diff --git a/src/GPU/Install.sh b/src/GPU/Install.sh index 32ee689be..4f1659989 100644 --- a/src/GPU/Install.sh +++ b/src/GPU/Install.sh @@ -1,148 +1,155 @@ # Install/unInstall package files in LAMMPS # edit 2 Makefile.package files to include/exclude GPU info # do not install child files if parent does not exist if (test $1 = 1) then if (test -e ../Makefile.package) then sed -i -e 's/[^ \t]*gpu[^ \t]* //' ../Makefile.package sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/gpu |' ../Makefile.package sed -i -e 's|^PKG_LIB =[ \t]*|&-lgpu |' ../Makefile.package sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(gpu_SYSINC) |' ../Makefile.package sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(gpu_SYSLIB) |' ../Makefile.package sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(gpu_SYSPATH) |' ../Makefile.package fi if (test -e ../Makefile.package.settings) then sed -i -e '/^include.*gpu.*$/d' ../Makefile.package.settings sed -i '4 i include ..\/..\/lib\/gpu\/Makefile.lammps' ../Makefile.package.settings fi if (test -e ../pair_gayberne.cpp) then cp pair_gayberne_gpu.cpp .. cp pair_gayberne_gpu.h .. cp pair_resquared_gpu.cpp .. cp pair_resquared_gpu.h .. fi if (test -e ../pair_lj_cut_coul_long.cpp) then cp pair_lj_cut_coul_long_gpu.cpp .. cp pair_lj_cut_coul_long_gpu.h .. fi if (test -e ../pair_lj_class2.cpp) then cp pair_lj_class2_gpu.cpp .. cp pair_lj_class2_gpu.h .. fi if (test -e ../pair_lj_class2_coul_long.cpp) then cp pair_lj_class2_coul_long_gpu.cpp .. cp pair_lj_class2_coul_long_gpu.h .. fi if (test -e ../pair_lj_charmm_coul_long.cpp) then cp pair_lj_charmm_coul_long_gpu.cpp .. cp pair_lj_charmm_coul_long_gpu.h .. fi + if (test -e ../pair_coul_long.cpp) then + cp pair_coul_long_gpu.cpp .. + cp pair_coul_long_gpu.h .. + fi + if (test -e ../pair_cg_cmm.cpp) then cp pair_cg_cmm_gpu.cpp .. cp pair_cg_cmm_gpu.h .. fi if (test -e ../pair_cg_cmm_coul_long.cpp) then cp pair_cg_cmm_coul_long_gpu.cpp .. cp pair_cg_cmm_coul_long_gpu.h .. cp pair_cg_cmm_coul_msm.cpp .. cp pair_cg_cmm_coul_msm.h .. cp pair_cg_cmm_coul_msm_gpu.cpp .. cp pair_cg_cmm_coul_msm_gpu.h .. fi if (test -e ../pppm.cpp) then cp pppm_gpu.cpp .. cp pppm_gpu.h .. fi cp pair_lj_cut_gpu.cpp .. cp pair_morse_gpu.cpp .. cp pair_lj96_cut_gpu.cpp .. cp pair_lj_expand_gpu.cpp .. cp pair_lj_cut_coul_cut_gpu.cpp .. cp pair_lj_cut_tgpu.cpp .. cp fix_gpu.cpp .. cp pair_lj_cut_gpu.h .. cp pair_morse_gpu.h .. cp pair_lj96_cut_gpu.h .. cp pair_lj_expand_gpu.h .. cp pair_lj_cut_coul_cut_gpu.h .. cp pair_lj_cut_tgpu.h .. cp fix_gpu.h .. cp gpu_extra.h .. cp pair_omp_gpu.cpp .. cp pair_lj_cut_tgpu.cpp .. cp pair_omp_gpu.h .. cp pair_lj_cut_tgpu.h .. elif (test $1 = 0) then if (test -e ../Makefile.package) then sed -i -e 's/[^ \t]*gpu[^ \t]* //' ../Makefile.package fi if (test -e ../Makefile.package.settings) then sed -i -e '/^include.*gpu.