rinvO = do_invsqrt(rsqO);
do_3_invsqrt(rsqM,rsqH1,rsqH2,&rinvM,&rinvH1,&rinvH2);
zero_highest_2_elements_in_vector(&rinvO);
zero_highest_2_elements_in_vector(&rsqO);
zero_highest_2_elements_in_3_vectors(&rinvM,&rinvH1,&rinvH2);
r = vec_madd(rsqO,rinvO,nul);
tja = ntiA+2*type[jnra];
tjb = ntiA+2*type[jnrb];
/* load 2 j charges and multiply by iq */
jq=load_2_float(charge+jnra,charge+jnrb);
load_2_pair(vdwparam+tja,vdwparam+tjb,&c6,&c12);
do_vonly_2_ljtable_lj(VFtab,vec_madd(r,tsc,nul),&VVd,&VVr);
Vvdwtot = vec_madd(c6,VVd,Vvdwtot);
Vvdwtot = vec_madd(c12,VVr,Vvdwtot);
qqH = vec_madd(iqH,jq,nul);
qqM = vec_madd(iqM,jq,nul);
vctot = vec_madd(qqM,rinvM,vctot);
vctot = vec_madd(qqH,rinvH1,vctot);
vctot = vec_madd(qqH,rinvH2,vctot);
}
else if(k<nj1)
{
jnra = jjnr[k];
j3a = 3*jnra;
transpose_1_to_3(load_xyz(pos+j3a),&dMx,&dMy,&dMz);
dOx = vec_sub(iOx,dMx);
dOy = vec_sub(iOy,dMy);
dOz = vec_sub(iOz,dMz);
dH1x = vec_sub(iH1x,dMx);
dH1y = vec_sub(iH1y,dMy);
dH1z = vec_sub(iH1z,dMz);
dH2x = vec_sub(iH2x,dMx);
dH2y = vec_sub(iH2y,dMy);
dH2z = vec_sub(iH2z,dMz);
dMx = vec_sub(iMx,dMx);
dMy = vec_sub(iMy,dMy);
dMz = vec_sub(iMz,dMz);
rsqO = vec_madd(dOx,dOx,nul);
rsqH1 = vec_madd(dH1x,dH1x,nul);
rsqH2 = vec_madd(dH2x,dH2x,nul);
rsqM = vec_madd(dMx,dMx,nul);
rsqO = vec_madd(dOy,dOy,rsqO);
rsqH1 = vec_madd(dH1y,dH1y,rsqH1);
rsqH2 = vec_madd(dH2y,dH2y,rsqH2);
rsqM = vec_madd(dMy,dMy,rsqM);
rsqO = vec_madd(dOz,dOz,rsqO);
rsqH1 = vec_madd(dH1z,dH1z,rsqH1);
rsqH2 = vec_madd(dH2z,dH2z,rsqH2);
rsqM = vec_madd(dMz,dMz,rsqM);
rinvO = do_invsqrt(rsqO);
do_3_invsqrt(rsqM,rsqH1,rsqH2,&rinvM,&rinvH1,&rinvH2);
zero_highest_3_elements_in_vector(&rinvO);
zero_highest_3_elements_in_vector(&rsqO);
zero_highest_3_elements_in_3_vectors(&rinvH1,&rinvH2,&rinvM);
r = vec_madd(rsqO,rinvO,nul);
jq=load_1_float(charge+jnra);
tja = ntiA+2*type[jnra];
/* load 1 j charge and multiply by iq */
load_1_pair(vdwparam+tja,&c6,&c12);
do_vonly_1_ljtable_lj(VFtab,vec_madd(r,tsc,nul),&VVd,&VVr);
Vvdwtot = vec_madd(c6,VVd,Vvdwtot);
Vvdwtot = vec_madd(c12,VVr,Vvdwtot);
qqH = vec_madd(iqH,jq,nul);
qqM = vec_madd(iqM,jq,nul);
vctot = vec_madd(qqM,rinvM,vctot);
vctot = vec_madd(qqH,rinvH1,vctot);
vctot = vec_madd(qqH,rinvH2,vctot);
}
/* update outer data */
add_vector_to_float(Vc+gid[n],vctot);
add_vector_to_float(Vvdw+gid[n],Vvdwtot);
ninner += nj1 - nj0;
}
#ifdef GMX_THREADS
nouter += nn1 - nn0;
} while (nn1<nri);
#else
nouter = nri;
#endif
*outeriter = nouter;
*inneriter = ninner;
}
void
nb_kernel010nf_ppc_altivec(int * p_nri,
int iinr[],
int jindex[],
int jjnr[],
int shift[],
float shiftvec[],
float fshift[],
int gid[],
float pos[],
float faction[],
float charge[],
float * p_facel,
float * p_krf,
float * p_crf,
float Vc[],
int type[],
int * p_ntype,
float vdwparam[],
float Vvdw[],
float * p_tabscale,
float VFtab[],
float invsqrta[],
float dvda[],
float * p_gbtabscale,
float GBtab[],
int * p_nthreads,
int * count,
void * mtx,
int * outeriter,
int * inneriter,
float * work)
{
vector float ix,iy,iz,shvec;
vector float nul;
vector float dx,dy,dz;
vector float Vvdwtot,c6,c12;
vector float rinvsq,rsq,rinvsix;
int n,k,ii,is3,ii3,nj0,nj1;
int jnra,jnrb,jnrc,jnrd;
int j3a,j3b,j3c,j3d;
int nri, ntype, nouter, ninner;
int ntiA,tja,tjb,tjc,tjd;
#ifdef GMX_THREAD_SHM_FDECOMP
int nn0, nn1;
#endif
nouter = 0;
ninner = 0;
nri = *p_nri;
ntype = *p_ntype;
nul=vec_zero();
#ifdef GMX_THREAD_SHM_FDECOMP
nthreads = *p_nthreads;
do {
tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
nn0 = *count;
nn1 = nn0+(nri-nn0)/(2*nthreads)+3;
*count = nn1;
tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
if(nn1>nri) nn1=nri;
for(n=nn0; (n<nn1); n++) {
#if 0
} /* maintain correct indentation even with conditional left braces */
#endif
#else /* without tMPI_Threads */
for(n=0;n<nri;n++) {
#endif
is3 = 3*shift[n];
shvec = load_xyz(shiftvec+is3);
ii = iinr[n];
ii3 = 3*ii;
ix = load_xyz(pos+ii3);
Vvdwtot = nul;
ix = vec_add(ix,shvec);
nj0 = jindex[n];
nj1 = jindex[n+1];
splat_xyz_to_vectors(ix,&ix,&iy,&iz);
ntiA = 2*ntype*type[ii];
for(k=nj0; k<(nj1-3); k+=4) {
jnra = jjnr[k];
jnrb = jjnr[k+1];
jnrc = jjnr[k+2];
jnrd = jjnr[k+3];
j3a = 3*jnra;
j3b = 3*jnrb;
j3c = 3*jnrc;
j3d = 3*jnrd;
transpose_4_to_3(load_xyz(pos+j3a),
load_xyz(pos+j3b),
load_xyz(pos+j3c),
load_xyz(pos+j3d),&dx,&dy,&dz);
dx = vec_sub(ix,dx);
dy = vec_sub(iy,dy);
dz = vec_sub(iz,dz);
rsq = vec_madd(dx,dx,nul);
rsq = vec_madd(dy,dy,rsq);
rsq = vec_madd(dz,dz,rsq);
rinvsq = do_recip(rsq);
rinvsix = vec_madd(rinvsq,rinvsq,nul);
rinvsix = vec_madd(rinvsix,rinvsq,nul);
tja = ntiA+2*type[jnra];
tjb = ntiA+2*type[jnrb];
tjc = ntiA+2*type[jnrc];
tjd = ntiA+2*type[jnrd];
load_4_pair(vdwparam+tja,vdwparam+tjb,vdwparam+tjc,vdwparam+tjd,&c6,&c12);
Vvdwtot = vec_nmsub(c6,rinvsix,Vvdwtot);
Vvdwtot = vec_madd(c12,
vec_madd(rinvsix,rinvsix,nul),
Vvdwtot);
}
if(k<(nj1-1)) {
jnra = jjnr[k];
jnrb = jjnr[k+1];
j3a = 3*jnra;
j3b = 3*jnrb;
transpose_2_to_3(load_xyz(pos+j3a),
load_xyz(pos+j3b),&dx,&dy,&dz);
dx = vec_sub(ix,dx);
dy = vec_sub(iy,dy);
dz = vec_sub(iz,dz);
rsq = vec_madd(dx,dx,nul);
rsq = vec_madd(dy,dy,rsq);
rsq = vec_madd(dz,dz,rsq);
rinvsq = do_recip(rsq);
zero_highest_2_elements_in_vector(&rinvsq);
rinvsix = vec_madd(rinvsq,rinvsq,nul);
rinvsix = vec_madd(rinvsix,rinvsq,nul);
tja = ntiA+2*type[jnra];
tjb = ntiA+2*type[jnrb];
load_2_pair(vdwparam+tja,vdwparam+tjb,&c6,&c12);
Vvdwtot = vec_nmsub(c6,rinvsix,Vvdwtot);
Vvdwtot = vec_madd(c12,
vec_madd(rinvsix,rinvsix,nul),
Vvdwtot);
k += 2;
}
if((nj1-nj0) & 0x1) {
jnra = jjnr[k];
j3a = 3*jnra;
transpose_1_to_3(load_xyz(pos+j3a),&dx,&dy,&dz);
dx = vec_sub(ix,dx);
dy = vec_sub(iy,dy);
dz = vec_sub(iz,dz);
rsq = vec_madd(dx,dx,nul);
rsq = vec_madd(dy,dy,rsq);
rsq = vec_madd(dz,dz,rsq);
rinvsq = do_recip(rsq);
