Merge branch 'master' into more-internal-convenience (e6c4036a) · Commits · 郑智淋 / lammps

doc/src/pair_eim.rst

+2 −2

Original line number	Original line	Diff line number	Diff line
	@@ -48,7 +48,7 @@ and :math:`sigma_i` are calculated as
	\sigma_i = & \sum_{j=i_1}^{i_N} q_j \cdot \psi_{ij} \left(r_{ij}\right) \\		\sigma_i = & \sum_{j=i_1}^{i_N} q_j \cdot \psi_{ij} \left(r_{ij}\right) \\
	E_i\left(q_i,\sigma_i\right) = & \frac{1}{2} \cdot q_i \cdot \sigma_i		E_i\left(q_i,\sigma_i\right) = & \frac{1}{2} \cdot q_i \cdot \sigma_i

	where :math:`\eta_{ji} is a pairwise function describing electron flow from atom		where :math:`\eta_{ji}` is a pairwise function describing electron flow from atom
	I to atom J, and :math:`\psi_{ij}` is another pairwise function. The multi-body		I to atom J, and :math:`\psi_{ij}` is another pairwise function. The multi-body
	nature of the EIM potential is a result of the embedding energy term.		nature of the EIM potential is a result of the embedding energy term.
	A complete list of all the pair functions used in EIM is summarized		A complete list of all the pair functions used in EIM is summarized
	@@ -63,7 +63,7 @@ below
	\right.\\		\right.\\
	\eta_{ji} = & A_{\eta,ij}\left(\chi_j-\chi_i\right)f_c\left(r,r_{s,\eta,ij},r_{c,\eta,ij}\right) \\		\eta_{ji} = & A_{\eta,ij}\left(\chi_j-\chi_i\right)f_c\left(r,r_{s,\eta,ij},r_{c,\eta,ij}\right) \\
	\psi_{ij}\left(r\right) = & A_{\psi,ij}\exp\left(-\zeta_{ij}r\right)f_c\left(r,r_{s,\psi,ij},r_{c,\psi,ij}\right) \\		\psi_{ij}\left(r\right) = & A_{\psi,ij}\exp\left(-\zeta_{ij}r\right)f_c\left(r,r_{s,\psi,ij},r_{c,\psi,ij}\right) \\
	f_{c}\left(r,r_p,r_c\right) = & 0.510204 \mathrm{erfc}\left[\frac{1.64498\left(2r-r_p-r_c\right)}{r_c-r_p}\right] - 0.010204		f_{c}\left(r,r_p,r_c\right) = & 0.510204 \cdot \mathrm{erfc}\left[\frac{1.64498\left(2r-r_p-r_c\right)}{r_c-r_p}\right] - 0.010204

	Here :math:`E_b, r_e, r_(c,\phi), \alpha, \beta, A_(\psi), \zeta, r_(s,\psi),		Here :math:`E_b, r_e, r_(c,\phi), \alpha, \beta, A_(\psi), \zeta, r_(s,\psi),
	r_(c,\psi), A_(\eta), r_(s,\eta), r_(c,\eta), \chi,` and pair function type		r_(c,\psi), A_(\eta), r_(s,\eta), r_(c,\eta), \chi,` and pair function type

examples/threebody/Si.sw

deleted100644 → 0

+1 −18

Original line number	Original line	Diff line number	Diff line
	# DATE: 2007-06-11 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Stillinger and Weber, Phys Rev B, 31, 5262, (1985)
	# Stillinger-Weber parameters for various elements and mixtures
	# multiple entries can be added to this file, LAMMPS reads the ones it needs
	# these entries are in LAMMPS "metal" units:
	# epsilon = eV; sigma = Angstroms
	# other quantities are unitless

	# format of a single entry (one or more lines):
	# element 1, element 2, element 3,
	# epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol

	# Here are the original parameters in metal units, for Silicon from:
	#
	# Stillinger and Weber, Phys. Rev. B, v. 31, p. 5262, (1985)
	#

	Si Si Si 2.1683 2.0951 1.80 21.0 1.20 -0.333333333333
	7.049556277 0.6022245584 4.0 0.0 0.0

examples/threebody/Si.sw

0 → 120000

+1 −18

Original line number	Original line	Diff line number	Diff line
			../../potentials/Si.sw
			No newline at end of file

potentials/MOH.nb3b.harmonic

+1 −1

Original line number	Original line	Diff line number	Diff line
	# DATE: 2016-07-29 UNITS: metal CONTRIBUTOR: Todd Zeitler, tzeitle@sandia.gov CITATION: none		# DATE: 2016-07-29 UNITS: real CONTRIBUTOR: Todd Zeitler, tzeitle@sandia.gov CITATION: none
	# nb3b/harmonic (nonbonded 3-body harmonic) parameters for various elements		# nb3b/harmonic (nonbonded 3-body harmonic) parameters for various elements
	#		#
	# multiple entries can be added to this file, LAMMPS reads the ones it needs		# multiple entries can be added to this file, LAMMPS reads the ones it needs