*$/d' ../Makefile.package.settings fi rm -f ../pppm_gpu.cpp rm -f ../pair_gayberne_gpu.cpp rm -f ../pair_resquared_gpu.cpp rm -f ../pair_lj_cut_gpu.cpp rm -f ../pair_morse_gpu.cpp rm -f ../pair_lj96_cut_gpu.cpp rm -f ../pair_lj_expand_gpu.cpp rm -f ../pair_lj_cut_coul_cut_gpu.cpp rm -f ../pair_lj_cut_coul_long_gpu.cpp rm -f ../pair_lj_class2_gpu.cpp rm -f ../pair_lj_class2_coul_long_gpu.cpp rm -f ../pair_lj_charmm_coul_long_gpu.cpp rm -f ../pair_lj_cut_tgpu.cpp + rm -f ../pair_coul_long_gpu.cpp rm -f ../pair_cg_cmm_gpu.cpp rm -f ../pair_cg_cmm_coul_long_gpu.cpp rm -f ../pair_cg_cmm_coul_msm.cpp rm -f ../pair_cg_cmm_coul_msm_gpu.cpp rm -f ../fix_gpu.cpp rm -f ../pair_omp_gpu.cpp rm -f ../pair_lj_cut_tgpu.cpp rm -f ../pppm_gpu.h rm -f ../pair_gayberne_gpu.h rm -f ../pair_resquared_gpu.h rm -f ../pair_lj_cut_gpu.h rm -f ../pair_morse_gpu.h rm -f ../pair_lj96_cut_gpu.h rm -f ../pair_lj_expand_gpu.h rm -f ../pair_lj_cut_coul_cut_gpu.h rm -f ../pair_lj_cut_coul_long_gpu.h rm -f ../pair_lj_class2_gpu.h rm -f ../pair_lj_class2_coul_long_gpu.h rm -f ../pair_lj_charmm_coul_long_gpu.h rm -f ../pair_lj_cut_tgpu.h + rm -f ../pair_coul_long_gpu.h rm -f ../pair_cg_cmm_gpu.h rm -f ../pair_cg_cmm_coul_long_gpu.h rm -f ../pair_cg_cmm_coul_msm.h rm -f ../pair_cg_cmm_coul_msm_gpu.h rm -f ../fix_gpu.h rm -f ../gpu_extra.h rm -f ../pair_omp_gpu.h rm -f ../pair_lj_cut_tgpu.h fi diff --git a/src/GPU/Package.sh b/src/GPU/Package.sh index 60aa6820c..2eb20755e 100644 --- a/src/GPU/Package.sh +++ b/src/GPU/Package.sh @@ -1,50 +1,56 @@ # Update package files in LAMMPS # cp package file to src if doesn't exist or is different # do not copy gayberne files if non-GPU version does not exist for file in *.cpp *.h; do if (test $file = pair_gayberne_gpu.cpp -a ! -e ../pair_gayberne.cpp) then continue fi if (test $file = pair_gayberne_gpu.h -a ! -e ../pair_gayberne.cpp) then continue fi if (test $file = pair_lj_cut_coul_long_gpu.cpp -a ! -e ../pair_lj_cut_coul_long.cpp) then continue fi if (test $file = pair_lj_cut_coul_long_gpu.h -a ! -e ../pair_lj_cut_coul_long.cpp) then continue fi + if (test $file = pair_coul_long_gpu.cpp -a ! -e ../pair_coul_long.cpp) then + continue + fi + if (test $file = pair_coul_long_gpu.h -a ! -e ../pair_coul_long.cpp) then + continue + fi if (test $file = pair_cg_cmm_gpu.cpp -a ! -e ../pair_cg_cmm.cpp) then continue fi if (test $file = pair_cg_cmm_gpu.h -a ! -e ../pair_cg_cmm.cpp) then continue fi if (test $file = pair_cg_cmm_coul_long_gpu.cpp -a ! -e ../pair_cg_cmm_coul_long.cpp) then continue fi if (test $file = pair_cg_cmm_coul_long_gpu.h -a ! -e ../pair_cg_cmm_coul_long.cpp) then continue fi if (test $file = pair_cg_cmm_coul_msm.cpp -a ! -e ../pair_cg_cmm.cpp) then continue fi if (test $file = pair_cg_cmm_coul_msm.h -a ! -e ../pair_cg_cmm.cpp) then continue fi if (test $file = pair_cg_cmm_coul_msm_gpu.cpp -a ! -e ../pair_cg_cmm.cpp) then continue fi if (test $file = pair_cg_cmm_coul_msm_gpu.h -a ! -e ../pair_cg_cmm.cpp) then continue fi if (test ! -e ../$file) then echo " creating src/$file" cp $file .. elif (test "`diff --brief $file ../$file`" != "") then echo " updating src/$file" cp $file .. fi done diff --git a/src/GPU/pair_cg_cmm_coul_long_gpu.cpp b/src/GPU/pair_cg_cmm_coul_long_gpu.cpp index 153cb98a9..d19b2d651 100644 --- a/src/GPU/pair_cg_cmm_coul_long_gpu.cpp +++ b/src/GPU/pair_cg_cmm_coul_long_gpu.cpp @@ -1,340 +1,340 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov 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: Mike Brown (SNL) ------------------------------------------------------------------------- */ #include "lmptype.h" #include "math.h" #include "stdio.h" #include "stdlib.h" #include "pair_cg_cmm_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "integrate.h" #include "memory.h" #include "error.h" #include "neigh_request.h" #include "universe.h" #include "update.h" #include "domain.h" #include "string.h" #include "kspace.h" #include "gpu_extra.h" #define MIN(a,b) ((a) < (b) ? (a) : (b)) #define MAX(a,b) ((a) > (b) ? (a) : (b)) #define EWALD_F 1.12837917 #define EWALD_P 0.3275911 #define A1 0.254829592 #define A2 -0.284496736 #define A3 1.421413741 #define A4 -1.453152027 #define A5 1.061405429 // External functions from cuda library for atom decomposition int cmml_gpu_init(const int ntypes, double **cutsq, int **cg_type, double **host_lj1, double **host_lj2, double **host_lj3, double **host_lj4, double **offset, double *special_lj, const int nlocal, const int nall, const int max_nbors, const int maxspecial, const double cell_size, int &gpu_mode, FILE *screen, double **host_cut_ljsq, double host_cut_coulsq, double *host_special_coul, const double qqrd2e, const double g_ewald); void cmml_gpu_clear(); int ** cmml_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x, int *host_type, double *sublo, double *subhi, int *tag, int **nspecial, int **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_q, double *boxlo, double *prd); void cmml_gpu_compute(const int ago, const int inum, 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, double *host_q, const int nlocal, double *boxlo, double *prd); double cmml_gpu_bytes(); using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ PairCGCMMCoulLongGPU::PairCGCMMCoulLongGPU(LAMMPS *lmp) : PairCGCMMCoulLong(lmp), gpu_mode(GPU_PAIR) { respa_enable = 0; cpu_time = 0.0; } /* ---------------------------------------------------------------------- free all arrays ------------------------------------------------------------------------- */ PairCGCMMCoulLongGPU::~PairCGCMMCoulLongGPU() { cmml_gpu_clear(); } /* ---------------------------------------------------------------------- */ void PairCGCMMCoulLongGPU::compute(int eflag, int vflag) { if (eflag || vflag) ev_setup(eflag,vflag); else evflag = vflag_fdotr = 0; int nall = atom->nlocal + atom->nghost; int inum, host_start; bool success = true; int *ilist, *numneigh, **firstneigh; if (gpu_mode == GPU_NEIGH) { inum = atom->nlocal; firstneigh = cmml_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, domain->sublo, domain->subhi, atom->tag, atom->nspecial, atom->special, eflag, vflag, eflag_atom, vflag_atom, host_start, &ilist, &numneigh, cpu_time, success, atom->q, domain->boxlo, domain->prd); } else { inum = list->inum; ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; cmml_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->q, atom->nlocal, domain->boxlo, domain->prd); } if (!success) error->one("Out of memory on GPGPU"); if (host_start<inum) { cpu_time = MPI_Wtime(); cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh); cpu_time = MPI_Wtime() - cpu_time; } } /* ---------------------------------------------------------------------- init specific to this pair style ------------------------------------------------------------------------- */ void PairCGCMMCoulLongGPU::init_style() { cut_respa = NULL; if (!atom->q_flag) - error->all("Pair style cg/cmm/coul/long requires atom attribute q"); + error->all("Pair