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Added the GPU version of pair edpd and mdpd

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This commit is contained in:
Trung Nguyen
2023-12-05 13:34:37 -06:00
parent 086cf49a8c
commit fe96d9f836
12 changed files with 2535 additions and 0 deletions
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lib/gpu/lal_edpd.cpp Normal file
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/***************************************************************************
edpd.cpp
-------------------
Trung Dac Nguyen (U Chicago)
Class for acceleration of the edpd pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : September 2023
email : ndactrung@gmail.com
***************************************************************************/
#if defined(USE_OPENCL)
#include "edpd_cl.h"
#elif defined(USE_CUDART)
const char *edpd=0;
#else
#include "edpd_cubin.h"
#endif
#include "lal_edpd.h"
#include <cassert>
namespace LAMMPS_AL {
#define EDPDT EDPD<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
template <class numtyp, class acctyp>
EDPDT::EDPD() : BaseDPD<numtyp,acctyp>(), _allocated(false) {
_max_q_size = 0;
}
template <class numtyp, class acctyp>
EDPDT::~EDPD() {
clear();
}
template <class numtyp, class acctyp>
int EDPDT::bytes_per_atom(const int max_nbors) const {
return this->bytes_per_atom_atomic(max_nbors);
}
template <class numtyp, class acctyp>
int EDPDT::init(const int ntypes,
double **host_cutsq, double **host_a0,
double **host_gamma, double **host_cut,
double **host_power, double **host_kappa,
double **host_powerT, double **host_cutT,
double ***host_sc, double ***host_kc, double *host_mass,
double *host_special_lj,
const int power_flag, const int kappa_flag,
const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size,
const double gpu_split, FILE *_screen) {
const int max_shared_types=this->device->max_shared_types();
int onetype=0;
#ifdef USE_OPENCL
if (maxspecial==0)
for (int i=1; i<ntypes; i++)
for (int j=i; j<ntypes; j++)
if (host_cutsq[i][j]>0) {
if (onetype>0)
onetype=-1;
else if (onetype==0)
onetype=i*max_shared_types+j;
}
if (onetype<0) onetype=0;
#endif
int success;
int extra_fields = 4; // round up to accomodate quadruples of numtyp values
// T and cv
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,
gpu_split,_screen,edpd,"k_edpd",onetype,extra_fields);
if (success!=0)
return success;
// If atom type constants fit in shared memory use fast kernel
int lj_types=ntypes;
shared_types=false;
if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
lj_types=max_shared_types;
shared_types=true;
}
_lj_types=lj_types;
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<lj_types*lj_types; i++)
host_write[i]=0.0;
coeff.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,coeff,host_write,host_a0,host_gamma,
host_cut);
coeff2.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,coeff2,host_write,host_power,host_kappa,
host_powerT,host_cutT);
UCL_H_Vec<int> dview_mass(ntypes, *(this->ucl_device), UCL_WRITE_ONLY);
for (int i = 0; i < ntypes; i++)
dview_mass[i] = host_mass[i];
mass.alloc(ntypes,*(this->ucl_device), UCL_READ_ONLY);
ucl_copy(mass,dview_mass,false);
if (host_sc) {
UCL_H_Vec<numtyp4> dview(lj_types*lj_types,*(this->ucl_device),UCL_WRITE_ONLY);;
sc.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
int n = 0;
for (int i = 1; i < ntypes; i++)
for (int j = 1; j < ntypes; j++) {
dview[n].x = host_sc[i][j][0];
dview[n].y = host_sc[i][j][1];
dview[n].z = host_sc[i][j][2];
dview[n].w = host_sc[i][j][3];
n++;
}
ucl_copy(sc,dview,false);
}
if (host_kc) {
UCL_H_Vec<numtyp4> dview(lj_types*lj_types,*(this->ucl_device),UCL_WRITE_ONLY);;
kc.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
int n = 0;
for (int i = 1; i < ntypes; i++)
for (int j = 1; j < ntypes; j++) {
dview[n].x = host_kc[i][j][0];
dview[n].y = host_kc[i][j][1];
dview[n].z = host_kc[i][j][2];
dview[n].w = host_kc[i][j][3];
n++;
}
ucl_copy(kc,dview,false);
}
UCL_H_Vec<numtyp> host_rsq(lj_types*lj_types,*(this->ucl_device),
UCL_WRITE_ONLY);
cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack1(ntypes,lj_types,cutsq,host_rsq,host_cutsq);
double special_sqrt[4];
special_sqrt[0] = sqrt(host_special_lj[0]);
special_sqrt[1] = sqrt(host_special_lj[1]);
special_sqrt[2] = sqrt(host_special_lj[2]);
special_sqrt[3] = sqrt(host_special_lj[3]);
UCL_H_Vec<double> dview;
sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
dview.view(host_special_lj,4,*(this->ucl_device));
ucl_copy(sp_lj,dview,false);
sp_sqrt.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
dview.view(special_sqrt,4,*(this->ucl_device));
ucl_copy(sp_sqrt,dview,false);
_power_flag = power_flag;
_kappa_flag = kappa_flag;
// allocate per-atom array Q
int ef_nall=nall;
if (ef_nall==0)
ef_nall=2000;
_max_q_size=static_cast<int>(static_cast<double>(ef_nall)*1.10);
Q.alloc(_max_q_size,*(this->ucl_device),UCL_READ_WRITE,UCL_READ_WRITE);
_allocated=true;
this->_max_bytes=coeff.row_bytes()+coeff2.row_bytes()+Q.row_bytes()+
sc.row_bytes()+kc.row_bytes()+mass.row_bytes()+cutsq.row_bytes()+sp_lj.row_bytes()+sp_sqrt.row_bytes();
return 0;
}
template <class numtyp, class acctyp>
void EDPDT::clear() {
if (!_allocated)
return;
_allocated=false;
coeff.clear();
coeff2.clear();
sc.clear();
kc.clear();
Q.clear();
mass.clear();
cutsq.clear();
sp_lj.clear();
sp_sqrt.clear();
this->clear_atomic();
}
template <class numtyp, class acctyp>
double EDPDT::host_memory_usage() const {
return this->host_memory_usage_atomic()+sizeof(EDPD<numtyp,acctyp>);
}
template <class numtyp, class acctyp>
void EDPDT::update_flux(void **flux_ptr) {
*flux_ptr=Q.host.begin();
Q.update_host(_max_q_size,false);
}
// ---------------------------------------------------------------------------
// Calculate energies, forces, and torques
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int EDPDT::loop(const int eflag, const int vflag) {
int nall = this->atom->nall();
// Resize Q array if necessary
if (nall > _max_q_size) {
_max_q_size=static_cast<int>(static_cast<double>(nall)*1.10);
Q.resize(_max_q_size);
}
// signal that we need to transfer extra data from the host
this->atom->extra_data_unavail();
numtyp4 *pextra=reinterpret_cast<numtyp4*>(&(this->atom->extra[0]));
int n = 0;
int nstride = 1;
for (int i = 0; i < nall; i++) {
int idx = n+i*nstride;
numtyp4 v;
v.x = edpd_temp[i];
v.y = edpd_cv[i];
v.z = 0;
v.w = 0;
pextra[idx] = v;
}
this->atom->add_extra_data();
// 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)));
int ainum=this->ans->inum();
int nbor_pitch=this->nbor->nbor_pitch();
this->time_pair.start();
if (shared_types) {
this->k_pair_sel->set_size(GX,BX);
this->k_pair_sel->run(&this->atom->x, &this->atom->extra, &coeff, &coeff2, &mass,
&sc, &kc, &sp_lj, &sp_sqrt, &this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &Q, &eflag, &vflag,
&_power_flag, &_kappa_flag, &ainum, &nbor_pitch,
&this->atom->v, &cutsq, &this->_dtinvsqrt, &this->_seed,
&this->_timestep, &this->_threads_per_atom);
} else {
this->k_pair.set_size(GX,BX);
