428 lines
18 KiB
C++
428 lines
18 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://lammps.sandia.gov/, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Trung Dac Nguyen (ORNL)
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------------------------------------------------------------------------- */
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#include "pair_dpd_tstat_gpu.h"
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#include "atom.h"
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#include "domain.h"
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#include "error.h"
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#include "force.h"
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#include "gpu_extra.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "neighbor.h"
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#include "suffix.h"
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#include "update.h"
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#include <cmath>
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using namespace LAMMPS_NS;
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// External functions from cuda library for atom decomposition
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int dpd_tstat_gpu_init(const int ntypes, double **cutsq, double **host_a0,
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double **host_gamma, double **host_sigma, double **host_cut,
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double *special_lj, const int inum,
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const int nall, const int max_nbors, const int maxspecial,
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const double cell_size, int &gpu_mode, FILE *screen);
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void dpd_tstat_gpu_clear();
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int ** dpd_tstat_gpu_compute_n(const int ago, const int inum_full,
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const int nall, double **host_x, int *host_type,
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double *sublo, double *subhi, tagint *tag,
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int **nspecial, tagint **special, const bool eflag,
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const bool vflag, 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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double **host_v, const double dtinvsqrt,
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const int seed, const int timestep,
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double *boxlo, double *prd);
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void dpd_tstat_gpu_compute(const int ago, const int inum_full, const int nall,
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double **host_x, int *host_type, int *ilist, int *numj,
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int **firstneigh, const bool eflag, const bool vflag,
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const bool eatom, const bool vatom, int &host_start,
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const double cpu_time, bool &success, tagint *tag,
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double **host_v, const double dtinvsqrt,
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const int seed, const int timestep,
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const int nlocal, double *boxlo, double *prd);
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void dpd_tstat_gpu_update_coeff(int ntypes, double **host_a0,
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double **host_gamma, double **host_sigma,
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double **host_cut);
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double dpd_tstat_gpu_bytes();
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#define EPSILON 1.0e-10
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//#define _USE_UNIFORM_SARU_LCG
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//#define _USE_UNIFORM_SARU_TEA8
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//#define _USE_GAUSSIAN_SARU_LCG
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#if !defined(_USE_UNIFORM_SARU_LCG) && !defined(_USE_UNIFORM_SARU_TEA8) && !defined(_USE_GAUSSIAN_SARU_LCG)
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#define _USE_UNIFORM_SARU_LCG
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#endif
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// References:
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// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128.
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// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201.
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// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19
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#define LCGA 0x4beb5d59 // Full period 32 bit LCG
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#define LCGC 0x2600e1f7
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#define oWeylPeriod 0xda879add // Prime period 3666320093
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#define oWeylOffset 0x8009d14b
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#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */
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// specifically implemented for steps = 1; high = 1.0; low = -1.0
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// returns uniformly distributed random numbers u in [-1.0;1.0]
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// using the inherent LCG, then multiply u with sqrt(3) to "match"
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// with a normal random distribution.
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// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
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// Curly brackets to make variables local to the scope.
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#ifdef _USE_UNIFORM_SARU_LCG
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#define numtyp double
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#define SQRT3 (numtyp)1.7320508075688772935274463
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#define saru(seed1, seed2, seed, timestep, randnum) { \
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unsigned int seed3 = seed + timestep; \
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seed3^=(seed1<<7)^(seed2>>6); \
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seed2+=(seed1>>4)^(seed3>>15); \
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seed1^=(seed2<<9)+(seed3<<8); \
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seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
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seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
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seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
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seed2+=seed1*seed3; \
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seed1+=seed3 ^ (seed2>>2); \
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seed2^=((signed int)seed2)>>17; \
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unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
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unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
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state = state + (wstate*(wstate^0xdddf97f5)); \
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wstate = 0xABCB96F7 + (wstate>>1); \
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state = LCGA*state + LCGC; \
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wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
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unsigned int v = (state ^ (state>>26)) + wstate; \
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unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
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randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
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}
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#endif
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// specifically implemented for steps = 1; high = 1.0; low = -1.0
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// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
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// then multiply u with sqrt(3) to "match" with a normal random distribution
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// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
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#ifdef _USE_UNIFORM_SARU_TEA8
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#define numtyp double
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#define SQRT3 (numtyp)1.7320508075688772935274463
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#define k0 0xA341316C
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#define k1 0xC8013EA4
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#define k2 0xAD90777D
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#define k3 0x7E95761E
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#define delta 0x9e3779b9
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#define rounds 8
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#define saru(seed1, seed2, seed, timestep, randnum) { \
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unsigned int seed3 = seed + timestep; \
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seed3^=(seed1<<7)^(seed2>>6); \
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seed2+=(seed1>>4)^(seed3>>15); \
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seed1^=(seed2<<9)+(seed3<<8); \
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seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
