Merge pull request #39 from lammps/master (e82999ec) · Commits · 郑智淋 / lammps

doc/src/rerun.txt

+8 −0

Original line number	Diff line number	Diff line
		@@ -107,6 +107,14 @@ However if you specify a series of dump files in an incorrect order
		(with respect to the timesteps they contain), you may skip large
		numbers of snapshots

		Note that the dump files specified as part of the {dump} keyword can
		be parallel files, i.e. written as multiple files either per processor
		and/or per snapshot. If that is the case they will also be read in
		parallel which can make the rerun command operate dramatically faster
		for large systems. See the doc page for the "read_dump"_read_dump and
		"dump"_dump.html commands which describe how to read and write
		parallel dump files.

		The {first}, {last}, {every}, {skip} keywords determine which
		snapshots are read from the dump file(s). Snapshots are skipped until
		they have a timestamp >= {Nfirst}. When a snapshot with a timestamp >

+8 −8

Original line number	Diff line number	Diff line
		@@ -1434,14 +1434,6 @@ void PairReaxCKokkos<DeviceType>::allocate_array()
		d_CdDelta = typename AT::t_ffloat_1d("reax/c/kk:CdDelta",nmax);
		d_sum_ovun = typename AT::t_ffloat_2d_dl("reax/c/kk:sum_ovun",nmax,3);

		// FixReaxCSpecies
		if (fixspecies_flag) {
		memoryKK->destroy_kokkos(k_tmpid,tmpid);
		memoryKK->destroy_kokkos(k_tmpbo,tmpbo);
		memoryKK->create_kokkos(k_tmpid,tmpid,nmax,MAXSPECBOND,"pair:tmpid");
		memoryKK->create_kokkos(k_tmpbo,tmpbo,nmax,MAXSPECBOND,"pair:tmpbo");
		}

		// FixReaxCBonds
		d_abo = typename AT::t_ffloat_2d("reax/c/kk:abo",nmax,maxbo);
		d_neighid = typename AT::t_tagint_2d("reax/c/kk:neighid",nmax,maxbo);
		@@ -4237,6 +4229,14 @@ void PairReaxCKokkos<DeviceType>::pack_bond_buffer_item(int i, int &j, const boo
		template<class DeviceType>
		void PairReaxCKokkos<DeviceType>::FindBondSpecies()
		{

		if (nmax > k_tmpid.extent(0)) {
		memoryKK->destroy_kokkos(k_tmpid,tmpid);
		memoryKK->destroy_kokkos(k_tmpbo,tmpbo);
		memoryKK->create_kokkos(k_tmpid,tmpid,nmax,MAXSPECBOND,"pair:tmpid");
		memoryKK->create_kokkos(k_tmpbo,tmpbo,nmax,MAXSPECBOND,"pair:tmpbo");
		}

		copymode = 1;
		Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxFindBondSpeciesZero>(0,nmax),*this);

+3 −0

+2 −0

Original line number	Diff line number	Diff line
		@@ -290,6 +290,8 @@ FixBondReact::FixBondReact(LAMMPS lmp, int narg, char *arg) :
		open(files[i]);
		onemol = atom->molecules[unreacted_mol[i]];
		twomol = atom->molecules[reacted_mol[i]];
		onemol->check_attributes(0);
		twomol->check_attributes(0);
		if (onemol->natoms != twomol->natoms)
		error->all(FLERR,"Post-reacted template must contain the same "
		"number of atoms as the pre-reacted template");

+436 −436