zero_highest_3_elements_in_vector(&rinvsq);
rinvsix = vec_madd(rinvsq,rinvsq,nul);
rinvsix = vec_madd(rinvsix,rinvsq,nul);
tja = ntiA+2*type[jnra];
load_1_pair(vdwparam+tja,&c6,&c12);
Vvdwtot = vec_nmsub(c6,rinvsix,Vvdwtot);
Vvdwtot = vec_madd(c12,
vec_madd(rinvsix,rinvsix,nul),
Vvdwtot);
}
/* update outer data */
add_vector_to_float(Vvdw+gid[n],Vvdwtot);
ninner += nj1 - nj0;
}
#ifdef GMX_THREAD_SHM_FDECOMP
nouter += nn1 - nn0;
} while (nn1<nri);
#else
nouter = nri;
#endif
*outeriter = nouter;
*inneriter = ninner;
}
void
nb_kernel100nf_ppc_altivec(int * p_nri,
int iinr[],
int jindex[],
int jjnr[],
int shift[],
float shiftvec[],
float fshift[],
int gid[],
float pos[],
float faction[],
float charge[],
float * p_facel,
float * p_krf,
float * p_crf,
float Vc[],
int type[],
int * p_ntype,
float vdwparam[],
float Vvdw[],
float * p_tabscale,
float VFtab[],
float invsqrta[],
float dvda[],
float * p_gbtabscale,
float GBtab[],
int * p_nthreads,
int * count,
void * mtx,
int * outeriter,
int * inneriter,
float * work)
{
vector float ix,iy,iz,shvec;
vector float vfacel,nul;
vector float dx,dy,dz;
vector float vctot,qq,iq;
vector float rinv,rsq;
int n,k,ii,is3,ii3,nj0,nj1;
int jnra,jnrb,jnrc,jnrd;
int j3a,j3b,j3c,j3d;
int nri, ntype, nouter, ninner;
#ifdef GMX_THREADS
int nn0, nn1;
#endif
nouter = 0;
ninner = 0;
nri = *p_nri;
ntype = *p_ntype;
nul=vec_zero();
vfacel=load_float_and_splat(p_facel);
#ifdef GMX_THREADS
nthreads = *p_nthreads;
do {
gmx_thread_mutex_lock((gmx_thread_mutex_t *)mtx);
nn0 = *count;
nn1 = nn0+(nri-nn0)/(2*nthreads)+3;
*count = nn1;
gmx_thread_mutex_unlock((gmx_thread_mutex_t *)mtx);
if(nn1>nri) nn1=nri;
for(n=nn0; (n<nn1); n++) {
#if 0
} /* maintain correct indentation even with conditional left braces */
#endif
#else /* without gmx_threads */
for(n=0;n<nri;n++) {
#endif
is3 = 3*shift[n];
shvec = load_xyz(shiftvec+is3);
ii = iinr[n];
ii3 = 3*ii;
ix = load_xyz(pos+ii3);
vctot = nul;
ix = vec_add(ix,shvec);
nj0 = jindex[n];
nj1 = jindex[n+1];
splat_xyz_to_vectors(ix,&ix,&iy,&iz);
iq = vec_madd(load_float_and_splat(charge+ii),vfacel,nul);
for(k=nj0; k<(nj1-3); k+=4) {
jnra = jjnr[k];
jnrb = jjnr[k+1];
jnrc = jjnr[k+2];
jnrd = jjnr[k+3];
j3a = 3*jnra;
j3b = 3*jnrb;
j3c = 3*jnrc;
j3d = 3*jnrd;
transpose_4_to_3(load_xyz(pos+j3a),
load_xyz(pos+j3b),
load_xyz(pos+j3c),
load_xyz(pos+j3d),&dx,&dy,&dz);
dx = vec_sub(ix,dx);
dy = vec_sub(iy,dy);
dz = vec_sub(iz,dz);
rsq = vec_madd(dx,dx,nul);
rsq = vec_madd(dy,dy,rsq);
rsq = vec_madd(dz,dz,rsq);
rinv = do_invsqrt(rsq);
/* load 4 j charges and multiply by iq */
qq = vec_madd(load_4_float(charge+jnra,charge+jnrb,
charge+jnrc,charge+jnrd),iq,nul);
vctot = vec_madd(qq,rinv,vctot);
}
if(k<(nj1-1)) {
jnra = jjnr[k];
jnrb = jjnr[k+1];
j3a = 3*jnra;
j3b = 3*jnrb;
transpose_2_to_3(load_xyz(pos+j3a),
load_xyz(pos+j3b),&dx,&dy,&dz);
dx = vec_sub(ix,dx);
dy = vec_sub(iy,dy);
dz = vec_sub(iz,dz);
rsq = vec_madd(dx,dx,nul);
rsq = vec_madd(dy,dy,rsq);
rsq = vec_madd(dz,dz,rsq);
rinv = do_invsqrt(rsq);
zero_highest_2_elements_in_vector(&rinv);
/* load 2 j charges and multiply by iq */
qq = vec_madd(load_2_float(charge+jnra,charge+jnrb),iq,nul);
vctot = vec_madd(qq,rinv,vctot);
k += 2;
}
if((nj1-nj0) & 0x1) {
jnra = jjnr[k];
j3a = 3*jnra;
transpose_1_to_3(load_xyz(pos+j3a),&dx,&dy,&dz);
dx = vec_sub(ix,dx);
dy = vec_sub(iy,dy);
dz = vec_sub(iz,dz);
rsq = vec_madd(dx,dx,nul);
rsq = vec_madd(dy,dy,rsq);
rsq = vec_madd(dz,dz,rsq);
rinv = do_invsqrt(rsq);
zero_highest_3_elements_in_vector(&rinv);
/* load 1 j charge and multiply by iq */
qq = vec_madd(load_1_float(charge+jnra),iq,nul);
vctot = vec_madd(qq,rinv,vctot);
}
/* update outer data */
add_vector_to_float(Vc+gid[n],vctot);
ninner += nj1 - nj0;
}
#ifdef GMX_THREADS
nouter += nn1 - nn0;
} while (nn1<nri);
#else
nouter = nri;
#endif
*outeriter = nouter;
*inneriter = ninner;
}
int main(int argc, char **argv) {
printf("ERKALE - Basis set tools from Hel.\n");
print_copyright();
print_license();
#ifdef SVNRELEASE
printf("At svn revision %s.\n\n",SVNREVISION);
#endif
print_hostname();
if(argc<3) {
printf("Usage: %s input.gbs command\n\n",argv[0]);
help();
return 0;
}
// Get filename
std::string filein(argv[1]);
// Load input
BasisSetLibrary bas;
bas.load_gaussian94(filein);
// Get command
std::string cmd(argv[2]);
// and determine what to do.
if(stricmp(cmd,"cholesky")==0) {
// Print completeness profile.
if(argc!=7) {
printf("\nUsage: %s input.gbs cholesky thr maxam ovlthr output.gbs\n",argv[0]);
return 1;
}
double thr(atof(argv[3]));
int maxam(atoi(argv[4]));
double ovlthr(atof(argv[5]));
std::string outfile(argv[6]);
if(maxam>=LIBINT_MAX_AM) {
printf("Setting maxam = %i because limitations in used version of LIBINT.\n",LIBINT_MAX_AM-1);
maxam=LIBINT_MAX_AM-1;
}
init_libint_base();
BasisSetLibrary ret=bas.cholesky_set(thr,maxam,ovlthr);
ret.save_gaussian94(outfile);
} else if(stricmp(cmd,"completeness")==0) {
// Print completeness profile.
if(argc!=5 && argc!=6) {
printf("\nUsage: %s input.gbs completeness element output.dat (coulomb)\n",argv[0]);
return 1;
}
std::string el(argv[3]);
std::string fileout(argv[4]);
bool coulomb=false;
if(argc==6)
coulomb=atoi(argv[5]);
// Get wanted element from basis
ElementBasisSet elbas=bas.get_element(el);
// Compute completeness profile
compprof_t prof=compute_completeness(elbas,-10.0,10.0,2001,coulomb);
// Print profile in output file
FILE *out=fopen(fileout.c_str(),"w");
for(size_t i=0;i<prof.lga.size();i++) {
// Value of scanning exponent
fprintf(out,"%13e",prof.lga[i]);
// Print completeness of shells
for(size_t j=0;j<prof.shells.size();j++)
fprintf(out,"\t%13e",prof.shells[j].Y[i]);
fprintf(out,"\n");
}
fclose(out);
} else if(stricmp(cmd,"composition")==0) {
// Determine composition of basis set.
