Merge pull request #330 from akohlmey/collected-small-bugfixes

"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

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

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

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:

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

   suffix

   tad

   temper

   temper_grem

   thermo

   thermo_modify

   thermo_style

   compute_erotate_sphere_atom

   compute_event_displace

   compute_fep

   compute_global_atom

   compute_group_group

   compute_gyration

   compute_gyration_chunk

[Description:]

This fix implements the molecular dynamics version of the generalized

replica exchange method (gREM) originally developed by "(Kim)"_#Kim,

replica exchange method (gREM) originally developed by "(Kim)"_#Kim2010,

which uses non-Boltzmann ensembles to sample over first order phase

transitions. The is done by defining replicas with an enthalpy

dependent effective temperature

:line

:link(Kim)

:link(Kim2010)

[(Kim)] Kim, Keyes, Straub, J Chem. Phys, 132, 224107 (2010).

:link(Malolepsza)