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patch_5Oct
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patch_6Oct
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BIN
doc/src/JPG/gran_funnel.png
Normal file
BIN
doc/src/JPG/gran_funnel.png
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Binary file not shown.
|
After Width: | Height: | Size: 117 KiB |
BIN
doc/src/JPG/gran_funnel_small.jpg
Normal file
BIN
doc/src/JPG/gran_funnel_small.jpg
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Binary file not shown.
|
After Width: | Height: | Size: 2.2 KiB |
BIN
doc/src/JPG/gran_mixer.png
Normal file
BIN
doc/src/JPG/gran_mixer.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 224 KiB |
BIN
doc/src/JPG/gran_mixer_small.jpg
Normal file
BIN
doc/src/JPG/gran_mixer_small.jpg
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Binary file not shown.
|
After Width: | Height: | Size: 3.0 KiB |
@ -1,7 +1,7 @@
|
||||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="5 Oct 2016 version">
|
||||
<META NAME="docnumber" CONTENT="6 Oct 2016 version">
|
||||
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
|
||||
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
|
||||
</HEAD>
|
||||
@ -21,7 +21,7 @@
|
||||
<H1></H1>
|
||||
|
||||
LAMMPS Documentation :c,h3
|
||||
5 Oct 2016 version :c,h4
|
||||
6 Oct 2016 version :c,h4
|
||||
|
||||
Version info: :h4
|
||||
|
||||
|
||||
@ -599,6 +599,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
|
||||
"viscous"_fix_viscous.html,
|
||||
"wall/colloid"_fix_wall.html,
|
||||
"wall/gran"_fix_wall_gran.html,
|
||||
"wall/gran/region"_fix_wall_gran_region.html,
|
||||
"wall/harmonic"_fix_wall.html,
|
||||
"wall/lj1043"_fix_wall.html,
|
||||
"wall/lj126"_fix_wall.html,
|
||||
|
||||
@ -37,7 +37,7 @@ pitfalls or alternatives.
|
||||
|
||||
Please see some of the closed issues for examples of how to
|
||||
suggest code enhancements, submit proposed changes, or report
|
||||
elated issues and how they are resoved.
|
||||
possible bugs and how they are resoved.
|
||||
|
||||
As an alternative to using GitHub, you may e-mail the
|
||||
"core developers"_http://lammps.sandia.gov/authors.html or send
|
||||
|
||||
@ -135,7 +135,7 @@ and angular momentum of a particle. If the {vel} option is set to
|
||||
{yes}, then ghost atoms store these quantities; if {no} then they do
|
||||
not. The {yes} setting is needed by some pair styles which require
|
||||
the velocity state of both the I and J particles to compute a pairwise
|
||||
I,J interaction.
|
||||
I,J interaction, as well as by some compute and fix commands.
|
||||
|
||||
Note that if the "fix deform"_fix_deform.html command is being used
|
||||
with its "remap v" option enabled, then the velocities for ghost atoms
|
||||
|
||||
@ -52,7 +52,7 @@ The KSpace contribution is calculated using the method in
|
||||
"(Heyes)"_#Heyes for the Ewald method and a related method for PPPM,
|
||||
as specified by the "kspace_style pppm"_kspace_style.html command.
|
||||
For PPPM, the calcluation requires 1 extra FFT each timestep that
|
||||
per-atom energy is calculated. Thie "document"_PDF/kspace.pdf
|
||||
per-atom energy is calculated. This "document"_PDF/kspace.pdf
|
||||
describes how the long-range per-atom energy calculation is performed.
|
||||
|
||||
Various fixes can contribute to the per-atom potential energy of the
|
||||
|
||||
@ -129,8 +129,6 @@ The attributes that start with "a", "d", "i", refer to similar values
|
||||
for "angles"_angle_style.html, "dihedrals"_dihedral_style.html, and
|
||||
"impropers"_improper_style.html.
|
||||
|
||||
The optional {cutoff} keyword
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a local vector or local array depending on the
|
||||
|
||||
0
doc/src/compute_temp_asphere.txt
Executable file → Normal file
0
doc/src/compute_temp_asphere.txt
Executable file → Normal file
0
doc/src/compute_temp_body.txt
Executable file → Normal file
0
doc/src/compute_temp_body.txt
Executable file → Normal file
0
doc/src/compute_temp_sphere.txt
Executable file → Normal file
0
doc/src/compute_temp_sphere.txt
Executable file → Normal file
0
doc/src/fix_bond_break.txt
Executable file → Normal file
0
doc/src/fix_bond_break.txt
Executable file → Normal file
0
doc/src/fix_bond_create.txt
Executable file → Normal file
0
doc/src/fix_bond_create.txt
Executable file → Normal file
0
doc/src/fix_bond_swap.txt
Executable file → Normal file
0
doc/src/fix_bond_swap.txt
Executable file → Normal file
0
doc/src/fix_lb_fluid.txt
Executable file → Normal file
0
doc/src/fix_lb_fluid.txt
Executable file → Normal file
0
doc/src/fix_lb_momentum.txt
Executable file → Normal file
0
doc/src/fix_lb_momentum.txt
Executable file → Normal file
0
doc/src/fix_lb_pc.txt
Executable file → Normal file
0
doc/src/fix_lb_pc.txt
Executable file → Normal file
0
doc/src/fix_lb_rigid_pc_sphere.txt
Executable file → Normal file
0
doc/src/fix_lb_rigid_pc_sphere.txt
Executable file → Normal file
0
doc/src/fix_lb_viscous.txt
Executable file → Normal file
0
doc/src/fix_lb_viscous.txt
Executable file → Normal file
0
doc/src/fix_nph_asphere.txt
Executable file → Normal file
0
doc/src/fix_nph_asphere.txt
Executable file → Normal file
0
doc/src/fix_nph_body.txt
Executable file → Normal file
0
doc/src/fix_nph_body.txt
Executable file → Normal file
0
doc/src/fix_nph_sphere.txt
Executable file → Normal file
0
doc/src/fix_nph_sphere.txt
Executable file → Normal file
0
doc/src/fix_npt_asphere.txt
Executable file → Normal file
0
doc/src/fix_npt_asphere.txt
Executable file → Normal file
0
doc/src/fix_npt_body.txt
Executable file → Normal file
0
doc/src/fix_npt_body.txt
Executable file → Normal file
0
doc/src/fix_npt_sphere.txt
Executable file → Normal file
0
doc/src/fix_npt_sphere.txt
Executable file → Normal file
0
doc/src/fix_nve_asphere.txt
Executable file → Normal file
0
doc/src/fix_nve_asphere.txt
Executable file → Normal file
0
doc/src/fix_nve_asphere_noforce.txt
Executable file → Normal file
0
doc/src/fix_nve_asphere_noforce.txt
Executable file → Normal file
0
doc/src/fix_nve_body.txt
Executable file → Normal file
0
doc/src/fix_nve_body.txt
Executable file → Normal file
0
doc/src/fix_nve_line.txt
Executable file → Normal file
0
doc/src/fix_nve_line.txt
Executable file → Normal file
0
doc/src/fix_nve_sphere.txt
Executable file → Normal file
0
doc/src/fix_nve_sphere.txt
Executable file → Normal file
0
doc/src/fix_nve_tri.txt
Executable file → Normal file
0
doc/src/fix_nve_tri.txt
Executable file → Normal file
0
doc/src/fix_nvt_asphere.txt
Executable file → Normal file
0
doc/src/fix_nvt_asphere.txt
Executable file → Normal file
0
doc/src/fix_nvt_body.txt
Executable file → Normal file
0
doc/src/fix_nvt_body.txt
Executable file → Normal file
0
doc/src/fix_nvt_sphere.txt
Executable file → Normal file
0
doc/src/fix_nvt_sphere.txt
Executable file → Normal file
@ -75,7 +75,7 @@ but no more than max_steps will be taken. If max_steps is reached, an error warn
|
||||
is printed and the simulation is stopped.
|
||||
|
||||
After each ODE step, the solution error {e} is tested and weighted using the absTol
|
||||
and relTol values. The error vector is weighted as {e} / (relTol * | {u} | + absTol)
|
||||
and relTol values. The error vector is weighted as {e} / (relTol * |{u}| + absTol)
|
||||
where {u} is the solution vector. If the norm of the error is <= 1, the solution is
|
||||
accepted, {h} is increased by a proportional amount, and the next ODE step is begun.
|
||||
Otherwise, {h} is shrunk and the ODE step is repeated.
|
||||
|
||||
0
doc/src/fix_ti_spring.txt
Executable file → Normal file
0
doc/src/fix_ti_spring.txt
Executable file → Normal file
@ -163,6 +163,8 @@ Any dimension (xyz) that has a granular wall must be non-periodic.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix move"_fix_move.html, "pair_style granular"_pair_gran.html
|
||||
"fix move"_fix_move.html,
|
||||
"fix wall/gran/region"_fix_wall_gran_region.html,
|
||||
"pair_style granular"_pair_gran.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
199
doc/src/fix_wall_gran_region.txt
Normal file
199
doc/src/fix_wall_gran_region.txt
Normal file
@ -0,0 +1,199 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix wall/gran/region command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID wall/gran/region fstyle Kn Kt gamma_n gamma_t xmu dampflag wallstyle regionID :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
wall/region = style name of this fix command :l
|
||||
fstyle = style of force interactions between particles and wall :l
|
||||
possible choices: hooke, hooke/history, hertz/history :pre
|
||||
Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) :l
|
||||
Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) :l
|
||||
gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l
|
||||
gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l
|
||||
xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l
|
||||
dampflag = 0 or 1 if tangential damping force is excluded or included :l
|
||||
wallstyle = region (see "fix wall/gran"_fix_wall_gran.html for options for other kinds of walls) :l
|
||||
region-ID = region whose boundary will act as wall :l,ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Treat the surface of the geometric region defined by the {region-ID}
|
||||
as a bounding frictional wall which interacts with nearby finite-size
|
||||
granular particles when they are close enough to touch the wall. See
|
||||
the "fix wall/region"_fix_wall_region.html and "fix
|
||||
wall/gran"_fix_wall_gran.html commands for related kinds of walls for
|
||||
non-granular particles and simpler wall geometries, respectively.
|
||||
|
||||
Here are snapshots of example models using this command.