this->k_pair.run(&this->atom->x, &this->atom->extra, &coeff, &coeff2, &mass,
&sc, &kc, &_lj_types, &sp_lj, &sp_sqrt,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &Q, &eflag, &vflag,
&_power_flag, &_kappa_flag, &ainum, &nbor_pitch,
&this->atom->v, &cutsq, &this->_dtinvsqrt, &this->_seed,
&this->_timestep, &this->_threads_per_atom);
}
this->time_pair.stop();
return GX;
}
template <class numtyp, class acctyp>
void EDPDT::update_coeff(int ntypes, double **host_a0, double **host_gamma,
double **host_sigma, double **host_cut)
{
UCL_H_Vec<numtyp> host_write(_lj_types*_lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
this->atom->type_pack4(ntypes,_lj_types,coeff,host_write,host_a0,host_gamma,
host_sigma,host_cut);
}
// ---------------------------------------------------------------------------
// Get the extra data pointers from host
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void EDPDT::get_extra_data(double *host_T, double *host_cv) {
edpd_temp = host_T;
edpd_cv = host_cv;
}
template class EDPD<PRECISION,ACC_PRECISION>;
}

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// **************************************************************************
// edpd.cu
// -------------------
// Trung Dac Nguyen (U Chicago)
//
// Device code for acceleration of the edpd pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________
//
// begin : September 2023
// email : ndactrung@gmail.com
// ***************************************************************************
#if defined(NV_KERNEL) || defined(USE_HIP)
#include "lal_aux_fun1.h"
#ifndef _DOUBLE_DOUBLE
_texture( pos_tex,float4);
_texture( vel_tex,float4);
#else
_texture_2d( pos_tex,int4);
_texture_2d( vel_tex,int4);
#endif
#else
#define pos_tex x_
#define vel_tex v_
#endif
#define EPSILON (numtyp)1.0e-10
//#define _USE_UNIFORM_SARU_LCG
//#define _USE_UNIFORM_SARU_TEA8
//#define _USE_GAUSSIAN_SARU_LCG
#if !defined(_USE_UNIFORM_SARU_LCG) && !defined(_USE_UNIFORM_SARU_TEA8) && !defined(_USE_GAUSSIAN_SARU_LCG)
#define _USE_UNIFORM_SARU_LCG
#endif
// References:
// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128.
// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201.
// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19
#define LCGA 0x4beb5d59 /* Full period 32 bit LCG */
#define LCGC 0x2600e1f7
#define oWeylPeriod 0xda879add /* Prime period 3666320093 */
#define oWeylOffset 0x8009d14b
#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0]
// using the inherent LCG, then multiply u with sqrt(3) to "match"
// with a normal random distribution.
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
// Curly brackets to make variables local to the scope.
#ifdef _USE_UNIFORM_SARU_LCG
#define SQRT3 (numtyp)1.7320508075688772935274463
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
unsigned int v = (state ^ (state>>26)) + wstate; \
unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
// then multiply u with sqrt(3) to "match" with a normal random distribution
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
#ifdef _USE_UNIFORM_SARU_TEA8
#define SQRT3 (numtyp)1.7320508075688772935274463
#define k0 0xA341316C
#define k1 0xC8013EA4
#define k2 0xAD90777D
#define k3 0x7E95761E
#define delta 0x9e3779b9
#define rounds 8
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
unsigned int sum = 0; \
for (int i=0; i < rounds; i++) { \
sum += delta; \
state += ((wstate<<4) + k0)^(wstate + sum)^((wstate>>5) + k1); \
wstate += ((state<<4) + k2)^(state + sum)^((state>>5) + k3); \
} \
unsigned int v = (state ^ (state>>26)) + wstate; \
unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
// and uses the polar method (Marsaglia's) to transform to a normal random value
// This is used to compared with CPU DPD using RandMars::gaussian()
#ifdef _USE_GAUSSIAN_SARU_LCG
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state=0x12345678; \
unsigned int wstate=12345678; \
state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
unsigned int v, s; \
numtyp r1, r2, rsq; \
while (1) { \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
v = (state ^ (state>>26)) + wstate; \
s = (signed int)((v^(v>>20))*0x6957f5a7); \
r1 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
v = (state ^ (state>>26)) + wstate; \
s = (signed int)((v^(v>>20))*0x6957f5a7); \
r2 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
rsq = r1 * r1 + r2 * r2; \
if (rsq < (numtyp)1.0) break; \
} \
numtyp fac = ucl_sqrt((numtyp)-2.0*log(rsq)/rsq); \
randnum = r2*fac; \
}
#endif
#if (SHUFFLE_AVAIL == 0)
#define store_heatflux(Qi, ii, inum, tid, t_per_atom, offset, Q) \
if (t_per_atom>1) { \
simdsync(); \
simd_reduce_add1(t_per_atom, red_acc, offset, tid, Qi); \
} \
if (offset==0 && ii<inum) { \
Q[ii]=Qi; \
}
#else
#define store_heatflux(Qi, ii, inum, tid, t_per_atom, offset, Q) \
if (t_per_atom>1) { \
simd_reduce_add1(t_per_atom,Qi); \
} \
if (offset==0 && ii<inum) { \
Q[ii]=Qi; \
}
#endif
#define MIN(A,B) ((A) < (B) ? (A) : (B))
#define MAX(A,B) ((A) < (B) ? (B) : (A))
// note the change in coeff: coeff.x = a0, coeff.y = gamma, coeff.z = cut (no sigma)
__kernel void k_edpd(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff,
const __global numtyp4 *restrict coeff2,
const __global numtyp *restrict mass,
const __global numtyp4 *restrict sc,
const __global numtyp4 *restrict kc,
const int lj_types,
const __global numtyp *restrict sp_lj,
const __global numtyp *restrict sp_sqrt,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
__global acctyp *restrict Q,
const int eflag, const int vflag,
const int power_flag, const int kappa_flag,
const int inum, const int nbor_pitch,
const __global numtyp4 *restrict v_,
const __global numtyp *restrict cutsq,
const numtyp dtinvsqrt, const int seed,
const int timestep, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
int n_stride;
local_allocate_store_pair();
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp energy, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
acctyp Qi = (acctyp)0;
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int itype=ix.w;
numtyp mass_itype = mass[itype];
numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
int itag=iv.w;
const numtyp4 Tcvi = extra[i];
numtyp Ti = Tcvi.x;
numtyp cvi = Tcvi.y;
numtyp factor_dpd;
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
factor_dpd = sp_lj[sbmask(j)];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
int jtag=jv.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
int mtype=itype*lj_types+jtype;
if (rsq<cutsq[mtype]) {
numtyp r=ucl_sqrt(rsq);
if (r < EPSILON) continue;
numtyp rinv=ucl_recip(r);
numtyp delvx = iv.x - jv.x;
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp dot = delx*delvx + dely*delvy + delz*delvz;
numtyp vijeij = dot*rinv;
const numtyp coeffx=coeff[mtype].x; // a0[itype][jtype]
const numtyp coeffy=coeff[mtype].y; // gamma[itype][jtype]
const numtyp coeffz=coeff[mtype].z; // cut[itype][jtype]
const numtyp4 Tcvj = extra[j];
numtyp Tj = Tcvj.x;
numtyp cvj = Tcvj.y;
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;
}