if(argc!=3 && argc!=4) {
printf("\nUsage: %s input.gbs composition (El)\n",argv[0]);
return 1;
}
// Elemental basis sets
std::vector<ElementBasisSet> elbases;
if(argc==4)
elbases.push_back(bas.get_element(argv[3]));
else
elbases=bas.get_elements();
printf("\n");
printf("el at# [npr|nbf] [primitive|contracted(?)]\n");
printf("-------------------------------------------\n");
// Loop over elements
for(size_t iel=0;iel<elbases.size();iel++) {
// Get the basis set
ElementBasisSet elbas=elbases[iel];
// Decontracted basis
ElementBasisSet eldec(elbas);
eldec.decontract();
// Get the shells
std::vector<FunctionShell> sh=elbas.get_shells();
std::vector<FunctionShell> decsh=eldec.get_shells();
// Count the shells
arma::imat Nsh(max_am,2);
Nsh.zeros();
for(size_t ish=0;ish<decsh.size();ish++)
Nsh(decsh[ish].get_am(),0)++;
for(size_t ish=0;ish<sh.size();ish++)
Nsh(sh[ish].get_am(),1)++;
// Determine if basis set is contracted and the amount of
// functions
bool contr=false;
size_t nbf=0;
size_t nprim=0;
for(int am=0;am<max_am;am++) {
// Number of primitives
nprim+=Nsh(am,0)*(2*am+1);
// Number of contracted functions
nbf+=Nsh(am,1)*(2*am+1);
}
if(nbf!=nprim)
contr=true;
// Print composition
printf("%-2s %3i ",elbas.get_symbol().c_str(),(int) elbas.get_number());
if(contr) {
// Print amount of functions
char cmp[20];
sprintf(cmp,"[%i|%i]",(int) nprim,(int) nbf);
printf("%10s [",cmp);
// Print primitives
for(int am=0;am<max_am;am++)
if(Nsh(am,0)>0)
printf("%i%c",Nsh(am,0),tolower(shell_types[am]));
// Print contractions
printf("|");
for(int am=0;am<max_am;am++)
if(Nsh(am,0)!=Nsh(am,1))
printf("%i%c",Nsh(am,1),tolower(shell_types[am]));
printf("]\n");
} else {
printf("%10i ",(int) nbf);
for(int am=0;am<max_am;am++)
if(Nsh(am,0)>0)
printf("%i%c",Nsh(am,0),tolower(shell_types[am]));
printf("\n");
}
}
} else if(stricmp(cmd,"daug")==0 || stricmp(cmd,"taug")==0) {
// Augment basis set
if(argc!=4) {
printf("\nUsage: %s input.gbs %s output.gbs\n",argv[0],tolower(cmd).c_str());
return 1;
}
int naug;
if(stricmp(cmd,"daug")==0)
naug=1;
else
naug=2;
std::string fileout(argv[3]);
bas.augment(naug);
bas.save_gaussian94(fileout);
} else if(stricmp(cmd,"decontract")==0) {
// Decontract basis set.
if(argc!=4) {
printf("\nUsage: %s input.gbs decontract output.gbs\n",argv[0]);
return 1;
}
std::string fileout(argv[3]);
bas.decontract();
bas.save_gaussian94(fileout);
} else if(stricmp(cmd,"densityfit")==0) {
// Generate density fitted set
if(argc!=6) {
printf("\nUsage: %s input.gbs densityfit lval fsam output.gbs\n",argv[0]);
return 1;
}
int lval(atoi(argv[3]));
double fsam(atof(argv[4]));
std::string fileout(argv[5]);
BasisSetLibrary dfit(bas.density_fitting(lval,fsam));
dfit.save_gaussian94(fileout);
} else if(stricmp(cmd,"dump")==0) {
// Dump wanted element.
if(argc!=5 && argc!=6) {
printf("\nUsage: %s input.gbs dump element output.gbs (number)\n",argv[0]);
return 1;
}
std::string el(argv[3]);
std::string fileout(argv[4]);
int no=0;
if(argc==6)
no=atoi(argv[5]);
// Save output
BasisSetLibrary elbas;
elbas.add_element(bas.get_element(el,no));
elbas.save_gaussian94(fileout);
} else if(stricmp(cmd,"dumpdec")==0) {
// Dump wanted element in decontracted form.
if(argc!=5 && argc!=6) {
printf("\nUsage: %s input.gbs dumpdec element output.gbs (number)\n",argv[0]);
return 1;
}
std::string el(argv[3]);
std::string fileout(argv[4]);
int no=0;
if(argc==6)
no=atoi(argv[5]);
// Save output
BasisSetLibrary elbas;
bas.decontract();
elbas.add_element(bas.get_element(el,no));
elbas.save_gaussian94(fileout);
} else if(stricmp(cmd,"genbas")==0) {
// Generate basis set for xyz file
if(argc!=5) {
printf("\nUsage: %s input.gbs genbas system.xyz output.gbs\n",argv[0]);
return 1;
}
// Load atoms from xyz file
std::vector<atom_t> atoms=load_xyz(argv[3]);
// Output file
std::string fileout(argv[4]);
// Save output
BasisSetLibrary elbas;
// Collect elements
std::vector<ElementBasisSet> els=bas.get_elements();
// Loop over atoms in system
for(size_t iat=0;iat<atoms.size();iat++) {
bool found=false;
// First, check if there is a special basis for the atom.
for(size_t iel=0;iel<els.size();iel++)
if(stricmp(atoms[iat].el,els[iel].get_symbol())==0 && atoms[iat].num == els[iel].get_number()) {
// Yes, add it.
elbas.add_element(els[iel]);
found=true;
break;
}
// Otherwise, check if a general basis is already in the basis
if(!found) {
std::vector<ElementBasisSet> added=elbas.get_elements();
for(size_t j=0;j<added.size();j++)
if(added[j].get_number()==0 && stricmp(atoms[iat].el,added[j].get_symbol())==0)
found=true;
}
// If general basis not found, add it.
if(!found) {
for(size_t iel=0;iel<els.size();iel++)
if(stricmp(atoms[iat].el,els[iel].get_symbol())==0 && els[iel].get_number()==0) {
// Yes, add it.
elbas.add_element(els[iel]);
found=true;
break;
}
}
if(!found) {
std::ostringstream oss;
oss << "Basis set for element " << atoms[iat].el << " does not exist in " << filein << "!\n";
throw std::runtime_error(oss.str());
}
}
elbas.save_gaussian94(fileout);
} else if(stricmp(cmd,"merge")==0) {
// Merge functions with too big overlap
if(argc!=5) {
printf("\nUsage: %s input.gbs merge cutoff output.gbs\n",argv[0]);
return 1;
}
// Cutoff value
double cutoff=atof(argv[3]);
bas.merge(cutoff);
bas.save_gaussian94(argv[4]);
} else if(stricmp(cmd,"norm")==0) {
// Normalize basis
if(argc!=4) {
printf("\nUsage: %s input.gbs norm output.gbs\n",argv[0]);
return 1;
}
std::string fileout=argv[3];
bas.normalize();
bas.save_gaussian94(fileout);
} else if(stricmp(cmd,"orth")==0) {
// Orthogonalize basis
if(argc!=4) {
printf("\nUsage: %s input.gbs orth output.gbs\n",argv[0]);
return 1;
}
std::string fileout=argv[3];
bas.orthonormalize();
bas.save_gaussian94(fileout);
} else if(stricmp(cmd,"overlap")==0) {
// Primitive overlap
if(argc!=4) {
printf("\nUsage: %s input.gbs overlap element\n",argv[0]);
return 1;
}
// Get element basis set
ElementBasisSet elbas=bas.get_element(argv[3]);
elbas.decontract();
// Loop over angular momentum
for(int am=0;am<=elbas.get_max_am();am++) {
// Get primitives
arma::vec exps;
arma::mat contr;
elbas.get_primitives(exps,contr,am);
// Compute overlap matrix
arma::mat S=overlap(exps,exps,am);
// Print out overlap
printf("*** %c shell ***\n",shell_types[am]);
exps.t().print("Exponents");
printf("\n");
S.print("Overlap");
printf("\n");
}
} else if(stricmp(cmd,"Porth")==0) {
// P-orthogonalize basis
if(argc!=6) {
printf("\nUsage: %s input.gbs Porth cutoff Cortho output.gbs\n",argv[0]);
return 1;
}
double cutoff=atof(argv[3]);
double Cortho=atof(argv[4]);
std::string fileout=argv[5];
bas.P_orthogonalize(cutoff,Cortho);
bas.save_gaussian94(fileout);
} else if(stricmp(cmd,"prodset")==0) {
// Generate product set
if(argc!=6) {
printf("\nUsage: %s input.gbs prodset lval fsam output.gbs\n",argv[0]);
return 1;
}
int lval(atoi(argv[3]));
double fsam(atof(argv[4]));
std::string fileout(argv[5]);
BasisSetLibrary dfit(bas.product_set(lval,fsam));
dfit.save_gaussian94(fileout);
} else if(stricmp(cmd,"save")==0) {
// Save basis
if(argc!=4) {
printf("\nUsage: %s input.gbs save output.gbs\n",argv[0]);
return 1;
}
std::string fileout=argv[3];
bas.save_gaussian94(fileout);
} else if(stricmp(cmd,"savecfour")==0) {
// Save basis in CFOUR format
if(argc!=5) {
printf("\nUsage: %s input.gbs savecfour name basis.cfour\n",argv[0]);
return 1;
}
std::string fileout=argv[3];
std::string name=argv[4];
bas.save_cfour(name,fileout);
} else if(stricmp(cmd,"savedalton")==0) {
// Save basis in Dalton format
if(argc!=4) {
printf("\nUsage: %s input.gbs savedalton output.dal\n",argv[0]);
return 1;
}
std::string fileout=argv[3];
bas.save_dalton(fileout);
} else if(stricmp(cmd,"savemolpro")==0) {
// Save basis in Molpro format
if(argc!=4) {
printf("\nUsage: %s input.gbs savemolpro output.mol\n",argv[0]);
return 1;
}
std::string fileout=argv[3];
bas.save_molpro(fileout);
} else if(stricmp(cmd,"sort")==0) {
// Sort basis set
if(argc!=4) {
printf("\nUsage: %s input.gbs sort output.gbs\n",argv[0]);
return 1;
}
std::string fileout=argv[3];
bas.sort();
bas.save_gaussian94(fileout);
} else {
printf("\nInvalid command.\n");
help();
}
return 0;
}
int main(int argc, char **argv) {
#ifdef _OPENMP
printf("ERKALE - Geometry optimization from Hel, OpenMP version, running on %i cores.\n",omp_get_max_threads());
#else
printf("ERKALE - Geometry optimization from Hel, serial version.\n");
#endif
print_copyright();
print_license();
#ifdef SVNRELEASE
printf("At svn revision %s.\n\n",SVNREVISION);
#endif
print_hostname();
if(argc!=2) {
printf("Usage: $ %s runfile\n",argv[0]);
return 0;
}
// Initialize libint
init_libint_base();
// Initialize libderiv
init_libderiv_base();
Timer tprog;
tprog.print_time();
// Parse settings
Settings set;
set.add_scf_settings();
set.add_string("SaveChk","File to use as checkpoint","erkale.chk");
set.add_string("LoadChk","File to load old results from","");
set.add_bool("ForcePol","Force polarized calculation",false);
set.add_bool("FreezeCore","Freeze the atomic cores?",false);
set.add_string("Optimizer","Optimizer to use: CGFR, CGPR, BFGS, BFGS2 (default), SD","BFGS2");
set.add_int("MaxSteps","Maximum amount of geometry steps",256);
set.add_string("Criterion","Convergence criterion to use: LOOSE, NORMAL, TIGHT, VERYTIGHT","NORMAL");
set.add_string("OptMovie","xyz movie to store progress in","optimize.xyz");
set.add_string("Result","File to save optimized geometry in","optimized.xyz");
set.set_string("Logfile","erkale_geom.log");
set.parse(std::string(argv[1]),true);
set.print();
bool verbose=set.get_bool("Verbose");
int maxiter=set.get_int("MaxSteps");
std::string optmovie=set.get_string("OptMovie");
std::string result=set.get_string("Result");
// Interpret optimizer
enum minimizer alg;
std::string method=set.get_string("Optimizer");
if(stricmp(method,"CGFR")==0)
alg=gCGFR;
else if(stricmp(method,"CGPR")==0)
alg=gCGPR;
else if(stricmp(method,"BFGS")==0)
alg=gBFGS;
else if(stricmp(method,"BFGS2")==0)
alg=gBFGS2;
else if(stricmp(method,"SD")==0)
alg=gSD;
else {
ERROR_INFO();
throw std::runtime_error("Unknown optimization method.\n");
}
// Interpret optimizer
enum convergence crit;
method=set.get_string("Criterion");
if(stricmp(method,"LOOSE")==0)
crit=LOOSE;
else if(stricmp(method,"NORMAL")==0)
crit=NORMAL;
else if(stricmp(method,"TIGHT")==0)
crit=TIGHT;
else if(stricmp(method,"VERYTIGHT")==0)
crit=VERYTIGHT;
else {
ERROR_INFO();
throw std::runtime_error("Unknown optimization method.\n");
}
// Redirect output?
