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Updated pair coul/long/cs and born/coul/long/cs; updated gpu neighbor builds to support core-shell styles where r2 can be tiny.

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This commit is contained in:
Trung Nguyen
2018-06-19 15:50:02 -05:00
parent 6842a527e0
commit 70a7b37614
3 changed files with 92 additions and 83 deletions
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81
lib/gpu/lal_born_coul_long_cs.cu
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@ -9,7 +9,7 @@
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) // This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________ // __________________________________________________________________________
// //
// begin : // begin : June 2018
// email : trung.nguyen@northwestern.edu // email : trung.nguyen@northwestern.edu
// ***************************************************************************/ // ***************************************************************************/
@ -29,15 +29,19 @@ texture<int2> q_tex;
#define q_tex q_ #define q_tex q_
#endif #endif
#define B0 (numtyp)-0.1335096380159268 // Note: EWALD_P is different from that in lal_preprocessor.h
#define B1 (numtyp)-2.57839507e-1 // acctyp is needed for these parameters
#define B2 (numtyp)-1.37203639e-1 #define CS_EWALD_P (acctyp)9.95473818e-1
#define B3 (numtyp)-8.88822059e-3 #define B0 (acctyp)-0.1335096380159268
#define B4 (numtyp)-5.80844129e-3 #define B1 (acctyp)-2.57839507e-1
#define B5 (numtyp)1.14652755e-1 #define B2 (acctyp)-1.37203639e-1
#define EPSILON (numtyp)1.0e-20 #define B3 (acctyp)-8.88822059e-3
#define EPS_EWALD (numtyp)1.0e-6 #define B4 (acctyp)-5.80844129e-3
#define EPS_EWALD_SQR (numtyp)1.0e-12 #define B5 (acctyp)1.14652755e-1
#define EPSILON (acctyp)(1.0e-20)
#define EPS_EWALD (acctyp)(1.0e-6)
#define EPS_EWALD_SQR (acctyp)(1.0e-12)
__kernel void k_born_coul_long_cs(const __global numtyp4 *restrict x_, __kernel void k_born_coul_long_cs(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict coeff1, const __global numtyp4 *restrict coeff1,
@ -105,39 +109,37 @@ __kernel void k_born_coul_long_cs(const __global numtyp4 *restrict x_,
int mtype=itype*lj_types+jtype; int mtype=itype*lj_types+jtype;
if (rsq<cutsq_sigma[mtype].x) { // cutsq if (rsq<cutsq_sigma[mtype].x) { // cutsq
numtyp forcecoul, forceborn, force, r6inv, prefactor, _erfc; numtyp forcecoul,forceborn,force,r6inv,prefactor,_erfc,rexp;
numtyp rexp = (numtyp)0.0;
rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
numtyp r2inv = ucl_recip(rsq);
if (rsq < cut_coulsq) { if (rsq < cut_coulsq) {
rsq += EPSILON; numtyp r = ucl_sqrt(rsq);
numtyp r2inv = ucl_recip(rsq);
numtyp r = ucl_rsqrt(r2inv);
fetch(prefactor,j,q_tex); fetch(prefactor,j,q_tex);
prefactor *= qqrd2e * qtmp; prefactor *= qqrd2e * qtmp;
if (factor_coul<(numtyp)1.0) { if (factor_coul<(numtyp)1.0) {
numtyp grij = g_ewald * (r+EPS_EWALD); numtyp grij = g_ewald * (r+EPS_EWALD);
numtyp expm2 = ucl_exp(-grij*grij); numtyp expm2 = ucl_exp(-grij*grij);
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij); numtyp t = ucl_recip((numtyp)1.0 + CS_EWALD_P*grij);
numtyp u = (numtyp)1.0 - t; numtyp u = (numtyp)1.0 - t;