|
||||
Corresponding input scripts can be found in examples/granregion.
|
||||
Click on the images to see a bigger picture. Movies of these
|
||||
simulations are "here on the Movies
|
||||
page"_http://lammps.sandia.gov/movies.html#granregion.html of the
|
||||
LAMMPS web site.
|
||||
|
||||
:image(JPG/gran_funnel_small.jpg,JPG/gran_funnel.png)
|
||||
:image(JPG/gran_mixer_small.jpg,JPG/gran_mixer.png)
|
||||
|
||||
:line
|
||||
|
||||
The distance between a particle and the region boundary is the
|
||||
distance to the nearest point on the region surface. The force the
|
||||
wall exerts on the particle is along the direction between that point
|
||||
and the particle center, which is the direction normal to the surface
|
||||
at that point. Note that if the region surface is comprised of
|
||||
multiple "faces", then each face can exert a force on the particle if
|
||||
it is close enough. E.g. for "region_style block"_region.html, a
|
||||
particle in the interior, near a corner of the block, could feel wall
|
||||
forces from 1, 2, or 3 faces of the block.
|
||||
|
||||
Regions are defined using the "region"_region.html command. Note that
|
||||
the region volume can be interior or exterior to the bounding surface,
|
||||
which will determine in which direction the surface interacts with
|
||||
particles, i.e. the direction of the surface normal. The exception to
|
||||
this is if one or more {open} options are specified for the region
|
||||
command, in which case particles interact with both the interior and
|
||||
exterior surfaces of regions.
|
||||
|
||||
Regions can either be primitive shapes (block, sphere, cylinder, etc)
|
||||
or combinations of primitive shapes specified via the {union} or
|
||||
{intersect} region styles. These latter styles can be used to
|
||||
construct particle containers with complex shapes. Regions can also
|
||||
move dynamically via the "region"_region.html command keywords (move)
|
||||
and {rotate}, or change their shape by use of variables as inputs to
|
||||
the "region"_region.html command. If such a region is used with this
|
||||
fix, then the region surface will move in time in the corresponding
|
||||
manner.
|
||||
|
||||
NOTE: As discussed on the "region"_region.html command doc page,
|
||||
regions in LAMMPS do not get wrapped across periodic boundaries. It
|
||||
is up to you to ensure that the region location with respect to
|
||||
periodic or non-periodic boundaries is specified appropriately via the
|
||||
"region"_region.html and "boundary"_boundary.html commands when using
|
||||
a region as a wall that bounds particle motion.
|
||||
|
||||
NOTE: For primitive regions with sharp corners and/or edges (e.g. a
|
||||
block or cylinder), wall/particle forces are computed accurately for
|
||||
both interior and exterior regions. For {union} and {intersect}
|
||||
regions, additional sharp corners and edges may be present due to the
|
||||
intersection of the surfaces of 2 or more primitive volumes. These
|
||||
corners and edges can be of two types: concave or convex. Concave
|
||||
points/edges are like the corners of a cube as seen by particles in
|
||||
the interior of a cube. Wall/particle forces around these features
|
||||
are computed correctly. Convex points/edges are like the corners of a
|
||||
cube as seen by particles exterior to the cube, i.e. the points jut
|
||||
into the volume where particles are present. LAMMPS does NOT compute
|
||||
the location of these convex points directly, and hence wall/particle
|
||||
forces in the cutoff volume around these points suffer from
|
||||
inaccuracies. The basic problem is that the outward normal of the
|
||||
surface is not continuous at these points. This can cause particles
|
||||
to feel no force (they don't "see" the wall) when in one location,
|
||||
then move a distance epsilon, and suddenly feel a large force because
|
||||
they now "see" the wall. In a worst-case scenario, this can blow
|
||||
particles out of the simulation box. Thus, as a general rule you
|
||||
should not use the fix wall/gran/region command with {union} or
|
||||
{interesect} regions that have convex points or edges resulting from
|
||||
the union/intersection (convex points/edges in the union/intersection
|
||||
due to a single sub-region are still OK).
|
||||
|
||||
NOTE: Similarly, you should not define {union} or {intersert} regions
|
||||
for use with this command that share an overlapping common face that
|
||||
is part of the overall outer boundary (interior boundary is OK), even
|
||||
if the face is smooth. E.g. two regions of style block in a {union}
|
||||
region, where the two blocks overlap on one or more of their faces.
|
||||
This is because LAMMPS discards points that are part of multiple
|
||||
sub-regions when calculating wall/particle interactions, to avoid
|
||||
double-counting the interaction. Having two coincident faces could
|
||||
cause the face to become invisible to the particles. The solution is
|
||||
to make the two faces differ by epsilon in their position.
|
||||
|
||||
The nature of the wall/particle interactions are determined by the
|
||||
{fstyle} setting. It can be any of the styles defined by the
|
||||
"pair_style granular"_pair_gran.html commands. Currently this is
|
||||
{hooke}, {hooke/history}, or {hertz/history}. The equation for the
|
||||
force between the wall and particles touching it is the same as the
|
||||
corresponding equation on the "pair_style granular"_pair_gran.html doc
|
||||
page, but the effective radius is calculated using the radius of the
|
||||
particle and the radius of curvature of the wall at the contact point.
|
||||
|
||||
Specifically, delta = radius - r = overlap of particle with wall,
|
||||
m_eff = mass of particle, and RiRj/Ri+Rj is the effective radius, with
|
||||
Rj replaced by the radius of curvature of the wall at the contact
|
||||
point. The radius of curvature can be negative for a concave wall
|
||||
section, e.g. the interior of cylinder. For a flat wall, delta =
|
||||
radius - r = overlap of particle with wall, m_eff = mass of particle,
|
||||
and the effective radius of contact is just the radius of the
|
||||
particle.
|
||||
|
||||
The parameters {Kn}, {Kt}, {gamma_n}, {gamma_t}, {xmu} and {dampflag}
|
||||
have the same meaning and units as those specified with the
|
||||
"pair_style granular"_pair_gran.html commands. This means a NULL can
|
||||
be used for either {Kt} or {gamma_t} as described on that page. If a
|
||||
NULL is used for {Kt}, then a default value is used where {Kt} = 2/7
|
||||
{Kn}. If a NULL is used for {gamma_t}, then a default value is used
|
||||
where {gamma_t} = 1/2 {gamma_n}.
|
||||
|
||||
Note that you can choose a different force styles and/or different
|
||||
values for the 6 wall/particle coefficients than for particle/particle
|
||||
interactions. E.g. if you wish to model the wall as a different
|
||||
material.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
Similiar to "fix wall/gran"_fix_wall_gran.html command, this fix
|
||||
writes the shear friction state of atoms interacting with the wall to
|
||||
"binary restart files"_restart.html, so that a simulation can continue
|
||||
correctly if granular potentials with shear "history" effects are
|
||||
being used. This fix also includes info about a moving region in the
|
||||
restart file. See the "read_restart"_read_restart.html command for
|
||||
info on how to re-specify a fix in an input script that reads a
|
||||
restart file, so that the operation of the fix continues in an
|
||||
uninterrupted fashion.
|
||||
|
||||
Note that info about region definitions is NOT included in restart
|
||||
files. So you must re-define your region and if it is a moving
|
||||
region, define its motion attributes in a way that is consistent with
|
||||
the simulation that wrote the restart file. In particular, if you
|
||||
want to change its motion attributes (e.g. its velocity), then you
|
||||
should insure the postition/orientation of the region at the initial
|
||||
restart timestep is the same as it was on the timestep the restart
|
||||
file was written. If this is not possible, then you may need to
|
||||
ignore info in the restart file by defining a new fix wall/gran/region
|
||||
command in your restart script (e.g. with a different fix ID).
|
||||
|
||||
None of the "fix_modify"_fix_modify.html options are relevant to this
|
||||
fix. No global or per-atom quantities are stored by this fix for
|
||||
access by various "output commands"_Section_howto.html#howto_15. No
|
||||
parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command. This fix is not invoked during "energy
|
||||
minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the GRANULAR package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix_move"_fix_move.html,
|
||||
"fix wall/gran"_fix_wall_gran.html,
|
||||
"fix wall/region"_fix_wall_region.html,
|
||||
"pair_style granular"_pair_gran.html,
|
||||
"region"_region.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
0
doc/src/min_style.txt
Executable file → Normal file
0
doc/src/min_style.txt
Executable file → Normal file
0
doc/src/pair_dipole.txt
Executable file → Normal file
0
doc/src/pair_dipole.txt
Executable file → Normal file
0
doc/src/pair_gayberne.txt
Executable file → Normal file
0
doc/src/pair_gayberne.txt
Executable file → Normal file
@ -41,7 +41,9 @@ supplemental information of the following paper: "(Chenoweth et al.,
|
||||
2008)"_#Chenoweth_2008. The version integrated into LAMMPS matches
|
||||
the most up-to-date version of ReaxFF as of summer 2010. For more
|
||||
technical details about the pair reax/c implementation of ReaxFF, see
|
||||
the "(Aktulga)"_#Aktulga paper.
|
||||
the "(Aktulga)"_#Aktulga paper. The {reax/c} style was initially
|
||||
implemented as a stand-alone C code and is now integrated into LAMMPS
|
||||
as a package.
|
||||
|
||||
The {reax/c/kk} style is a Kokkos version of the ReaxFF potential that is
|
||||
derived from the {reax/c} style. The Kokkos version can run on GPUs and
|
||||
@ -167,7 +169,7 @@ variable eb equal c_reax\[1\]
|
||||
variable ea equal c_reax\[2\]
|
||||
\[...\]
|
||||
variable eqeq equal c_reax\[14\]
|
||||
thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre
|
||||
thermo_style custom step temp epair v_eb v_ea \[...\] v_eqeq :pre
|
||||
|
||||
Only a single pair_coeff command is used with the {reax/c} style which
|
||||
specifies a ReaxFF potential file with parameters for all needed
|
||||
@ -237,7 +239,7 @@ nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms)
|
||||
regarding the bonded interactions. (default value = 5.0)
|
||||
|
||||
hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen
|
||||
bond interactions.(default value = 7.5. Value of 0.0 turns off
|
||||
bond interactions.(default value = 7.5. A value of 0.0 turns off
|
||||
hydrogen bonds)
|
||||
|
||||
bond_graph_cutoff: is the threshold used in determining what is a
|
||||
|
||||
0
doc/src/pair_resquared.txt
Executable file → Normal file
0
doc/src/pair_resquared.txt
Executable file → Normal file
0
doc/src/pair_smtbq.txt
Executable file → Normal file
0
doc/src/pair_smtbq.txt
Executable file → Normal file
@ -74,11 +74,14 @@ larger version of your molecule as a pre-processing step and input a
|
||||
new data file to LAMMPS.
|
||||
|
||||
If the current simulation was read in from a restart file (before a
|
||||
run is performed), there can have been no fix information stored in
|
||||
run is performed), there must not be any fix information stored in
|
||||
the file for individual atoms. Similarly, no fixes can be defined at
|
||||
the time the replicate command is used that require vectors of atom
|
||||
information to be stored. This is because the replicate command does
|
||||
not know how to replicate that information for new atoms it creates.
|
||||
To work around this restriction, restart files may be converted into
|
||||
data files and fixes may be undefined via the "unfix"_unfix.html
|
||||
command before and redefined after the replicate command.
