Merge pull request #695 from timattox/USER-DPD_small_updates (b1b4a52b) · Commits · 郑智淋 / lammps

src/KOKKOS/npair_ssa_kokkos.cpp

+9 −2

Original line number	Diff line number	Diff line
		@@ -70,6 +70,7 @@ void NPairSSAKokkos<DeviceType>::copy_neighbor_info()
		k_ex2_bit = neighborKK->k_ex2_bit;
		k_ex_mol_group = neighborKK->k_ex_mol_group;
		k_ex_mol_bit = neighborKK->k_ex_mol_bit;
		k_ex_mol_intra = neighborKK->k_ex_mol_intra;
		}

		/* ----------------------------------------------------------------------
		@@ -217,8 +218,12 @@ int NPairSSAKokkosExecute<DeviceType>::exclusion(const int &i,const int &j,

		if (nex_mol) {
		for (m = 0; m < nex_mol; m++)
		if (mask(i) & ex_mol_bit(m) && mask(j) & ex_mol_bit(m) &&
		molecule(i) == molecule(j)) return 1;
		if (ex_mol_intra[m]) { // intra-chain: exclude i-j pair if on same molecule
		if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
		molecule[i] == molecule[j]) return 1;
		} else // exclude i-j pair if on different molecules
		if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
		molecule[i] != molecule[j]) return 1;
		}

		return 0;
		@@ -418,6 +423,7 @@ fprintf(stdout, "tota%03d total %3d could use %6d inums, expected %6d inums. inu
		nex_mol,
		k_ex_mol_group.view<DeviceType>(),
		k_ex_mol_bit.view<DeviceType>(),
		k_ex_mol_intra.view<DeviceType>(),
		bboxhi,bboxlo,
		domain->xperiodic,domain->yperiodic,domain->zperiodic,
		domain->xprd_half,domain->yprd_half,domain->zprd_half);
		@@ -432,6 +438,7 @@ fprintf(stdout, "tota%03d total %3d could use %6d inums, expected %6d inums. inu
		k_ex2_bit.sync<DeviceType>();
		k_ex_mol_group.sync<DeviceType>();
		k_ex_mol_bit.sync<DeviceType>();
		k_ex_mol_intra.sync<DeviceType>();
		k_bincount.sync<DeviceType>();
		k_bins.sync<DeviceType>();
		k_gbincount.sync<DeviceType>();

src/KOKKOS/npair_ssa_kokkos.h

+4 −0

Original line number	Diff line number	Diff line
		@@ -76,6 +76,7 @@ class NPairSSAKokkos : public NPair {
		DAT::tdual_int_1d k_ex1_bit,k_ex2_bit;
		DAT::tdual_int_1d k_ex_mol_group;
		DAT::tdual_int_1d k_ex_mol_bit;
		DAT::tdual_int_1d k_ex_mol_intra;

		// data from NBinSSA class

		@@ -123,6 +124,7 @@ class NPairSSAKokkosExecute
		const int nex_mol;
		const typename AT::t_int_1d_const ex_mol_group;
		const typename AT::t_int_1d_const ex_mol_bit;
		const typename AT::t_int_1d_const ex_mol_intra;

		// data from NBinSSA class

		@@ -233,6 +235,7 @@ class NPairSSAKokkosExecute
		const int & _nex_mol,
		const typename AT::t_int_1d_const & _ex_mol_group,
		const typename AT::t_int_1d_const & _ex_mol_bit,
		const typename AT::t_int_1d_const & _ex_mol_intra,
		const X_FLOAT _bboxhi, const X_FLOAT _bboxlo,
		const int & _xperiodic, const int & _yperiodic, const int & _zperiodic,
		const int & _xprd_half, const int & _yprd_half, const int & _zprd_half):
		@@ -266,6 +269,7 @@ class NPairSSAKokkosExecute
		ex1_group(_ex1_group),ex2_group(_ex2_group),
		ex1_bit(_ex1_bit),ex2_bit(_ex2_bit),nex_mol(_nex_mol),
		ex_mol_group(_ex_mol_group),ex_mol_bit(_ex_mol_bit),
		ex_mol_intra(_ex_mol_intra),
		xperiodic(_xperiodic),yperiodic(_yperiodic),zperiodic(_zperiodic),
		xprd_half(_xprd_half),yprd_half(_yprd_half),zprd_half(_zprd_half) {

src/USER-DPD/nbin_ssa.h

+5 −68

Original line number	Diff line number	Diff line
		@@ -23,6 +23,8 @@ NBinStyle(ssa,
		#define LMP_NBIN_SSA_H