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seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
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seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
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seed2+=seed1*seed3; \
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seed1+=seed3 ^ (seed2>>2); \
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seed2^=((signed int)seed2)>>17; \
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unsigned int state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
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unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8); \
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state = state + (wstate*(wstate^0xdddf97f5)); \
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wstate = 0xABCB96F7 + (wstate>>1); \
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unsigned int sum = 0; \
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for (int i=0; i < rounds; i++) { \
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sum += delta; \
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state += ((wstate<<4) + k0)^(wstate + sum)^((wstate>>5) + k1); \
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wstate += ((state<<4) + k2)^(state + sum)^((state>>5) + k3); \
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} \
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unsigned int v = (state ^ (state>>26)) + wstate; \
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unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7); \
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randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0); \
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}
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#endif
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// specifically implemented for steps = 1; high = 1.0; low = -1.0
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// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
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// and uses the polar method (Marsaglia's) to transform to a normal random value
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// This is used to compared with CPU DPD using RandMars::gaussian()
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#ifdef _USE_GAUSSIAN_SARU_LCG
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#define numtyp double
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#define saru(seed1, seed2, seed, timestep, randnum) { \
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unsigned int seed3 = seed + timestep; \
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seed3^=(seed1<<7)^(seed2>>6); \
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seed2+=(seed1>>4)^(seed3>>15); \
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seed1^=(seed2<<9)+(seed3<<8); \
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seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1)); \
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seed2+=0x72BE1579*((seed1<<4) ^ (seed3>>16)); \
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seed1^=0x3F38A6ED*((seed3>>5) ^ (((signed int)seed2)>>22)); \
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seed2+=seed1*seed3; \
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seed1+=seed3 ^ (seed2>>2); \
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seed2^=((signed int)seed2)>>17; \
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unsigned int state=0x12345678; \
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unsigned int wstate=12345678; \
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state = 0x79dedea3*(seed1^(((signed int)seed1)>>14)); \
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wstate = (state + seed2) ^ (((signed int)state)>>8); \
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state = state + (wstate*(wstate^0xdddf97f5)); \
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wstate = 0xABCB96F7 + (wstate>>1); \
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unsigned int v, s; \
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numtyp r1, r2, rsq; \
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while (1) { \
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state = LCGA*state + LCGC; \
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wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
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v = (state ^ (state>>26)) + wstate; \
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s = (signed int)((v^(v>>20))*0x6957f5a7); \
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r1 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
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state = LCGA*state + LCGC; \
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wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
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v = (state ^ (state>>26)) + wstate; \
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s = (signed int)((v^(v>>20))*0x6957f5a7); \
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r2 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0; \
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rsq = r1 * r1 + r2 * r2; \
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if (rsq < (numtyp)1.0) break; \
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} \
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numtyp fac = sqrt((numtyp)-2.0*log(rsq)/rsq); \
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randnum = r2*fac; \
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}
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#endif
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/* ---------------------------------------------------------------------- */
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PairDPDTstatGPU::PairDPDTstatGPU(LAMMPS *lmp) : PairDPDTstat(lmp),
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gpu_mode(GPU_FORCE)
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{
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respa_enable = 0;
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reinitflag = 0;
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cpu_time = 0.0;
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suffix_flag |= Suffix::GPU;
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GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
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}
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/* ----------------------------------------------------------------------
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free all arrays
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------------------------------------------------------------------------- */
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PairDPDTstatGPU::~PairDPDTstatGPU()
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{
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dpd_tstat_gpu_clear();
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}
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/* ---------------------------------------------------------------------- */
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void PairDPDTstatGPU::compute(int eflag, int vflag)
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{
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ev_init(eflag,vflag);
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// adjust sigma if target T is changing
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if (t_start != t_stop) {
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double delta = update->ntimestep - update->beginstep;
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if (delta != 0.0) delta /= update->endstep - update->beginstep;
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temperature = t_start + delta * (t_stop-t_start);
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double boltz = force->boltz;
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for (int i = 1; i <= atom->ntypes; i++)
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for (int j = i; j <= atom->ntypes; j++)
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sigma[i][j] = sigma[j][i] = sqrt(2.0*boltz*temperature*gamma[i][j]);
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dpd_tstat_gpu_update_coeff(atom->ntypes+1, a0, gamma, sigma, cut);
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}
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int nall = atom->nlocal + atom->nghost;
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int inum, host_start;
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double dtinvsqrt = 1.0/sqrt(update->dt);
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bool success = true;
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int *ilist, *numneigh, **firstneigh;
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if (gpu_mode != GPU_FORCE) {
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double sublo[3],subhi[3];
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if (domain->triclinic == 0) {
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sublo[0] = domain->sublo[0];
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sublo[1] = domain->sublo[1];
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sublo[2] = domain->sublo[2];
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subhi[0] = domain->subhi[0];
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subhi[1] = domain->subhi[1];
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subhi[2] = domain->subhi[2];
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} else {
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domain->bbox(domain->sublo_lamda,domain->subhi_lamda,sublo,subhi);
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}
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inum = atom->nlocal;
