Added classes for hippo/gpu, refactored BaseAmoeba and made room for the dispersion real-space term in hippo
This commit is contained in:
Trung Nguyen
430
lib/gpu/lal_hippo.cpp
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430
lib/gpu/lal_hippo.cpp
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/***************************************************************************
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hippo.cpp
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-------------------
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Trung Dac Nguyen (Northwestern)
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Class for acceleration of the hippo pair style.
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__________________________________________________________________________
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This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
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__________________________________________________________________________
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begin :
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email : trung.nguyen@northwestern.edu
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***************************************************************************/
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#if defined(USE_OPENCL)
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#include "hippo_cl.h"
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#elif defined(USE_CUDART)
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const char *hippo=0;
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#else
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#include "hippo_cubin.h"
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#endif
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#include "lal_hippo.h"
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#include <cassert>
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namespace LAMMPS_AL {
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#define HippoT Hippo<numtyp, acctyp>
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extern Device<PRECISION,ACC_PRECISION> device;
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template <class numtyp, class acctyp>
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HippoT::Hippo() : BaseAmoeba<numtyp,acctyp>(),
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_allocated(false) {
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}
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template <class numtyp, class acctyp>
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HippoT::~Hippo() {
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clear();
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k_dispersion.clear();
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}
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template <class numtyp, class acctyp>
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int HippoT::bytes_per_atom(const int max_nbors) const {
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return this->bytes_per_atom_atomic(max_nbors);
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}
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template <class numtyp, class acctyp>
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int HippoT::init(const int ntypes, const int max_amtype, const int max_amclass,
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const double *host_pdamp, const double *host_thole,
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const double *host_dirdamp, const int *host_amtype2class,
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const double *host_special_hal,
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const double *host_special_repel,
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const double *host_special_disp,
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const double *host_special_mpole,
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const double *host_special_polar_wscale,
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const double *host_special_polar_piscale,
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const double *host_special_polar_pscale,
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const double *host_csix, const double *host_adisp,
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const int nlocal, const int nall, const int max_nbors,
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const int maxspecial, const int maxspecial15,
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const double cell_size, const double gpu_split, FILE *_screen,
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const double polar_dscale, const double polar_uscale) {
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int success;
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success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,maxspecial15,
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cell_size,gpu_split,_screen,hippo,
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"k_hippo_multipole",
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"k_hippo_udirect2b", "k_hippo_umutual2b",
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"k_hippo_polar", "k_hippo_short_nbor");
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if (success!=0)
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return success;
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k_dispersion.set_function(*(this->pair_program),"k_hippo_dispersion");
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// If atom type constants fit in shared memory use fast kernel
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int lj_types=ntypes;
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shared_types=false;
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int max_shared_types=this->device->max_shared_types();
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if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
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lj_types=max_shared_types;
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shared_types=true;
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}
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_lj_types=lj_types;
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// Allocate a host write buffer for data initialization
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UCL_H_Vec<numtyp4> host_write(max_amtype, *(this->ucl_device), UCL_WRITE_ONLY);
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for (int i = 0; i < max_amtype; i++) {
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host_write[i].x = host_pdamp[i];
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host_write[i].y = host_thole[i];
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host_write[i].z = host_dirdamp[i];
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host_write[i].w = host_amtype2class[i];
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}
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coeff_amtype.alloc(max_amtype,*(this->ucl_device), UCL_READ_ONLY);
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ucl_copy(coeff_amtype,host_write,false);
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UCL_H_Vec<numtyp4> host_write2(max_amclass, *(this->ucl_device), UCL_WRITE_ONLY);
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for (int i = 0; i < max_amclass; i++) {