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
|
||||
@ -74,6 +74,7 @@ eim: NaCl using the EIM potential
|
||||
ellipse: ellipsoidal particles in spherical solvent, 2d system
|
||||
flow: Couette and Poiseuille flow in a 2d channel
|
||||
friction: frictional contact of spherical asperities between 2d surfaces
|
||||
granregion: use of fix wall/region/gran as boundary on granular particles
|
||||
hugoniostat: Hugoniostat shock dynamics
|
||||
indent: spherical indenter into a 2d solid
|
||||
kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
|
||||
|
||||
@ -18,6 +18,5 @@ thermo 10
|
||||
timestep 0.001
|
||||
|
||||
dump 1 all custom 10 dump.gap id fx fy fz
|
||||
dump_modify 1 format "%d %20.15g %20.15g %20.15g"
|
||||
|
||||
run 40
|
||||
|
||||
@ -18,6 +18,5 @@ thermo 10
|
||||
timestep 0.001
|
||||
|
||||
dump 1 all custom 10 dump.sw id fx fy fz
|
||||
dump_modify 1 format "%d %20.15g %20.15g %20.15g"
|
||||
|
||||
run 1
|
||||
|
||||
@ -1,225 +0,0 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
# 2d circle of particles inside a box with LJ walls
|
||||
|
||||
variable b index 0
|
||||
|
||||
variable x index 50
|
||||
variable y index 20
|
||||
variable d index 20
|
||||
variable v index 5
|
||||
variable w index 2
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style bond
|
||||
boundary f f p
|
||||
|
||||
lattice hex 0.85
|
||||
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
|
||||
region box block 0 $x 0 $y -0.5 0.5
|
||||
region box block 0 50 0 $y -0.5 0.5
|
||||
region box block 0 50 0 20 -0.5 0.5
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 6
|
||||
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 10
|
||||
create_atoms 1 region circle
|
||||
Created 361 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 0.5 87287 loop geom
|
||||
velocity all set $v $w 0 sum yes
|
||||
velocity all set 5 $w 0 sum yes
|
||||
velocity all set 5 2 0 sum yes
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 10.0 1.0 2.5
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 10.0 1.2
|
||||
|
||||
# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
|
||||
|
||||
special_bonds lj/coul 0 1 1
|
||||
0 = max # of 1-2 neighbors
|
||||
1 = max # of special neighbors
|
||||
create_bonds all all 1 1.0 1.5
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Added 1014 bonds, new total = 1014
|
||||
6 = max # of 1-2 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
|
||||
|
||||
comm_style tiled
|
||||
comm_modify cutoff 7.5
|
||||
fix 10 all balance 50 0.9 rcb
|
||||
|
||||
#compute 1 all property/atom proc
|
||||
#variable p atom (c_1%10)+1
|
||||
#dump 2 all custom 50 tmp.dump id v_p x y z
|
||||
|
||||
#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
|
||||
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
||||
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
thermo_style custom step temp epair press f_10[3] f_10
|
||||
thermo 100
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 7.5
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Memory usage per processor = 4.49421 Mbytes
|
||||
Step Temp E_pair Press f_10[3] f_10
|
||||
0 25.701528 -2.2032569 3.1039469 3.2354571 1.0526316
|
||||
100 27.623422 -6.228166 2.6542136 1.2631579 1.0083102
|
||||
200 33.35302 -15.746749 3.2018248 1.2963989 1.0193906
|
||||
300 39.17734 -24.1557 4.9116986 1.2963989 1.0193906
|
||||
400 41.660701 -27.615203 8.6214679 1.3518006 1.0083102
|
||||
500 37.154928 -24.096947 3.2656178 1.3296399 1.0193906
|
||||
600 35.059889 -21.524278 2.3728491 1.3296399 1.0083102
|
||||
700 36.70511 -21.983922 3.299538 1.3296399 1.0083102
|
||||
800 39.54394 -25.667546 4.3058382 1.3961219 1.0083102
|
||||
900 37.868974 -24.379807 5.3176538 1.3518006 1.0083102
|
||||
1000 36.721328 -23.341363 5.8700266 1.3407202 1.0083102
|
||||
1100 35.646239 -23.3255 3.3762843 1.1855956 1.0083102
|
||||
1200 31.452912 -20.792985 5.4901357 1.1966759 1.0083102
|
||||
1300 32.276549 -21.245929 6.4153084 1.2077562 1.0193906
|
||||
1400 29.452751 -20.724401 2.174752 1.1855956 1.0083102
|
||||
1500 28.014757 -18.893532 1.7482766 1.1634349 1.0083102
|
||||
1600 26.222645 -16.78953 0.93944237 1.1966759 1.0304709
|
||||
1700 25.711888 -15.792639 0.20021405 1.0969529 1.0083102
|
||||
1800 24.412639 -13.217606 0.7091708 1.1966759 1.0083102
|
||||
1900 25.644324 -13.020594 1.3661224 1.1412742 1.0083102
|
||||
2000 24.556667 -13.580087 0.80121134 1.0637119 1.0083102
|
||||
2100 25.23657 -13.560862 1.2349706 1.1191136 1.0193906
|
||||
2200 26.456985 -13.804729 1.27046 1.1412742 1.0193906
|
||||
2300 26.416685 -13.212452 1.4096744 1.1412742 1.0083102
|
||||
2400 25.472914 -12.472527 1.5408641 1.1412742 1.0083102
|
||||
2500 25.216305 -12.597474 0.84328282 1.1412742 1.0083102
|
||||
2600 24.107024 -12.455199 1.5587978 1.2409972 1.0193906
|
||||
2700 26.840175 -15.533209 1.2944973 1.1745152 1.0083102
|
||||
2800 26.149759 -14.83948 4.0371126 1.0747922 1.0083102
|
||||
2900 24.651151 -14.934342 2.7634302 1.0747922 1.0193906
|
||||
3000 21.873123 -13.366381 -0.18605935 1.1301939 1.0083102
|
||||
3100 19.974658 -10.620844 -0.16366371 1.0637119 1.0193906
|
||||
3200 20.926558 -10.336663 -0.73116364 1.1080332 1.0083102
|
||||
3300 20.473772 -10.588752 -0.66017168 1.0858726 1.0304709
|
||||
3400 22.476649 -11.87982 1.0141731 1.0747922 1.0083102
|
||||
3500 24.02361 -12.532787 1.4116935 1.1191136 1.0083102
|
||||
3600 22.922792 -12.328391 -0.27783338 1.0969529 1.0083102
|
||||
3700 21.772971 -10.716922 0.95739835 1.1523546 1.0083102
|
||||
3800 21.597174 -10.839031 0.67958603 1.1191136 1.0193906
|
||||
3900 21.883448 -11.258422 -0.40592732 1.0637119 1.0193906
|
||||
4000 22.815486 -10.891868 1.6123322 1.1301939 1.0193906
|
||||
4100 23.276599 -11.400134 0.65653972 1.0415512 1.0193906
|
||||
4200 22.543441 -11.530245 0.074132899 1.1523546 1.0193906
|
||||
4300 22.863379 -10.809451 0.27552824 1.1412742 1.0193906
|
||||
4400 22.475073 -11.125735 1.7708547 1.1191136 1.0193906
|
||||
4500 23.500125 -11.680919 0.91347563 1.0858726 1.0083102
|
||||
4600 21.1812 -11.767353 0.095659263 1.1191136 1.0193906
|
||||
4700 22.950759 -12.108158 0.083009642 1.1966759 1.0083102
|
||||
4800 22.12306 -11.455893 0.47932308 1.1080332 1.0083102
|
||||
4900 23.297573 -11.823246 0.93733479 1.0969529 1.0083102
|
||||
5000 22.98743 -12.014836 0.36186604 1.1080332 1.0083102
|
||||
5100 23.081456 -11.54226 0.73473004 1.0747922 1.0193906
|
||||
5200 20.980311 -11.493036 -0.71555187 1.0637119 1.0193906
|
||||
5300 21.468406 -11.18497 0.54579843 1.0304709 1.0193906
|
||||
5400 22.75839 -10.856825 0.94407228 1.1191136 1.0083102
|
||||
5500 22.705652 -12.112469 0.4753399 1.1412742 1.0083102
|
||||
5600 22.391177 -12.530712 1.0180383 1.1412742 1.0083102
|
||||
5700 21.832834 -11.368512 0.88281166 1.0415512 1.0083102
|
||||
5800 22.850002 -11.948876 -0.46874747 1.0747922 1.0083102
|
||||
5900 21.135991 -12.358431 -0.48932559 1.0526316 1.0193906
|
||||
6000 22.071115 -11.433484 0.49653696 1.0747922 1.0304709
|
||||
6100 21.91427 -11.458553 -0.030708226 1.0637119 1.0193906
|
||||
6200 24.173206 -13.110269 -0.13661363 1.1412742 1.0083102
|
||||
6300 22.204413 -11.373556 1.6254012 1.0747922 1.0304709
|
||||
6400 23.259022 -11.634614 1.4472592 1.1412742 1.0193906
|
||||
6500 22.185287 -11.606998 0.66488201 1.0415512 1.0083102
|
||||
6600 21.329653 -10.989853 0.31700842 1.1301939 1.0083102
|
||||
6700 21.903749 -10.335477 1.3749575 1.0637119 1.0083102
|
||||
6800 21.188714 -10.545014 1.3448408 1.0415512 1.0083102
|
||||
6900 22.683005 -11.254371 0.5048545 1.1523546 1.0193906
|
||||
