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Added the dispersion real space term, which is for HIPPO.

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This commit is contained in:
Trung Nguyen
2021-09-21 10:55:38 -05:00
parent 42034bd1c9
commit a2fd784034
9 changed files with 234 additions and 28 deletions
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49
lib/gpu/lal_amoeba.cpp
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@ -62,9 +62,9 @@ int AmoebaT::init(const int ntypes, const int max_amtype, const int max_amclass,
int success;
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,maxspecial15,
cell_size,gpu_split,_screen,amoeba,
"k_amoeba_multipole", "k_amoeba_udirect2b",
"k_amoeba_umutual2b", "k_amoeba_polar",
"k_amoeba_short_nbor");
"k_amoeba_dispersion", "k_amoeba_multipole",
"k_amoeba_udirect2b", "k_amoeba_umutual2b",
"k_amoeba_polar", "k_amoeba_short_nbor");
if (success!=0)
return success;
@ -150,7 +150,48 @@ double AmoebaT::host_memory_usage() const {
}
// ---------------------------------------------------------------------------
// Calculate the polar real-space term, returning tep
// Calculate the dispersion real-space term, returning tep
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int AmoebaT::dispersion_real(const int eflag, const int vflag) {
int ainum=this->ans->inum();
if (ainum == 0)
return 0;
int _nall=this->atom->nall();
int nbor_pitch=this->nbor->nbor_pitch();
// Compute the block size and grid size to keep all cores busy
const int BX=this->block_size();
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
(BX/this->_threads_per_atom)));
this->time_pair.start();
// Build the short neighbor list for the cutoff off2_mpole,
// at this point mpole is the first kernel in a time step
this->k_short_nbor.set_size(GX,BX);
this->k_short_nbor.run(&this->atom->x, &this->nbor->dev_nbor,
&this->_nbor_data->begin(),
&this->dev_short_nbor, &this->_off2_disp, &ainum,
&nbor_pitch, &this->_threads_per_atom);
printf("launching dispersion\n");
this->k_dispersion.set_size(GX,BX);
this->k_dispersion.run(&this->atom->x, &this->atom->extra,
&coeff_amtype, &coeff_amclass, &sp_nonpolar,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->dev_short_nbor,
&this->ans->force, &this->ans->engv,
&eflag, &vflag, &ainum, &_nall, &nbor_pitch,
&this->_threads_per_atom, &this->_aewald,
&this->_off2_disp);
this->time_pair.stop();
return GX;
}
// ---------------------------------------------------------------------------
// Calculate the multipole real-space term, returning tep
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int AmoebaT::multipole_real(const int eflag, const int vflag) {

11
lib/gpu/lal_amoeba.cu
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@ -413,7 +413,7 @@ __kernel void k_amoeba_dispersion(const __global numtyp4 *restrict x_,
const __global numtyp *restrict extra,
const __global numtyp4 *restrict coeff_amtype,
const __global numtyp4 *restrict coeff_amclass,
const __global numtyp4 *restrict sp_disp,
const __global numtyp4 *restrict sp_nonpolar,
const __global int *dev_nbor,
const __global int *dev_packed,
const __global int *dev_short_nbor,
@ -422,8 +422,7 @@ __kernel void k_amoeba_dispersion(const __global numtyp4 *restrict x_,
const int eflag, const int vflag, const int inum,
const int nall, const int nbor_pitch,
const int t_per_atom, const numtyp aewald,
const numtyp felec, const numtyp off2,
const numtyp polar_dscale, const numtyp polar_uscale)
const numtyp off2)
{
int tid, ii, offset, i;
atom_info(t_per_atom,ii,tid,offset);
@ -876,9 +875,11 @@ __kernel void k_amoeba_multipole(const __global numtyp4 *restrict x_,
// accumulate tq
store_answers_amoeba_tq(tq,ii,inum,tid,t_per_atom,offset,i,tep);
// accumate force, energy and virial
// accumate force, energy and virial: use _acc if not the first kernel
store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,
offset,eflag,vflag,ans,engv);
//store_answers_acc(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,
// offset,eflag,vflag,ans,engv,NUM_BLOCKS_X);
}
/* ----------------------------------------------------------------------
@ -1785,7 +1786,7 @@ __kernel void k_amoeba_polar(const __global numtyp4 *restrict x_,
// accumate force, energy and virial
//store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,
// offset,eflag,vflag,ans,engv);
// offset,eflag,vflag,ans,engv);
store_answers_acc(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,
offset,eflag,vflag,ans,engv,NUM_BLOCKS_X);
}