_erfc = t * ((numtyp)1.0 + u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2; _erfc = t * ((numtyp)1.0 + u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
prefactor /= (r+EPS_EWALD); prefactor /= (r+EPS_EWALD);
forcecoul = prefactor * (_erfc + EWALD_F*grij*expm2 - ((numtyp)1.0-factor_coul)); forcecoul = prefactor * (_erfc + EWALD_F*grij*expm2 - ((numtyp)1.0-factor_coul));
// Additionally r2inv needs to be accordingly modified since the later
// scaling of the overall force shall be consistent
r2inv = ucl_recip(rsq + EPS_EWALD_SQR); r2inv = ucl_recip(rsq + EPS_EWALD_SQR);
forcecoul *= r2inv;
} else { } else {
numtyp grij = g_ewald * r; numtyp grij = g_ewald * r;
numtyp expm2 = ucl_exp(-grij*grij); numtyp expm2 = ucl_exp(-grij*grij);
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij); numtyp t = ucl_recip((numtyp)1.0 + CS_EWALD_P*grij);
numtyp u = (numtyp)1.0 - t; numtyp u = (numtyp)1.0 - t;
_erfc = t * ((numtyp)1.0 + u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2; _erfc = t * ((numtyp)1.0 + u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
prefactor /= r; prefactor /= r;
forcecoul = prefactor*(_erfc + EWALD_F*grij*expm2); forcecoul = prefactor*(_erfc + EWALD_F*grij*expm2);
forcecoul *= r2inv;
} }
} else forcecoul = (numtyp)0.0; } else forcecoul = (numtyp)0.0;
numtyp r2inv = ucl_recip(rsq);
if (rsq < cutsq_sigma[mtype].y) { // cut_ljsq if (rsq < cutsq_sigma[mtype].y) { // cut_ljsq
numtyp r = ucl_sqrt(rsq); numtyp r = ucl_sqrt(rsq);
rexp = ucl_exp((cutsq_sigma[mtype].z-r)*coeff1[mtype].x); rexp = ucl_exp((cutsq_sigma[mtype].z-r)*coeff1[mtype].x);
@ -146,7 +148,7 @@ __kernel void k_born_coul_long_cs(const __global numtyp4 *restrict x_,
+ coeff1[mtype].w*r2inv*r6inv)*factor_lj; + coeff1[mtype].w*r2inv*r6inv)*factor_lj;
} else forceborn = (numtyp)0.0; } else forceborn = (numtyp)0.0;
force = forceborn*r2inv + forcecoul; force = (forcecoul + forceborn) * r2inv;
f.x+=delx*force; f.x+=delx*force;
f.y+=dely*force; f.y+=dely*force;
@ -154,9 +156,9 @@ __kernel void k_born_coul_long_cs(const __global numtyp4 *restrict x_,
if (eflag>0) { if (eflag>0) {
if (rsq < cut_coulsq) { if (rsq < cut_coulsq) {
e_coul += prefactor*_erfc; numtyp e = prefactor*_erfc;
if (factor_coul<(numtyp)1.0) if (factor_coul<(numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor;
e_coul -= ((numtyp)1.0-factor_coul)*prefactor; e_coul += e;
} }
if (rsq < cutsq_sigma[mtype].y) { if (rsq < cutsq_sigma[mtype].y) {
numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv
@ -248,39 +250,38 @@ __kernel void k_born_coul_long_cs_fast(const __global numtyp4 *restrict x_,
numtyp rsq = delx*delx+dely*dely+delz*delz; numtyp rsq = delx*delx+dely*dely+delz*delz;
if (rsq<cutsq_sigma[mtype].x) { // cutsq if (rsq<cutsq_sigma[mtype].x) { // cutsq
numtyp forcecoul, forceborn, force, r6inv, prefactor, _erfc; numtyp forcecoul,forceborn,force,r6inv,prefactor,_erfc,rexp;
numtyp rexp = (numtyp)0.0;
rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
numtyp r2inv = ucl_recip(rsq);
if (rsq < cut_coulsq) { if (rsq < cut_coulsq) {
rsq += EPSILON; numtyp r = ucl_sqrt(rsq);
numtyp r2inv = ucl_recip(rsq);
numtyp r = ucl_rsqrt(r2inv);
fetch(prefactor,j,q_tex); fetch(prefactor,j,q_tex);
prefactor *= qqrd2e * qtmp; prefactor *= qqrd2e * qtmp;
if (factor_coul<(numtyp)1.0) { if (factor_coul<(numtyp)1.0) {