7000 21.224439 -9.7325551 0.71666112 1.0637119 1.0083102
|
||||
7100 21.712624 -10.594397 0.3657261 1.0858726 1.0193906
|
||||
7200 22.115857 -10.479237 0.95528164 1.0969529 1.0193906
|
||||
7300 22.075732 -11.255 -0.35340754 1.0526316 1.0193906
|
||||
7400 21.659767 -10.238454 -0.063639729 1.1523546 1.0083102
|
||||
7500 21.966354 -10.654264 0.36298903 1.0747922 1.0083102
|
||||
7600 21.541195 -11.151416 0.96453416 1.1080332 1.0193906
|
||||
7700 23.517228 -12.266781 0.49603585 1.1523546 1.0193906
|
||||
7800 21.665911 -11.832323 0.47104209 1.1080332 1.0083102
|
||||
7900 23.469372 -12.358423 -0.757413 1.0747922 1.0193906
|
||||
8000 21.699467 -11.462824 -0.73009236 1.0415512 1.0083102
|
||||
8100 21.583783 -10.21474 0.98837038 1.0969529 1.0193906
|
||||
8200 21.804998 -10.916922 -0.53268178 1.0858726 1.0083102
|
||||
8300 21.291145 -10.875356 0.81277146 1.0858726 1.0193906
|
||||
8400 21.939964 -10.726547 0.95830844 1.0415512 1.0193906
|
||||
8500 23.600157 -11.041255 -0.14583876 1.0747922 1.0083102
|
||||
8600 22.37787 -10.946852 1.0360646 1.0415512 1.0083102
|
||||
8700 23.591205 -11.524803 1.1877377 1.0526316 1.0304709
|
||||
8800 22.567007 -11.4629 0.4360461 1.0526316 1.0083102
|
||||
8900 22.11289 -11.772849 -0.019132631 1.0304709 1.0193906
|
||||
9000 22.814946 -11.705633 0.59029789 1.0747922 1.0083102
|
||||
9100 22.58487 -11.431283 0.9884223 1.1634349 1.0083102
|
||||
9200 23.283939 -11.825534 0.68358625 1.0637119 1.0083102
|
||||
9300 23.292444 -11.365494 0.78631005 1.0526316 1.0083102
|
||||
9400 21.748634 -10.16176 0.59185916 1.0969529 1.0083102
|
||||
9500 21.644797 -10.00944 1.1450108 1.0637119 1.0304709
|
||||
9600 23.01957 -10.683211 1.5735291 1.0637119 1.0193906
|
||||
9700 21.207989 -10.344668 0.34401867 1.0969529 1.0083102
|
||||
9800 22.035363 -10.849581 -0.14118639 1.0304709 1.0083102
|
||||
9900 21.839653 -10.008407 0.96570633 1.0526316 1.0193906
|
||||
10000 22.845561 -10.238723 0.74236932 1.0858726 1.0083102
|
||||
Loop time of 0.812716 on 4 procs for 10000 steps with 361 atoms
|
||||
|
||||
Performance: 5315508.362 tau/day, 12304.418 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.12434 | 0.13482 | 0.14506 | 2.5 | 16.59
|
||||
Bond | 0.053339 | 0.058165 | 0.062916 | 1.9 | 7.16
|
||||
Neigh | 0.28554 | 0.29233 | 0.29933 | 0.9 | 35.97
|
||||
Comm | 0.16602 | 0.19226 | 0.21833 | 4.3 | 23.66
|
||||
Output | 0.0017536 | 0.0019155 | 0.0022504 | 0.4 | 0.24
|
||||
Modify | 0.040126 | 0.040341 | 0.04054 | 0.1 | 4.96
|
||||
Other | | 0.09288 | | | 11.43
|
||||
|
||||
Nlocal: 90.25 ave 91 max 90 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 198.25 ave 206 max 191 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 667.75 ave 751 max 627 min
|
||||
Histogram: 2 0 1 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2671
|
||||
Ave neighs/atom = 7.39889
|
||||
Ave special neighs/atom = 5.61773
|
||||
Neighbor list builds = 4832
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,202 +0,0 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
# 2d circle of particles inside a box with LJ walls
|
||||
|
||||
variable b index 0
|
||||
|
||||
variable x index 50
|
||||
variable y index 20
|
||||
variable d index 20
|
||||
variable v index 5
|
||||
variable w index 2
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
boundary f f p
|
||||
|
||||
lattice hex 0.85
|
||||
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
|
||||
region box block 0 $x 0 $y -0.5 0.5
|
||||
region box block 0 50 0 $y -0.5 0.5
|
||||
region box block 0 50 0 20 -0.5 0.5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 10
|
||||
create_atoms 1 region circle
|
||||
Created 361 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 0.5 87287 loop geom
|
||||
velocity all set $v $w 0 sum yes
|
||||
velocity all set 5 $w 0 sum yes
|
||||
velocity all set 5 2 0 sum yes
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 10.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
|
||||
|
||||
comm_style tiled
|
||||
fix 10 all balance 50 0.9 rcb
|
||||
|
||||
#compute 1 all property/atom proc
|
||||
#variable p atom c_1%10
|
||||
#dump 2 all custom 50 tmp.dump id v_p x y z
|
||||
|
||||
#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
|
||||
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
||||
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
thermo_style custom step temp epair press f_10[3] f_10
|
||||
thermo 100
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Memory usage per processor = 2.48839 Mbytes
|
||||
Step Temp E_pair Press f_10[3] f_10
|
||||
0 25.701528 -29.143179 -1.2407285 3.2354571 1.0526316
|
||||
100 26.269576 -29.713313 7.9052334 1.2742382 1.0304709
|
||||
200 26.368336 -29.809962 1.6412462 1.2520776 1.0083102
|
||||
300 26.479082 -29.920083 2.3678653 1.2299169 1.0193906
|
||||
400 26.522239 -29.965537 6.6787858 1.1855956 1.0193906
|
||||
500 25.725591 -29.168034 0.67065285 1.2520776 1.0083102
|
||||
600 26.247693 -29.692706 7.9887712 1.3074792 1.0083102
|
||||
700 26.237368 -29.676926 1.5987214 1.2409972 1.0083102
|
||||
800 25.889643 -29.431589 4.6160859 1.2631579 1.0083102
|
||||
900 23.635295 -27.372963 9.029962 1.1634349 1.0083102
|
||||
1000 22.571904 -25.87422 1.8936085 1.1301939 1.0193906
|
||||
1100 17.493795 -21.447274 9.502619 1.0858726 1.0193906
|
||||
1200 17.214459 -20.726965 6.3578917 1.0304709 1.0193906
|
||||
1300 16.424084 -19.757322 3.9028131 1.1191136 1.0083102
|
||||
1400 15.026954 -18.109911 1.7623684 1.0858726 1.0193906
|
||||
1500 13.640678 -16.740794 1.5347425 1.0858726 1.0193906
|
||||
1600 13.618211 -16.610276 1.9480883 1.0747922 1.0083102
|
||||
1700 13.266465 -16.300632 1.6890777 1.0637119 1.0193906
|
||||
1800 12.178444 -15.175544 2.1018989 1.0304709 1.0083102
|
||||
1900 12.131633 -15.075269 2.0174899 1.0526316 1.0193906
|
||||
2000 12.290785 -15.185923 1.8747772 1.0415512 1.0193906
|
||||
2100 12.02255 -14.947108 1.086185 1.0747922 1.0083102
|
||||
2200 11.733238 -14.620414 0.93934447 1.0526316 1.0193906
|
||||
2300 12.180779 -15.092283 1.1969416 1.0526316 1.0083102
|
||||
2400 11.721247 -14.503377 1.3759878 1.1080332 1.0083102
|
||||
2500 11.609116 -14.371603 2.0315139 1.0747922 1.0083102
|
||||
2600 11.712503 -14.494711 1.7236598 1.0415512 1.0193906
|
||||
2700 10.932816 -13.665751 1.2772732 1.0415512 1.0083102
|
||||
2800 10.418752 -13.183889 1.2940564 1.0415512 1.0193906
|
||||
2900 10.668297 -13.404525 0.90378659 1.0304709 1.0083102
|
||||
3000 10.562215 -13.581566 1.0507999 1.0083102 1.0193906
|
||||
3100 10.283188 -13.016565 1.0685664 1.0526316 1.0193906
|
||||
3200 10.424678 -13.136756 1.4038511 1.0193906 1.0083102
|
||||
3300 10.207304 -12.901323 1.3077174 1.0415512 1.0193906
|
||||
3400 10.143301 -12.802915 1.2776266 1.0415512 1.0193906
|
||||
3500 9.8449452 -12.507639 1.5455496 1.0637119 1.0083102
|
||||
3600 9.5629038 -12.204164 0.84971204 1.0304709 1.0083102
|
||||
3700 9.1851938 -11.809431 1.0102805 1.0304709 1.0193906
|
||||
3800 9.3305969 -11.989086 0.69923461 1.0193906 1.0083102
|
||||
3900 9.2415243 -11.880498 1.2471235 1.0637119 1.0193906
|
||||
4000 8.8240051 -11.417696 0.60781901 1.0304709 1.0083102
|
||||
4100 8.9126422 -11.503716 0.96900558 1.0083102 1.0083102
|
||||
4200 8.3738185 -10.93925 0.84927158 1.0193906 1.0083102
|
||||
4300 8.2401487 -10.90291 0.97775564 1.0083102 1.0083102
|
||||
4400 8.061288 -10.722169 1.4106859 1.0193906 1.0193906
|
||||
4500 7.8900038 -10.422818 0.67651486 1.0193906 1.0193906
|
||||
4600 7.8306694 -10.363812 0.83437455 1.0193906 1.0193906
|
||||
4700 8.1116499 -10.712008 0.58885383 1.0304709 1.0193906
|
||||