std::string logfile=set.get_string("Logfile");
if(stricmp(logfile,"stdout")!=0) {
// Redirect stdout to file
FILE *outstream=freopen(logfile.c_str(),"w",stdout);
if(outstream==NULL) {
ERROR_INFO();
throw std::runtime_error("Unable to redirect output!\n");
} else
fprintf(stderr,"\n");
}
// Read in atoms.
std::string atomfile=set.get_string("System");
const std::vector<atom_t> origgeom=load_xyz(atomfile);
std::vector<atom_t> atoms(origgeom);
// Are any atoms fixed?
std::vector<size_t> dofidx;
for(size_t i=0;i<atoms.size();i++) {
bool fixed=false;
if(atoms[i].el.size()>3)
if(stricmp(atoms[i].el.substr(atoms[i].el.size()-3),"-Fx")==0) {
fixed=true;
atoms[i].el=atoms[i].el.substr(0,atoms[i].el.size()-3);
}
// Add to degrees of freedom
if(!fixed)
dofidx.push_back(i);
}
// Read in basis set
BasisSetLibrary baslib;
std::string basfile=set.get_string("Basis");
baslib.load_gaussian94(basfile);
printf("\n");
// Save to output
save_xyz(atoms,"Initial configuration",optmovie,false);
// Minimizer options
opthelper_t pars;
pars.atoms=atoms;
pars.baslib=baslib;
pars.set=set;
pars.dofidx=dofidx;
/* Starting point */
gsl_vector *x = gsl_vector_alloc (3*dofidx.size());
for(size_t i=0;i<dofidx.size();i++) {
gsl_vector_set(x,3*i,atoms[dofidx[i]].x);
gsl_vector_set(x,3*i+1,atoms[dofidx[i]].y);
gsl_vector_set(x,3*i+2,atoms[dofidx[i]].z);
}
// GSL status
int status;
const gsl_multimin_fdfminimizer_type *T;
gsl_multimin_fdfminimizer *s;
gsl_multimin_function_fdf minimizer;
minimizer.n = x->size;
minimizer.f = calc_E;
minimizer.df = calc_f;
minimizer.fdf = calc_Ef;
minimizer.params = (void *) &pars;
if(alg==gCGFR) {
T = gsl_multimin_fdfminimizer_conjugate_fr;
if(verbose) printf("Using Fletcher-Reeves conjugate gradients.\n");
} else if(alg==gCGPR) {
T = gsl_multimin_fdfminimizer_conjugate_pr;
if(verbose) printf("Using Polak-Ribière conjugate gradients.\n");
} else if(alg==gBFGS) {
T = gsl_multimin_fdfminimizer_vector_bfgs;
if(verbose) printf("Using the BFGS minimizer.\n");
} else if(alg==gBFGS2) {
T = gsl_multimin_fdfminimizer_vector_bfgs2;
if(verbose) printf("Using the BFGS2 minimizer.\n");
} else if(alg==gSD) {
T = gsl_multimin_fdfminimizer_steepest_descent;
if(verbose) printf("Using the steepest descent minimizer.\n");
} else {
ERROR_INFO();
throw std::runtime_error("Unsupported minimizer\n");
}
// Run an initial calculation
double oldE=calc_E(x,minimizer.params);
// Turn off verbose setting
pars.set.set_bool("Verbose",false);
// and load from old checkpoint
pars.set.set_string("LoadChk",pars.set.get_string("SaveChk"));
// Initialize minimizer
s = gsl_multimin_fdfminimizer_alloc (T, minimizer.n);
// Use initial step length of 0.02 bohr, and a line search accuracy
// 1e-1 (recommended in the GSL manual for BFGS)
gsl_multimin_fdfminimizer_set (s, &minimizer, x, 0.02, 1e-1);
// Store old force
arma::mat oldf=interpret_force(s->gradient);
fprintf(stderr,"Geometry optimizer initialized in %s.\n",tprog.elapsed().c_str());
fprintf(stderr,"Entering minimization loop with %s optimizer.\n",set.get_string("Optimizer").c_str());
fprintf(stderr,"%4s %16s %10s %10s %9s %9s %9s %9s %s\n","iter","E","dE","dE/dEproj","disp max","disp rms","f max","f rms", "titer");
std::vector<atom_t> oldgeom(atoms);
bool convd=false;
int iter;
for(iter=1;iter<=maxiter;iter++) {
printf("\nGeometry iteration %i\n",(int) iter);
fflush(stdout);
Timer titer;
status = gsl_multimin_fdfminimizer_iterate (s);
if (status) {
fprintf(stderr,"GSL encountered error: \"%s\".\n",gsl_strerror(status));
break;
}
// New geometry is
std::vector<atom_t> geom=get_atoms(s->x,pars);
// Calculate displacements
double dmax, drms;
get_displacement(geom, oldgeom, dmax, drms);
// Calculate projected change of energy
double dEproj=calculate_projection(geom,oldgeom,oldf,pars.dofidx);
// Actual change of energy is
double dE=s->f - oldE;
// Switch geometries
oldgeom=geom;
// Save old force
// Get forces
double fmax, frms;
get_forces(s->gradient, fmax, frms);
// Save geometry step
char comment[80];
sprintf(comment,"Step %i",(int) iter);
save_xyz(get_atoms(s->x,pars),comment,optmovie,true);
// Check convergence
bool fmaxconv=false, frmsconv=false;
bool dmaxconv=false, drmsconv=false;
switch(crit) {
case(LOOSE):
if(fmax < 2.5e-3)
fmaxconv=true;
if(frms < 1.7e-3)
frmsconv=true;
if(dmax < 1.0e-2)
dmaxconv=true;
if(drms < 6.7e-3)
drmsconv=true;
break;
case(NORMAL):
if(fmax < 4.5e-4)
fmaxconv=true;
if(frms < 3.0e-4)
frmsconv=true;
if(dmax < 1.8e-3)
dmaxconv=true;
if(drms < 1.2e-3)
drmsconv=true;
break;
case(TIGHT):
if(fmax < 1.5e-5)
fmaxconv=true;
if(frms < 1.0e-5)
frmsconv=true;
if(dmax < 6.0e-5)
dmaxconv=true;
if(drms < 4.0e-5)
drmsconv=true;
break;
case(VERYTIGHT):
if(fmax < 2.0e-6)
fmaxconv=true;
if(frms < 1.0e-6)
frmsconv=true;
if(dmax < 6.0e-6)
dmaxconv=true;
if(drms < 4.0e-6)
drmsconv=true;
break;
default:
ERROR_INFO();
throw std::runtime_error("Not implemented!\n");
}
// Converged?