numtyp grij = g_ewald * (r+EPS_EWALD); numtyp grij = g_ewald * (r+EPS_EWALD);
numtyp expm2 = ucl_exp(-grij*grij); numtyp expm2 = ucl_exp(-grij*grij);
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij); numtyp t = ucl_recip((numtyp)1.0 + CS_EWALD_P*grij);
numtyp u = (numtyp)1.0 - t; numtyp u = (numtyp)1.0 - t;
_erfc = t * ((numtyp)1.0 + u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2; _erfc = t * ((numtyp)1.0 + u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
prefactor /= (r+EPS_EWALD); prefactor /= (r+EPS_EWALD);
forcecoul = prefactor * (_erfc + EWALD_F*grij*expm2 - ((numtyp)1.0-factor_coul)); forcecoul = prefactor * (_erfc + EWALD_F*grij*expm2 - ((numtyp)1.0-factor_coul));
// Additionally r2inv needs to be accordingly modified since the later
// scaling of the overall force shall be consistent
r2inv = ucl_recip(rsq + EPS_EWALD_SQR); r2inv = ucl_recip(rsq + EPS_EWALD_SQR);
forcecoul *= r2inv;
} else { } else {
numtyp grij = g_ewald * r; numtyp grij = g_ewald * r;
numtyp expm2 = ucl_exp(-grij*grij); numtyp expm2 = ucl_exp(-grij*grij);
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij); numtyp t = ucl_recip((numtyp)1.0 + CS_EWALD_P*grij);
numtyp u = (numtyp)1.0 - t; numtyp u = (numtyp)1.0 - t;
_erfc = t * ((numtyp)1.0 + u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2; _erfc = t * ((numtyp)1.0 + u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
prefactor /= r; prefactor /= r;
forcecoul = prefactor*(_erfc + EWALD_F*grij*expm2); forcecoul = prefactor*(_erfc + EWALD_F*grij*expm2);
forcecoul *= r2inv;
} }
} else forcecoul = (numtyp)0.0; } else forcecoul = (numtyp)0.0;
numtyp r2inv = ucl_recip(rsq);
if (rsq < cutsq_sigma[mtype].y) { // cut_ljsq if (rsq < cutsq_sigma[mtype].y) { // cut_ljsq
numtyp r = ucl_sqrt(rsq); numtyp r = ucl_sqrt(rsq);
rexp = ucl_exp((cutsq_sigma[mtype].z-r)*coeff1[mtype].x); rexp = ucl_exp((cutsq_sigma[mtype].z-r)*coeff1[mtype].x);
@ -289,7 +290,7 @@ __kernel void k_born_coul_long_cs_fast(const __global numtyp4 *restrict x_,
+ coeff1[mtype].w*r2inv*r6inv)*factor_lj; + coeff1[mtype].w*r2inv*r6inv)*factor_lj;
} else forceborn = (numtyp)0.0; } else forceborn = (numtyp)0.0;
force = forceborn*r2inv + forcecoul; force = (forcecoul + forceborn) * r2inv;
f.x+=delx*force; f.x+=delx*force;
f.y+=dely*force; f.y+=dely*force;
@ -297,9 +298,9 @@ __kernel void k_born_coul_long_cs_fast(const __global numtyp4 *restrict x_,
if (eflag>0) { if (eflag>0) {
if (rsq < cut_coulsq) { if (rsq < cut_coulsq) {
e_coul += prefactor*_erfc; numtyp e = prefactor*_erfc;
if (factor_coul<(numtyp)1.0) if (factor_coul<(numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor;
e_coul -= ((numtyp)1.0-factor_coul)*prefactor; e_coul += e;
} }
if (rsq < cutsq_sigma[mtype].y) { if (rsq < cutsq_sigma[mtype].y) {
numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv

56
lib/gpu/lal_coul_long_cs.cu
View File

@ -29,6 +29,20 @@ texture<int2> q_tex;
#define q_tex q_ #define q_tex q_
#endif #endif
// Note: EWALD_P is different from that in lal_preprocessor.h
// acctyp is needed for these parameters
#define CS_EWALD_P (acctyp)9.95473818e-1
#define B0 (acctyp)-0.1335096380159268
#define B1 (acctyp)-2.57839507e-1
#define B2 (acctyp)-1.37203639e-1
#define B3 (acctyp)-8.88822059e-3
