Merge remote-tracking branch 'charlie/chem_snap' into ml_chem_snap (b84a2481) · Commits · 郑智淋 / lammps

cmake/2826.patch

deleted100644 → 0

+0 −13

Original line number	Diff line number	Diff line
		diff --git a/lib/kokkos/containers/src/Kokkos_ScatterView.hpp b/lib/kokkos/containers/src/Kokkos_ScatterView.hpp
		index a8c05e3..1d83aed 100644
		--- a/lib/kokkos/containers/src/Kokkos_ScatterView.hpp
		+++ b/lib/kokkos/containers/src/Kokkos_ScatterView.hpp
		@@ -681,7 +681,7 @@ class ScatterView<DataType
		,contribution>
		{
		public:
		- typedef Kokkos::View<DataType, Layout, ExecSpace> original_view_type;
		+ typedef Kokkos::View<DataType, Layout, Kokkos::Device<ExecSpace, Kokkos::Cuda::memory_space> > original_view_type;
		typedef typename original_view_type::value_type original_value_type;
		typedef typename original_view_type::reference_type original_reference_type;
		friend class ScatterAccess<DataType, Op, ExecSpace, Layout, ScatterNonDuplicated, contribution, ScatterNonAtomic>;

cmake/Modules/Packages/KOKKOS.cmake

+20 −10

Original line number	Diff line number	Diff line
		if(PKG_KOKKOS)
		find_package(Kokkos 3 QUIET)
		if(Kokkos_FOUND)
		set(DOWNLOAD_KOKKOS_DEFAULT OFF)
		else()
		set(DOWNLOAD_KOKKOS_DEFAULT ON)
		endif()
		option(DOWNLOAD_KOKKOS "Download the KOKKOS library instead of using an already installed one" ${DOWNLOAD_KOKKOS_DEFAULT})
		option(EXTERNAL_KOKKOS "Build against external kokkos library" OFF)
		option(DOWNLOAD_KOKKOS "Download the KOKKOS library instead of using the bundled one" OFF)
		if(DOWNLOAD_KOKKOS)
		if(CMAKE_VERSION VERSION_LESS 3.11)
		message(FATAL_ERROR "Downloading kokkos currently only works with cmake-3.11 and higher")
		endif()
		message(STATUS "KOKKOS download requested - we will build our own")
		# Workaround for cross compilation with MinGW where ${CMAKE_INSTALL_LIBDIR}
		# is a full path, so we need to remove the prefix
		string(REPLACE ${CMAKE_INSTALL_PREFIX} "" _KOKKOS_LIBDIR ${CMAKE_INSTALL_LIBDIR})
		file(DOWNLOAD https://github.com/kokkos/kokkos/compare/3.0.00...stanmoore1:lammps.diff ${CMAKE_CURRENT_BINARY_DIR}/kokkos-lammps.patch)
		include(ExternalProject)
		ExternalProject_Add(kokkos_build
		URL https://github.com/kokkos/kokkos/archive/3.0.00.tar.gz
		URL_MD5 281c7093aa3a603276e93abdf4be23b9
		PATCH_COMMAND patch -p3 < ${CMAKE_CURRENT_SOURCE_DIR}/2826.patch
		PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/kokkos-lammps.patch
		CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}
		-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
		-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
		@@ -26,13 +25,24 @@ if(PKG_KOKKOS)
		set(KOKKOS_LIBRARIES ${INSTALL_DIR}/${_KOKKOS_LIBDIR}/libkokkoscore.a)
		set(KOKKOS_INCLUDE_DIRS ${INSTALL_DIR}/include)
		include_directories(${KOKKOS_INCLUDE_DIRS})
		list(APPEND LAMMPS_LINK_LIBS ${KOKKOS_LIBRARIES})
		else()
		list(APPEND LAMMPS_LINK_LIBS ${KOKKOS_LIBRARIES} ${CMAKE_DL_LIBS})
		elseif(EXTERNAL_KOKKOS)
		find_package(Kokkos 3)
		if(NOT Kokkos_FOUND)
		message(FATAL_ERROR "KOKKOS library not found, help CMake to find it by setting KOKKOS_LIBRARY, or set DOWNLOAD_KOKKOS=ON to download it")
		endif()
		list(APPEND LAMMPS_LINK_LIBS Kokkos::kokkos)
		else()
		set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
		set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
		add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})