const static char cconv[]=" *";
double dEfrac;
if(dEproj!=0.0)
dEfrac=dE/dEproj;
else
dEfrac=0.0;
fprintf(stderr,"%4d % 16.8f % .3e % .3e %.3e%c %.3e%c %.3e%c %.3e%c %s\n", (int) iter, s->f, dE, dEfrac, dmax, cconv[dmaxconv], drms, cconv[drmsconv], fmax, cconv[fmaxconv], frms, cconv[frmsconv], titer.elapsed().c_str());
fflush(stderr);
convd=dmaxconv && drmsconv && fmaxconv && frmsconv;
if(convd) {
fprintf(stderr,"Converged.\n");
break;
}
// Store old energy
oldE=s->f;
// Store old force
oldf=interpret_force(s->gradient);
}
if(convd)
save_xyz(get_atoms(s->x,pars),"Optimized geometry",result);
gsl_multimin_fdfminimizer_free (s);
gsl_vector_free (x);
if(iter==maxiter && !convd) {
printf("Geometry convergence was not achieved!\n");
}
printf("Running program took %s.\n",tprog.elapsed().c_str());
return 0;
}
void
nb_kernel231_ppc_altivec (int * p_nri,
int iinr[],
int jindex[],
int jjnr[],
int shift[],
float shiftvec[],
float fshift[],
int gid[],
float pos[],
float faction[],
float charge[],
float * p_facel,
float * p_krf,
float * p_crf,
float Vc[],
int type[],
int * p_ntype,
float vdwparam[],
float Vvdw[],
float * p_tabscale,
float VFtab[],
float invsqrta[],
float dvda[],
float * p_gbtabscale,
float GBtab[],
int * p_nthreads,
int * count,
void * mtx,
int * outeriter,
int * inneriter,
float * work)
{
vector float vkrf,vcrf;
vector float iOx,iOy,iOz,iH1x,iH1y,iH1z,iH2x,iH2y,iH2z;
vector float dOx,dOy,dOz,dH1x,dH1y,dH1z,dH2x,dH2y,dH2z;
vector float vfacel,vcoulO,vcoulH1,vcoulH2,nul;
vector float Vvdwtot,c6,c12,VVd,VVr,FFd,FFr,tsc,r;
vector float fsO,fsH1,fsH2,krsqO,krsqH1,krsqH2;
vector float vctot,qqO,qqH,iqO,iqH,jq;
vector float fiOx,fiOy,fiOz,fiH1x,fiH1y,fiH1z,fiH2x,fiH2y,fiH2z;
vector float tmp1,tmp2,tmp3,tmp4;
vector float rinvO,rinvH1,rinvH2,rinvsqH1,rinvsqH2;
vector float rsqO,rsqH1,rsqH2;
int n,k,ii,is3,ii3,ntiA,nj0,nj1;
int jnra,jnrb,jnrc,jnrd;
int j3a,j3b,j3c,j3d;
int nri, ntype, nouter, ninner;
int tja,tjb,tjc,tjd;
#ifdef GMX_THREAD_SHM_FDECOMP
int nn0, nn1;
#endif
nouter = 0;
ninner = 0;
nri = *p_nri;
ntype = *p_ntype;
nul=vec_zero();
tsc=load_float_and_splat(p_tabscale);
vfacel=load_float_and_splat(p_facel);
vkrf=load_float_and_splat(p_krf);
vcrf=load_float_and_splat(p_crf);
ii = iinr[0];
iqO = vec_madd(load_float_and_splat(charge+ii),vfacel,nul);
iqH = vec_madd(load_float_and_splat(charge+ii+1),vfacel,nul);
ntiA = 2*ntype*type[ii];
#ifdef GMX_THREAD_SHM_FDECOMP
nthreads = *p_nthreads;
do {
tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
nn0 = *count;
nn1 = nn0+(nri-nn0)/(2*nthreads)+3;
*count = nn1;
tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
if(nn1>nri) nn1=nri;
for(n=nn0; (n<nn1); n++) {
#if 0
} /* maintain correct indentation even with conditional left braces */
#endif
#else /* without tMPI_Threads */
for(n=0;n<nri;n++) {
#endif
is3 = 3*shift[n];
ii = iinr[n];
ii3 = 3*ii;
load_1_3atoms_shift_and_splat(pos+ii3,shiftvec+is3,&iOx,&iOy,&iOz,
&iH1x,&iH1y,&iH1z,&iH2x,&iH2y,&iH2z);
vctot = nul;
Vvdwtot = nul;
fiOx = nul;
fiOy = nul;
fiOz = nul;
fiH1x = nul;
fiH1y = nul;
fiH1z = nul;
fiH2x = nul;
fiH2y = nul;
fiH2z = nul;
nj0 = jindex[n];
nj1 = jindex[n+1];
for(k=nj0; k<(nj1-3); k+=4) {
jnra = jjnr[k];
jnrb = jjnr[k+1];
jnrc = jjnr[k+2];
jnrd = jjnr[k+3];
j3a = 3*jnra;
j3b = 3*jnrb;
j3c = 3*jnrc;
j3d = 3*jnrd;
transpose_4_to_3(load_xyz(pos+j3a),
load_xyz(pos+j3b),
load_xyz(pos+j3c),
load_xyz(pos+j3d),&dH2x,&dH2y,&dH2z);
dOx = vec_sub(iOx,dH2x);
dOy = vec_sub(iOy,dH2y);
dOz = vec_sub(iOz,dH2z);
dH1x = vec_sub(iH1x,dH2x);
dH1y = vec_sub(iH1y,dH2y);
dH1z = vec_sub(iH1z,dH2z);
dH2x = vec_sub(iH2x,dH2x);
dH2y = vec_sub(iH2y,dH2y);
dH2z = vec_sub(iH2z,dH2z);
rsqO = vec_madd(dOx,dOx,nul);
rsqH1 = vec_madd(dH1x,dH1x,nul);
rsqH2 = vec_madd(dH2x,dH2x,nul);
rsqO = vec_madd(dOy,dOy,rsqO);
rsqH1 = vec_madd(dH1y,dH1y,rsqH1);
rsqH2 = vec_madd(dH2y,dH2y,rsqH2);
rsqO = vec_madd(dOz,dOz,rsqO);
rsqH1 = vec_madd(dH1z,dH1z,rsqH1);
rsqH2 = vec_madd(dH2z,dH2z,rsqH2);
do_3_invsqrt(rsqO,rsqH1,rsqH2,&rinvO,&rinvH1,&rinvH2);
rinvsqH1 = vec_madd(rinvH1,rinvH1,nul);
rinvsqH2 = vec_madd(rinvH2,rinvH2,nul);
r = vec_madd(rinvO,rsqO,nul);
tja = ntiA+2*type[jnra];
tjb = ntiA+2*type[jnrb];
tjc = ntiA+2*type[jnrc];
tjd = ntiA+2*type[jnrd];
/* load 4 j charges and multiply by iq */
jq=load_4_float(charge+jnra,charge+jnrb,
charge+jnrc,charge+jnrd);
load_4_pair(vdwparam+tja,vdwparam+tjb,vdwparam+tjc,vdwparam+tjd,&c6,&c12);
do_4_ljtable_lj(VFtab,vec_madd(r,tsc,nul),&VVd,&FFd,&VVr,&FFr);
Vvdwtot = vec_madd(c6,VVd,Vvdwtot);
tmp1 = vec_nmsub(c6,FFd,nul);
Vvdwtot = vec_madd(c12,VVr,Vvdwtot);
tmp1 = vec_nmsub(c12,FFr,tmp1);
tmp1 = vec_madd(tmp1,tsc,nul);
qqO = vec_madd(iqO,jq,nul);
qqH = vec_madd(iqH,jq,nul);
krsqO = vec_madd(vkrf,rsqO,nul);
krsqH1 = vec_madd(vkrf,rsqH1,nul);
krsqH2 = vec_madd(vkrf,rsqH2,nul);
fsO = vec_nmsub(vec_two(),krsqO,rinvO);
vcoulO = vec_add(rinvO,krsqO);
vcoulH1 = vec_add(rinvH1,krsqH1);
fsO = vec_madd(qqO,fsO,nul);
vcoulH2 = vec_add(rinvH2,krsqH2);
vcoulO = vec_sub(vcoulO,vcrf);
vcoulH1 = vec_sub(vcoulH1,vcrf);
vcoulH2 = vec_sub(vcoulH2,vcrf);
vctot = vec_madd(qqO,vcoulO,vctot);
fsH1 = vec_nmsub(vec_two(),krsqH1,rinvH1);
fsH2 = vec_nmsub(vec_two(),krsqH2,rinvH2);
vctot = vec_madd(qqH,vcoulH1,vctot);
fsO = vec_madd(fsO,rinvO,tmp1);
fsO = vec_madd(fsO,rinvO,nul);
fsH1 = vec_madd(fsH1,qqH,nul);
fsH2 = vec_madd(fsH2,qqH,nul);
vctot = vec_madd(qqH,vcoulH2,vctot);
fsH1 = vec_madd(fsH1,rinvsqH1,nul);
fsH2 = vec_madd(fsH2,rinvsqH2,nul);
fiOx = vec_madd(fsO,dOx,fiOx); /* +=fx */
dOx = vec_nmsub(fsO,dOx,nul); /* -fx */
fiOy = vec_madd(fsO,dOy,fiOy); /* +=fy */
dOy = vec_nmsub(fsO,dOy,nul); /* -fy */
fiOz = vec_madd(fsO,dOz,fiOz); /* +=fz */
dOz = vec_nmsub(fsO,dOz,nul); /* -fz */
fiH1x = vec_madd(fsH1,dH1x,fiH1x); /* +=fx */