style cg/cmm/coul/long/gpu requires atom attribute q"); if (force->newton_pair) - error->all("Cannot use newton pair with GPU cg/cmm pair style"); + error->all("Cannot use newton pair with cg/cmm/coul/long/gpu pair style"); // Repeat cutsq calculation because done after call to init_style double maxcut = -1.0; double cut; 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)) { cut = init_one(i,j); cut *= cut; if (cut > maxcut) maxcut = cut; cutsq[i][j] = cutsq[j][i] = cut; } else cutsq[i][j] = cutsq[j][i] = 0.0; } } double cell_size = sqrt(maxcut) + neighbor->skin; // insure use of KSpace long-range solver, set g_ewald if (force->kspace == NULL) error->all("Pair style is incompatible with KSpace style"); g_ewald = force->kspace->g_ewald; // setup force tables if (ncoultablebits) init_tables(); int maxspecial=0; if (atom->molecular) maxspecial=atom->maxspecial; int success = cmml_gpu_init(atom->ntypes+1, cutsq, cg_type, lj1, lj2, lj3, lj4, offset, force->special_lj, atom->nlocal, atom->nlocal+atom->nghost, 300, maxspecial, cell_size, gpu_mode, screen, cut_ljsq, cut_coulsq_global, force->special_coul, force->qqrd2e, g_ewald); GPU_EXTRA::check_flag(success,error,world); if (gpu_mode != GPU_NEIGH) { int irequest = neighbor->request(this); neighbor->requests[irequest]->half = 0; neighbor->requests[irequest]->full = 1; } } /* ---------------------------------------------------------------------- */ double PairCGCMMCoulLongGPU::memory_usage() { double bytes = Pair::memory_usage(); return bytes + cmml_gpu_bytes(); } /* ---------------------------------------------------------------------- */ void PairCGCMMCoulLongGPU::cpu_compute(int start, int inum, int eflag, int vflag, int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype,itable; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz; double fraction,table; double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj; double grij,expm2,prefactor,t,erfc; int *jlist; double rsq; double **x = atom->x; double **f = atom->f; double *q = atom->q; int *type = atom->type; int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; double *special_coul = force->special_coul; double *special_lj = force->special_lj; double qqrd2e = force->qqrd2e; // loop over neighbors of my atoms for (ii = start; ii < inum; ii++) { i = ilist[ii]; qtmp = q[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; itype = type[i]; jlist = firstneigh[i]; jnum = numneigh[i]; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; factor_lj = special_lj[sbmask(j)]; factor_coul = special_coul[sbmask(j)]; j &= NEIGHMASK; const double delx = xtmp - x[j][0]; const double dely = ytmp - x[j][1]; const double delz = ztmp - x[j][2]; const double rsq = delx*delx + dely*dely + delz*delz; const int jtype = type[j]; double evdwl = 0.0; double ecoul = 0.0; double fpair = 0.0; if (rsq < cutsq[itype][jtype]) { const double r2inv = 1.0/rsq; const int cgt=cg_type[itype][jtype]; double forcelj = 0.0; double forcecoul = 0.0; if (rsq < cut_ljsq[itype][jtype]) { forcelj=factor_lj; if (eflag) evdwl=factor_lj; if (cgt == CG_LJ12_4) { const double r4inv=r2inv*r2inv; forcelj *= r4inv*(lj1[itype][jtype]*r4inv*r4inv - lj2[itype][jtype]); if (eflag) { evdwl *= r4inv*(lj3[itype][jtype]*r4inv*r4inv - lj4[itype][jtype]) - offset[itype][jtype]; } } else if (cgt == CG_LJ9_6) { const double r3inv = r2inv*sqrt(r2inv); const double r6inv = r3inv*r3inv; forcelj *= r6inv*(lj1[itype][jtype]*r3inv - lj2[itype][jtype]); if (eflag) { evdwl *= r6inv*(lj3[itype][jtype]*r3inv - lj4[itype][jtype]) - offset[itype][jtype]; } } else { const double r6inv = r2inv*r2inv*r2inv; forcelj *= r6inv*(lj1[itype][jtype]*r6inv - lj2[itype][jtype]); if (eflag) { evdwl *= r6inv*(lj3[itype][jtype]*r6inv - lj4[itype][jtype]) - offset[itype][jtype]; } } } if (rsq < cut_coulsq_global) { if (!ncoultablebits || rsq <= tabinnersq) { const double r = sqrt(rsq); const double grij = g_ewald * r; const double expm2 = exp(-grij*grij); const double t = 1.0 / (1.0 + EWALD_P*grij); const double erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; const double prefactor = qqrd2e * qtmp*q[j]/r; forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); if (eflag) ecoul = prefactor*erfc; if (factor_coul < 1.0) { forcecoul -= (1.0-factor_coul)*prefactor; if (eflag) ecoul -= (1.0-factor_coul)*prefactor; } } else { union_int_float_t rsq_lookup; rsq_lookup.f = rsq; int itable = rsq_lookup.i & ncoulmask; itable >>= ncoulshiftbits; const double fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable]; const double table = ftable[itable] + fraction*dftable[itable]; forcecoul = qtmp*q[j] * table; if (eflag) { const double table2 = etable[itable] + fraction*detable[itable]; ecoul = qtmp*q[j] * table2; } if (factor_coul < 1.0) { const double table2 = ctable[itable] + fraction*dctable[itable]; const double prefactor = qtmp*q[j] * table2; forcecoul -= (1.0-factor_coul)*prefactor; if (eflag) ecoul -= (1.0-factor_coul)*prefactor; } } } fpair = (forcecoul + forcelj) * r2inv; f[i][0] += delx*fpair; f[i][1] += dely*fpair; f[i][2] += delz*fpair; if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz); } } } } diff --git a/src/GPU/pair_cg_cmm_coul_msm_gpu.cpp b/src/GPU/pair_cg_cmm_coul_msm_gpu.cpp index e88144bea..d946b739d 100644 --- a/src/GPU/pair_cg_cmm_coul_msm_gpu.cpp +++ b/src/GPU/pair_cg_cmm_coul_msm_gpu.cpp @@ -1,309 +1,309 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov 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: Mike Brown (SNL) ------------------------------------------------------------------------- */ #include "math.h" #include "stdio.h" #include "stdlib.h" #include "pair_cg_cmm_coul_msm_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "integrate.h" #include "memory.h" #include "error.h" #include "neigh_request.h" #include "universe.h" #include "update.h" #include "domain.h" #include "string.h" #include "kspace.h" #include "gpu_extra.h" #define MIN(a,b) ((a) < (b) ? (a) : (b)) #define MAX(a,b) ((a) > (b) ? (a) : (b)) enum {C3=0,C4=1}; // External functions from cuda library for atom decomposition int cmmm_gpu_init(const int ntypes, double **cutsq, int **cg_type, double **host_lj1, double **host_lj2, double **host_lj3, double **host_lj4, double **offset, double *special_lj, const int nlocal, const int nall, const int max_nbors, const int maxspecial, const double cell_size, int &gpu_mode, FILE *screen, double **host_cut_ljsq, double host_cut_coulsq, double *host_special_coul, const double qqrd2e, const int smooth); void cmmm_gpu_clear(); int ** cmmm_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x, int *host_type, double *sublo, double *subhi, int *tag, int **nspecial, int **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_q, double *boxlo, double *prd); void cmmm_gpu_compute(const int ago, const int inum, 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, double *host_q, const int nlocal, double *boxlo, double *prd); double cmmm_gpu_bytes(); using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ PairCGCMMCoulMSMGPU::PairCGCMMCoulMSMGPU(LAMMPS *lmp) : PairCGCMMCoulMSM(lmp), gpu_mode(GPU_PAIR) { respa_enable = 0; cpu_time = 0.0; } /* ---------------------------------------------------------------------- free all arrays ------------------------------------------------------------------------- */ PairCGCMMCoulMSMGPU::~PairCGCMMCoulMSMGPU() { cmmm_gpu_clear(); } /* ---------------------------------------------------------------------- */ void PairCGCMMCoulMSMGPU::compute(int eflag, int vflag) { if (eflag || vflag) ev_setup(eflag,vflag); else evflag = vflag_fdotr = 0; int nall = atom->nlocal + atom->nghost; int inum, host_start; bool success = true; int *ilist, *numneigh, **firstneigh; if (gpu_mode == GPU_NEIGH) { inum = atom->nlocal; firstneigh = cmmm_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, domain->sublo, domain->subhi, atom->tag, atom->nspecial, atom->special, eflag, vflag, eflag_atom, vflag_atom, host_start, &ilist, &numneigh, cpu_time, success, atom->q, domain->boxlo, domain->prd); } else { inum = list->inum; ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; cmmm_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->q, atom->nlocal, domain->boxlo, domain->prd); } if (!success) error->one("Out of memory on GPGPU"); if (host_start<inum) { cpu_time = MPI_Wtime(); cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh); cpu_time = MPI_Wtime() - cpu_time; } } /* ---------------------------------------------------------------------- init specific to this pair style ------------------------------------------------------------------------- */ void PairCGCMMCoulMSMGPU::init_style() { PairCGCMMCoulMSM::init_style(); if (force->newton_pair) - error->all("Cannot use newton pair with GPU cg/cmm pair style"); + error->all("Cannot use newton pair with cg/cmm/coul/msm/gpu pair style"); // Repeat cutsq calculation because done after call to init_style double maxcut = -1.0; double cut; 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)) { cut = init_one(i,j); cut *= cut; if (cut > maxcut) maxcut = cut; cutsq[i][j] = cutsq[j][i] = cut; } else cutsq[i][j] = cutsq[j][i] = 0.0; } } double cell_size = sqrt(maxcut) + neighbor->skin; int maxspecial=0; if (atom->molecular) maxspecial=atom->maxspecial; int success = cmmm_gpu_init(atom->ntypes+1, cutsq, cg_type, lj1, lj2, lj3, lj4, offset, force->special_lj, atom->nlocal, atom->nlocal+atom->nghost, 300, maxspecial, cell_size, gpu_mode, screen, cut_ljsq, cut_coulsq_global, force->special_coul, force->qqrd2e,_smooth); GPU_EXTRA::check_flag(success,error,world); if (gpu_mode != GPU_NEIGH) { int irequest = neighbor->request(this); neighbor->requests[irequest]->half = 0; neighbor->requests[irequest]->full = 1; } } /* ---------------------------------------------------------------------- */ double