4800 8.0508103 -10.576232 0.52562827 1.0193906 1.0083102
|
||||
4900 7.8161815 -10.368333 0.89724847 1.0415512 1.0083102
|
||||
5000 7.4940002 -9.9763835 1.215446 1.0304709 1.0083102
|
||||
5100 7.9981403 -10.510786 1.0948502 1.0304709 1.0193906
|
||||
5200 7.7674668 -10.259031 0.81850586 1.0304709 1.0193906
|
||||
5300 7.9627913 -10.465018 0.75004253 1.0304709 1.0083102
|
||||
5400 7.8093696 -10.371624 0.75451812 1.0193906 1.0083102
|
||||
5500 8.1189569 -10.623288 0.91908416 1.0304709 1.0083102
|
||||
5600 7.5970957 -10.070305 0.84265844 1.0415512 1.0083102
|
||||
5700 7.4322203 -9.9176252 0.32608772 1.0304709 1.0083102
|
||||
5800 7.8210607 -10.311444 0.95696619 1.0304709 1.0083102
|
||||
5900 7.6181913 -10.111225 1.1341946 1.0193906 1.0083102
|
||||
6000 7.2217555 -9.7122281 0.75858423 1.0637119 1.0083102
|
||||
6100 7.3643302 -9.851242 0.5240439 1.0193906 1.0193906
|
||||
6200 7.0281589 -9.4834454 0.59523945 1.0526316 1.0193906
|
||||
6300 7.1383115 -9.6099868 0.87558078 1.0193906 1.0193906
|
||||
6400 7.2136999 -9.6965877 0.88426542 1.0304709 1.0083102
|
||||
6500 7.1710521 -9.7082917 1.2055959 1.0415512 1.0193906
|
||||
6600 7.4150515 -9.9376614 0.48201097 1.0304709 1.0083102
|
||||
6700 6.8701427 -9.3844769 0.72785561 1.0526316 1.0193906
|
||||
6800 6.8486978 -9.3256413 0.93231327 1.0193906 1.0083102
|
||||
6900 6.583533 -9.0068813 0.51281911 1.0193906 1.0193906
|
||||
7000 6.7199396 -9.1773668 0.12636874 1.0193906 1.0083102
|
||||
7100 6.5193695 -8.9553058 1.0423295 1.0083102 1.0193906
|
||||
7200 6.4868896 -8.9090695 0.49867926 1.0083102 1.0193906
|
||||
7300 6.2975635 -8.7775483 0.49072731 1.0415512 1.0083102
|
||||
7400 6.4966155 -8.9410837 0.52952897 1.0193906 1.0083102
|
||||
7500 6.7100139 -9.166691 0.82930078 1.0193906 1.0083102
|
||||
7600 6.3569418 -8.7843554 0.93473251 1.0193906 1.0083102
|
||||
7700 6.122789 -8.5434369 0.33725874 1.0526316 1.0083102
|
||||
7800 6.0249595 -8.4453069 0.52784464 1.0193906 1.0083102
|
||||
7900 6.6673238 -9.1166487 0.93753595 1.0193906 1.0083102
|
||||
8000 6.4177253 -8.8896071 0.57421674 1.0193906 1.0193906
|
||||
8100 5.965959 -8.3655023 0.42043964 1.0304709 1.0193906
|
||||
8200 6.3325216 -8.758339 0.76723151 1.0193906 1.0193906
|
||||
8300 6.4992751 -8.943922 0.86331769 1.0526316 1.0193906
|
||||
8400 6.1834495 -8.6059885 0.43133079 1.0415512 1.0193906
|
||||
8500 6.2567239 -8.6758815 0.8551113 1.0083102 1.0193906
|
||||
8600 6.1232623 -8.5905174 0.6014726 1.0304709 1.0083102
|
||||
8700 6.6650376 -9.0949995 0.46866086 1.0637119 1.0193906
|
||||
8800 6.6103957 -9.0116868 0.84371859 1.0083102 1.0193906
|
||||
8900 5.8867946 -8.3162884 0.64216189 1.0415512 1.0193906
|
||||
9000 5.685369 -8.0652138 0.32067903 1.0304709 1.0083102
|
||||
9100 6.2783881 -8.6826466 0.36419567 1.0415512 1.0304709
|
||||
9200 6.0162211 -8.4584809 0.58707128 1.0083102 1.0083102
|
||||
9300 5.9900511 -8.3949266 0.62037401 1.0304709 1.0193906
|
||||
9400 6.2686573 -8.6713334 0.81204427 1.0415512 1.0083102
|
||||
9500 6.0317917 -8.4325112 0.63221293 1.0304709 1.0193906
|
||||
9600 5.8217003 -8.256407 0.816143 1.0304709 1.0083102
|
||||
9700 5.6011023 -7.9966077 0.4114902 1.0304709 1.0193906
|
||||
9800 5.6339982 -8.0317639 0.32315576 1.0083102 1.0083102
|
||||
9900 5.8044743 -8.1942271 0.62892477 1.0193906 1.0083102
|
||||
10000 6.1722678 -8.5642925 0.80423557 1.0304709 1.0083102
|
||||
Loop time of 0.39332 on 4 procs for 10000 steps with 361 atoms
|
||||
|
||||
Performance: 10983420.832 tau/day, 25424.585 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.067888 | 0.075593 | 0.091022 | 3.3 | 19.22
|
||||
Neigh | 0.071147 | 0.075568 | 0.085203 | 2.1 | 19.21
|
||||
Comm | 0.10841 | 0.12918 | 0.14463 | 4.0 | 32.84
|
||||
Output | 0.0017445 | 0.001877 | 0.0022032 | 0.4 | 0.48
|
||||
Modify | 0.038837 | 0.039568 | 0.040469 | 0.3 | 10.06
|
||||
Other | | 0.07153 | | | 18.19
|
||||
|
||||
Nlocal: 90.25 ave 91 max 90 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 22.25 ave 27 max 16 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 268.25 ave 400 max 133 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 1073
|
||||
Ave neighs/atom = 2.9723
|
||||
Neighbor list builds = 3611
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
225
examples/balance/log.5Oct16.balance.bond.fast.g++.4
Normal file
225
examples/balance/log.5Oct16.balance.bond.fast.g++.4
Normal file
@ -0,0 +1,225 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 2d circle of particles inside a box with LJ walls
|
||||
|
||||
variable b index 0
|
||||
|
||||
variable x index 50
|
||||
variable y index 20
|
||||
variable d index 20
|
||||
variable v index 5
|
||||
variable w index 2
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style bond
|
||||
boundary f f p
|
||||
|
||||
lattice hex 0.85
|
||||
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
|
||||
region box block 0 $x 0 $y -0.5 0.5
|
||||
region box block 0 50 0 $y -0.5 0.5
|
||||
region box block 0 50 0 20 -0.5 0.5
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 6
|
||||
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 10
|
||||
create_atoms 1 region circle
|
||||
Created 361 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 0.5 87287 loop geom
|
||||
velocity all set $v $w 0 sum yes
|
||||
velocity all set 5 $w 0 sum yes
|
||||
velocity all set 5 2 0 sum yes
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 10.0 1.0 2.5
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 10.0 1.2
|
||||
|
||||
# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
|
||||
|
||||
special_bonds lj/coul 0 1 1
|
||||
0 = max # of 1-2 neighbors
|
||||
1 = max # of special neighbors
|
||||
create_bonds all all 1 1.0 1.5
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Added 1014 bonds, new total = 1014
|
||||
6 = max # of 1-2 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
|
||||
|
||||
comm_style tiled
|
||||
comm_modify cutoff 10.0 # because bonds stretch a long ways
|
||||
fix 10 all balance 50 0.9 rcb
|
||||
|
||||
#compute 1 all property/atom proc
|
||||
#variable p atom (c_1%10)+1
|
||||
#dump 2 all custom 50 tmp.dump id v_p x y z
|
||||
|
||||
#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
|
||||
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
||||
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
thermo_style custom step temp epair press f_10[3] f_10
|
||||
thermo 100
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 10
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Memory usage per processor = 4.49479 Mbytes
|
||||
Step Temp E_pair Press f_10[3] f_10
|
||||
0 25.701528 -2.2032569 3.1039469 3.2354571 1.0526316
|
||||
100 27.623422 -6.228166 2.6542136 1.2631579 1.0083102
|
||||
200 33.35302 -15.746749 3.2018248 1.2963989 1.0193906
|
||||
300 39.17734 -24.1557 4.9116986 1.2963989 1.0193906
|
||||
400 41.660701 -27.615203 8.6214679 1.3518006 1.0083102
|
||||
500 37.154928 -24.096947 3.2656178 1.3296399 1.0193906
|
||||
600 35.05989 -21.524279 2.3728488 1.3296399 1.0083102
|
||||
700 36.705654 -21.984526 3.2984899 1.3296399 1.0083102
|
||||
800 39.631254 -25.783472 4.1595658 1.3961219 1.0083102
|
||||
900 38.122407 -24.836728 5.3619155 1.3628809 1.0083102
|
||||
1000 38.369965 -25.098561 4.5613077 1.3074792 1.0083102
|
||||
1100 36.448264 -25.295817 4.0134469 1.1966759 1.0193906
|
||||
1200 33.216313 -21.813423 4.48954 1.1634349 1.0304709
|
||||
1300 30.361077 -20.323335 4.8079549 1.0637119 1.0083102
|
||||
1400 29.368132 -18.532543 3.8449914 1.1191136 1.0083102
|
||||
1500 27.699395 -15.990271 2.1565226 1.1523546 1.0304709