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host_write2[i].x = host_csix[i];
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host_write2[i].y = host_adisp[i];
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host_write2[i].z = (numtyp)0;
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host_write2[i].w = (numtyp)0;
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}
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coeff_amclass.alloc(max_amclass,*(this->ucl_device), UCL_READ_ONLY);
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ucl_copy(coeff_amclass,host_write2,false);
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UCL_H_Vec<numtyp4> dview(5, *(this->ucl_device), UCL_WRITE_ONLY);
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sp_polar.alloc(5,*(this->ucl_device),UCL_READ_ONLY);
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for (int i=0; i<5; i++) {
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dview[i].x=host_special_polar_wscale[i];
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dview[i].y=host_special_polar_piscale[i];
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dview[i].z=host_special_polar_pscale[i];
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dview[i].w=host_special_mpole[i];
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}
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ucl_copy(sp_polar,dview,5,false);
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sp_nonpolar.alloc(5,*(this->ucl_device),UCL_READ_ONLY);
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for (int i=0; i<5; i++) {
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dview[i].x=host_special_hal[i];
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dview[i].y=host_special_repel[i];
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dview[i].z=host_special_disp[i];
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dview[i].w=(numtyp)0;
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}
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ucl_copy(sp_nonpolar,dview,5,false);
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_polar_dscale = polar_dscale;
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_polar_uscale = polar_uscale;
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_allocated=true;
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this->_max_bytes=coeff_amtype.row_bytes() + coeff_amclass.row_bytes()
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+ sp_polar.row_bytes() + sp_nonpolar.row_bytes() + this->_tep.row_bytes();
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return 0;
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}
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template <class numtyp, class acctyp>
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void HippoT::clear() {
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if (!_allocated)
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return;
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_allocated=false;
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coeff_amtype.clear();
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coeff_amclass.clear();
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sp_polar.clear();
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sp_nonpolar.clear();
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this->clear_atomic();
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}
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template <class numtyp, class acctyp>
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double HippoT::host_memory_usage() const {
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return this->host_memory_usage_atomic()+sizeof(Hippo<numtyp,acctyp>);
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}
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// ---------------------------------------------------------------------------
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// Reneighbor on GPU if necessary, and then compute dispersion real-space
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// ---------------------------------------------------------------------------
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template <class numtyp, class acctyp>
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int** HippoT::compute_dispersion_real(const int ago, const int inum_full,
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const int nall, double **host_x,
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int *host_type, int *host_amtype,
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int *host_amgroup, double **host_rpole,
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double *sublo, double *subhi, tagint *tag,
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int **nspecial, tagint **special,
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int *nspecial15, tagint **special15,
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const bool eflag_in, const bool vflag_in,
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const bool eatom, const bool vatom,
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int &host_start, int **ilist, int **jnum,
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const double cpu_time, bool &success,
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const double aewald, const double off2_disp,
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double *host_q, double *boxlo, double *prd) {
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this->acc_timers();
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int eflag, vflag;
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if (eatom) eflag=2;
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else if (eflag_in) eflag=1;
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else eflag=0;
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if (vatom) vflag=2;
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else if (vflag_in) vflag=1;
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else vflag=0;
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#ifdef LAL_NO_BLOCK_REDUCE
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if (eflag) eflag=2;
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if (vflag) vflag=2;
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#endif
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this->set_kernel(eflag,vflag);
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// reallocate per-atom arrays, transfer data from the host
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// and build the neighbor lists if needed
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// NOTE:
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// For now we invoke precompute() again here,
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// to be able to turn on/off the udirect2b kernel (which comes before this)
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// Once all the kernels are ready, precompute() is needed only once
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// in the first kernel in a time step.
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// We only need to cast uind and uinp from host to device here
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// if the neighbor lists are rebuilt and other per-atom arrays
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// (x, type, amtype, amgroup, rpole) are ready on the device.