#define B4 (acctyp)-5.80844129e-3
#define B5 (acctyp)1.14652755e-1
#define EPSILON (acctyp)(1.0e-20)
#define EPS_EWALD (acctyp)(1.0e-6)
#define EPS_EWALD_SQR (acctyp)(1.0e-12)
#if (ARCH < 300) #if (ARCH < 300)
#define store_answers_lq(f, e_coul, virial, ii, inum, tid, \ #define store_answers_lq(f, e_coul, virial, ii, inum, tid, \
@ -123,16 +137,6 @@ texture<int2> q_tex;
#endif #endif
#define B0 (numtyp)-0.1335096380159268
#define B1 (numtyp)-2.57839507e-1
#define B2 (numtyp)-1.37203639e-1
#define B3 (numtyp)-8.88822059e-3
#define B4 (numtyp)-5.80844129e-3
#define B5 (numtyp)1.14652755e-1
#define EPSILON (numtyp)1.0e-20
#define EPS_EWALD (numtyp)1.0e-6
#define EPS_EWALD_SQR (numtyp)1.0e-12
__kernel void k_coul_long_cs(const __global numtyp4 *restrict x_, __kernel void k_coul_long_cs(const __global numtyp4 *restrict x_,
const __global numtyp *restrict scale, const __global numtyp *restrict scale,
const int lj_types, const int lj_types,
@ -191,7 +195,7 @@ __kernel void k_coul_long_cs(const __global numtyp4 *restrict x_,
int mtype=itype*lj_types+jtype; int mtype=itype*lj_types+jtype;
if (rsq < cut_coulsq) { if (rsq < cut_coulsq) {
rsq += EPSILON; rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
numtyp force,prefactor,_erfc; numtyp force,prefactor,_erfc;
numtyp r2inv = ucl_recip(rsq); numtyp r2inv = ucl_recip(rsq);
@ -201,17 +205,19 @@ __kernel void k_coul_long_cs(const __global numtyp4 *restrict x_,
if (factor_coul<(numtyp)1.0) { if (factor_coul<(numtyp)1.0) {
numtyp grij = g_ewald * (r+EPS_EWALD); numtyp grij = g_ewald * (r+EPS_EWALD);
numtyp expm2 = ucl_exp(-grij*grij); numtyp expm2 = ucl_exp(-grij*grij);
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij); numtyp t = ucl_recip((numtyp)1.0 + CS_EWALD_P*grij);
numtyp u = (numtyp)1.0 - t; numtyp u = (numtyp)1.0 - t;
_erfc = t * ((numtyp)1.0 + u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2; _erfc = t * ((numtyp)1.0 + u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
prefactor /= (r+EPS_EWALD); prefactor /= (r+EPS_EWALD);
force = prefactor * (_erfc + EWALD_F*grij*expm2 - ((numtyp)1.0-factor_coul)); force = prefactor * (_erfc + EWALD_F*grij*expm2 - ((numtyp)1.0-factor_coul));
// Additionally r2inv needs to be accordingly modified since the later
// scaling of the overall force shall be consistent
r2inv = ucl_recip(rsq + EPS_EWALD_SQR); r2inv = ucl_recip(rsq + EPS_EWALD_SQR);
force *= r2inv; force *= r2inv;
} else { } else {
numtyp grij = g_ewald * r; numtyp grij = g_ewald * r;
numtyp expm2 = ucl_exp(-grij*grij); numtyp expm2 = ucl_exp(-grij*grij);
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij); numtyp t = ucl_recip((numtyp)1.0 + CS_EWALD_P*grij);
numtyp u = (numtyp)1.0 - t; numtyp u = (numtyp)1.0 - t;
_erfc = t * ((numtyp)1.0 + u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2; _erfc = t * ((numtyp)1.0 + u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
prefactor /= r; prefactor /= r;
@ -224,9 +230,9 @@ __kernel void k_coul_long_cs(const __global numtyp4 *restrict x_,
f.z+=delz*force; f.z+=delz*force;
if (eflag>0) { if (eflag>0) {
e_coul += prefactor*_erfc; numtyp e = prefactor*_erfc;
if (factor_coul<(numtyp)1.0) if (factor_coul<(numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor;