numtyp randnum = (numtyp)0.0;
saru(tag1, tag2, seed, timestep, randnum);
numtyp T_ij=(numtyp)0.5*(Ti+Tj);
numtyp4 T_pow;
T_pow.x = T_ij - (numtyp)1.0;
T_pow.y = T_pow.x*T_pow.x;
T_pow.z = T_pow.x*T_pow.y;
T_pow.w = T_pow.x*T_pow.z;
numtyp coeff2x = coeff2[mtype].x; //power[itype][jtype]
numtyp coeff2y = coeff2[mtype].y; //kappa[itype][jtype]
numtyp coeff2z = coeff2[mtype].z; //powerT[itype][jtype]
numtyp coeff2w = coeff2[mtype].w; //cutT[itype][jtype]
numtyp power_d = coeff2x;
if (power_flag) {
numtyp factor = (numtyp)1.0;
factor += sc[mtype].x*T_pow.x + sc[mtype].y*T_pow.y +
sc[mtype].z*T_pow.z + sc[mtype].w*T_pow.w;
power_d *= factor;
}
power_d = MAX((numtyp)0.01,power_d);
numtyp wc = (numtyp)1.0 - r/coeffz; // cut[itype][jtype]
wc = MAX((numtyp)0.0,MIN((numtyp)1.0,wc));
numtyp wr = ucl_pow(wc, (numtyp)0.5*power_d);
numtyp kboltz = (numtyp)1.0;
numtyp GammaIJ = coeffy; // gamma[itype][jtype]
numtyp SigmaIJ = (numtyp)4.0*GammaIJ*kboltz*Ti*Tj/(Ti+Tj);
SigmaIJ = ucl_sqrt(SigmaIJ);
numtyp force = coeffx*T_ij*wc; // a0[itype][jtype]
force -= GammaIJ *wr*wr *dot*rinv;
force += SigmaIJ * wr *randnum * dtinvsqrt;
force *= factor_dpd*rinv;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
// heat transfer
if (r < coeff2w) {
numtyp wrT = (numtyp)1.0 - r/coeff2w;
wrT = MAX((numtyp)0.0,MIN((numtyp)1.0,wrT));
wrT = ucl_pow(wrT, (numtyp)0.5*coeff2z); // powerT[itype][jtype]
numtyp randnumT = (numtyp)0;
saru(tag1, tag2, seed+tag1+tag2, timestep, randnumT); // randomT->gaussian();
randnumT = MAX((numtyp)-5.0,MIN(randnum,(numtyp)5.0));
numtyp kappaT = coeff2y; // kappa[itype][jtype]
if (kappa_flag) {
numtyp factor = (numtyp)1.0;
factor += kc[mtype].x*T_pow.x + kc[mtype].y*T_pow.y +
kc[mtype].z*T_pow.z + kc[mtype].w*T_pow.w;
kappaT *= factor;
}
numtyp kij = cvi*cvj*kappaT * T_ij*T_ij;
numtyp alphaij = ucl_sqrt((numtyp)2.0*kboltz*kij);
numtyp dQc = kij * wrT*wrT * (Tj - Ti)/(Ti*Tj);
numtyp dQd = wr*wr*( GammaIJ * vijeij*vijeij - SigmaIJ*SigmaIJ/mass_itype ) - SigmaIJ * wr *vijeij *randnum;
dQd /= (cvi+cvj);
numtyp dQr = alphaij * wrT * dtinvsqrt * randnumT;
Qi += (dQc + dQd + dQr );
}
if (EVFLAG && eflag) {
numtyp e = (numtyp)0.5*coeffx*T_ij*coeffz * wc*wc;
energy+=factor_dpd*e;
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
ans,engv);
store_heatflux(Qi,ii,inum,tid,t_per_atom,offset,Q);
}
__kernel void k_edpd_fast(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff_in,
const __global numtyp4 *restrict coeff2_in,
const __global numtyp *restrict mass,
const __global numtyp4 *restrict sc_in,
const __global numtyp4 *restrict kc_in,
const __global numtyp *restrict sp_lj_in,
const __global numtyp *restrict sp_sqrt_in,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
__global acctyp *restrict Q,
const int eflag, const int vflag,
const int power_flag, const int kappa_flag,
const int inum, const int nbor_pitch,
const __global numtyp4 *restrict v_,
const __global numtyp *restrict cutsq,
const numtyp dtinvsqrt, const int seed,
const int timestep, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
#ifndef ONETYPE
__local numtyp4 coeff[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 coeff2[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 sc[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 kc[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp sp_lj[4];
__local numtyp sp_sqrt[4];
if (tid<4) {
sp_lj[tid]=sp_lj_in[tid];
sp_sqrt[tid]=sp_sqrt_in[tid];
}
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
coeff[tid]=coeff_in[tid];
coeff2[tid]=coeff2_in[tid];
sc[tid]=sc_in[tid];
kc[tid]=kc_in[tid];
}
__syncthreads();
#else
const numtyp coeffx=coeff_in[ONETYPE].x; // a0[itype][jtype]
const numtyp coeffy=coeff_in[ONETYPE].y; // gamma[itype][jtype]
const numtyp coeffz=coeff_in[ONETYPE].z; // cut[itype][jtype]
const numtyp coeff2x=coeff2_in[ONETYPE].x; // power[itype][jtype]
const numtyp coeff2y=coeff2_in[ONETYPE].y; // kappa[itype][jtype]
const numtyp coeff2z=coeff2_in[ONETYPE].z; // powerT[itype][jtype]
const numtyp coeff2w=coeff2_in[ONETYPE].w; // cutT[itype][jtype]
const numtyp cutsq_p=cutsq[ONETYPE];
const numtyp scx=sc_in[ONETYPE].x;
const numtyp scy=sc_in[ONETYPE].y;
const numtyp scz=sc_in[ONETYPE].z;
const numtyp scw=sc_in[ONETYPE].w;
const numtyp kcx=kc_in[ONETYPE].x;
const numtyp kcy=kc_in[ONETYPE].y;
const numtyp kcz=kc_in[ONETYPE].z;
const numtyp kcw=kc_in[ONETYPE].w;
#endif
int n_stride;
local_allocate_store_pair();
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp energy, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
acctyp Qi = (acctyp)0;
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int iw=ix.w;
numtyp mass_itype = mass[iw];
#ifndef ONETYPE
int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
#endif
numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
int itag=iv.w;
const numtyp4 Tcvi = extra[i];
numtyp Ti = Tcvi.x;
numtyp cvi = Tcvi.y;
#ifndef ONETYPE
numtyp factor_dpd;
#endif
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
#ifndef ONETYPE
factor_dpd = sp_lj[sbmask(j)];
j &= NEIGHMASK;
#endif
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
#ifndef ONETYPE
int mtype=itype+jx.w;
const numtyp cutsq_p=cutsq[mtype];
#endif
numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
int jtag=jv.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
if (rsq<cutsq_p) {
numtyp r=ucl_sqrt(rsq);
if (r < EPSILON) continue;
numtyp rinv=ucl_recip(r);
numtyp delvx = iv.x - jv.x;
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp dot = delx*delvx + dely*delvy + delz*delvz;
numtyp vijeij = dot*rinv;
#ifndef ONETYPE
const numtyp coeffx=coeff[mtype].x; // a0[itype][jtype]
const numtyp coeffy=coeff[mtype].y; // gamma[itype][jtype]
const numtyp coeffz=coeff[mtype].z; // cut[itype][jtype]
const numtyp coeff2x=coeff2[mtype].x; // power[itype][jtype]
const numtyp coeff2y=coeff2[mtype].y; // kappa[itype][jtype]
const numtyp coeff2z=coeff2[mtype].z; // powerT[itype][jtype]
const numtyp coeff2w=coeff2[mtype].w; // cutT[itype][jtype]
const numtyp scx = sc[mtype].x;
const numtyp scy = sc[mtype].y;
const numtyp scz = sc[mtype].z;
const numtyp scw = sc[mtype].w;
const numtyp kcx = kc[mtype].x;
const numtyp kcy = kc[mtype].y;
const numtyp kcz = kc[mtype].z;
const numtyp kcw = kc[mtype].w;
#endif
const numtyp4 Tcvj = extra[j];
numtyp Tj = Tcvj.x;
numtyp cvj = Tcvj.y;
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;
}
numtyp randnum = (numtyp)0.0;
saru(tag1, tag2, seed, timestep, randnum);
numtyp T_ij=(numtyp)0.5*(Ti+Tj);
numtyp4 T_pow;
T_pow.x = T_ij - (numtyp)1.0;
T_pow.y = T_pow.x*T_pow.x;
T_pow.z = T_pow.x*T_pow.y;
T_pow.w = T_pow.x*T_pow.z;
numtyp power_d = coeff2x; // power[itype][jtype]
if (power_flag) {
numtyp factor = (numtyp)1.0;
factor += scx*T_pow.x + scy*T_pow.y + scz*T_pow.z + scw*T_pow.w;
power_d *= factor;
}
power_d = MAX((numtyp)0.01,power_d);
numtyp wc = (numtyp)1.0 - r/coeffz; // cut[itype][jtype]
wc = MAX((numtyp)0.0,MIN((numtyp)1.0,wc));
numtyp wr = ucl_pow((numtyp)wc, (numtyp)0.5*power_d);
numtyp kboltz = (numtyp)1.0;
numtyp GammaIJ = coeffy; // gamma[itype][jtype]