PairCGCMMCoulMSMGPU::memory_usage() { double bytes = Pair::memory_usage(); return bytes + cmmm_gpu_bytes(); } /* ---------------------------------------------------------------------- */ void PairCGCMMCoulMSMGPU::cpu_compute(int start, int inum, int eflag, int vflag, int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype,itable; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz; double fraction,table; double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj; double grij,expm2,prefactor,t,erfc; int *jlist; double rsq; double **x = atom->x; double **f = atom->f; double *q = atom->q; int *type = atom->type; int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; double *special_coul = force->special_coul; double *special_lj = force->special_lj; double qqrd2e = force->qqrd2e; // loop over neighbors of my atoms for (ii = start; ii < inum; ii++) { i = ilist[ii]; qtmp = q[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; itype = type[i]; jlist = firstneigh[i]; jnum = numneigh[i]; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; factor_lj = special_lj[sbmask(j)]; factor_coul = special_coul[sbmask(j)]; j &= NEIGHMASK; const double delx = xtmp - x[j][0]; const double dely = ytmp - x[j][1]; const double delz = ztmp - x[j][2]; const double rsq = delx*delx + dely*dely + delz*delz; const int jtype = type[j]; double evdwl = 0.0; double ecoul = 0.0; double fpair = 0.0; if (rsq < cutsq[itype][jtype]) { const double r2inv = 1.0/rsq; const int cgt=cg_type[itype][jtype]; double forcelj = 0.0; double forcecoul = 0.0; if (rsq < cut_ljsq[itype][jtype]) { forcelj=factor_lj; if (eflag) evdwl=factor_lj; if (cgt == CG_LJ12_4) { const double r4inv=r2inv*r2inv; forcelj *= r4inv*(lj1[itype][jtype]*r4inv*r4inv - lj2[itype][jtype]); if (eflag) { evdwl *= r4inv*(lj3[itype][jtype]*r4inv*r4inv - lj4[itype][jtype]) - offset[itype][jtype]; } } else if (cgt == CG_LJ9_6) { const double r3inv = r2inv*sqrt(r2inv); const double r6inv = r3inv*r3inv; forcelj *= r6inv*(lj1[itype][jtype]*r3inv - lj2[itype][jtype]); if (eflag) { evdwl *= r6inv*(lj3[itype][jtype]*r3inv - lj4[itype][jtype]) - offset[itype][jtype]; } } else { const double r6inv = r2inv*r2inv*r2inv; forcelj *= r6inv*(lj1[itype][jtype]*r6inv - lj2[itype][jtype]); if (eflag) { evdwl *= r6inv*(lj3[itype][jtype]*r6inv - lj4[itype][jtype]) - offset[itype][jtype]; } } } if (rsq < cut_coulsq_global) { const double ir = 1.0/sqrt(rsq); const double prefactor = qqrd2e * qtmp*q[j]; const double r2_ia2 = rsq*_ia2; const double r4_ia4 = r2_ia2*r2_ia2; if (_smooth==C3) { forcecoul = prefactor*(_ia3*(-4.375+5.25*r2_ia2-1.875*r4_ia4)- ir/rsq); if (eflag) ecoul = prefactor*(ir+_ia*(2.1875-2.1875*r2_ia2+ 1.3125*r4_ia4-0.3125*r2_ia2*r4_ia4)); } else { const double r6_ia6 = r2_ia2*r4_ia4; forcecoul = prefactor*(_ia3*(-6.5625+11.8125*r2_ia2-8.4375*r4_ia4+ 2.1875*r6_ia6)-ir/rsq); if (eflag) ecoul = prefactor*(ir+_ia*(2.4609375-3.28125*r2_ia2+ 2.953125*r4_ia4-1.40625*r6_ia6+ 0.2734375*r4_ia4*r4_ia4)); } if (factor_coul < 1.0) { forcecoul -= (1.0-factor_coul)*prefactor*ir; if (eflag) ecoul -= (1.0-factor_coul)*prefactor*ir; } } fpair = forcecoul + forcelj * r2inv; f[i][0] += delx*fpair; f[i][1] += dely*fpair; f[i][2] += delz*fpair; if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz); } } } }