dOx = vec_nmsub(fsH1,dH1x,dOx); /* -fx */
fiH1y = vec_madd(fsH1,dH1y,fiH1y); /* +=fy */
dOy = vec_nmsub(fsH1,dH1y,dOy); /* -fy */
fiH1z = vec_madd(fsH1,dH1z,fiH1z); /* +=fz */
dOz = vec_nmsub(fsH1,dH1z,dOz); /* -fz */
fiH2x = vec_madd(fsH2,dH2x,fiH2x); /* +=fx */
dOx = vec_nmsub(fsH2,dH2x,dOx); /* -fx */
fiH2y = vec_madd(fsH2,dH2y,fiH2y); /* +=fy */
dOy = vec_nmsub(fsH2,dH2y,dOy); /* -fy */
fiH2z = vec_madd(fsH2,dH2z,fiH2z); /* +=fz */
dOz = vec_nmsub(fsH2,dH2z,dOz); /* -fz */
transpose_3_to_4(dOx,dOy,dOz,&tmp1,&tmp2,&tmp3,&tmp4);
add_xyz_to_mem(faction+j3a,tmp1);
add_xyz_to_mem(faction+j3b,tmp2);
add_xyz_to_mem(faction+j3c,tmp3);
add_xyz_to_mem(faction+j3d,tmp4);
}
if(k<(nj1-2)) {
jnra = jjnr[k];
jnrb = jjnr[k+1];
jnrc = jjnr[k+2];
j3a = 3*jnra;
j3b = 3*jnrb;
j3c = 3*jnrc;
transpose_4_to_3(load_xyz(pos+j3a),
load_xyz(pos+j3b),
load_xyz(pos+j3c),nul,&dH2x,&dH2y,&dH2z);
dOx = vec_sub(iOx,dH2x);
dOy = vec_sub(iOy,dH2y);
dOz = vec_sub(iOz,dH2z);
dH1x = vec_sub(iH1x,dH2x);
dH1y = vec_sub(iH1y,dH2y);
dH1z = vec_sub(iH1z,dH2z);
dH2x = vec_sub(iH2x,dH2x);
dH2y = vec_sub(iH2y,dH2y);
dH2z = vec_sub(iH2z,dH2z);
rsqO = vec_madd(dOx,dOx,nul);
rsqH1 = vec_madd(dH1x,dH1x,nul);
rsqH2 = vec_madd(dH2x,dH2x,nul);
rsqO = vec_madd(dOy,dOy,rsqO);
rsqH1 = vec_madd(dH1y,dH1y,rsqH1);
rsqH2 = vec_madd(dH2y,dH2y,rsqH2);
rsqO = vec_madd(dOz,dOz,rsqO);
rsqH1 = vec_madd(dH1z,dH1z,rsqH1);
rsqH2 = vec_madd(dH2z,dH2z,rsqH2);
zero_highest_element_in_3_vectors(&rsqO,&rsqH1,&rsqH2);
do_3_invsqrt(rsqO,rsqH1,rsqH2,&rinvO,&rinvH1,&rinvH2);
zero_highest_element_in_3_vectors(&rinvO,&rinvH1,&rinvH2);
r = vec_madd(rinvO,rsqO,nul);
rinvsqH1 = vec_madd(rinvH1,rinvH1,nul);
rinvsqH2 = vec_madd(rinvH2,rinvH2,nul);
jq=load_3_float(charge+jnra,charge+jnrb,charge+jnrc);
tja = ntiA+2*type[jnra];
tjb = ntiA+2*type[jnrb];
tjc = ntiA+2*type[jnrc];
load_3_pair(vdwparam+tja,vdwparam+tjb,vdwparam+tjc,&c6,&c12);
do_3_ljtable_lj(VFtab,vec_madd(r,tsc,nul),&VVd,&FFd,&VVr,&FFr);
Vvdwtot = vec_madd(c6,VVd,Vvdwtot);
tmp1 = vec_nmsub(c6,FFd,nul);
Vvdwtot = vec_madd(c12,VVr,Vvdwtot);
tmp1 = vec_nmsub(c12,FFr,tmp1);
tmp1 = vec_madd(tmp1,tsc,nul);
qqO = vec_madd(iqO,jq,nul);
qqH = vec_madd(iqH,jq,nul);
krsqO = vec_madd(vkrf,rsqO,nul);
krsqH1 = vec_madd(vkrf,rsqH1,nul);
krsqH2 = vec_madd(vkrf,rsqH2,nul);
fsO = vec_nmsub(vec_two(),krsqO,rinvO);
vcoulO = vec_add(rinvO,krsqO);
vcoulH1 = vec_add(rinvH1,krsqH1);
fsO = vec_madd(qqO,fsO,nul);
vcoulH2 = vec_add(rinvH2,krsqH2);
vcoulO = vec_sub(vcoulO,vcrf);
vcoulH1 = vec_sub(vcoulH1,vcrf);
vcoulH2 = vec_sub(vcoulH2,vcrf);
vctot = vec_madd(qqO,vcoulO,vctot);
fsH1 = vec_nmsub(vec_two(),krsqH1,rinvH1);
fsH2 = vec_nmsub(vec_two(),krsqH2,rinvH2);
vctot = vec_madd(qqH,vcoulH1,vctot);
fsO = vec_madd(fsO,rinvO,tmp1);
fsO = vec_madd(fsO,rinvO,nul);
fsH1 = vec_madd(fsH1,qqH,nul);
fsH2 = vec_madd(fsH2,qqH,nul);
vctot = vec_madd(qqH,vcoulH2,vctot);
fsH1 = vec_madd(fsH1,rinvsqH1,nul);
fsH2 = vec_madd(fsH2,rinvsqH2,nul);
fiOx = vec_madd(fsO,dOx,fiOx); /* +=fx */
dOx = vec_nmsub(fsO,dOx,nul); /* -fx */
fiOy = vec_madd(fsO,dOy,fiOy); /* +=fy */
dOy = vec_nmsub(fsO,dOy,nul); /* -fy */
fiOz = vec_madd(fsO,dOz,fiOz); /* +=fz */
dOz = vec_nmsub(fsO,dOz,nul); /* -fz */
fiH1x = vec_madd(fsH1,dH1x,fiH1x); /* +=fx */
dOx = vec_nmsub(fsH1,dH1x,dOx); /* -fx */
fiH1y = vec_madd(fsH1,dH1y,fiH1y); /* +=fy */
dOy = vec_nmsub(fsH1,dH1y,dOy); /* -fy */
fiH1z = vec_madd(fsH1,dH1z,fiH1z); /* +=fz */
dOz = vec_nmsub(fsH1,dH1z,dOz); /* -fz */
fiH2x = vec_madd(fsH2,dH2x,fiH2x); /* +=fx */
dOx = vec_nmsub(fsH2,dH2x,dOx); /* -fx */
fiH2y = vec_madd(fsH2,dH2y,fiH2y); /* +=fy */
dOy = vec_nmsub(fsH2,dH2y,dOy); /* -fy */
fiH2z = vec_madd(fsH2,dH2z,fiH2z); /* +=fz */
dOz = vec_nmsub(fsH2,dH2z,dOz); /* -fz */
transpose_4_to_3(dOx,dOy,dOz,nul,&tmp1,&tmp2,&tmp3);
add_xyz_to_mem(faction+j3a,tmp1);
add_xyz_to_mem(faction+j3b,tmp2);
add_xyz_to_mem(faction+j3c,tmp3);
} else if(k<(nj1-1)) {
jnra = jjnr[k];
jnrb = jjnr[k+1];
j3a = 3*jnra;
j3b = 3*jnrb;
transpose_2_to_3(load_xyz(pos+j3a),
load_xyz(pos+j3b),&dH2x,&dH2y,&dH2z);
dOx = vec_sub(iOx,dH2x);
dOy = vec_sub(iOy,dH2y);
dOz = vec_sub(iOz,dH2z);
dH1x = vec_sub(iH1x,dH2x);
dH1y = vec_sub(iH1y,dH2y);
dH1z = vec_sub(iH1z,dH2z);
dH2x = vec_sub(iH2x,dH2x);
dH2y = vec_sub(iH2y,dH2y);
dH2z = vec_sub(iH2z,dH2z);
rsqO = vec_madd(dOx,dOx,nul);
rsqH1 = vec_madd(dH1x,dH1x,nul);
rsqH2 = vec_madd(dH2x,dH2x,nul);
rsqO = vec_madd(dOy,dOy,rsqO);
rsqH1 = vec_madd(dH1y,dH1y,rsqH1);
rsqH2 = vec_madd(dH2y,dH2y,rsqH2);
rsqO = vec_madd(dOz,dOz,rsqO);
rsqH1 = vec_madd(dH1z,dH1z,rsqH1);
rsqH2 = vec_madd(dH2z,dH2z,rsqH2);
zero_highest_2_elements_in_3_vectors(&rsqO,&rsqH1,&rsqH2);
do_3_invsqrt(rsqO,rsqH1,rsqH2,&rinvO,&rinvH1,&rinvH2);
zero_highest_2_elements_in_3_vectors(&rinvO,&rinvH1,&rinvH2);
r = vec_madd(rinvO,rsqO,nul);
rinvsqH1 = vec_madd(rinvH1,rinvH1,nul);
rinvsqH2 = vec_madd(rinvH2,rinvH2,nul);
tja = ntiA+2*type[jnra];
tjb = ntiA+2*type[jnrb];
/* load 2 j charges and multiply by iq */
jq=load_2_float(charge+jnra,charge+jnrb);
load_2_pair(vdwparam+tja,vdwparam+tjb,&c6,&c12);
do_2_ljtable_lj(VFtab,vec_madd(r,tsc,nul),&VVd,&FFd,&VVr,&FFr);
Vvdwtot = vec_madd(c6,VVd,Vvdwtot);
tmp1 = vec_nmsub(c6,FFd,nul);
Vvdwtot = vec_madd(c12,VVr,Vvdwtot);
tmp1 = vec_nmsub(c12,FFr,tmp1);
tmp1 = vec_madd(tmp1,tsc,nul);
qqO = vec_madd(iqO,jq,nul);
qqH = vec_madd(iqH,jq,nul);
krsqO = vec_madd(vkrf,rsqO,nul);
krsqH1 = vec_madd(vkrf,rsqH1,nul);
krsqH2 = vec_madd(vkrf,rsqH2,nul);
fsO = vec_nmsub(vec_two(),krsqO,rinvO);
vcoulO = vec_add(rinvO,krsqO);
vcoulH1 = vec_add(rinvH1,krsqH1);
fsO = vec_madd(qqO,fsO,nul);
vcoulH2 = vec_add(rinvH2,krsqH2);
vcoulO = vec_sub(vcoulO,vcrf);
vcoulH1 = vec_sub(vcoulH1,vcrf);
vcoulH2 = vec_sub(vcoulH2,vcrf);
vctot = vec_madd(qqO,vcoulO,vctot);