|
||||
1600 25.304973 -14.626675 0.91025038 1.1301939 1.0083102
|
||||
1700 26.335273 -14.499134 1.2878263 1.1855956 1.0083102
|
||||
1800 25.755278 -13.121269 0.78425366 1.1745152 1.0193906
|
||||
1900 25.454743 -13.903724 -0.16644734 1.1080332 1.0083102
|
||||
2000 25.54829 -13.271068 1.9214248 1.0969529 1.0083102
|
||||
2100 26.663083 -13.423796 1.9699997 1.1080332 1.0083102
|
||||
2200 27.707332 -13.759474 1.5528121 1.1412742 1.0304709
|
||||
2300 26.649636 -14.246313 0.91466777 1.1412742 1.0193906
|
||||
2400 25.92802 -13.16271 1.0298936 1.1301939 1.0193906
|
||||
2500 24.992275 -12.299161 1.3078979 1.1301939 1.0083102
|
||||
2600 26.235185 -13.363142 2.0756764 1.2188366 1.0083102
|
||||
2700 27.235116 -15.57943 2.1120604 1.1745152 1.0083102
|
||||
2800 25.313585 -14.352196 2.1442169 1.0637119 1.0083102
|
||||
2900 23.472278 -13.686216 0.69404738 1.0637119 1.0193906
|
||||
3000 21.02552 -11.646464 0.56287643 1.0747922 1.0083102
|
||||
3100 20.746946 -10.721207 -0.67351842 1.0858726 1.0193906
|
||||
3200 20.330655 -10.307715 -0.30221601 1.0637119 1.0083102
|
||||
3300 22.84995 -11.104879 0.0039310975 1.1191136 1.0083102
|
||||
3400 23.23878 -11.827018 0.80792932 1.1301939 1.0193906
|
||||
3500 25.262491 -12.191616 0.83249221 1.0747922 1.0193906
|
||||
3600 25.08542 -13.10456 1.3164581 1.0969529 1.0193906
|
||||
3700 22.649046 -11.300822 0.20123604 1.0526316 1.0193906
|
||||
3800 20.516849 -9.7738907 -0.45160364 1.0637119 1.0083102
|
||||
3900 20.227823 -9.8156456 -1.4386994 1.0637119 1.0083102
|
||||
4000 21.511004 -9.6074826 0.83933362 1.1080332 1.0083102
|
||||
4100 24.569081 -12.671563 0.60105671 1.0858726 1.0193906
|
||||
4200 24.739215 -11.654269 0.66172409 1.0969529 1.0083102
|
||||
4300 22.433043 -10.921392 1.2813391 1.1634349 1.0083102
|
||||
4400 22.520504 -10.59901 0.10799908 1.0193906 1.0083102
|
||||
4500 21.799185 -9.5801426 0.057062661 1.1191136 1.0193906
|
||||
4600 22.537171 -9.9647087 -0.70915155 1.1412742 1.0083102
|
||||
4700 22.380783 -10.974234 -0.73703011 1.0858726 1.0083102
|
||||
4800 23.991602 -11.171402 1.3314176 1.0415512 1.0193906
|
||||
4900 23.077116 -12.281132 0.73818416 1.0858726 1.0083102
|
||||
5000 23.180253 -11.702364 0.84176858 1.1080332 1.0193906
|
||||
5100 21.079712 -11.204743 0.50038687 1.0747922 1.0083102
|
||||
5200 21.348945 -10.802581 -0.28651467 1.1634349 1.0193906
|
||||
5300 21.332913 -10.352697 0.46738209 1.0858726 1.0193906
|
||||
5400 22.283885 -10.635637 -0.31446485 1.0415512 1.0083102
|
||||
5500 21.404737 -9.7733531 0.61106958 1.0858726 1.0193906
|
||||
5600 23.013417 -10.291315 1.0562031 1.0969529 1.0083102
|
||||
5700 22.087964 -10.931365 0.071180576 1.0415512 1.0193906
|
||||
5800 24.011278 -11.080032 1.3901123 1.0637119 1.0193906
|
||||
5900 22.320482 -10.616071 0.57726663 1.1412742 1.0193906
|
||||
6000 23.348377 -12.116776 0.59306932 1.1191136 1.0193906
|
||||
6100 22.20822 -11.545749 0.035299394 1.0747922 1.0193906
|
||||
6200 22.810467 -10.598645 0.3296656 1.0415512 1.0083102
|
||||
6300 21.398957 -10.058479 0.66795602 1.0415512 1.0193906
|
||||
6400 21.945005 -10.358622 -1.0094405 1.0415512 1.0083102
|
||||
6500 22.906408 -10.767788 1.0948374 1.0858726 1.0083102
|
||||
6600 23.326617 -11.264481 0.82773039 1.0747922 1.0083102
|
||||
6700 22.491386 -10.27014 0.043938534 1.0526316 1.0193906
|
||||
6800 22.294374 -10.664685 0.048726237 1.1191136 1.0083102
|
||||
6900 22.221286 -10.697394 1.0354647 1.0415512 1.0193906
|
||||
7000 21.693738 -10.009277 0.64426437 1.0858726 1.0083102
|
||||
7100 22.775615 -11.372061 0.069159076 1.1191136 1.0193906
|
||||
7200 22.274683 -11.583382 -0.35907789 1.0858726 1.0193906
|
||||
7300 21.410706 -11.005479 -0.66394825 1.1080332 1.0083102
|
||||
7400 21.910735 -9.9354265 0.78899083 1.0526316 1.0083102
|
||||
7500 21.526738 -9.7787506 -0.38232161 1.0415512 1.0083102
|
||||
7600 21.833898 -10.289457 0.058939882 1.0747922 1.0193906
|
||||
7700 21.606736 -9.6807332 0.50127515 1.0526316 1.0083102
|
||||
7800 22.294657 -10.790285 0.8685065 1.0637119 1.0083102
|
||||
7900 23.269713 -11.375434 0.84634431 1.0969529 1.0304709
|
||||
8000 22.865151 -10.960251 1.0270422 1.0526316 1.0304709
|
||||
8100 21.656008 -10.504825 1.2228537 1.0304709 1.0193906
|
||||
8200 24.494122 -12.282009 0.16316531 1.0526316 1.0193906
|
||||
8300 22.974267 -11.287149 -0.035076799 1.0747922 1.0193906
|
||||
8400 21.052237 -11.243181 -0.099450689 1.0747922 1.0193906
|
||||
8500 22.661383 -11.090107 -0.22913242 1.0969529 1.0193906
|
||||
8600 21.403272 -9.5267458 -0.28047198 1.0637119 1.0193906
|
||||
8700 22.786699 -10.403836 0.40752047 1.0415512 1.0193906
|
||||
8800 24.504694 -10.706052 1.1870205 1.0969529 1.0193906
|
||||
8900 23.22256 -11.182967 0.64166445 1.0747922 1.0304709
|
||||
9000 23.734203 -10.422277 1.3143506 1.1191136 1.0304709
|
||||
9100 23.517258 -11.247418 -0.13540081 1.0193906 1.0193906
|
||||
9200 23.128204 -9.9181617 1.0928284 1.1412742 1.0083102
|
||||
9300 23.281107 -10.523942 0.011923998 1.0969529 1.0193906
|
||||
9400 21.800282 -10.359413 -0.62145559 1.1412742 1.0193906
|
||||
9500 24.910955 -11.786562 1.6227559 1.1301939 1.0193906
|
||||
9600 24.331432 -11.802048 0.62882542 1.1191136 1.0083102
|
||||
9700 22.340782 -10.531555 0.29842716 1.0415512 1.0193906
|
||||
9800 22.371239 -10.384104 0.34253854 1.0415512 1.0083102
|
||||
9900 22.289367 -9.9488634 0.29499176 1.1412742 1.0083102
|
||||
10000 22.518865 -10.279548 -0.48356734 1.1745152 1.0083102
|
||||
Loop time of 0.879172 on 4 procs for 10000 steps with 361 atoms
|
||||
|
||||
Performance: 4913715.115 tau/day, 11374.341 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11586 | 0.13009 | 0.14055 | 2.7 | 14.80
|
||||
Bond | 0.054003 | 0.058475 | 0.063238 | 1.8 | 6.65
|
||||
Neigh | 0.2865 | 0.29554 | 0.3049 | 1.2 | 33.62
|
||||
Comm | 0.20988 | 0.24193 | 0.27748 | 4.9 | 27.52
|
||||
Output | 0.0021532 | 0.0023131 | 0.00266 | 0.4 | 0.26
|
||||
Modify | 0.043945 | 0.045592 | 0.047122 | 0.6 | 5.19
|
||||
Other | | 0.1052 | | | 11.97
|
||||
|
||||
Nlocal: 90.25 ave 91 max 90 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 250.25 ave 257 max 247 min
|
||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||
Neighs: 624.75 ave 739 max 519 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 2499
|
||||
Ave neighs/atom = 6.92244
|
||||
Ave special neighs/atom = 5.61773
|
||||
Neighbor list builds = 4881
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 2d circle of particles inside a box with LJ walls
|
||||
|
||||
variable b index 0
|
||||
@ -108,9 +108,9 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
1300 0.32952819 0 0.124902 1.0083102 1.0083102
|
||||
1400 0.34497365 0 0.12662081 1.0193906 1.0083102
|
||||
1500 0.33429243 0 0.096230972 1.0526316 1.0193906
|
||||
1600 0.33765387 0 0.025800542 1.0304709 1.0193906
|
||||
1600 0.33765387 0 0.025800542 1.0304709 1.0083102
|
||||
1700 0.35134464 0 -0.04422593 1.0415512 1.0083102
|
||||
1800 0.35003859 0 -0.096745576 1.0304709 1.0083102
|
||||
1800 0.35003859 0 -0.096745576 1.0304709 1.0193906
|
||||
1900 0.33839618 0 -0.095465943 1.0193906 1.0083102
|
||||
2000 0.33732078 0 -0.094652802 1.0083102 1.0083102
|
||||
2100 0.34552238 0 -0.076729261 1.0304709 1.0083102
|
||||
@ -181,9 +181,9 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
8600 0.33761673 0 -0.07069818 1.0193906 1.0083102
|
||||
8700 0.34495452 0 -0.022458056 1.0193906 1.0193906
|
||||
8800 0.33502983 0 0.027742411 1.0304709 1.0083102
|
||||
8900 0.35418591 0 0.092390134 1.0083102 1.0193906
|
||||
8900 0.35418591 0 0.092390134 1.0083102 1.0083102
|
||||