9
lib/gpu/lal_amoeba.h
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@ -38,9 +38,11 @@ class Amoeba : public BaseAmoeba<numtyp, acctyp> {
* - -4 if the GPU library was not compiled for GPU
* - -5 Double precision is not supported on card **/
int init(const int ntypes, const int max_amtype, const int max_amclass,
const double *host_pdamp, const double *host_thole, const double *host_dirdamp,
const int *host_amtype2class, const double *host_special_mpole,
const double *host_special_hal, const double *host_special_repel,
const double *host_pdamp, const double *host_thole,
const double *host_dirdamp, const int *host_amtype2class,
const double *host_special_mpole,
const double *host_special_hal,
const double *host_special_repel,
const double *host_special_disp,
const double *host_special_polar_wscale,
const double *host_special_polar_piscale,
@ -91,6 +93,7 @@ class Amoeba : public BaseAmoeba<numtyp, acctyp> {
protected:
bool _allocated;
int dispersion_real(const int eflag, const int vflag);
int multipole_real(const int eflag, const int vflag);
int udirect2b(const int eflag, const int vflag);
int umutual2b(const int eflag, const int vflag);

17
lib/gpu/lal_amoeba_ext.cpp
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@ -117,6 +117,23 @@ void amoeba_gpu_clear() {
AMOEBAMF.clear();
}
int** amoeba_gpu_compute_dispersion_real(const int ago, const int inum_full,
const int nall, double **host_x, int *host_type,
int *host_amtype, int *host_amgroup, double **host_rpole,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, int *nspecial15, tagint** special15,
const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, const double aewald, const double off2,
double *host_q, double *boxlo, double *prd) {
return AMOEBAMF.compute_dispersion_real(ago, inum_full, nall, host_x, host_type,
host_amtype, host_amgroup, host_rpole, sublo, subhi,
tag, nspecial, special, nspecial15, special15,
eflag, vflag, eatom, vatom, host_start, ilist, jnum,
cpu_time, success, aewald, off2, host_q, boxlo, prd);
}
int** amoeba_gpu_compute_multipole_real(const int ago, const int inum_full,
const int nall, double **host_x, int *host_type,
int *host_amtype, int *host_amgroup, double **host_rpole,