src/KOKKOS/sna_kokkos_impl.h

+6 −9

Original line number	Original line	Diff line number	Diff line
	@@ -552,10 +552,7 @@ void SNAKokkos<DeviceType>::compute_bi(const int& iatom_mod, const int& jjb, con
	int idouble = 0;		int idouble = 0;
	for (int elem1 = 0; elem1 < nelements; elem1++) {		for (int elem1 = 0; elem1 < nelements; elem1++) {
	for (int elem2 = 0; elem2 < nelements; elem2++) {		for (int elem2 = 0; elem2 < nelements; elem2++) {
	const int jalloy = idouble;

	for (int elem3 = 0; elem3 < nelements; elem3++) {		for (int elem3 = 0; elem3 < nelements; elem3++) {
	const int jjballoy = itriple;

	double sumzu = 0.0;		double sumzu = 0.0;
	double sumzu_temp = 0.0;		double sumzu_temp = 0.0;
	@@ -566,7 +563,7 @@ void SNAKokkos<DeviceType>::compute_bi(const int& iatom_mod, const int& jjb, con
	const int jjz_index = jjz+mb*(j+1)+ma;		const int jjz_index = jjz+mb*(j+1)+ma;
	if (2*mb == j) return; // I think we can remove this?		if (2*mb == j) return; // I think we can remove this?
	const auto utot = ulisttot_pack(iatom_mod, jju_index, elem3, iatom_div);		const auto utot = ulisttot_pack(iatom_mod, jju_index, elem3, iatom_div);
	const auto zloc = zlist_pack(iatom_mod, jjz_index, jalloy, iatom_div);		const auto zloc = zlist_pack(iatom_mod, jjz_index, idouble, iatom_div);
	sumzu_temp += utot.re * zloc.re + utot.im * zloc.im;		sumzu_temp += utot.re * zloc.re + utot.im * zloc.im;
	}		}
	}		}
	@@ -582,7 +579,7 @@ void SNAKokkos<DeviceType>::compute_bi(const int& iatom_mod, const int& jjb, con
	const int jjz_index = jjz+(mb-1)*(j+1)+(j+1)+ma;		const int jjz_index = jjz+(mb-1)*(j+1)+(j+1)+ma;

	const auto utot = ulisttot_pack(iatom_mod, jju_index, elem3, iatom_div);		const auto utot = ulisttot_pack(iatom_mod, jju_index, elem3, iatom_div);
	const auto zloc = zlist_pack(iatom_mod, jjz_index, jalloy, iatom_div);		const auto zloc = zlist_pack(iatom_mod, jjz_index, idouble, iatom_div);
	sumzu_temp += utot.re * zloc.re + utot.im * zloc.im;		sumzu_temp += utot.re * zloc.re + utot.im * zloc.im;

	}		}
	@@ -593,7 +590,7 @@ void SNAKokkos<DeviceType>::compute_bi(const int& iatom_mod, const int& jjb, con
	const int jjz_index = jjz+(mb-1)*(j+1)+(j+1)+ma;		const int jjz_index = jjz+(mb-1)*(j+1)+(j+1)+ma;

	const auto utot = ulisttot_pack(iatom_mod, jju_index, elem3, iatom_div);		const auto utot = ulisttot_pack(iatom_mod, jju_index, elem3, iatom_div);
	const auto zloc = zlist_pack(iatom_mod, jjz_index, jalloy, iatom_div);		const auto zloc = zlist_pack(iatom_mod, jjz_index, idouble, iatom_div);
	sumzu += 0.5 * (utot.re * zloc.re + utot.im * zloc.im);		sumzu += 0.5 * (utot.re * zloc.re + utot.im * zloc.im);
	} // end if jeven		} // end if jeven

	@@ -607,7 +604,7 @@ void SNAKokkos<DeviceType>::compute_bi(const int& iatom_mod, const int& jjb, con
	sumzu -= bzero[j];		sumzu -= bzero[j];
	}		}
	}		}
	blist_pack(iatom_mod, jjb, jjballoy, iatom_div) = sumzu;		blist_pack(iatom_mod, jjb, itriple, iatom_div) = sumzu;
	//} // end loop over j		//} // end loop over j
	//} // end loop over j1, j2		//} // end loop over j1, j2
	itriple++;		itriple++;
	@@ -1078,7 +1075,7 @@ void SNAKokkos<DeviceType>::compute_bi_cpu(const typename Kokkos::TeamPolicy<Dev
	int idouble = 0;		int idouble = 0;
	for (int elem1 = 0; elem1 < nelements; elem1++) {		for (int elem1 = 0; elem1 < nelements; elem1++) {
	for (int elem2 = 0; elem2 < nelements; elem2++) {		for (int elem2 = 0; elem2 < nelements; elem2++) {
	const auto jalloy = idouble;		auto jalloy = idouble; // must be non-const to work around gcc compiler bug
	for (int elem3 = 0; elem3 < nelements; elem3++) {		for (int elem3 = 0; elem3 < nelements; elem3++) {
	Kokkos::parallel_for(Kokkos::TeamThreadRange(team,idxb_max),		Kokkos::parallel_for(Kokkos::TeamThreadRange(team,idxb_max),
	[&] (const int& jjb) {		[&] (const int& jjb) {
	@@ -1146,7 +1143,7 @@ void SNAKokkos<DeviceType>::compute_bi_cpu(const typename Kokkos::TeamPolicy<Dev
	}		}
	}		}

	blist(jjb, jjballoy, iatom) = sumzu;		blist(jjb, itriple, iatom) = sumzu;
	});		});
	});		});
	//} // end loop over j		//} // end loop over j

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