fsH1 = vec_nmsub(vec_two(),krsqH1,rinvH1);
fsH2 = vec_nmsub(vec_two(),krsqH2,rinvH2);
vctot = vec_madd(qqH,vcoulH1,vctot);
fsO = vec_madd(fsO,rinvO,tmp1);
fsO = vec_madd(fsO,rinvO,nul);
fsH1 = vec_madd(fsH1,qqH,nul);
fsH2 = vec_madd(fsH2,qqH,nul);
vctot = vec_madd(qqH,vcoulH2,vctot);
fsH1 = vec_madd(fsH1,rinvsqH1,nul);
fsH2 = vec_madd(fsH2,rinvsqH2,nul);
fiOx = vec_madd(fsO,dOx,fiOx); /* +=fx */
dOx = vec_nmsub(fsO,dOx,nul); /* -fx */
fiOy = vec_madd(fsO,dOy,fiOy); /* +=fy */
dOy = vec_nmsub(fsO,dOy,nul); /* -fy */
fiOz = vec_madd(fsO,dOz,fiOz); /* +=fz */
dOz = vec_nmsub(fsO,dOz,nul); /* -fz */
fiH1x = vec_madd(fsH1,dH1x,fiH1x); /* +=fx */
dOx = vec_nmsub(fsH1,dH1x,dOx); /* -fx */
fiH1y = vec_madd(fsH1,dH1y,fiH1y); /* +=fy */
dOy = vec_nmsub(fsH1,dH1y,dOy); /* -fy */
fiH1z = vec_madd(fsH1,dH1z,fiH1z); /* +=fz */
dOz = vec_nmsub(fsH1,dH1z,dOz); /* -fz */
fiH2x = vec_madd(fsH2,dH2x,fiH2x); /* +=fx */
dOx = vec_nmsub(fsH2,dH2x,dOx); /* -fx */
fiH2y = vec_madd(fsH2,dH2y,fiH2y); /* +=fy */
dOy = vec_nmsub(fsH2,dH2y,dOy); /* -fy */
fiH2z = vec_madd(fsH2,dH2z,fiH2z); /* +=fz */
dOz = vec_nmsub(fsH2,dH2z,dOz); /* -fz */
transpose_3_to_2(dOx,dOy,dOz,&tmp1,&tmp2);
add_xyz_to_mem(faction+j3a,tmp1);
add_xyz_to_mem(faction+j3b,tmp2);
} else if(k<nj1) {
jnra = jjnr[k];
j3a = 3*jnra;
transpose_1_to_3(load_xyz(pos+j3a),&dH2x,&dH2y,&dH2z);
dOx = vec_sub(iOx,dH2x);
dOy = vec_sub(iOy,dH2y);
dOz = vec_sub(iOz,dH2z);
dH1x = vec_sub(iH1x,dH2x);
dH1y = vec_sub(iH1y,dH2y);
dH1z = vec_sub(iH1z,dH2z);
dH2x = vec_sub(iH2x,dH2x);
dH2y = vec_sub(iH2y,dH2y);
dH2z = vec_sub(iH2z,dH2z);
rsqO = vec_madd(dOx,dOx,nul);
rsqH1 = vec_madd(dH1x,dH1x,nul);
rsqH2 = vec_madd(dH2x,dH2x,nul);
rsqO = vec_madd(dOy,dOy,rsqO);
rsqH1 = vec_madd(dH1y,dH1y,rsqH1);
rsqH2 = vec_madd(dH2y,dH2y,rsqH2);
rsqO = vec_madd(dOz,dOz,rsqO);
rsqH1 = vec_madd(dH1z,dH1z,rsqH1);
rsqH2 = vec_madd(dH2z,dH2z,rsqH2);
zero_highest_3_elements_in_3_vectors(&rsqO,&rsqH1,&rsqH2);
do_3_invsqrt(rsqO,rsqH1,rsqH2,&rinvO,&rinvH1,&rinvH2);
zero_highest_3_elements_in_3_vectors(&rinvO,&rinvH1,&rinvH2);
r = vec_madd(rinvO,rsqO,nul);
rinvsqH1 = vec_madd(rinvH1,rinvH1,nul);
rinvsqH2 = vec_madd(rinvH2,rinvH2,nul);
tja = ntiA+2*type[jnra];
/* load 1 j charges and multiply by iq */
jq=load_1_float(charge+jnra);
load_1_pair(vdwparam+tja,&c6,&c12);
do_1_ljtable_lj(VFtab,vec_madd(r,tsc,nul),&VVd,&FFd,&VVr,&FFr);
Vvdwtot = vec_madd(c6,VVd,Vvdwtot);
tmp1 = vec_nmsub(c6,FFd,nul);
Vvdwtot = vec_madd(c12,VVr,Vvdwtot);
tmp1 = vec_nmsub(c12,FFr,tmp1);
tmp1 = vec_madd(tmp1,tsc,nul);
qqO = vec_madd(iqO,jq,nul);
qqH = vec_madd(iqH,jq,nul);
krsqO = vec_madd(vkrf,rsqO,nul);
krsqH1 = vec_madd(vkrf,rsqH1,nul);
krsqH2 = vec_madd(vkrf,rsqH2,nul);
fsO = vec_nmsub(vec_two(),krsqO,rinvO);
vcoulO = vec_add(rinvO,krsqO);
vcoulH1 = vec_add(rinvH1,krsqH1);
fsO = vec_madd(qqO,fsO,nul);
vcoulH2 = vec_add(rinvH2,krsqH2);
vcoulO = vec_sub(vcoulO,vcrf);
vcoulH1 = vec_sub(vcoulH1,vcrf);
vcoulH2 = vec_sub(vcoulH2,vcrf);
vctot = vec_madd(qqO,vcoulO,vctot);
fsH1 = vec_nmsub(vec_two(),krsqH1,rinvH1);
fsH2 = vec_nmsub(vec_two(),krsqH2,rinvH2);
vctot = vec_madd(qqH,vcoulH1,vctot);
fsO = vec_madd(fsO,rinvO,tmp1);
fsO = vec_madd(fsO,rinvO,nul);
fsH1 = vec_madd(fsH1,qqH,nul);
fsH2 = vec_madd(fsH2,qqH,nul);
vctot = vec_madd(qqH,vcoulH2,vctot);
fsH1 = vec_madd(fsH1,rinvsqH1,nul);
fsH2 = vec_madd(fsH2,rinvsqH2,nul);
fiOx = vec_madd(fsO,dOx,fiOx); /* +=fx */
dOx = vec_nmsub(fsO,dOx,nul); /* -fx */
fiOy = vec_madd(fsO,dOy,fiOy); /* +=fy */
dOy = vec_nmsub(fsO,dOy,nul); /* -fy */
fiOz = vec_madd(fsO,dOz,fiOz); /* +=fz */
dOz = vec_nmsub(fsO,dOz,nul); /* -fz */
fiH1x = vec_madd(fsH1,dH1x,fiH1x); /* +=fx */
dOx = vec_nmsub(fsH1,dH1x,dOx); /* -fx */
fiH1y = vec_madd(fsH1,dH1y,fiH1y); /* +=fy */
dOy = vec_nmsub(fsH1,dH1y,dOy); /* -fy */
fiH1z = vec_madd(fsH1,dH1z,fiH1z); /* +=fz */
dOz = vec_nmsub(fsH1,dH1z,dOz); /* -fz */
fiH2x = vec_madd(fsH2,dH2x,fiH2x); /* +=fx */
dOx = vec_nmsub(fsH2,dH2x,dOx); /* -fx */
fiH2y = vec_madd(fsH2,dH2y,fiH2y); /* +=fy */
dOy = vec_nmsub(fsH2,dH2y,dOy); /* -fy */
fiH2z = vec_madd(fsH2,dH2z,fiH2z); /* +=fz */
dOz = vec_nmsub(fsH2,dH2z,dOz); /* -fz */
transpose_3_to_1(dOx,dOy,dOz,&tmp1);
add_xyz_to_mem(faction+j3a,tmp1);
}
/* update outer data */
update_i_3atoms_forces(faction+ii3,fshift+is3,
fiOx,fiOy,fiOz,fiH1x,fiH1y,fiH1z,
fiH2x,fiH2y,fiH2z);
add_vector_to_float(Vc+gid[n],vctot);
add_vector_to_float(Vvdw+gid[n],Vvdwtot);
ninner += nj1 - nj0;
}
#ifdef GMX_THREAD_SHM_FDECOMP
nouter += nn1 - nn0;
} while (nn1<nri);
#else
nouter = nri;
#endif
*outeriter = nouter;
*inneriter = ninner;
}
void
nb_kernel400_ppc_altivec (int * p_nri,
int iinr[],
int jindex[],
int jjnr[],
int shift[],
float shiftvec[],
float fshift[],
int gid[],
float pos[],
float faction[],
float charge[],
float * p_facel,
float * p_krf,
float * p_crf,
float Vc[],
int type[],
int * p_ntype,
float vdwparam[],
float Vvdw[],
float * p_tabscale,
float VFtab[],
float invsqrta[],
float dvda[],
float * p_gbtabscale,
float GBtab[],
int * p_nthreads,
int * count,
void * mtx,
int * outeriter,
int * inneriter,
float * work)
{
vector float ix,iy,iz,shvec;
vector float vfacel,fs,nul;
vector float dx,dy,dz;
vector float vctot,qq,iq;
vector float fix,fiy,fiz;
vector float tmp1,tmp2,tmp3,tmp4;
vector float rinv,r,rsq,VVc,FFc;
vector float isai,isaj,isaprod,gbtsc,dvdasum,dvdaj,dvdatmp,gbscale,half;
int n,k,ii,is3,ii3,nj0,nj1;
int jnra,jnrb,jnrc,jnrd;
int j3a,j3b,j3c,j3d;
int nri, ntype, nouter, ninner;
#ifdef GMX_THREADS
int nn0, nn1;
#endif
nouter = 0;
ninner = 0;
nri = *p_nri;
ntype = *p_ntype;
nul=vec_zero();
half=vec_half();
vfacel=load_float_and_splat(p_facel);
gbtsc=load_float_and_splat(p_gbtabscale);
#ifdef GMX_THREADS
nthreads = *p_nthreads;