numtyp SigmaIJ = (numtyp)4.0*GammaIJ*kboltz*Ti*Tj/(Ti+Tj);
SigmaIJ = ucl_sqrt(SigmaIJ);
numtyp force = coeffx*T_ij*wc; // a0[itype][jtype]
force -= GammaIJ *wr*wr *dot*rinv;
force += SigmaIJ* wr *randnum * dtinvsqrt;
#ifndef ONETYPE
force *= factor_dpd*rinv;
#else
force *= rinv;
#endif
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
// heat transfer
if (r < coeff2w) {
numtyp wrT = (numtyp)1.0 - r/coeff2w;
wrT = MAX((numtyp)0.0,MIN((numtyp)1.0,wrT));
wrT = ucl_pow(wrT, (numtyp)0.5*coeff2z); // powerT[itype][jtype]
numtyp randnumT = (numtyp)0;
saru(tag1, tag2, seed+tag1+tag2, timestep, randnumT); // randomT->gaussian();
randnumT = MAX((numtyp)-5.0,MIN(randnum,(numtyp)5.0));
numtyp kappaT = coeff2y; // kappa[itype][jtype]
if (kappa_flag) {
numtyp factor = (numtyp)1.0;
factor += kcx*T_pow.x + kcy*T_pow.y + kcz*T_pow.z + kcw*T_pow.w;
kappaT *= factor;
}
numtyp kij = cvi*cvj*kappaT * T_ij*T_ij;
numtyp alphaij = ucl_sqrt((numtyp)2.0*kboltz*kij);
numtyp dQc = kij * wrT*wrT * (Tj - Ti )/(Ti*Tj);
numtyp dQd = wr*wr*( GammaIJ * vijeij*vijeij - SigmaIJ*SigmaIJ/mass_itype ) - SigmaIJ * wr *vijeij *randnum;
dQd /= (cvi+cvj);
numtyp dQr = alphaij * wrT * dtinvsqrt * randnumT;
Qi += (dQc + dQd + dQr );
}
if (EVFLAG && eflag) {
numtyp e = (numtyp)0.5*coeffx*T_ij*coeffz * wc*wc;
#ifndef ONETYPE
energy+=factor_dpd*e;
#else
energy+=e;
#endif
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag, ans,engv);
store_heatflux(Qi,ii,inum,tid,t_per_atom,offset,Q);
}

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/***************************************************************************
edpd.h
-------------------
Trung Dac Nguyen (U Chicago)
Class for acceleration of the dpd pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : September 2023
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_DPD_H
#define LAL_DPD_H
#include "lal_base_dpd.h"
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class EDPD : public BaseDPD<numtyp, acctyp> {
public:
EDPD();
~EDPD();
/// Clear any previous data and set up for a new LAMMPS run
/** \param max_nbors initial number of rows in the neighbor matrix
* \param cell_size cutoff + skin
* \param gpu_split fraction of particles handled by device
*
* Returns:
* - 0 if successful
* - -1 if fix gpu not found
* - -3 if there is an out of memory error
* - -4 if the GPU library was not compiled for GPU
* - -5 Double precision is not supported on card **/
int init(const int ntypes, double **host_cutsq, double **host_a0,
double **host_gamma, double **host_cut, double **host_power,
double **host_kappa, double **host_powerT, double **host_cutT,
double ***host_sc, double ***host_kc, double *host_mass,
double *host_special_lj, const int power_flag, const int kappa_flag,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, const double gpu_split,
FILE *screen);
/// Clear all host and device data
/** \note This is called at the beginning of the init() routine **/
void clear();
/// Returns memory usage on device per atom
int bytes_per_atom(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage() const;
/// Update coeff if needed (tstat only)
void update_coeff(int ntypes, double **host_a0, double **host_gamma,
double **host_sigma, double **host_cut);
void get_extra_data(double *host_T, double *host_cv);
/// copy Q (flux) from device to host
void update_flux(void **flux_ptr);
// --------------------------- TYPE DATA --------------------------
/// coeff.x = a0, coeff.y = gamma, coeff.z = cut
UCL_D_Vec<numtyp4> coeff;
/// coeff2.x = power, coeff2.y = kappa, coeff2.z = powerT, coeff2.w = cutT
UCL_D_Vec<numtyp4> coeff2;
UCL_D_Vec<numtyp4> kc, sc;
UCL_D_Vec<numtyp> cutsq;
/// per-type array
UCL_D_Vec<numtyp> mass;
/// Special LJ values
UCL_D_Vec<numtyp> sp_lj, sp_sqrt;
/// If atom type constants fit in shared memory, use fast kernels
bool shared_types;
/// Number of atom types
int _lj_types;
/// Per-atom arrays
UCL_Vector<acctyp,acctyp> Q;
int _max_q_size;
int _power_flag, _kappa_flag;
/// pointer to host data
double *edpd_temp, *edpd_cv;
private:
bool _allocated;
int loop(const int eflag, const int vflag);
};
}
#endif

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/***************************************************************************
edpd_ext.cpp
-------------------
Trung Dac Nguyen (U Chicago)
Functions for LAMMPS access to edpd acceleration routines.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : September 2023
email : ndactrung@gmail.com
***************************************************************************/
#include <iostream>
#include <cassert>
#include <cmath>
#include "lal_edpd.h"
using namespace std;
using namespace LAMMPS_AL;
static EDPD<PRECISION,ACC_PRECISION> EDPDMF;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int edpd_gpu_init(const int ntypes, double **cutsq, double **host_a0,
double **host_gamma, double **host_cut, double **host_power,
double **host_kappa, double **host_powerT, double **host_cutT,
double ***host_sc, double ***host_kc, double *host_mass,
double *special_lj, const int power_flag, const int kappa_flag,
const int inum, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen) {
EDPDMF.clear();
gpu_mode=EDPDMF.device->gpu_mode();
double gpu_split=EDPDMF.device->particle_split();
int first_gpu=EDPDMF.device->first_device();
int last_gpu=EDPDMF.device->last_device();
int world_me=EDPDMF.device->world_me();
int gpu_rank=EDPDMF.device->gpu_rank();
int procs_per_gpu=EDPDMF.device->procs_per_gpu();
EDPDMF.device->init_message(screen,"edpd",first_gpu,last_gpu);
bool message=false;
if (EDPDMF.device->replica_me()==0 && screen)
message=true;
if (message) {
fprintf(screen,"Initializing Device and compiling on process 0...");
fflush(screen);
}
int init_ok=0;
if (world_me==0)
init_ok=EDPDMF.init(ntypes, cutsq, host_a0, host_gamma, host_cut,
host_power, host_kappa, host_powerT,
host_cutT, host_sc, host_kc, host_mass,
special_lj, power_flag, kappa_flag,
inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen);
EDPDMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
last_gpu,i);
fflush(screen);
}
if (gpu_rank==i && world_me!=0)
init_ok=EDPDMF.init(ntypes, cutsq, host_a0, host_gamma, host_cut,
host_power, host_kappa, host_powerT, host_cutT,
host_sc, host_kc, host_mass,
special_lj, power_flag, kappa_flag,
inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen);
EDPDMF.device->serialize_init();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
if (init_ok==0)
EDPDMF.estimate_gpu_overhead();
return init_ok;
}
void edpd_gpu_clear() {
EDPDMF.clear();
}
int ** edpd_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
tagint **special, 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,
double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
double *boxlo, double *prd) {
return EDPDMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
subhi, tag, nspecial, special, eflag, vflag, eatom,
vatom, host_start, ilist, jnum, cpu_time, success,
host_v, dtinvsqrt, seed, timestep, boxlo, prd);
}
void edpd_gpu_compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *tag,