77
lib/gpu/lal_base_amoeba.cpp
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@ -33,6 +33,7 @@ template <class numtyp, class acctyp>
BaseAmoebaT::~BaseAmoeba() {
delete ans;
delete nbor;
k_dispersion.clear();
k_multipole.clear();
k_udirect2b.clear();
k_umutual2b.clear();
@ -54,6 +55,7 @@ int BaseAmoebaT::init_atomic(const int nlocal, const int nall,
const int maxspecial15,
const double cell_size, const double gpu_split,
FILE *_screen, const void *pair_program,
const char *k_name_dispersion,
const char *k_name_multipole,
const char *k_name_udirect2b,
const char *k_name_umutual2b,
@ -90,8 +92,8 @@ int BaseAmoebaT::init_atomic(const int nlocal, const int nall,
_block_size=device->pair_block_size();
_block_bio_size=device->block_bio_pair();
compile_kernels(*ucl_device,pair_program,k_name_multipole,k_name_udirect2b,
k_name_umutual2b,k_name_polar,k_name_short_nbor);
compile_kernels(*ucl_device,pair_program,k_name_dispersion,k_name_multipole,
k_name_udirect2b, k_name_umutual2b,k_name_polar,k_name_short_nbor);
if (_threads_per_atom>1 && gpu_nbor==0) {
nbor->packing(true);
@ -427,7 +429,74 @@ int** BaseAmoebaT::precompute(const int ago, const int inum_full, const int nall
}
// ---------------------------------------------------------------------------
// Reneighbor on GPU if necessary, and then compute polar real-space
// Reneighbor on GPU if necessary, and then compute dispersion real-space
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int** BaseAmoebaT::compute_dispersion_real(const int ago, const int inum_full,
const int nall, double **host_x,
int *host_type, int *host_amtype,
int *host_amgroup, double **host_rpole,
double *sublo, double *subhi, tagint *tag,
int **nspecial, tagint **special,
int *nspecial15, tagint **special15,
const bool eflag_in, const bool vflag_in,
const bool eatom, const bool vatom,
int &host_start, int **ilist, int **jnum,
const double cpu_time, bool &success,
const double aewald, const double off2_disp,
double *host_q, double *boxlo, double *prd) {
acc_timers();
int eflag, vflag;
if (eatom) eflag=2;
else if (eflag_in) eflag=1;
else eflag=0;
if (vatom) vflag=2;
else if (vflag_in) vflag=1;
else vflag=0;
#ifdef LAL_NO_BLOCK_REDUCE
if (eflag) eflag=2;
if (vflag) vflag=2;
#endif
set_kernel(eflag,vflag);
// reallocate per-atom arrays, transfer data from the host
// and build the neighbor lists if needed
// NOTE:
// For now we invoke precompute() again here,
// to be able to turn on/off the udirect2b kernel (which comes before this)
// Once all the kernels are ready, precompute() is needed only once
// in the first kernel in a time step.
// We only need to cast uind and uinp from host to device here
// if the neighbor lists are rebuilt and other per-atom arrays
// (x, type, amtype, amgroup, rpole) are ready on the device.
int** firstneigh = nullptr;
firstneigh = precompute(ago, inum_full, nall, host_x, host_type,
host_amtype, host_amgroup, host_rpole,
nullptr, nullptr, sublo, subhi, tag,
nspecial, special, nspecial15, special15,
eflag_in, vflag_in, eatom, vatom,
host_start, ilist, jnum, cpu_time,
success, host_q, boxlo, prd);
_off2_disp = off2_disp;
_aewald = aewald;
const int red_blocks=dispersion_real(eflag,vflag);
// leave the answers (forces, energies and virial) on the device,
// only copy them back in the last kernel (polar_real)
//ans->copy_answers(eflag_in,vflag_in,eatom,vatom,red_blocks);
//device->add_ans_object(ans);
hd_balancer.stop_timer();
return firstneigh; // nbor->host_jlist.begin()-host_start;
}
// ---------------------------------------------------------------------------
// Reneighbor on GPU if necessary, and then compute multipole real-space
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int** BaseAmoebaT::compute_multipole_real(const int ago, const int inum_full,
@ -816,6 +885,7 @@ void BaseAmoebaT::cast_extra_data(int* amtype, int* amgroup, double** rpole,
template <class numtyp, class acctyp>
void BaseAmoebaT::compile_kernels(UCL_Device &dev, const void *pair_str,
const char *kname_dispersion,
const char *kname_multipole,
const char *kname_udirect2b,
const char *kname_umutual2b,
@ -829,6 +899,7 @@ void BaseAmoebaT::compile_kernels(UCL_Device &dev, const void *pair_str,
std::string oclstring = device->compile_string()+" -DEVFLAG=1";
pair_program->load_string(pair_str,oclstring.c_str(),nullptr,screen);
k_dispersion.set_function(*pair_program,kname_dispersion);
k_multipole.set_function(*pair_program,kname_multipole);
k_udirect2b.set_function(*pair_program,kname_udirect2b);
k_umutual2b.set_function(*pair_program,kname_umutual2b);

31
lib/gpu/lal_base_amoeba.h
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@ -54,9 +54,9 @@ class BaseAmoeba {
int init_atomic(const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const int maxspecial15, const double cell_size,
const double gpu_split, FILE *screen, const void *pair_program,
const char *kname_multipole, const char *kname_udirect2b,
const char *kname_umutual2b, const char *kname_polar,
const char *kname_short_nbor);
const char *kname_dispersion, const char *kname_multipole,
const char *kname_udirect2b, const char *kname_umutual2b,
const char *kname_polar, const char *kname_short_nbor);
/// Estimate the overhead for GPU context changes and CPU driver
void estimate_gpu_overhead(const int add_kernels=0);
@ -142,6 +142,18 @@ class BaseAmoeba {
int **&ilist, int **&numj, const double cpu_time, bool &success,
double *charge, double *boxlo, double *prd);
/// Compute dispersion real-space with device neighboring
int** compute_dispersion_real(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *host_amtype,
int *host_amgroup, double **host_rpole, double *sublo, double *subhi,
tagint *tag, int **nspecial, tagint **special,
int *nspecial15, tagint **special15,
const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **numj, const double cpu_time, bool &success,
const double aewald, const double off2_disp, double *charge,
double *boxlo, double *prd);
/// Compute multipole real-space with device neighboring
int** compute_multipole_real(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *host_amtype,
@ -257,8 +269,8 @@ class BaseAmoeba {
// ------------------------- DEVICE KERNELS -------------------------
UCL_Program *pair_program;
UCL_Kernel k_multipole, k_udirect2b, k_umutual2b, k_polar, k_special15;
UCL_Kernel k_short_nbor;
UCL_Kernel k_dispersion, k_multipole, k_udirect2b, k_umutual2b, k_polar;
UCL_Kernel k_special15, k_short_nbor;
inline int block_size() { return _block_size; }
inline void set_kernel(const int eflag, const int vflag) {}
@ -276,13 +288,14 @@ class BaseAmoeba {
UCL_D_Vec<int> *_nbor_data;
numtyp _aewald,_felec;
numtyp _off2_hal,_off2_repulse,_off2_dispersion,_off2_mpole,_off2_polar;
numtyp _off2_hal,_off2_repulse,_off2_disp,_off2_mpole,_off2_polar;
void compile_kernels(UCL_Device &dev, const void *pair_string,
const char *kname_multipole, const char *kname_udirect2b,
const char *kname_umutual2b, const char *kname_polar,
const char *kname_short_nbor);
const char *kname_dispersion, const char *kname_multipole,
const char *kname_udirect2b, const char *kname_umutual2b,
const char *kname_polar, const char *kname_short_nbor);
virtual int dispersion_real(const int eflag, const int vflag) = 0;
virtual int multipole_real(const int eflag, const int vflag) = 0;
virtual int udirect2b(const int eflag, const int vflag) = 0;
virtual int umutual2b(const int eflag, const int vflag) = 0;