9000 0.31648387 0 0.12467398 1.0193906 1.0083102
|
||||
9100 0.33994825 0 0.14460327 1.0193906 1.0083102
|
||||
9100 0.33994825 0 0.14460327 1.0193906 1.0193906
|
||||
9200 0.33822571 0 0.11273284 1.0193906 1.0083102
|
||||
9300 0.33260773 0 0.060063671 1.0083102 1.0193906
|
||||
9400 0.36140305 0 0.021427642 1.0193906 1.0083102
|
||||
@ -192,18 +192,18 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
9700 0.32088235 0 -0.12027075 1.0193906 1.0083102
|
||||
9800 0.3320823 0 -0.11602794 1.0415512 1.0083102
|
||||
9900 0.33916442 0 -0.080281044 1.0083102 1.0083102
|
||||
10000 0.34852268 0 -0.01000914 1.0193906 1.0083102
|
||||
10000 0.34852268 0 -0.01000914 1.0193906 1.0193906
|
||||
10100 0.32955942 0 0.04258493 1.0083102 1.0083102
|
||||
10200 0.34487898 0 0.086971308 1.0304709 1.0083102
|
||||
10300 0.32325593 0 0.11558149 1.0304709 1.0193906
|
||||
10400 0.30927871 0 0.12239437 1.0083102 1.0083102
|
||||
10300 0.32325593 0 0.11558149 1.0304709 1.0083102
|
||||
10400 0.30927871 0 0.12239437 1.0083102 1.0193906
|
||||
10500 0.33176799 0 0.12285937 1.0193906 1.0083102
|
||||
10600 0.35120027 0 0.084897432 1.0083102 1.0083102
|
||||
10700 0.33129697 0 0.0053089279 1.0193906 1.0193906
|
||||
10800 0.36028769 0 -0.04280715 1.0193906 1.0083102
|
||||
10900 0.35552287 0 -0.084955999 1.0193906 1.0193906
|
||||
10900 0.35552287 0 -0.084955999 1.0193906 1.0304709
|
||||
11000 0.3406024 0 -0.096554577 1.0083102 1.0083102
|
||||
11100 0.33041202 0 -0.10703492 1.0304709 1.0193906
|
||||
11100 0.33041202 0 -0.10703492 1.0304709 1.0083102
|
||||
11200 0.32442686 0 -0.084328121 1.0304709 1.0083102
|
||||
11300 0.35952468 0 -0.020191965 1.0304709 1.0193906
|
||||
11400 0.34610624 0 0.03440148 1.0193906 1.0083102
|
||||
@ -214,7 +214,7 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
11900 0.33836678 0 0.067253864 1.0193906 1.0193906
|
||||
12000 0.34853314 0 0.03201448 1.0193906 1.0083102
|
||||
12100 0.34600048 0 -0.034833402 1.0304709 1.0083102
|
||||
12200 0.33145631 0 -0.09865675 1.0193906 1.0083102
|
||||
12200 0.33145631 0 -0.09865675 1.0193906 1.0193906
|
||||
12300 0.32848884 0 -0.1248489 1.0193906 1.0193906
|
||||
12400 0.3321344 0 -0.11266575 1.0083102 1.0083102
|
||||
12500 0.32622305 0 -0.061634993 1.0304709 1.0083102
|
||||
@ -225,11 +225,11 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
13000 0.31993287 0 0.13879926 1.0193906 1.0193906
|
||||
13100 0.3422918 0 0.11978905 1.0083102 1.0083102
|
||||
13200 0.33055236 0 0.062620483 1.0193906 1.0083102
|
||||
13300 0.34652207 0 0.0043833459 1.0304709 1.0083102
|
||||
13400 0.33574661 0 -0.04691024 1.0304709 1.0083102
|
||||
13500 0.33940837 0 -0.074241604 1.0304709 1.0083102
|
||||
13600 0.32093414 0 -0.1078027 1.0193906 1.0193906
|
||||
13700 0.34336597 0 -0.10544097 1.0193906 1.0193906
|
||||
13300 0.34652207 0 0.0043833459 1.0304709 1.0193906
|
||||
13400 0.33574661 0 -0.04691024 1.0304709 1.0193906
|
||||
13500 0.33940837 0 -0.074241604 1.0304709 1.0193906
|
||||
13600 0.32093414 0 -0.1078027 1.0193906 1.0083102
|
||||
13700 0.34336597 0 -0.10544097 1.0193906 1.0083102
|
||||
13800 0.35806461 0 -0.072531559 1.0193906 1.0083102
|
||||
13900 0.35209713 0 -0.018851408 1.0083102 1.0083102
|
||||
14000 0.35702629 0 0.061046366 1.0083102 1.0083102
|
||||
@ -240,18 +240,18 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
14500 0.35022184 0 0.083558031 1.0083102 1.0193906
|
||||
14600 0.34823843 0 0.024605569 1.0083102 1.0083102
|
||||
14700 0.35298973 0 -0.040418888 1.0193906 1.0083102
|
||||
14800 0.33679845 0 -0.10067728 1.0193906 1.0193906
|
||||
14800 0.33679845 0 -0.10067728 1.0193906 1.0083102
|
||||
14900 0.32790966 0 -0.10925568 1.0193906 1.0083102
|
||||
15000 0.34208495 0 -0.09568004 1.0193906 1.0083102
|
||||
15100 0.33647529 0 -0.055652929 1.0083102 1.0083102
|
||||
15200 0.35328398 0 -0.020236536 1.0193906 1.0193906
|
||||
15300 0.34252669 0 0.026434179 1.0083102 1.0193906
|
||||
15400 0.34409435 0 0.094410599 1.0304709 1.0083102
|
||||
15500 0.32288994 0 0.12034455 1.0415512 1.0193906
|
||||
15500 0.32288994 0 0.12034455 1.0415512 1.0083102
|
||||
15600 0.32109689 0 0.13645185 1.0193906 1.0083102
|
||||
15700 0.33681572 0 0.098607746 1.0415512 1.0193906
|
||||
15700 0.33681572 0 0.098607746 1.0415512 1.0083102
|
||||
15800 0.33635195 0 0.05570715 1.0193906 1.0193906
|
||||
15900 0.34289757 0 0.013849092 1.0304709 1.0083102
|
||||
15900 0.34289757 0 0.013849092 1.0304709 1.0193906
|
||||
16000 0.34225547 0 -0.035597548 1.0304709 1.0083102
|
||||
16100 0.33660991 0 -0.076931881 1.0193906 1.0193906
|
||||
16200 0.32802152 0 -0.12765884 1.0083102 1.0083102
|
||||
@ -261,23 +261,23 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
16600 0.35109001 0 0.041251169 1.0304709 1.0083102
|
||||
16700 0.34336905 0 0.077996627 1.0193906 1.0083102
|
||||
16800 0.33277414 0 0.11053634 1.0083102 1.0083102
|
||||
16900 0.32183338 0 0.11680626 1.0193906 1.0193906
|
||||
16900 0.32183338 0 0.11680626 1.0193906 1.0083102
|
||||
17000 0.34044352 0 0.10806555 1.0193906 1.0083102
|
||||
17100 0.32967873 0 0.067759786 1.0304709 1.0193906
|
||||
17200 0.36172278 0 -0.0048631904 1.0304709 1.0083102
|
||||
17300 0.35619435 0 -0.04215545 1.0193906 1.0083102
|
||||
17400 0.34540936 0 -0.093994174 1.0193906 1.0193906
|
||||
17400 0.34540936 0 -0.093994174 1.0193906 1.0083102
|
||||
17500 0.33193585 0 -0.098831315 1.0083102 1.0193906
|
||||
17600 0.3544756 0 -0.085660403 1.0193906 1.0083102
|
||||
17700 0.34505209 0 -0.069640515 1.0304709 1.0193906
|
||||
17800 0.36291124 0 -0.0063088133 1.0083102 1.0193906
|
||||
17900 0.34255705 0 0.046794555 1.0304709 1.0083102
|
||||
18000 0.34163238 0 0.11767705 1.0193906 1.0083102
|
||||
18000 0.34163238 0 0.11767705 1.0193906 1.0193906
|
||||
18100 0.3466445 0 0.1351712 1.0415512 1.0193906
|
||||
18200 0.33037668 0 0.12703659 1.0083102 1.0083102
|
||||
18300 0.33677404 0 0.10956306 1.0083102 1.0304709
|
||||
18400 0.34978954 0 0.087193072 1.0193906 1.0193906
|
||||
18500 0.33354363 0 0.051095814 1.0526316 1.0193906
|
||||
18500 0.33354363 0 0.051095814 1.0526316 1.0083102
|
||||
18600 0.34651729 0 0.0056245561 1.0304709 1.0193906
|
||||
18700 0.32622232 0 -0.047319269 1.0083102 1.0193906
|
||||
18800 0.32978847 0 -0.054929416 1.0304709 1.0193906
|
||||
@ -298,8 +298,8 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
20300 0.34195438 0 0.072811099 1.0304709 1.0193906
|
||||
20400 0.31249563 0 0.10063541 1.0415512 1.0083102
|
||||
20500 0.31544938 0 0.1405794 1.0083102 1.0083102
|
||||
20600 0.30071644 0 0.12763486 1.0193906 1.0193906
|
||||
20700 0.2890265 0 0.1136651 1.0083102 1.0193906
|
||||
20600 0.30071644 0 0.12763486 1.0193906 1.0304709
|
||||
20700 0.2890265 0 0.1136651 1.0083102 1.0083102
|
||||
20800 0.28962296 0 0.094481978 1.0193906 1.0083102
|
||||
20900 0.29447212 0 0.0967165 1.0193906 1.0193906
|
||||
21000 0.31159961 0 0.067307231 1.0083102 1.0083102
|
||||
@ -314,7 +314,7 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
21900 0.32451958 0 0.068935768 1.0304709 1.0193906
|
||||
22000 0.35219298 0 0.067161227 1.0193906 1.0193906
|
||||
22100 0.34857705 0 0.032731746 1.0193906 1.0083102
|
||||
22200 0.34750227 0 0.0056917695 1.0193906 1.0193906
|
||||
22200 0.34750227 0 0.0056917695 1.0193906 1.0083102
|
||||
22300 0.34766017 0 -0.0027090483 1.0193906 1.0083102
|
||||
22400 0.33426062 0 -0.023196063 1.0304709 1.0193906
|
||||
22500 0.34174625 0 -0.025019717 1.0083102 1.0083102
|
||||
@ -328,15 +328,15 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
23300 0.32965664 0 0.035989589 1.0193906 1.0083102
|
||||