		set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
		${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
		${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
		${LAMMPS_LIB_KOKKOS_BIN_DIR})
		include_directories(${Kokkos_INCLUDE_DIRS})
		list(APPEND LAMMPS_LINK_LIBS kokkos)
		endif()
		add_definitions(-DLMP_KOKKOS)

src/SNAP/compute_snap.cpp

+6 −4

Original line number	Diff line number	Diff line
		@@ -40,7 +40,7 @@ ComputeSnap::ComputeSnap(LAMMPS lmp, int narg, char *arg) :
		extarray = 0;

		double rfac0, rmin0;
		int twojmax, switchflag, bzeroflag, bnormflag;
		int twojmax, switchflag, bzeroflag;
		radelem = NULL;
		wjelem = NULL;

		@@ -54,7 +54,6 @@ ComputeSnap::ComputeSnap(LAMMPS lmp, int narg, char *arg) :
		rmin0 = 0.0;
		switchflag = 1;
		bzeroflag = 1;
		bnormflag = 0;
		quadraticflag = 0;
		alloyflag = 0;
		wselfallflag = 0;
		@@ -113,10 +112,9 @@ ComputeSnap::ComputeSnap(LAMMPS lmp, int narg, char *arg) :
		quadraticflag = atoi(arg[iarg+1]);
		iarg += 2;
		} else if (strcmp(arg[iarg],"alloyflag") == 0) {
		if (iarg+2+ntypes > narg)
		if (iarg+2 > narg)
		error->all(FLERR,"Illegal compute snap command");
		alloyflag = 1;
		bnormflag = 1;
		memory->create(map,ntypes+1,"compute_snap:map");
		nelements = force->inumeric(FLERR,arg[iarg+1]);
		for(int i = 0; i < ntypes; i++) {
		@@ -168,6 +166,8 @@ ComputeSnap::~ComputeSnap()
		memory->destroy(wjelem);
		memory->destroy(cutsq);
		delete snaptr;

		if (alloyflag) memory->destroy(map);
		}

		/* ---------------------------------------------------------------------- */
		@@ -541,6 +541,8 @@ double ComputeSnap::memory_usage()
		sizeof(double); // snapall
		bytes += nmaxsize_peratom sizeof(double); // snap_peratom
		bytes += snaptr->memory_usage(); // SNA object
		int n = atom->ntypes+1;
		bytes += n*sizeof(int); // map

		return bytes;
		}

src/SNAP/pair_snap.cpp

+18 −5

Original line number	Diff line number	Diff line
		@@ -162,7 +162,10 @@ void PairSNAP::compute(int eflag, int vflag)

		// compute Ui, Yi for atom I

		if (alloyflag)
		snaptr->compute_ui(ninside, ielem);
		else
		snaptr->compute_ui(ninside, 0);

		// for neighbors of I within cutoff:
		// compute Fij = dEi/dRj = -dEi/dRi
		@@ -175,8 +178,12 @@ void PairSNAP::compute(int eflag, int vflag)

		for (int jj = 0; jj < ninside; jj++) {
		int j = snaptr->inside[jj];
		if(alloyflag)
		snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
		snaptr->rcutij[jj],jj, snaptr->element[jj]);
		else
		snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
		snaptr->rcutij[jj],jj, 0);

		snaptr->compute_deidrj(fij);