double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
const int nlocal, double *boxlo, double *prd) {
EDPDMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
tag, host_v, dtinvsqrt, seed, timestep, nlocal, boxlo, prd);
}
void edpd_gpu_get_extra_data(double *host_T, double *host_cv) {
EDPDMF.get_extra_data(host_T, host_cv);
}
void edpd_gpu_update_flux(void **flux_ptr) {
EDPDMF.update_flux(flux_ptr);
}
double edpd_gpu_bytes() {
return EDPDMF.host_memory_usage();
}

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/***************************************************************************
mdpd.cpp
-------------------
Trung Dac Nguyen (U Chicago)
Class for acceleration of the mdpd pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : September 2023
email : ndactrung@gmail.com
***************************************************************************/
#if defined(USE_OPENCL)
#include "mdpd_cl.h"
#elif defined(USE_CUDART)
const char *mdpd=0;
#else
#include "mdpd_cubin.h"
#endif
#include "lal_mdpd.h"
#include <cassert>
namespace LAMMPS_AL {
#define MDPDT MDPD<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
template <class numtyp, class acctyp>
MDPDT::MDPD() : BaseDPD<numtyp,acctyp>(), _allocated(false) {
}
template <class numtyp, class acctyp>
MDPDT::~MDPD() {
clear();
}
template <class numtyp, class acctyp>
int MDPDT::bytes_per_atom(const int max_nbors) const {
return this->bytes_per_atom_atomic(max_nbors);
}
template <class numtyp, class acctyp>
int MDPDT::init(const int ntypes,
double **host_cutsq, double **host_A_att, double **host_B_rep,
double **host_gamma, double **host_sigma,
double **host_cut, double **host_cut_r,
double *host_special_lj, const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size,
const double gpu_split, FILE *_screen) {
const int max_shared_types=this->device->max_shared_types();
int onetype=0;
#ifdef USE_OPENCL
if (maxspecial==0)
for (int i=1; i<ntypes; i++)
for (int j=i; j<ntypes; j++)
if (host_cutsq[i][j]>0) {
if (onetype>0)
onetype=-1;
else if (onetype==0)
onetype=i*max_shared_types+j;
}
if (onetype<0) onetype=0;
#endif
int success;
int extra_fields = 4; // round up to accomodate quadruples of numtyp values
// rho
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,
gpu_split,_screen,mdpd,"k_mdpd",onetype,extra_fields);
if (success!=0)
return success;
// If atom type constants fit in shared memory use fast kernel
int lj_types=ntypes;
shared_types=false;
if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
lj_types=max_shared_types;
shared_types=true;
}
_lj_types=lj_types;
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<lj_types*lj_types; i++)
host_write[i]=0.0;
coeff.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,coeff,host_write,host_A_att,host_B_rep,
host_gamma,host_sigma);
coeff2.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,lj_types,coeff2,host_write,host_cut,host_cut_r,
host_cutsq);
UCL_H_Vec<numtyp> host_rsq(lj_types*lj_types,*(this->ucl_device),
UCL_WRITE_ONLY);
cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack1(ntypes,lj_types,cutsq,host_rsq,host_cutsq);
double special_sqrt[4];
special_sqrt[0] = sqrt(host_special_lj[0]);
special_sqrt[1] = sqrt(host_special_lj[1]);
special_sqrt[2] = sqrt(host_special_lj[2]);
special_sqrt[3] = sqrt(host_special_lj[3]);
UCL_H_Vec<double> dview;
sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
dview.view(host_special_lj,4,*(this->ucl_device));
ucl_copy(sp_lj,dview,false);
sp_sqrt.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
dview.view(special_sqrt,4,*(this->ucl_device));
ucl_copy(sp_sqrt,dview,false);
// allocate per-atom array Q
int ef_nall=nall;
if (ef_nall==0)
ef_nall=2000;
_allocated=true;
this->_max_bytes=coeff.row_bytes()+coeff2.row_bytes()+cutsq.row_bytes()+
sp_lj.row_bytes()+sp_sqrt.row_bytes();
return 0;
}
template <class numtyp, class acctyp>
void MDPDT::clear() {
if (!_allocated)
return;
_allocated=false;
coeff.clear();
coeff2.clear();
cutsq.clear();
sp_lj.clear();
sp_sqrt.clear();
this->clear_atomic();
}
template <class numtyp, class acctyp>
double MDPDT::host_memory_usage() const {
return this->host_memory_usage_atomic()+sizeof(MDPD<numtyp,acctyp>);
}
// ---------------------------------------------------------------------------
// Calculate energies, forces, and torques
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int MDPDT::loop(const int eflag, const int vflag) {
int nall = this->atom->nall();
// signal that we need to transfer extra data from the host
this->atom->extra_data_unavail();
numtyp4 *pextra=reinterpret_cast<numtyp4*>(&(this->atom->extra[0]));
int n = 0;
int nstride = 1;
for (int i = 0; i < nall; i++) {
int idx = n+i*nstride;
numtyp4 v;
v.x = mdpd_rho[i];
v.y = 0;
v.z = 0;
v.w = 0;
pextra[idx] = v;
}
this->atom->add_extra_data();
// 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)));
int ainum=this->ans->inum();
int nbor_pitch=this->nbor->nbor_pitch();
this->time_pair.start();
if (shared_types) {
this->k_pair_sel->set_size(GX,BX);
this->k_pair_sel->run(&this->atom->x, &this->atom->extra, &coeff, &coeff2,
&sp_lj, &sp_sqrt, &this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &eflag, &vflag,
&ainum, &nbor_pitch, &this->atom->v, &cutsq, &this->_dtinvsqrt, &this->_seed,
&this->_timestep, &this->_threads_per_atom);
} else {
this->k_pair.set_size(GX,BX);
this->k_pair.run(&this->atom->x, &this->atom->extra, &coeff, &coeff2,
&_lj_types, &sp_lj, &sp_sqrt, &this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &eflag, &vflag,
&ainum, &nbor_pitch, &this->atom->v, &cutsq, &this->_dtinvsqrt, &this->_seed,
&this->_timestep, &this->_threads_per_atom);
}
this->time_pair.stop();
return GX;
}
// ---------------------------------------------------------------------------
// Get the extra data pointers from host
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void MDPDT::get_extra_data(double *host_rho) {
mdpd_rho = host_rho;
}
template class MDPD<PRECISION,ACC_PRECISION>;
}

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// **************************************************************************
// mdpd.cu
// -------------------
// Trung Dac Nguyen (ORNL)
//
// Device code for acceleration of the mdpd pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________
//
// begin : December 2023
// email : ndactrung@gmail.com
// ***************************************************************************
#if defined(NV_KERNEL) || defined(USE_HIP)
#include "lal_aux_fun1.h"
#ifndef _DOUBLE_DOUBLE
_texture( pos_tex,float4);
_texture( vel_tex,float4);
#else
_texture_2d( pos_tex,int4);
_texture_2d( vel_tex,int4);
#endif
#else
#define pos_tex x_
#define vel_tex v_
#endif
#define EPSILON (numtyp)1.0e-10
//#define _USE_UNIFORM_SARU_LCG
//#define _USE_UNIFORM_SARU_TEA8
//#define _USE_GAUSSIAN_SARU_LCG
#if !defined(_USE_UNIFORM_SARU_LCG) && !defined(_USE_UNIFORM_SARU_TEA8) && !defined(_USE_GAUSSIAN_SARU_LCG)
#define _USE_UNIFORM_SARU_LCG
#endif
// References:
// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128.
// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201.
// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19
#define LCGA 0x4beb5d59 /* Full period 32 bit LCG */
#define LCGC 0x2600e1f7
#define oWeylPeriod 0xda879add /* Prime period 3666320093 */
#define oWeylOffset 0x8009d14b
#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0]
// using the inherent LCG, then multiply u with sqrt(3) to "match"
// with a normal random distribution.
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
// Curly brackets to make variables local to the scope.
#ifdef _USE_UNIFORM_SARU_LCG
#define SQRT3 (numtyp)1.7320508075688772935274463
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
unsigned int v = (state ^ (state>>26)) + wstate; \
unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
// then multiply u with sqrt(3) to "match" with a normal random distribution
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
#ifdef _USE_UNIFORM_SARU_TEA8
#define SQRT3 (numtyp)1.7320508075688772935274463
#define k0 0xA341316C
#define k1 0xC8013EA4
#define k2 0xAD90777D
#define k3 0x7E95761E
#define delta 0x9e3779b9
#define rounds 8
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
unsigned int sum = 0; \
for (int i=0; i < rounds; i++) { \
sum += delta; \
state += ((wstate<<4) + k0)^(wstate + sum)^((wstate>>5) + k1); \
wstate += ((state<<4) + k2)^(state + sum)^((state>>5) + k3); \
} \
unsigned int v = (state ^ (state>>26)) + wstate; \
unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
}
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
// and uses the polar method (Marsaglia's) to transform to a normal random value
// This is used to compared with CPU DPD using RandMars::gaussian()
#ifdef _USE_GAUSSIAN_SARU_LCG
#define saru(seed1, seed2, seed, timestep, randnum) { \
unsigned int seed3 = seed + timestep; \
seed3^=(seed1<<7)^(seed2>>6); \
seed2+=(seed1>>4)^(seed3>>15); \
seed1^=(seed2<<9)+(seed3<<8); \
seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
seed2+=seed1*seed3; \
seed1+=seed3 ^ (seed2>>2); \
seed2^=((signed int)seed2)>>17; \
unsigned int state=0x12345678; \
unsigned int wstate=12345678; \
state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
wstate = (state + seed2) ^ (((signed int)state)>>8); \
state = state + (wstate*(wstate^0xdddf97f5)); \
wstate = 0xABCB96F7 + (wstate>>1); \
unsigned int v, s; \
numtyp r1, r2, rsq; \
while (1) { \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
v = (state ^ (state>>26)) + wstate; \
s = (signed int)((v^(v>>20))*0x6957f5a7); \
r1 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
state = LCGA*state + LCGC; \
wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
v = (state ^ (state>>26)) + wstate; \
s = (signed int)((v^(v>>20))*0x6957f5a7); \
r2 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
rsq = r1 * r1 + r2 * r2; \
if (rsq < (numtyp)1.0) break; \
} \
numtyp fac = ucl_sqrt((numtyp)-2.0*log(rsq)/rsq); \
randnum = r2*fac; \
}
#endif
#define MIN(A,B) ((A) < (B) ? (A) : (B))
#define MAX(A,B) ((A) < (B) ? (B) : (A))
// coeff.x = A_att, coeff.y = B_rep, coeff.z = gamma, coeff.w = sigma
// coeff2.x = cut, coeff2.y = cut_r, coeff2.z = cutsq
__kernel void k_mdpd(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff,
const __global numtyp4 *restrict coeff2,
const int lj_types,
const __global numtyp *restrict sp_lj,
const __global numtyp *restrict sp_sqrt,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag, const int inum,
const int nbor_pitch,
const __global numtyp4 *restrict v_,
const __global numtyp *restrict cutsq,
const numtyp dtinvsqrt, const int seed,
const int timestep, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
int n_stride;
local_allocate_store_pair();
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp energy, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int itype=ix.w;
numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
int itag=iv.w;
const numtyp rhoi = extra[i].x;
numtyp factor_dpd, factor_sqrt;
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
factor_dpd = sp_lj[sbmask(j)];
factor_sqrt = sp_sqrt[sbmask(j)];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
int jtag=jv.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
int mtype=itype*lj_types+jtype;
if (rsq<coeff2[mtype].z) { // cutsq[itype][jtype]
numtyp r=ucl_sqrt(rsq);
if (r < EPSILON) continue;
numtyp rinv=ucl_recip(r);
numtyp delvx = iv.x - jv.x;
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp dot = delx*delvx + dely*delvy + delz*delvz;
numtyp A_attij = coeff[mtype].x;
numtyp B_repij = coeff[mtype].y;
numtyp gammaij = coeff[mtype].z;
numtyp sigmaij = coeff[mtype].w;
numtyp cutij = coeff2[mtype].x;
numtyp cut_rij = coeff2[mtype].y;
numtyp cutsqij = coeff2[mtype].z;
numtyp wc = (numtyp)1.0 - r/cutij;
numtyp wc_r = (numtyp)1.0 - r/cut_rij;
wc_r = MAX(wc_r,(numtyp)0.0);
numtyp wr = wc;
const numtyp rhoj = extra[j].x;
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;
}
numtyp randnum = (numtyp)0.0;
saru(tag1, tag2, seed, timestep, randnum);
// conservative force = A_att * wc + B_rep*(rhoi+rhoj)*wc_r
// drag force = -gamma * wr^2 * (delx dot delv) / r
// random force = sigma * wr * rnd * dtinvsqrt;
numtyp force = A_attij*wc + B_repij*(rhoi+rhoj)*wc_r;
force -= gammaij*wr*wr*dot*rinv;
force += sigmaij*wr*randnum*dtinvsqrt;
force *= factor_dpd*rinv;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
if (EVFLAG && eflag) {
// unshifted eng of conservative term:
// eng shifted to 0.0 at cutoff
numtyp e = (numtyp)0.5*A_attij*cutij * wr*wr + (numtyp)0.5*B_repij*cut_rij*(rhoi+rhoj)*wc_r*wc_r;
energy+=factor_dpd*e;
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
ans,engv);
}
__kernel void k_mdpd_fast(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict extra,
const __global numtyp4 *restrict coeff_in,
const __global numtyp4 *restrict coeff2_in,
const __global numtyp *restrict sp_lj_in,
const __global numtyp *restrict sp_sqrt_in,
const __global int * dev_nbor,
const __global int * dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag, const int inum,
const int nbor_pitch,
const __global numtyp4 *restrict v_,
const __global numtyp *restrict cutsq,
const numtyp dtinvsqrt, const int seed,
const int timestep, const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
#ifndef ONETYPE
__local numtyp4 coeff[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 coeff2[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp sp_lj[4];
__local numtyp sp_sqrt[4];
if (tid<4) {
sp_lj[tid]=sp_lj_in[tid];
sp_sqrt[tid]=sp_sqrt_in[tid];
}
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
coeff[tid]=coeff_in[tid];
coeff2[tid]=coeff2_in[tid];
}
__syncthreads();
#else
const numtyp A_attij=coeff_in[ONETYPE].x;
const numtyp B_repij=coeff_in[ONETYPE].y;
const numtyp gammaij=coeff_in[ONETYPE].z;
const numtyp sigmaij=coeff_in[ONETYPE].w;
const numtyp cutij=coeff2_in[ONETYPE].x;
const numtyp cut_rij=coeff2_in[ONETYPE].y;
const numtyp cutsqij=coeff2_in[ONETYPE].z;
const numtyp cutsq_p=cutsq[ONETYPE];
#endif
int n_stride;
local_allocate_store_pair();
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp energy, virial[6];
if (EVFLAG) {
energy=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
if (ii<inum) {
int i, numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
#ifndef ONETYPE
int iw=ix.w;
int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
#endif
numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
int itag=iv.w;
const numtyp rhoi = extra[i].x;
#ifndef ONETYPE
numtyp factor_dpd;
#endif
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
#ifndef ONETYPE
factor_dpd = sp_lj[sbmask(j)];
j &= NEIGHMASK;
#endif
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
#ifndef ONETYPE
int mtype=itype+jx.w;
const numtyp cutsq_p=cutsq[mtype];