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int** firstneigh = nullptr;
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firstneigh = this->precompute(ago, inum_full, nall, host_x, host_type,
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host_amtype, host_amgroup, host_rpole,
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nullptr, nullptr, sublo, subhi, tag,
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nspecial, special, nspecial15, special15,
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eflag_in, vflag_in, eatom, vatom,
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host_start, ilist, jnum, cpu_time,
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success, host_q, boxlo, prd);
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this->_off2_disp = off2_disp;
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this->_aewald = aewald;
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const int red_blocks=dispersion_real(eflag,vflag);
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// leave the answers (forces, energies and virial) on the device,
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// only copy them back in the last kernel (polar_real)
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//ans->copy_answers(eflag_in,vflag_in,eatom,vatom,red_blocks);
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//device->add_ans_object(ans);
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this->hd_balancer.stop_timer();
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return firstneigh; // nbor->host_jlist.begin()-host_start;
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}
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// ---------------------------------------------------------------------------
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// Calculate the dispersion real-space term, returning tep
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// ---------------------------------------------------------------------------
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template <class numtyp, class acctyp>
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int HippoT::dispersion_real(const int eflag, const int vflag) {
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int ainum=this->ans->inum();
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if (ainum == 0)
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return 0;
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int _nall=this->atom->nall();
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int nbor_pitch=this->nbor->nbor_pitch();
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// Compute the block size and grid size to keep all cores busy
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const int BX=this->block_size();
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int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
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(BX/this->_threads_per_atom)));
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this->time_pair.start();
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// Build the short neighbor list for the cutoff off2_mpole,
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// at this point mpole is the first kernel in a time step
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this->k_short_nbor.set_size(GX,BX);
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this->k_short_nbor.run(&this->atom->x, &this->nbor->dev_nbor,
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&this->_nbor_data->begin(),
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&this->dev_short_nbor, &this->_off2_disp, &ainum,
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&nbor_pitch, &this->_threads_per_atom);
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k_dispersion.set_size(GX,BX);
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k_dispersion.run(&this->atom->x, &this->atom->extra,
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&coeff_amtype, &coeff_amclass, &sp_nonpolar,
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&this->nbor->dev_nbor, &this->_nbor_data->begin(),
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&this->dev_short_nbor,
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&this->ans->force, &this->ans->engv,
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&eflag, &vflag, &ainum, &_nall, &nbor_pitch,
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&this->_threads_per_atom, &this->_aewald,
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&this->_off2_disp);
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this->time_pair.stop();
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return GX;
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}
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// ---------------------------------------------------------------------------
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// Calculate the multipole real-space term, returning tep
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// ---------------------------------------------------------------------------
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template <class numtyp, class acctyp>
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int HippoT::multipole_real(const int eflag, const int vflag) {
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int ainum=this->ans->inum();
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if (ainum == 0)
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return 0;
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int _nall=this->atom->nall();
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int nbor_pitch=this->nbor->nbor_pitch();
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// Compute the block size and grid size to keep all cores busy
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const int BX=this->block_size();
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int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
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(BX/this->_threads_per_atom)));
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this->time_pair.start();
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// Build the short neighbor list for the cutoff off2_mpole,
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// at this point mpole is the first kernel in a time step
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this->k_short_nbor.set_size(GX,BX);
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this->k_short_nbor.run(&this->atom->x, &this->nbor->dev_nbor,
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&this->_nbor_data->begin(),
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&this->dev_short_nbor, &this->_off2_mpole, &ainum,
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&nbor_pitch, &this->_threads_per_atom);
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this->k_multipole.set_size(GX,BX);
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this->k_multipole.run(&this->atom->x, &this->atom->extra, &coeff_amtype, &sp_polar,
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&this->nbor->dev_nbor, &this->_nbor_data->begin(),
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&this->dev_short_nbor,
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&this->ans->force, &this->ans->engv, &this->_tep,
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&eflag, &vflag, &ainum, &_nall, &nbor_pitch,
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&this->_threads_per_atom, &this->_aewald, &this->_felec,
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&this->_off2_mpole, &_polar_dscale, &_polar_uscale);
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this->time_pair.stop();
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return GX;
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}
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// ---------------------------------------------------------------------------
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// Calculate the real-space permanent field, returning field and fieldp
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// ---------------------------------------------------------------------------
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template <class numtyp, class acctyp>
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int HippoT::udirect2b(const int eflag, const int vflag) {
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int ainum=this->ans->inum();
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if (ainum == 0)