		#include "nbin_standard.h"
		#include "math.h"
		#include "error.h"

		namespace LAMMPS_NS {

		@@ -47,79 +49,14 @@ class NBinSSA : public NBinStandard {

		bigint memory_usage();

		inline
		int coord2bin(const double & x,const double & y,const double & z) const
		{
		int ix,iy,iz;

		if (x >= bboxhi_[0])
		ix = static_cast<int> ((x-bboxhi_[0])*bininvx) + nbinx;
		else if (x >= bboxlo_[0]) {
		ix = static_cast<int> ((x-bboxlo_[0])*bininvx);
		ix = MIN(ix,nbinx-1);
		} else
		ix = static_cast<int> ((x-bboxlo_[0])*bininvx) - 1;

		if (y >= bboxhi_[1])
		iy = static_cast<int> ((y-bboxhi_[1])*bininvy) + nbiny;
		else if (y >= bboxlo_[1]) {
		iy = static_cast<int> ((y-bboxlo_[1])*bininvy);
		iy = MIN(iy,nbiny-1);
		} else
		iy = static_cast<int> ((y-bboxlo_[1])*bininvy) - 1;

		if (z >= bboxhi_[2])
		iz = static_cast<int> ((z-bboxhi_[2])*bininvz) + nbinz;
		else if (z >= bboxlo_[2]) {
		iz = static_cast<int> ((z-bboxlo_[2])*bininvz);
		iz = MIN(iz,nbinz-1);
		} else
		iz = static_cast<int> ((z-bboxlo_[2])*bininvz) - 1;

		return (iz-mbinzlo)mbinymbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
		}

		inline
		int coord2bin(const double & x,const double & y,const double & z, int* i) const
		{
		int ix,iy,iz;

		if (x >= bboxhi_[0])
		ix = static_cast<int> ((x-bboxhi_[0])*bininvx) + nbinx;
		else if (x >= bboxlo_[0]) {
		ix = static_cast<int> ((x-bboxlo_[0])*bininvx);
		ix = MIN(ix,nbinx-1);
		} else
		ix = static_cast<int> ((x-bboxlo_[0])*bininvx) - 1;

		if (y >= bboxhi_[1])
		iy = static_cast<int> ((y-bboxhi_[1])*bininvy) + nbiny;
		else if (y >= bboxlo_[1]) {
		iy = static_cast<int> ((y-bboxlo_[1])*bininvy);
		iy = MIN(iy,nbiny-1);
		} else
		iy = static_cast<int> ((y-bboxlo_[1])*bininvy) - 1;

		if (z >= bboxhi_[2])
		iz = static_cast<int> ((z-bboxhi_[2])*bininvz) + nbinz;
		else if (z >= bboxlo_[2]) {
		iz = static_cast<int> ((z-bboxlo_[2])*bininvz);
		iz = MIN(iz,nbinz-1);
		} else
		iz = static_cast<int> ((z-bboxlo_[2])*bininvz) - 1;

		i[0] = ix - mbinxlo;
		i[1] = iy - mbinylo;
		i[2] = iz - mbinzlo;

		return (iz-mbinzlo)mbinymbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
		}

		inline
		int coord2bin(const double & x,const double & y,const double & z, int &ixo, int &iyo, int &izo) const
		{
		int ix,iy,iz;

		if (!ISFINITE(x) \|\| !ISFINITE(y) \|\| !ISFINITE(z))
		error->one(FLERR,"Non-numeric positions - simulation unstable");

		if (x >= bboxhi_[0])
		ix = static_cast<int> ((x-bboxhi_[0])*bininvx) + nbinx;
		else if (x >= bboxlo_[0]) {

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