		@@ -329,9 +336,15 @@ void PairSNAP::compute_bispectrum()
		}
		}

		if (alloyflag)
		snaptr->compute_ui(ninside, ielem);
		else
		snaptr->compute_ui(ninside, 0);
		snaptr->compute_zi();
		if (alloyflag)
		snaptr->compute_bi(ielem);
		else
		snaptr->compute_bi(0);

		for (int icoeff = 0; icoeff < ncoeff; icoeff++){
		bispectrum[ii][icoeff] = snaptr->blist[icoeff];

src/SNAP/sna.cpp

+27 −77

Original line number	Diff line number	Diff line
		@@ -120,7 +120,11 @@ SNA::SNA(LAMMPS* lmp, double rfac0_in, int twojmax_in,
		bnorm_flag = alloy_flag_in;
		alloy_flag = alloy_flag_in;
		wselfall_flag = wselfall_flag_in;

		if (alloy_flag)
		nelements = nelements_in;
		else
		nelements = 1;

		twojmax = twojmax_in;

		@@ -277,8 +281,6 @@ void SNA::build_indexlist()
		idxz[idxz_count].mb1min = MAX(0, (2 * mb - j - j2 + j1) / 2);
		idxz[idxz_count].mb2max = (2 * mb - j - (2 * idxz[idxz_count].mb1min - j1) + j2) / 2;
		idxz[idxz_count].nb = MIN(j1, (2 * mb - j + j2 + j1) / 2) - idxz[idxz_count].mb1min + 1;
		idxz[idxz_count].ma = ma;
		idxz[idxz_count].mb = mb;
		// apply to z(j1,j2,j,ma,mb) to unique element of y(j)

		const int jju = idxu_block[j] + (j+1)*mb + ma;
		@@ -336,7 +338,6 @@ void SNA::compute_ui(int jnum, int ielem)
		// utot(j,ma,mb) += u(r0;j,ma,mb) for all j,ma,mb

		zero_uarraytot(ielem);
		addself_uarraytot(wself, ielem);

		for(int j = 0; j < jnum; j++) {
		x = rij[j][0];
		@@ -350,7 +351,10 @@ void SNA::compute_ui(int jnum, int ielem)
		z0 = r / tan(theta0);

		compute_uarray(x, y, z, z0, r, j);
		if (alloy_flag)
		add_uarraytot(r, wj[j], rcutij[j], j, element[j]);
		else
		add_uarraytot(r, wj[j], rcutij[j], j, 0);
		}

		}
		@@ -438,8 +442,6 @@ void SNA::compute_yi(const double* beta)
		int jju;
		double betaj;
		int itriple;
		int jelem;
		double temp;

		for(int ielem1 = 0; ielem1 < nelements; ielem1++)
		for(int j = 0; j <= twojmax; j++) {
		@@ -464,8 +466,6 @@ void SNA::compute_yi(const double* beta)
		const int mb1min = idxz[jjz].mb1min;
		const int mb2max = idxz[jjz].mb2max;
		const int nb = idxz[jjz].nb;
		const int ma = idxz[jjz].ma;
		const int mb = idxz[jjz].mb;

		const double *cgblock = cglist + idxcg_block[j1][j2][j];