2
src/AMOEBA/pair_amoeba.h
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@ -348,7 +348,7 @@ class PairAmoeba : public Pair {
int, double, double, double *);
void dispersion();
void dispersion_real();
virtual void dispersion_real();
void dispersion_kspace();
void multipole();

63
src/GPU/pair_amoeba_gpu.cpp
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@ -65,6 +65,17 @@ int amoeba_gpu_init(const int ntypes, const int max_amtype, const int max_amclas
const double polar_dscale, const double polar_uscale, int& tq_size);
void amoeba_gpu_clear();
int** amoeba_gpu_compute_dispersion_real(const int ago, const int inum_full,
const int nall, double **host_x, int *host_type,
int *host_amtype, int *host_amgroup, double **host_rpole,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, int *nspecial15, tagint** special15,
const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, const double aewald, const double off2,
double *host_q, double *boxlo, double *prd);
int ** amoeba_gpu_compute_multipole_real(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *host_amtype, int *host_amgroup,
double **host_rpole, double *sublo, double *subhi, tagint *tag,
@ -118,8 +129,8 @@ PairAmoebaGPU::PairAmoebaGPU(LAMMPS *lmp) : PairAmoeba(lmp), gpu_mode(GPU_FORCE)
tq_pinned = nullptr;
gpu_hal_ready = false;
gpu_repulsion_ready = false;
gpu_dispersion_real_ready = false;
gpu_repulsion_ready = false; // true for HIPPO
gpu_dispersion_real_ready = false; // true for HIPPO
gpu_multipole_real_ready = true;
gpu_udirect2b_ready = true;
gpu_umutual2b_ready = true;
@ -194,6 +205,54 @@ void PairAmoebaGPU::init_style()
/* ---------------------------------------------------------------------- */
void PairAmoebaGPU::dispersion_real()
{
if (!gpu_dispersion_real_ready) {
PairAmoeba::dispersion_real();
return;
}
int eflag=1, vflag=1;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
double sublo[3],subhi[3];
if (domain->triclinic == 0) {
sublo[0] = domain->sublo[0];
sublo[1] = domain->sublo[1];
sublo[2] = domain->sublo[2];
subhi[0] = domain->subhi[0];
subhi[1] = domain->subhi[1];
subhi[2] = domain->subhi[2];
} else {
domain->bbox(domain->sublo_lamda,domain->subhi_lamda,sublo,subhi);
}
inum = atom->nlocal;
// select the correct cutoff for the term
if (use_dewald) choose(DISP_LONG);
else choose(DISP);
firstneigh = amoeba_gpu_compute_dispersion_real(neighbor->ago, inum, nall, atom->x,
atom->type, amtype, amgroup, rpole,
sublo, subhi, atom->tag,
atom->nspecial, atom->special,
atom->nspecial15, atom->special15,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, aewald, off2, atom->q,
domain->boxlo, domain->prd);
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
}
/* ---------------------------------------------------------------------- */
void PairAmoebaGPU::multipole_real()
{
if (!gpu_multipole_real_ready) {

1
src/GPU/pair_amoeba_gpu.h
View File

@ -35,6 +35,7 @@ class PairAmoebaGPU : public PairAmoeba {
virtual void induce();
virtual void dispersion_real();
virtual void multipole_real();
virtual void udirect2b(double **, double **);
virtual void umutual2b(double **, double **);