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return 0;
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int _nall=this->atom->nall();
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int nbor_pitch=this->nbor->nbor_pitch();
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// Compute the block size and grid size to keep all cores busy
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const int BX=this->block_size();
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int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
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(BX/this->_threads_per_atom)));
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this->time_pair.start();
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// Build the short neighbor list if not done yet
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if (!this->short_nbor_polar_avail) {
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this->k_short_nbor.set_size(GX,BX);
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this->k_short_nbor.run(&this->atom->x, &this->nbor->dev_nbor,
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&this->_nbor_data->begin(),
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&this->dev_short_nbor, &this->_off2_polar, &ainum,
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&nbor_pitch, &this->_threads_per_atom);
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this->short_nbor_polar_avail = true;
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}
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this->k_udirect2b.set_size(GX,BX);
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this->k_udirect2b.run(&this->atom->x, &this->atom->extra, &coeff_amtype, &sp_polar,
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&this->nbor->dev_nbor, &this->_nbor_data->begin(),
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&this->dev_short_nbor,
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&this->_fieldp, &ainum, &_nall, &nbor_pitch,
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&this->_threads_per_atom, &this->_aewald, &this->_off2_polar,
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&_polar_dscale, &_polar_uscale);
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this->time_pair.stop();
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return GX;
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}
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// ---------------------------------------------------------------------------
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// Calculate the real-space induced field, returning field and fieldp
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// ---------------------------------------------------------------------------
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template <class numtyp, class acctyp>
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int HippoT::umutual2b(const int eflag, const int vflag) {
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int ainum=this->ans->inum();
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if (ainum == 0)
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return 0;
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int _nall=this->atom->nall();
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int nbor_pitch=this->nbor->nbor_pitch();
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// Compute the block size and grid size to keep all cores busy
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const int BX=this->block_size();
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int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
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(BX/this->_threads_per_atom)));
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this->time_pair.start();
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// Build the short neighbor list if not done yet
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if (!this->short_nbor_polar_avail) {
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this->k_short_nbor.set_size(GX,BX);
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this->k_short_nbor.run(&this->atom->x, &this->nbor->dev_nbor,
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&this->_nbor_data->begin(), &this->dev_short_nbor,
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&this->_off2_polar, &ainum, &nbor_pitch,
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&this->_threads_per_atom);
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this->short_nbor_polar_avail = true;
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}
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this->k_umutual2b.set_size(GX,BX);
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this->k_umutual2b.run(&this->atom->x, &this->atom->extra, &coeff_amtype, &sp_polar,
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&this->nbor->dev_nbor, &this->_nbor_data->begin(),
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&this->dev_short_nbor, &this->_fieldp, &ainum, &_nall,
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&nbor_pitch, &this->_threads_per_atom, &this->_aewald,
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&this->_off2_polar, &_polar_dscale, &_polar_uscale);
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this->time_pair.stop();
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return GX;
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}
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// ---------------------------------------------------------------------------
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// Calculate the polar real-space term, returning tep
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// ---------------------------------------------------------------------------
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template <class numtyp, class acctyp>
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int HippoT::polar_real(const int eflag, const int vflag) {
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int ainum=this->ans->inum();
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if (ainum == 0)
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return 0;
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int _nall=this->atom->nall();
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int nbor_pitch=this->nbor->nbor_pitch();
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// Compute the block size and grid size to keep all cores busy
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const int BX=this->block_size();
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int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
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(BX/this->_threads_per_atom)));
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this->time_pair.start();
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// Build the short neighbor list if not done yet
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if (!this->short_nbor_polar_avail) {
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this->k_short_nbor.set_size(GX,BX);
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this->k_short_nbor.run(&this->atom->x, &this->nbor->dev_nbor,
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&this->_nbor_data->begin(),
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&this->dev_short_nbor, &this->_off2_polar, &ainum,
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&nbor_pitch, &this->_threads_per_atom);
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this->short_nbor_polar_avail = true;
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}
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this->k_polar.set_size(GX,BX);
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this->k_polar.run(&this->atom->x, &this->atom->extra, &coeff_amtype, &sp_polar,
|
||||
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
|
||||
&this->dev_short_nbor,
|
||||
&this->ans->force, &this->ans->engv, &this->_tep,
|
||||
&eflag, &vflag, &ainum, &_nall, &nbor_pitch,
|
||||
&this->_threads_per_atom, &this->_aewald, &this->_felec,
|
||||
&this->_off2_polar, &_polar_dscale, &_polar_uscale);
|
||||
this->time_pair.stop();
|
||||
|
||||
// Signal that short nbor list is not avail for the next time step
|
||||
// do it here because polar_real() is the last kernel in a time step at this point
|
||||
|
||||
this->short_nbor_polar_avail = false;
|
||||
|
||||
return GX;
|
||||
}
|
||||
|
||||
template class Hippo<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
Reference in New Issue
Block a user