make MIN_HBONDS define for reax/c configurable via an input option (1418ec4a) · Commits · 郑智淋 / lammps

doc/src/pair_reaxc.rst

+8 −7

Changes for doc/src/pair_reaxc.rst: 8 added lines, 7 removed lines.
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		@@ -21,12 +21,13 @@ Syntax

		.. parsed-literal::

		keyword = checkqeq or lgvdw or safezone or mincap
		keyword = checkqeq or lgvdw or safezone or mincap or minhbonds
		checkqeq value = yes or no = whether or not to require qeq/reax fix
		enobonds value = yes or no = whether or not to tally energy of atoms with no bonds
		lgvdw value = yes or no = whether or not to use a low gradient vdW correction
		safezone = factor used for array allocation
		mincap = minimum size for array allocation
		minhbonds = minimum size use for storing hydrogen bonds

		Examples
		""""""""
		@@ -146,11 +147,11 @@ zero. The latter behavior is usual not desired, as it causes
		discontinuities in the potential energy when the bonding of an atom
		drops to zero.

		Optional keywords safezone and mincap are used for allocating
		reax/c arrays. Increasing these values can avoid memory problems,
		such as segmentation faults and bondchk failed errors, that could
		occur under certain conditions. These keywords are not used by the
		Kokkos version, which instead uses a more robust memory allocation
		Optional keywords safezone\ , mincap\ , and minhbonds are used
		for allocating reax/c arrays. Increasing these values can avoid memory
		problems, such as segmentation faults and bondchk failed errors, that
		could occur under certain conditions. These keywords are not used by
		the Kokkos version, which instead uses a more robust memory allocation
		scheme that checks if the sizes of the arrays have been exceeded and
		automatically allocates more memory.

		@@ -352,7 +353,7 @@ Default
		"""""""

		The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no,
		safezone = 1.2, mincap = 50.
		safezone = 1.2, mincap = 50, minhbonds = 25.

		----------

doc/utils/sphinx-config/false_positives.txt

+1 −0

Changes for doc/utils/sphinx-config/false_positives.txt: 1 added line, 0 removed lines.
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		@@ -1786,6 +1786,7 @@ Militzer
		Minary
		mincap
		Mindlin
		minhbonds
		mingw
		minima
		minimizations

src/USER-OMP/pair_reaxc_omp.cpp

+1 −1

Changes for src/USER-OMP/pair_reaxc_omp.cpp: 1 added line, 1 removed line.
Original line number	Diff line number	Diff line
		@@ -508,7 +508,7 @@ int PairReaxCOMP::estimate_reax_lists()
		num_nbrs += numneigh[i];
		}

		int new_estimate = MAX (num_nbrs, mincap*MIN_NBRS);
		int new_estimate = MAX(num_nbrs, mincap*REAX_MIN_NBRS);

		return new_estimate;
		}

src/USER-OMP/reaxc_forces_omp.cpp

+1 −1

Changes for src/USER-OMP/reaxc_forces_omp.cpp: 1 added line, 1 removed line.
Original line number	Diff line number	Diff line
		@@ -310,7 +310,7 @@ void Validate_ListsOMP(reax_system system, storage /workspace/, reax_list *
		Hindex = system->my_atoms[i].Hindex;
		if (Hindex > -1) {
		system->my_atoms[i].num_hbonds =
		(int)(MAX( Num_Entries(Hindex, hbonds)*saferzone, MIN_HBONDS ));
		(int)(MAX(Num_Entries(Hindex,hbonds)*saferzone,system->minhbonds));

		if (Hindex < numH-1)
		comp = Start_Index(Hindex+1, hbonds);

src/USER-OMP/reaxc_init_md_omp.cpp

+1 −1

Changes for src/USER-OMP/reaxc_init_md_omp.cpp: 1 added line, 1 removed line.
Original line number	Diff line number	Diff line
		@@ -68,7 +68,7 @@ int Init_ListsOMP(reax_system system, control_params control,
		system->my_atoms[i].num_hbonds = hb_top[i];
		total_hbonds += hb_top[i];
		}
		total_hbonds = (int)(MAX( total_hbondssaferzone, mincapMIN_HBONDS ));
		total_hbonds = (int)(MAX(total_hbondssaferzone,mincapsystem->minhbonds));

		if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
		*lists+HBONDS ) ) {

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