#endif
numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
int jtag=jv.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
if (rsq<cutsq_p) {
numtyp r=ucl_sqrt(rsq);
if (r < EPSILON) continue;
numtyp rinv=ucl_recip(r);
numtyp delvx = iv.x - jv.x;
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp dot = delx*delvx + dely*delvy + delz*delvz;
#ifndef ONETYPE
numtyp A_attij = coeff[mtype].x;
numtyp B_repij = coeff[mtype].y;
numtyp gammaij = coeff[mtype].z;
numtyp sigmaij = coeff[mtype].w;
numtyp cutij = coeff2[mtype].x;
numtyp cut_rij = coeff2[mtype].y;
numtyp cutsqij = coeff2[mtype].z;
#endif
numtyp wc = (numtyp)1.0 - r/cutij;
numtyp wc_r = (numtyp)1.0 - r/cut_rij;
wc_r = MAX(wc_r,(numtyp)0.0);
numtyp wr = wc;
const numtyp rhoj = extra[j].x;
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;
}
numtyp randnum = (numtyp)0.0;
saru(tag1, tag2, seed, timestep, randnum);
// conservative force = A_att * wc + B_rep*(rhoi+rhoj)*wc_r
// drag force = -gamma * wr^2 * (delx dot delv) / r
// random force = sigma * wr * rnd * dtinvsqrt;
numtyp force = A_attij*wc + B_repij*(rhoi+rhoj)*wc_r;
force -= gammaij*wr*wr*dot*rinv;
force += sigmaij*wr*randnum*dtinvsqrt;
#ifndef ONETYPE
force *= factor_dpd*rinv;
#else
force*=rinv;
#endif
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
if (EVFLAG && eflag) {
// unshifted eng of conservative term:
// eng shifted to 0.0 at cutoff
numtyp e = (numtyp)0.5*A_attij*cutij * wr*wr + (numtyp)0.5*B_repij*cut_rij*(rhoi+rhoj)*wc_r*wc_r;
#ifndef ONETYPE
energy+=factor_dpd*e;
#else
energy+=e;
#endif
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
ans,engv);
}

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/***************************************************************************
mdpd.h
-------------------
Trung Dac Nguyen (U Chicago)
Class for acceleration of the mdpd pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : December 2023
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_DPD_H
#define LAL_DPD_H
#include "lal_base_dpd.h"
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class MDPD : public BaseDPD<numtyp, acctyp> {
public:
MDPD();
~MDPD();
/// Clear any previous data and set up for a new LAMMPS run
/** \param max_nbors initial number of rows in the neighbor matrix
* \param cell_size cutoff + skin
* \param gpu_split fraction of particles handled by device
*
* Returns:
* - 0 if successful
* - -1 if fix gpu not found
* - -3 if there is an out of memory error
* - -4 if the GPU library was not compiled for GPU
* - -5 Double precision is not supported on card **/
int init(const int ntypes, double **host_cutsq,
double **host_A_att, double **host_B_rep,
double **host_gamma, double **host_sigma,
double **host_cut, double **host_cut_r, double *host_special_lj,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, const double gpu_split,
FILE *screen);
/// Clear all host and device data
/** \note This is called at the beginning of the init() routine **/
void clear();
/// Returns memory usage on device per atom
int bytes_per_atom(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage() const;
void get_extra_data(double *host_rho);
// --------------------------- TYPE DATA --------------------------
/// coeff.x = A_att, coeff.x = B_rep, coeff.z = gamma, coeff.w = sigma
UCL_D_Vec<numtyp4> coeff;
/// coeff2.x = cut, coeff2.y = cut_r, coeff2.z = cutsq
UCL_D_Vec<numtyp4> coeff2;
UCL_D_Vec<numtyp> cutsq;
/// Special LJ values
UCL_D_Vec<numtyp> sp_lj, sp_sqrt;
/// If atom type constants fit in shared memory, use fast kernels
bool shared_types;
/// Number of atom types
int _lj_types;
/// pointer to host data
double *mdpd_rho;
private:
bool _allocated;
int loop(const int eflag, const int vflag);
};
}
#endif

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/***************************************************************************
mdpd_ext.cpp
-------------------
Trung Dac Nguyen (U Chicago)
Functions for LAMMPS access to mdpd acceleration routines.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : December 2023
email : ndactrung@gmail.com
***************************************************************************/
#include <iostream>
#include <cassert>
#include <cmath>
#include "lal_mdpd.h"
using namespace std;
using namespace LAMMPS_AL;
static MDPD<PRECISION,ACC_PRECISION> MDPDMF;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int mdpd_gpu_init(const int ntypes, double **cutsq,
double **host_A_att, double **host_B_rep,
double **host_gamma, double **host_sigma,
double **host_cut, double **host_cut_r,
double *special_lj, const int inum,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen) {
MDPDMF.clear();
gpu_mode=MDPDMF.device->gpu_mode();
double gpu_split=MDPDMF.device->particle_split();
int first_gpu=MDPDMF.device->first_device();
int last_gpu=MDPDMF.device->last_device();
int world_me=MDPDMF.device->world_me();
int gpu_rank=MDPDMF.device->gpu_rank();
int procs_per_gpu=MDPDMF.device->procs_per_gpu();
MDPDMF.device->init_message(screen,"mdpd",first_gpu,last_gpu);
bool message=false;
if (MDPDMF.device->replica_me()==0 && screen)
message=true;
if (message) {
fprintf(screen,"Initializing Device and compiling on process 0...");
fflush(screen);
}
int init_ok=0;
if (world_me==0)
init_ok=MDPDMF.init(ntypes, cutsq, host_A_att, host_B_rep, host_gamma, host_sigma,
host_cut, host_cut_r, special_lj, inum, nall, max_nbors,
maxspecial, cell_size, gpu_split, screen);
MDPDMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
last_gpu,i);
fflush(screen);
}
if (gpu_rank==i && world_me!=0)
init_ok=MDPDMF.init(ntypes, cutsq, host_A_att, host_B_rep, host_gamma, host_sigma,
host_cut, host_cut_r, special_lj, inum, nall, max_nbors,
maxspecial, cell_size, gpu_split, screen);
MDPDMF.device->serialize_init();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
if (init_ok==0)
MDPDMF.estimate_gpu_overhead();
return init_ok;
}
void mdpd_gpu_clear() {
MDPDMF.clear();
}
int ** mdpd_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
tagint **special, 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,
double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
double *boxlo, double *prd) {
return MDPDMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
subhi, tag, nspecial, special, eflag, vflag, eatom,
vatom, host_start, ilist, jnum, cpu_time, success,
host_v, dtinvsqrt, seed, timestep, boxlo, prd);
}
void mdpd_gpu_compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *tag,
double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
const int nlocal, double *boxlo, double *prd) {
MDPDMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
tag, host_v, dtinvsqrt, seed, timestep, nlocal, boxlo, prd);
}
void mdpd_gpu_get_extra_data(double *host_rho) {
MDPDMF.get_extra_data(host_rho);
}
double mdpd_gpu_bytes() {
return MDPDMF.host_memory_usage();
}

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Dac Nguyen (U Chicago)
------------------------------------------------------------------------- */
#include "pair_edpd_gpu.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "info.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include "update.h"
#include <cmath>
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int edpd_gpu_init(const int ntypes, double **cutsq, double **host_a0, double **host_gamma,
double **host_cut, double **host_power, double **host_kappa,
double **host_powerT, double** host_cutT, double*** host_sc, double ***host_kc,
double *host_mass, double *special_lj, const int power_flag, const int kappa_flag,
const int inum, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode, FILE *screen);
void edpd_gpu_clear();
int **edpd_gpu_compute_n(const int ago, const int inum_full, const int nall, double **host_x,