do {
gmx_thread_mutex_lock((gmx_thread_mutex_t *)mtx);
nn0 = *count;
nn1 = nn0+(nri-nn0)/(2*nthreads)+3;
*count = nn1;
gmx_thread_mutex_unlock((gmx_thread_mutex_t *)mtx);
if(nn1>nri) nn1=nri;
for(n=nn0; (n<nn1); n++) {
#if 0
} /* maintain correct indentation even with conditional left braces */
#endif
#else /* without gmx_threads */
for(n=0;n<nri;n++) {
#endif
is3 = 3*shift[n];
shvec = load_xyz(shiftvec+is3);
ii = iinr[n];
ii3 = 3*ii;
ix = load_xyz(pos+ii3);
vctot = nul;
dvdasum = nul;
fix = nul;
fiy = nul;
fiz = nul;
ix = vec_add(ix,shvec);
nj0 = jindex[n];
nj1 = jindex[n+1];
splat_xyz_to_vectors(ix,&ix,&iy,&iz);
iq = vec_madd(load_float_and_splat(charge+ii),vfacel,nul);
isai = load_float_and_splat(invsqrta+ii);
for(k=nj0; k<(nj1-3); k+=4) {
jnra = jjnr[k];
jnrb = jjnr[k+1];
jnrc = jjnr[k+2];
jnrd = jjnr[k+3];
j3a = 3*jnra;
j3b = 3*jnrb;
j3c = 3*jnrc;
j3d = 3*jnrd;
transpose_4_to_3(load_xyz(pos+j3a),
load_xyz(pos+j3b),
load_xyz(pos+j3c),
load_xyz(pos+j3d),&dx,&dy,&dz);
dx = vec_sub(ix,dx);
dy = vec_sub(iy,dy);
dz = vec_sub(iz,dz);
rsq = vec_madd(dx,dx,nul);
rsq = vec_madd(dy,dy,rsq);
rsq = vec_madd(dz,dz,rsq);
rinv = do_invsqrt(rsq);
r = vec_madd(rinv,rsq,nul);
/* load 1/sqrt(a2) and multiply with 1/sqrt(a1) */
isaj = load_4_float(invsqrta+jnra,invsqrta+jnrb,
invsqrta+jnrc,invsqrta+jnrd);
isaprod = vec_madd(isai,isaj,nul);
/* load 4 j charges and multiply by iq and 1/sqrt(a1*a2) */
qq = vec_madd(load_4_float(charge+jnra,charge+jnrb,
charge+jnrc,charge+jnrd),iq,nul);
qq = vec_madd(isaprod,qq,nul);
gbscale = vec_madd(isaprod,gbtsc,nul);
do_4_ctable_coul(GBtab,vec_madd(r,gbscale,nul),&VVc,&FFc);
dvdaj = load_4_float(dvda+jnra,dvda+jnrb,
dvda+jnrc,dvda+jnrd);
fs = vec_madd(qq,FFc,nul);
fs = vec_madd(fs,gbscale,nul);
vctot = vec_madd(qq,VVc,vctot);
dvdatmp = vec_madd(fs,r,nul);
dvdatmp = vec_madd(qq,VVc,dvdatmp);
dvdasum = vec_sub(dvdasum,dvdatmp);
dvdaj = vec_sub(dvdaj,dvdatmp);
store_4_float(dvdaj,dvda+jnra,dvda+jnrb,dvda+jnrc,dvda+jnrd);
fs = vec_nmsub(fs,rinv,nul);
fix = vec_madd(fs,dx,fix); /* +=fx */
fiy = vec_madd(fs,dy,fiy); /* +=fy */
fiz = vec_madd(fs,dz,fiz); /* +=fz */
dx = vec_nmsub(dx,fs,nul); /* -fx */
dy = vec_nmsub(dy,fs,nul); /* -fy */
dz = vec_nmsub(dz,fs,nul); /* -fz */
transpose_3_to_4(dx,dy,dz,&tmp1,&tmp2,&tmp3,&tmp4);
add_xyz_to_mem(faction+j3a,tmp1);
add_xyz_to_mem(faction+j3b,tmp2);
add_xyz_to_mem(faction+j3c,tmp3);
add_xyz_to_mem(faction+j3d,tmp4);
}
if(k<(nj1-1)) {
jnra = jjnr[k];
jnrb = jjnr[k+1];
j3a = 3*jnra;
j3b = 3*jnrb;
transpose_2_to_3(load_xyz(pos+j3a),
load_xyz(pos+j3b),&dx,&dy,&dz);
dx = vec_sub(ix,dx);
dy = vec_sub(iy,dy);
dz = vec_sub(iz,dz);
rsq = vec_madd(dx,dx,nul);
rsq = vec_madd(dy,dy,rsq);
rsq = vec_madd(dz,dz,rsq);
zero_highest_2_elements_in_vector(&rsq);
rinv = do_invsqrt(rsq);
zero_highest_2_elements_in_vector(&rinv);
r = vec_madd(rinv,rsq,nul);
/* load 1/sqrt(a2) and multiply with 1/sqrt(a1) */
isaj = load_2_float(invsqrta+jnra,invsqrta+jnrb);
isaprod = vec_madd(isai,isaj,nul);
/* load 2 j charges and multiply by iq and 1/sqrt(a1*a2) */
qq = vec_madd(load_2_float(charge+jnra,charge+jnrb),iq,nul);
qq = vec_madd(isaprod,qq,nul);
gbscale = vec_madd(isaprod,gbtsc,nul);
do_2_ctable_coul(GBtab,vec_madd(r,gbscale,nul),&VVc,&FFc);
dvdaj = load_2_float(dvda+jnra,dvda+jnrb);
fs = vec_madd(qq,FFc,nul);
fs = vec_madd(fs,gbscale,nul);
vctot = vec_madd(qq,VVc,vctot);
dvdatmp = vec_madd(fs,r,nul);
dvdatmp = vec_madd(qq,VVc,dvdatmp);
dvdasum = vec_sub(dvdasum,dvdatmp);
dvdaj = vec_sub(dvdaj,dvdatmp);
store_2_float(dvdaj,dvda+jnra,dvda+jnrb);
fs = vec_nmsub(fs,rinv,nul);
fix = vec_madd(fs,dx,fix); /* +=fx */
fiy = vec_madd(fs,dy,fiy); /* +=fy */
fiz = vec_madd(fs,dz,fiz); /* +=fz */
dx = vec_nmsub(dx,fs,nul); /* -fx */
dy = vec_nmsub(dy,fs,nul); /* -fy */
dz = vec_nmsub(dz,fs,nul); /* -fz */
transpose_3_to_2(dx,dy,dz,&tmp1,&tmp2);
add_xyz_to_mem(faction+j3a,tmp1);
add_xyz_to_mem(faction+j3b,tmp2);
k += 2;
}
if((nj1-nj0) & 0x1) {
jnra = jjnr[k];
j3a = 3*jnra;
transpose_1_to_3(load_xyz(pos+j3a),&dx,&dy,&dz);
dx = vec_sub(ix,dx);
dy = vec_sub(iy,dy);
dz = vec_sub(iz,dz);
rsq = vec_madd(dx,dx,nul);
rsq = vec_madd(dy,dy,rsq);
rsq = vec_madd(dz,dz,rsq);
zero_highest_3_elements_in_vector(&rsq);
rinv = do_invsqrt(rsq);
zero_highest_3_elements_in_vector(&rinv);
r = vec_madd(rinv,rsq,nul);
/* load 1/sqrt(a2) and multiply with 1/sqrt(a1) */
isaj = load_1_float(invsqrta+jnra);
isaprod = vec_madd(isai,isaj,nul);
/* load 1 j charge and multiply by iq and 1/sqrt(a1*a2) */
qq = vec_madd(load_1_float(charge+jnra),iq,nul);
qq = vec_madd(isaprod,qq,nul);
gbscale = vec_madd(isaprod,gbtsc,nul);
do_1_ctable_coul(GBtab,vec_madd(r,gbscale,nul),&VVc,&FFc);
dvdaj = load_1_float(dvda+jnra);
fs = vec_madd(qq,FFc,nul);
fs = vec_madd(fs,gbscale,nul);
vctot = vec_madd(qq,VVc,vctot);
dvdatmp = vec_madd(fs,r,nul);
dvdatmp = vec_madd(qq,VVc,dvdatmp);
dvdasum = vec_sub(dvdasum,dvdatmp);
dvdaj = vec_sub(dvdaj,dvdatmp);
store_1_float(dvdaj,dvda+jnra);
fs = vec_nmsub(fs,rinv,nul);
fix = vec_madd(fs,dx,fix); /* +=fx */
fiy = vec_madd(fs,dy,fiy); /* +=fy */
fiz = vec_madd(fs,dz,fiz); /* +=fz */
dx = vec_nmsub(dx,fs,nul); /* -fx */
dy = vec_nmsub(dy,fs,nul); /* -fy */
dz = vec_nmsub(dz,fs,nul); /* -fz */
transpose_3_to_1(dx,dy,dz,&tmp1);
add_xyz_to_mem(faction+j3a,tmp1);
}
/* update outer data */
transpose_3_to_4(fix,fiy,fiz,&tmp1,&tmp2,&tmp3,&tmp4);
tmp1 = vec_add(tmp1,tmp3);
tmp2 = vec_add(tmp2,tmp4);
tmp1 = vec_add(tmp1,tmp2);
add_xyz_to_mem(faction+ii3,tmp1);
add_xyz_to_mem(fshift+is3,tmp1);
add_vector_to_float(Vc+gid[n],vctot);
add_vector_to_float(dvda+ii,dvdasum);
ninner += nj1 - nj0;
}
#ifdef GMX_THREADS
nouter += nn1 - nn0;
} while (nn1<nri);
#else
nouter = nri;
#endif
*outeriter = nouter;
*inneriter = ninner;
}