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firstneigh = dpd_tstat_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
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atom->type, sublo, subhi,
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atom->tag, atom->nspecial, atom->special,
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eflag, vflag, eflag_atom, vflag_atom,
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host_start, &ilist, &numneigh, cpu_time,
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success, atom->v, dtinvsqrt, seed,
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update->ntimestep,
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domain->boxlo, domain->prd);
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} else {
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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dpd_tstat_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
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ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
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vflag_atom, host_start, cpu_time, success,
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atom->tag, atom->v, dtinvsqrt, seed,
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update->ntimestep,
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atom->nlocal, domain->boxlo, domain->prd);
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}
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if (!success)
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error->one(FLERR,"Insufficient memory on accelerator");
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if (host_start<inum) {
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cpu_time = MPI_Wtime();
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cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
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cpu_time = MPI_Wtime() - cpu_time;
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}
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}
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/* ----------------------------------------------------------------------
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init specific to this pair style
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------------------------------------------------------------------------- */
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void PairDPDTstatGPU::init_style()
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{
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if (force->newton_pair)
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error->all(FLERR,"Cannot use newton pair with dpd/tstat/gpu pair style");
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// Repeat cutsq calculation because done after call to init_style
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double maxcut = -1.0;
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double mcut;
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for (int i = 1; i <= atom->ntypes; i++) {
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for (int j = i; j <= atom->ntypes; j++) {
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if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
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mcut = init_one(i,j);
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mcut *= mcut;
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if (mcut > maxcut)
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maxcut = mcut;
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cutsq[i][j] = cutsq[j][i] = mcut;
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} else
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cutsq[i][j] = cutsq[j][i] = 0.0;
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}
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}
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double cell_size = sqrt(maxcut) + neighbor->skin;
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int maxspecial=0;
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if (atom->molecular != Atom::ATOMIC)
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maxspecial=atom->maxspecial;
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int mnf = 5e-2 * neighbor->oneatom;
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int success = dpd_tstat_gpu_init(atom->ntypes+1, cutsq, a0, gamma, sigma,
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cut, force->special_lj, atom->nlocal,
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atom->nlocal+atom->nghost, mnf, maxspecial,
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cell_size, gpu_mode, screen);
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GPU_EXTRA::check_flag(success,error,world);
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if (gpu_mode == GPU_FORCE) {
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int irequest = neighbor->request(this,instance_me);
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neighbor->requests[irequest]->half = 0;
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neighbor->requests[irequest]->full = 1;
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}
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}
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/* ---------------------------------------------------------------------- */
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double PairDPDTstatGPU::memory_usage()
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{
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double bytes = Pair::memory_usage();
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return bytes + dpd_tstat_gpu_bytes();
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}
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/* ---------------------------------------------------------------------- */
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void PairDPDTstatGPU::cpu_compute(int start, int inum, int /* eflag */,
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int /* vflag */, int *ilist,
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int *numneigh, int **firstneigh) {
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int i,j,ii,jj,jnum,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz,fpair;
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double vxtmp,vytmp,vztmp,delvx,delvy,delvz;
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double rsq,r,rinv,dot,wd,randnum,factor_dpd;
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int *jlist;
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tagint itag,jtag;
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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int *type = atom->type;
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tagint *tag = atom->tag;
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double *special_lj = force->special_lj;
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double dtinvsqrt = 1.0/sqrt(update->dt);
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int timestep = (int)update->ntimestep;
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// loop over neighbors of my atoms
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for (ii = start; ii < inum; ii++) {
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i = ilist[ii];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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vxtmp = v[i][0];
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vytmp = v[i][1];
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vztmp = v[i][2];
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itype = type[i];
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itag = tag[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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factor_dpd = special_lj[sbmask(j)];
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j &= NEIGHMASK;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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jtype = type[j];
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jtag = tag[j];
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if (rsq < cutsq[itype][jtype]) {
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r = sqrt(rsq);
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if (r < EPSILON) continue; // r can be 0.0 in DPD systems
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rinv = 1.0/r;
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delvx = vxtmp - v[j][0];
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delvy = vytmp - v[j][1];
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delvz = vztmp - v[j][2];
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dot = delx*delvx + dely*delvy + delz*delvz;
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wd = 1.0 - r/cut[itype][jtype];
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unsigned int tag1=itag, tag2=jtag;
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if (tag1 > tag2) {
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tag1 = jtag; tag2 = itag;
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}
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randnum = 0.0;
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saru(tag1, tag2, seed, timestep, randnum);
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// conservative force = a0 * wd
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// drag force = -gamma * wd^2 * (delx dot delv) / r
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// random force = sigma * wd * rnd * dtinvsqrt;
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fpair = -gamma[itype][jtype]*wd*wd*dot*rinv;
|
||
fpair += sigma[itype][jtype]*wd*randnum*dtinvsqrt;
|
||
fpair *= factor_dpd*rinv;
|
||
|
||
f[i][0] += delx*fpair;
|
||
f[i][1] += dely*fpair;
|
||
f[i][2] += delz*fpair;
|
||
|
||
if (evflag) ev_tally_full(i,0.0,0.0,fpair,delx,dely,delz);
|
||
}
|
||
}
|
||
}
|
||
}
|