e_coul -= ((numtyp)1.0-factor_coul)*prefactor; e_coul += e;
} }
if (vflag>0) { if (vflag>0) {
virial[0] += delx*delx*force; virial[0] += delx*delx*force;
@ -304,7 +310,7 @@ __kernel void k_coul_long_cs_fast(const __global numtyp4 *restrict x_,
numtyp rsq = delx*delx+dely*dely+delz*delz; numtyp rsq = delx*delx+dely*dely+delz*delz;
if (rsq < cut_coulsq) { if (rsq < cut_coulsq) {
rsq += EPSILON; rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
numtyp force,prefactor,_erfc; numtyp force,prefactor,_erfc;
numtyp r2inv = ucl_recip(rsq); numtyp r2inv = ucl_recip(rsq);
@ -314,32 +320,34 @@ __kernel void k_coul_long_cs_fast(const __global numtyp4 *restrict x_,
if (factor_coul<(numtyp)1.0) { if (factor_coul<(numtyp)1.0) {
numtyp grij = g_ewald * (r+EPS_EWALD); numtyp grij = g_ewald * (r+EPS_EWALD);
numtyp expm2 = ucl_exp(-grij*grij); numtyp expm2 = ucl_exp(-grij*grij);
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij); numtyp t = ucl_recip((numtyp)1.0 + CS_EWALD_P*grij);
numtyp u = (numtyp)1.0 - t; numtyp u = (numtyp)1.0 - t;
_erfc = t * ((numtyp)1.0 + u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2; _erfc = t * ((numtyp)1.0 + u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
prefactor /= (r+EPS_EWALD); prefactor /= (r+EPS_EWALD);
force = prefactor * (_erfc + EWALD_F*grij*expm2 - ((numtyp)1.0-factor_coul)); force = prefactor * (_erfc + EWALD_F*grij*expm2 - ((numtyp)1.0-factor_coul));
// Additionally r2inv needs to be accordingly modified since the later
// scaling of the overall force shall be consistent
r2inv = ucl_recip(rsq + EPS_EWALD_SQR); r2inv = ucl_recip(rsq + EPS_EWALD_SQR);
force *= r2inv;
} else { } else {
numtyp grij = g_ewald * r; numtyp grij = g_ewald * r;
numtyp expm2 = ucl_exp(-grij*grij); numtyp expm2 = ucl_exp(-grij*grij);
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij); numtyp t = ucl_recip((numtyp)1.0 + CS_EWALD_P*grij);
numtyp u = (numtyp)1.0 - t; numtyp u = (numtyp)1.0 - t;
_erfc = t * ((numtyp)1.0 + u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2; _erfc = t * ((numtyp)1.0 + u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
prefactor /= r; prefactor /= r;
force = prefactor * (_erfc + EWALD_F*grij*expm2); force = prefactor * (_erfc + EWALD_F*grij*expm2);
force *= r2inv;
} }
force *= r2inv;
f.x+=delx*force; f.x+=delx*force;
f.y+=dely*force; f.y+=dely*force;
f.z+=delz*force; f.z+=delz*force;
if (eflag>0) { if (eflag>0) {
e_coul += prefactor*_erfc; numtyp e = prefactor*_erfc;
if (factor_coul<(numtyp)1.0) if (factor_coul<(numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor;
e_coul -= ((numtyp)1.0-factor_coul)*prefactor; e_coul += e;
} }
if (vflag>0) { if (vflag>0) {
virial[0] += delx*delx*force; virial[0] += delx*delx*force;

2
lib/gpu/lal_neighbor_gpu.cu
View File

@ -232,7 +232,7 @@ __kernel void calc_neigh_list_cell(const __global numtyp4 *restrict x_,
diff.z = atom_i.z - pos_sh[j].z; diff.z = atom_i.z - pos_sh[j].z;
r2 = diff.x*diff.x + diff.y*diff.y + diff.z*diff.z; r2 = diff.x*diff.x + diff.y*diff.y + diff.z*diff.z;
if (r2 < cell_size*cell_size && r2 > 1e-5) { if (r2 < cell_size*cell_size && pid_j != pid_i) { // && r2 > 1e-5
cnt++; cnt++;
if (cnt <= neigh_bin_size) { if (cnt <= neigh_bin_size) {
*neigh_list = pid_j; *neigh_list = pid_j;