neighbor list bug fixes, new compute coord/atom option (9b012758) · Commits · 郑智淋 / lammps

doc/src/JPG/tutorial_merged.png

−31.7 KiB (25.3 KiB)

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doc/src/JPG/tutorial_reverse_pull_request7.png

0 → 100644

+25.4 KiB

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doc/src/Section_packages.txt

+4 −3

Original line number	Diff line number	Diff line
		@@ -1153,7 +1153,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
		"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
		"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
		"USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
		"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc, dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
		"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc / dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
		"USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
		"USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
		"USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
		@@ -1610,6 +1610,7 @@ and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots
		in this format. See src/USER-NC-DUMP/README for more details.

		NetCDF files can be directly visualized with the following tools:

		Ovito (http://www.ovito.org/). Ovito supports the AMBER convention
		and all of the above extensions. :ulb,l
		VMD (http://www.ks.uiuc.edu/Research/vmd/) :l

doc/src/Section_start.txt

+7 −7

Original line number	Diff line number	Diff line
		@@ -1727,7 +1727,7 @@ thermodynamic state and a total run time for the simulation. It then
		appends statistics about the CPU time and storage requirements for the
		simulation. An example set of statistics is shown here:

		Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
		Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms :pre

		Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s
		97.0% CPU use with 4 MPI tasks x no OpenMP threads :pre
		@@ -1757,14 +1757,14 @@ Ave special neighs/atom = 2.34032
		Neighbor list builds = 26
		Dangerous builds = 0 :pre

		The first section provides a global loop timing summary. The loop time
		The first section provides a global loop timing summary. The {loop time}
		is the total wall time for the section. The {Performance} line is
		provided for convenience to help predicting the number of loop
		continuations required and for comparing performance with other
		similar MD codes. The CPU use line provides the CPU utilzation per
		continuations required and for comparing performance with other,
		similar MD codes. The {CPU use} line provides the CPU utilzation per
		MPI task; it should be close to 100% times the number of OpenMP
		threads (or 1). Lower numbers correspond to delays due to file I/O or
		insufficient thread utilization.
		threads (or 1 of no OpenMP). Lower numbers correspond to delays due
		to file I/O or insufficient thread utilization.

		The MPI task section gives the breakdown of the CPU run time (in
		seconds) into major categories:
		@@ -1791,7 +1791,7 @@ is present that also prints the CPU utilization in percent. In
		addition, when using {timer full} and the "package omp"_package.html
		command are active, a similar timing summary of time spent in threaded
		regions to monitor thread utilization and load balance is provided. A
		new entry is the {Reduce} section, which lists the time spend in
		new entry is the {Reduce} section, which lists the time spent in
		reducing the per-thread data elements to the storage for non-threaded
		computation. These thread timings are taking from the first MPI rank
		only and and thus, as the breakdown for MPI tasks can change from MPI

doc/src/accelerate_kokkos.txt

+2 −2

Original line number	Diff line number	Diff line
		@@ -110,14 +110,14 @@ mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis :p
		[Required hardware/software:]

		Kokkos support within LAMMPS must be built with a C++11 compatible
		compiler. If using gcc, version 4.8.1 or later is required.
		compiler. If using gcc, version 4.7.2 or later is required.

		To build with Kokkos support for CPUs, your compiler must support the
		OpenMP interface. You should have one or more multi-core CPUs so that
		multiple threads can be launched by each MPI task running on a CPU.

		To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
		version 6.5 or later must be installed on your system. See the
		version 7.5 or later must be installed on your system. See the
		discussion for the "GPU"_accelerate_gpu.html package for details of
		how to check and do this.

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