int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, 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, double **host_v,
const double dtinvsqrt, const int seed, const int timestep, double *boxlo,
double *prd);
void edpd_gpu_compute(const int ago, const int inum_full, const int nall, double **host_x,
int *host_type, int *ilist, int *numj, int **firstneigh, const bool eflag,
const bool vflag, const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *tag, double **host_v,
const double dtinvsqrt, const int seed, const int timestep, const int nlocal,
double *boxlo, double *prd);
void edpd_gpu_get_extra_data(double *host_T, double *host_cv);
void edpd_gpu_update_flux(void **flux_ptr);
double edpd_gpu_bytes();
#define EPSILON 1.0e-10
/* ---------------------------------------------------------------------- */
PairEDPDGPU::PairEDPDGPU(LAMMPS *lmp) : PairEDPD(lmp), gpu_mode(GPU_FORCE)
{
flux_pinned = nullptr;
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairEDPDGPU::~PairEDPDGPU()
{
edpd_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairEDPDGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
double dtinvsqrt = 1.0 / sqrt(update->dt);
bool success = true;
int *ilist, *numneigh, **firstneigh;
double *T = atom->edpd_temp;
double *cv = atom->edpd_cv;
edpd_gpu_get_extra_data(T, cv);
if (gpu_mode != GPU_FORCE) {
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;
firstneigh = edpd_gpu_compute_n(
neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom, vflag_atom, host_start, &ilist, &numneigh,
cpu_time, success, atom->v, dtinvsqrt, seed, update->ntimestep, domain->boxlo, domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
edpd_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success, atom->tag,
atom->v, dtinvsqrt, seed, update->ntimestep, atom->nlocal, domain->boxlo, domain->prd);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
// get the heat flux from device
double *Q = atom->edpd_flux;
edpd_gpu_update_flux(&flux_pinned);
int nlocal = atom->nlocal;
if (acc_float) {
auto flux_ptr = (float *)flux_pinned;
for (int i = 0; i < nlocal; i++)
Q[i] = flux_ptr[i];
} else {
auto flux_ptr = (double *)flux_pinned;
for (int i = 0; i < nlocal; i++)
Q[i] = flux_ptr[i];
}
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)
neighbor->build_topology();
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairEDPDGPU::init_style()
{
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double mcut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
mcut = init_one(i, j);
mcut *= mcut;
if (mcut > maxcut) maxcut = mcut;
cutsq[i][j] = cutsq[j][i] = mcut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success =
edpd_gpu_init(atom->ntypes + 1, cutsq, a0, gamma, cut, power, kappa,
powerT, cutT, sc, kc, atom->mass, force->special_lj,
power_flag, kappa_flag, atom->nlocal, atom->nlocal + atom->nghost,
mnf, maxspecial, cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success, error, world);
acc_float = Info::has_accelerator_feature("GPU", "precision", "single");
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ---------------------------------------------------------------------- */
double PairEDPDGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + edpd_gpu_bytes();
}

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(edpd/gpu,PairEDPDGPU);
// clang-format on
#else
#ifndef LMP_PAIR_EDPD_GPU_H
#define LMP_PAIR_EDPD_GPU_H
#include "pair_edpd.h"
namespace LAMMPS_NS {
class PairEDPDGPU : public PairEDPD {
public:
PairEDPDGPU(LAMMPS *lmp);
~PairEDPDGPU() override;
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int) override;
void init_style() override;
double memory_usage() override;
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
void *flux_pinned;
bool acc_float;
private:
int gpu_mode;
double cpu_time;
};
} // namespace LAMMPS_NS
#endif
#endif

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Dac Nguyen (U Chicago)
------------------------------------------------------------------------- */
#include "pair_mdpd_gpu.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "info.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include "update.h"
#include <cmath>
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int mdpd_gpu_init(const int ntypes, double **cutsq, double **host_A_att, double **host_B_rep,
double **host_gamma, double **host_sigma, double **host_cut, double **host_cut_r,
double *special_lj, const int inum, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode, FILE *screen);
void mdpd_gpu_clear();
int **mdpd_gpu_compute_n(const int ago, const int inum_full, const int nall, double **host_x,
int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, 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, double **host_v,
const double dtinvsqrt, const int seed, const int timestep, double *boxlo,
double *prd);
void mdpd_gpu_compute(const int ago, const int inum_full, const int nall, double **host_x,
int *host_type, int *ilist, int *numj, int **firstneigh, const bool eflag,
const bool vflag, const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *tag, double **host_v,
const double dtinvsqrt, const int seed, const int timestep, const int nlocal,
double *boxlo, double *prd);
void mdpd_gpu_get_extra_data(double *host_rho);
double mdpd_gpu_bytes();
#define EPSILON 1.0e-10
/* ---------------------------------------------------------------------- */
PairMDPDGPU::PairMDPDGPU(LAMMPS *lmp) : PairMDPD(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairMDPDGPU::~PairMDPDGPU()
{
mdpd_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairMDPDGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
double dtinvsqrt = 1.0 / sqrt(update->dt);
bool success = true;
int *ilist, *numneigh, **firstneigh;
double *rho = atom->rho;
mdpd_gpu_get_extra_data(rho);
if (gpu_mode != GPU_FORCE) {
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;
firstneigh = mdpd_gpu_compute_n(
neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom, vflag_atom, host_start, &ilist, &numneigh,
cpu_time, success, atom->v, dtinvsqrt, seed, update->ntimestep, domain->boxlo, domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
mdpd_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success, atom->tag,
atom->v, dtinvsqrt, seed, update->ntimestep, atom->nlocal, domain->boxlo, domain->prd);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)
neighbor->build_topology();
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairMDPDGPU::init_style()
{
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double mcut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
mcut = init_one(i, j);
mcut *= mcut;
if (mcut > maxcut) maxcut = mcut;
cutsq[i][j] = cutsq[j][i] = mcut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success =
mdpd_gpu_init(atom->ntypes + 1, cutsq, A_att, B_rep, gamma, sigma,
cut, cut_r, force->special_lj,
atom->nlocal, atom->nlocal + atom->nghost,
mnf, maxspecial, cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success, error, world);
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ---------------------------------------------------------------------- */
double PairMDPDGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + mdpd_gpu_bytes();
}

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(mdpd/gpu,PairMDPDGPU);
// clang-format on
#else
#ifndef LMP_PAIR_MDPD_GPU_H
#define LMP_PAIR_MDPD_GPU_H
#include "pair_mdpd.h"
namespace LAMMPS_NS {
class PairMDPDGPU : public PairMDPD {
public:
PairMDPDGPU(LAMMPS *lmp);
~PairMDPDGPU() override;
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int) override;
void init_style() override;
double memory_usage() override;
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
private:
int gpu_mode;
double cpu_time;
};
} // namespace LAMMPS_NS
#endif
#endif