Merge pull request #1769 from akohlmey/collected-small-fixes (39a26e6c) · Commits · 郑智淋 / lammps

doc/src/bond_table.rst

+3 −2

Original line number	Diff line number	Diff line
		@@ -119,8 +119,9 @@ the bond length r (in distance units), the 3rd value is the energy (in
		energy units), and the 4th is the force (in force units). The bond
		lengths must range from a LO value to a HI value, and increase from
		one line to the next. If the actual bond length is ever smaller than
		the LO value or larger than the HI value, then the bond energy and
		force is evaluated as if the bond were the LO or HI length.
		the LO value or larger than the HI value, then the calculation is
		aborted with an error, so it is advisable to cover the whole range
		of possible bond lengths.

		Note that one file can contain many sections, each with a tabulated
		potential. LAMMPS reads the file section by section until it finds

src/KOKKOS/pair_eam_kokkos.cpp

+1 −0

Original line number	Diff line number	Diff line
		@@ -37,6 +37,7 @@ template<class DeviceType>
		PairEAMKokkos<DeviceType>::PairEAMKokkos(LAMMPS *lmp) : PairEAM(lmp)
		{
		respa_enable = 0;
		single_enable = 0;

		atomKK = (AtomKokkos *) atom;
		execution_space = ExecutionSpaceFromDevice<DeviceType>::space;

src/MANYBODY/pair_eam.cpp

+19 −1

Original line number	Diff line number	Diff line
		@@ -43,6 +43,7 @@ PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp)
		nmax = 0;
		rho = NULL;
		fp = NULL;
		numforce = NULL;
		map = NULL;
		type2frho = NULL;

		@@ -77,6 +78,7 @@ PairEAM::~PairEAM()

		memory->destroy(rho);
		memory->destroy(fp);
		memory->destroy(numforce);

		if (allocated) {
		memory->destroy(setflag);
		@@ -151,9 +153,11 @@ void PairEAM::compute(int eflag, int vflag)
		if (atom->nmax > nmax) {
		memory->destroy(rho);
		memory->destroy(fp);
		memory->destroy(numforce);
		nmax = atom->nmax;
		memory->create(rho,nmax,"pair:rho");
		memory->create(fp,nmax,"pair:fp");
		memory->create(numforce,nmax,"pair:numforce");
		}

		double **x = atom->x;
		@@ -255,6 +259,7 @@ void PairEAM::compute(int eflag, int vflag)

		jlist = firstneigh[i];
		jnum = numneigh[i];
		numforce[i] = 0;

		for (jj = 0; jj < jnum; jj++) {
		j = jlist[jj];
		@@ -266,6 +271,7 @@ void PairEAM::compute(int eflag, int vflag)
		rsq = delxdelx + delydely + delz*delz;

		if (rsq < cutforcesq) {
		++numforce[i];
		jtype = type[j];
		r = sqrt(rsq);
		p = r*rdr + 1.0;
		@@ -802,6 +808,18 @@ double PairEAM::single(int i, int j, int itype, int jtype,
		double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip;
		double *coeff;

		if (numforce[i] > 0) {
		p = rho[i]*rdrho + 1.0;
		m = static_cast<int> (p);
		m = MAX(1,MIN(m,nrho-1));
		p -= m;
		p = MIN(p,1.0);
		coeff = frho_spline[type2frho[itype]][m];
		phi = ((coeff[3]p + coeff[4])p + coeff[5])*p + coeff[6];
		if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax);
		phi *= 1.0/static_cast<double>(numforce[i]);
		} else phi = 0.0;

		r = sqrt(rsq);
		p = r*rdr + 1.0;
		m = static_cast<int> (p);
		@@ -818,7 +836,7 @@ double PairEAM::single(int i, int j, int itype, int jtype,
		z2 = ((coeff[3]p + coeff[4])p + coeff[5])*p + coeff[6];

		recip = 1.0/r;
		phi = z2*recip;
		phi += z2*recip;
		phip = z2precip - phirecip;
		psip = fp[i]rhojp + fp[j]rhoip + phip;
		fforce = -psip*recip;

src/MANYBODY/pair_eam.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -70,6 +70,7 @@ class PairEAM : public Pair {
		// per-atom arrays

		double rho,fp;
		int *numforce;

		// potentials as file data

src/OPT/pair_eam_opt.cpp

+8 −4

Original line number	Diff line number	Diff line
		@@ -80,11 +80,13 @@ void PairEAMOpt::eval()
		// grow energy array if necessary

		if (atom->nmax > nmax) {
		memory->sfree(rho);
		memory->sfree(fp);
		memory->destroy(rho);
		memory->destroy(fp);
		memory->destroy(numforce);
		nmax = atom->nmax;
		rho = (double ) memory->smalloc(nmaxsizeof(double),"pair:rho");
		fp = (double ) memory->smalloc(nmaxsizeof(double),"pair:fp");
		memory->create(rho,nmax,"pair:rho");
		memory->create(fp,nmax,"pair:fp");
		memory->create(numforce,nmax,"pair:numforce");
		}

		double** _noalias x = atom->x;
		@@ -269,6 +271,7 @@ void PairEAMOpt::eval()

		fast_gamma_t* _noalias tabssi = &tabss[itype1ntypesnr];
		double* _noalias scale_i = scale[itype1+1]+1;
		numforce[i] = 0;

		for (jj = 0; jj < jnum; jj++) {
		j = jlist[jj];
		@@ -280,6 +283,7 @@ void PairEAMOpt::eval()
		double rsq = delxdelx + delydely + delz*delz;

		if (rsq < tmp_cutforcesq) {
		++numforce[i];
		jtype = type[j] - 1;
		double r = sqrt(rsq);
		double rhoip,rhojp,z2,z2p;

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