		@@ -518,65 +518,29 @@ void SNA::compute_yi(const double* beta)
		jju = idxz[jjz].jju;
		for(int elem3 = 0; elem3 < nelements; elem3++) {
		// pick out right beta value
		if (alloy_flag) {
		if (j >= j1) {
		const int jjb = idxb_block[j1][j2][j];
		itriple = ((elem3 * nelements + elem2) * nelements + elem1) * idxb_max + jjb;
		if (j1 ==j && j2 == j && elem1 == elem2 && elem1 == elem3) betaj = 3 * beta[itriple];
		else if (j1 == j && j2 == j && elem2 == elem3 && elem1!=elem3)
		betaj =
		2 * (beta[itriple] + beta[((elem1 * nelements + elem2) * nelements + elem3) * idxb_max + jjb]);
		else if (j1 == j && j2 == j && elem1 == elem2 && elem1 != elem3)
		betaj = beta[itriple] + beta[((elem2 * nelements + elem1) * nelements + elem3) * idxb_max + jjb] +
		beta[((elem1 * nelements + elem3) * nelements + elem2) * idxb_max + jjb];
		else if (j1 ==j && (elem1 == elem3 \|\| elem2 == elem3)) // this line covers quite a few cases
		betaj = 2 * beta[itriple];
		else if (j1 == j && j2 != j && elem2 == elem1 && elem1 != elem3)
		betaj = beta[itriple] + beta[((elem1 * nelements + elem2) * nelements + elem3) * idxb_max + jjb];
		else
		betaj = beta[((elem1 * nelements + elem2) * nelements + elem3) * idxb_max + jjb];
		itriple = ((elem1 * nelements + elem2) * nelements + elem3) * idxb_max + jjb;
		if (j1 == j) {
		if (j2 == j) betaj = 3*beta[itriple];
		else betaj = 2*beta[itriple];
		} else betaj = beta[itriple];
		} else if (j >= j2) {
		const int jjb = idxb_block[j][j2][j1];
		itriple = ((elem3 * nelements + elem2) * nelements + elem1) * idxb_max + jjb;
		if (j2 == j) {
		if (elem3 == elem2)
		betaj = 2 * beta[itriple];
		else if (elem1 == elem2)
		betaj = beta[itriple] + beta[((elem1 * nelements + elem3) * nelements + elem2) * idxb_max + jjb];
		else if (elem1 == elem3)
		betaj = beta[itriple] + beta[((elem2 * nelements + elem1) * nelements + elem3) * idxb_max + jjb];
		} else
		betaj = beta[itriple];
		if (j2 == j) betaj = 2*beta[itriple];
		else betaj = beta[itriple];
		} else {
		const int jjb = idxb_block[j2][j][j1];
		itriple = ((elem2 * nelements + elem3) * nelements + elem1) * idxb_max + jjb;
		betaj = beta[itriple];
		}
		} else {
		if (j >= j1) {
		const int jjb = idxb_block[j1][j2][j];
		if (j1 == j) {
		if (j2 == j) betaj = 3*beta[jjb];
		else betaj = 2*beta[jjb];
		} else betaj = beta[jjb];
		} else if (j >= j2) {
		const int jjb = idxb_block[j][j2][j1];
		if (j2 == j) betaj = 2*beta[jjb];
		else betaj = beta[jjb];
		} else {
		const int jjb = idxb_block[j2][j][j1];
		betaj = beta[jjb];
		}
		}

		if (!bnorm_flag && j1 > j)
		betaj *= (j1 + 1) / (j + 1.0);

		ylist_r[elem3 * idxu_max + jju] += betaj * ztmp_r;
		ylist_i[elem3 * idxu_max + jju] += betaj * ztmp_i;
		//if (elem3==0 && j ==4 && ma==2 && mb==0)
		// fprintf(screen, "%i %i %i %i %i %i %f %f %f\n", elem1, elem2, elem3, j, j1, j2, betaj, ztmp_r, ylist_r[elem3 * idxu_max + jju]);

		}
		} // end loop over jjz
		}
		@@ -1023,20 +987,6 @@ void SNA::zero_uarraytot(int ielem)
		}
		}

		/* ---------------------------------------------------------------------- */

		void SNA::addself_uarraytot(double wself_in, int ielem)
		{
		// for (int j = 0; j <= twojmax; j++) {
		// int jju = idxu_block[j];
		// for (int ma = 0; ma <= j; ma++) {
		// ulisttot_r[ielem*idxu_max+jju] = wself_in;
		// ulisttot_i[ielem*idxu_max+jju] = 0.0;
		// jju += j+2;
		// }
		// }
		}

		/* ----------------------------------------------------------------------
		add Wigner U-functions for one neighbor to the total
		------------------------------------------------------------------------- */

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