23400 0.30927749 0 0.024581106 1.0193906 1.0083102
|
||||
23500 0.32890632 0 0.01092479 1.0304709 1.0193906
|
||||
23600 0.34137438 0 0.0094839745 1.0193906 1.0193906
|
||||
23600 0.34137438 0 0.0094839745 1.0193906 1.0083102
|
||||
23700 0.34512638 0 -0.012392771 1.0304709 1.0193906
|
||||
23800 0.31781354 0 -0.012908449 1.0193906 1.0193906
|
||||
23900 0.32405513 0 -0.015018071 1.0415512 1.0083102
|
||||
23900 0.32405513 0 -0.015018071 1.0415512 1.0193906
|
||||
24000 0.33549728 0 -0.012812915 1.0193906 1.0193906
|
||||
24100 0.31368736 0 -0.020818372 1.0304709 1.0193906
|
||||
24200 0.33533836 0 0.0056121057 1.0083102 1.0193906
|
||||
24200 0.33533836 0 0.0056121057 1.0083102 1.0083102
|
||||
24300 0.32530627 0 0.018183931 1.0415512 1.0083102
|
||||
24400 0.31930662 0 0.027446878 1.0083102 1.0083102
|
||||
24400 0.31930662 0 0.027446878 1.0083102 1.0193906
|
||||
24500 0.33540302 0 0.040307455 1.0304709 1.0083102
|
||||
24600 0.34020431 0 0.027403921 1.0083102 1.0083102
|
||||
24700 0.3291814 0 0.01204865 1.0193906 1.0083102
|
||||
@ -357,29 +357,29 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
26200 0.35097144 0 0.012291703 1.0083102 1.0083102
|
||||
26300 0.34303792 0 0.00094823191 1.0083102 1.0193906
|
||||
26400 0.33632665 0 -0.0026904889 1.0193906 1.0193906
|
||||
26500 0.33580127 0 -0.0074168555 1.0193906 1.0083102
|
||||
26500 0.33580127 0 -0.0074168555 1.0193906 1.0193906
|
||||
26600 0.33063188 0 -0.020378601 1.0083102 1.0193906
|
||||
26700 0.33581846 0 -0.00084397268 1.0083102 1.0193906
|
||||
26800 0.32998532 0 0.015932208 1.0304709 1.0193906
|
||||
26800 0.32998532 0 0.015932208 1.0304709 1.0304709
|
||||
26900 0.33825444 0 0.010428603 1.0304709 1.0083102
|
||||
27000 0.32081518 0 0.019818223 1.0304709 1.0193906
|
||||
27100 0.31448098 0 0.020093416 1.0193906 1.0083102
|
||||
27200 0.32643684 0 0.021934917 1.0083102 1.0083102
|
||||
27300 0.33289466 0 0.023713072 1.0415512 1.0083102
|
||||
27400 0.32310744 0 0.024110945 1.0415512 1.0083102
|
||||
27500 0.33115619 0 0.0025776713 1.0304709 1.0193906
|
||||
27500 0.33115619 0 0.0025776713 1.0304709 1.0083102
|
||||
27600 0.33295887 0 -0.010710764 1.0304709 1.0193906
|
||||
27700 0.32968876 0 -0.0064595905 1.0193906 1.0193906
|
||||
27700 0.32968876 0 -0.0064595905 1.0193906 1.0083102
|
||||
27800 0.34064581 0 -0.0086519116 1.0193906 1.0083102
|
||||
27900 0.33559187 0 -0.0055753593 1.0083102 1.0083102
|
||||
28000 0.32300727 0 -0.0004153384 1.0304709 1.0083102
|
||||
28100 0.32147461 0 -0.0058543412 1.0083102 1.0083102
|
||||
28100 0.32147461 0 -0.0058543412 1.0083102 1.0193906
|
||||
28200 0.35532383 0 0.013646951 1.0304709 1.0083102
|
||||
28300 0.31507942 0 0.026532255 1.0415512 1.0083102
|
||||
28300 0.31507942 0 0.026532255 1.0415512 1.0193906
|
||||
28400 0.32711006 0 0.033214981 1.0193906 1.0083102
|
||||
28500 0.34472462 0 0.028050837 1.0304709 1.0193906
|
||||
28600 0.33708059 0 0.019115676 1.0083102 1.0083102
|
||||
28700 0.34478087 0 0.023743689 1.0304709 1.0193906
|
||||
28700 0.34478087 0 0.023743689 1.0304709 1.0083102
|
||||
28800 0.34546686 0 0.0081772997 1.0304709 1.0083102
|
||||
28900 0.34004886 0 0.017771865 1.0415512 1.0193906
|
||||
29000 0.33604232 0 -0.010505671 1.0304709 1.0193906
|
||||
@ -408,24 +408,24 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
31300 0.32372541 0 0.01215566 1.0083102 1.0083102
|
||||
31400 0.32734692 0 0.016229397 1.0083102 1.0083102
|
||||
31500 0.33089262 0 0.0060426618 1.0083102 1.0083102
|
||||
31600 0.34273493 0 -0.013456537 1.0083102 1.0083102
|
||||
31700 0.32723905 0 -0.019243766 1.0193906 1.0083102
|
||||
31600 0.34273493 0 -0.013456537 1.0083102 1.0193906
|
||||
31700 0.32723905 0 -0.019243766 1.0193906 1.0193906
|
||||
31800 0.33636488 0 0.0027814902 1.0083102 1.0083102
|
||||
31900 0.32834805 0 0.00706877 1.0083102 1.0193906
|
||||
31900 0.32834805 0 0.00706877 1.0083102 1.0083102
|
||||
32000 0.33995148 0 0.0018383309 1.0193906 1.0193906
|
||||
32100 0.33412282 0 0.0076455933 1.0083102 1.0083102
|
||||
32200 0.34334884 0 0.023586129 1.0083102 1.0083102
|
||||
32300 0.32778925 0 0.020564321 1.0193906 1.0083102
|
||||
32400 0.33163443 0 0.038878463 1.0193906 1.0083102
|
||||
32500 0.32290345 0 0.022247461 1.0193906 1.0193906
|
||||
32600 0.34113954 0 0.010966365 1.0304709 1.0193906
|
||||
32600 0.34113954 0 0.010966365 1.0304709 1.0083102
|
||||
32700 0.33390633 0 0.0037777555 1.0193906 1.0083102
|
||||
32800 0.34385341 0 0.010556575 1.0193906 1.0193906
|
||||
32900 0.32137047 0 0.00022027143 1.0526316 1.0193906
|
||||
33000 0.32079172 0 -0.017261272 1.0193906 1.0193906
|
||||
33100 0.33570882 0 -0.0051942206 1.0083102 1.0083102
|
||||
33200 0.34320894 0 -0.011515281 1.0304709 1.0083102
|
||||
33300 0.32794746 0 -0.0018153673 1.0083102 1.0193906
|
||||
33200 0.34320894 0 -0.011515281 1.0304709 1.0193906
|
||||
33300 0.32794746 0 -0.0018153673 1.0083102 1.0083102
|
||||
33400 0.33060982 0 0.027118146 1.0193906 1.0083102
|
||||
33500 0.33641809 0 0.02143035 1.0083102 1.0083102
|
||||
33600 0.33643061 0 0.020833068 1.0193906 1.0083102
|
||||
@ -434,7 +434,7 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
33900 0.31959761 0 0.021128147 1.0083102 1.0193906
|
||||
34000 0.33897984 0 0.015270986 1.0193906 1.0083102
|
||||
34100 0.32392267 0 0.0020130852 1.0304709 1.0193906
|
||||
34200 0.33084514 0 -0.024316708 1.0193906 1.0193906
|
||||
34200 0.33084514 0 -0.024316708 1.0193906 1.0083102
|
||||
34300 0.3342259 0 -0.0059047764 1.0193906 1.0304709
|
||||
34400 0.33385098 0 0.0063818721 1.0193906 1.0083102
|
||||
34500 0.33255603 0 -0.01023837 1.0083102 1.0304709
|
||||
@ -446,7 +446,7 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
35100 0.3124942 0 0.011316548 1.0193906 1.0193906
|
||||
35200 0.34486416 0 0.011670127 1.0193906 1.0193906
|
||||
35300 0.33275353 0 0.020491246 1.0193906 1.0193906
|
||||
35400 0.33618763 0 0.014678874 1.0083102 1.0193906
|
||||
35400 0.33618763 0 0.014678874 1.0083102 1.0083102
|
||||
35500 0.32352282 0 -0.018568683 1.0193906 1.0193906
|
||||
35600 0.32617903 0 -0.012796912 1.0193906 1.0193906
|
||||
35700 0.32378048 0 -0.021318585 1.0193906 1.0083102
|
||||
@ -459,15 +459,15 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
36400 0.32301096 0 0.019966746 1.0304709 1.0083102
|
||||
36500 0.35612028 0 0.036509556 1.0083102 1.0083102
|
||||
36600 0.33841597 0 -0.0042180605 1.0193906 1.0193906
|
||||
36700 0.34477654 0 -0.0052770853 1.0193906 1.0193906
|
||||
36700 0.34477654 0 -0.0052770853 1.0193906 1.0083102
|
||||
36800 0.33804317 0 -0.013751733 1.0083102 1.0083102
|
||||
36900 0.35003816 0 -0.0021184393 1.0083102 1.0193906
|
||||
36900 0.35003816 0 -0.0021184393 1.0083102 1.0083102
|
||||
37000 0.32965041 0 -0.020900951 1.0193906 1.0083102
|
||||
37100 0.34653095 0 -0.013667977 1.0193906 1.0083102
|
||||
37200 0.35019871 0 -0.0071740923 1.0083102 1.0193906
|
||||
37300 0.34859745 0 0.02006041 1.0304709 1.0083102
|
||||
37400 0.35739859 0 0.020892822 1.0193906 1.0083102
|
||||
37500 0.34128859 0 0.041072111 1.0193906 1.0083102
|
||||
37500 0.34128859 0 0.041072111 1.0193906 1.0193906
|
||||
37600 0.33781905 0 0.023376738 1.0193906 1.0083102
|
||||
37700 0.32961874 0 0.030953741 1.0193906 1.0083102
|
||||
37800 0.343987 0 0.029579795 1.0083102 1.0083102
|
||||
@ -481,7 +481,7 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
38600 0.32322402 0 0.053453832 1.0193906 1.0304709
|
||||
38700 0.33843057 0 0.076264534 1.0083102 1.0193906
|
||||
38800 0.31350741 0 0.064733869 1.0415512 1.0083102
|
||||
38900 0.31943061 0 0.067836769 1.0304709 1.0083102
|
||||
38900 0.31943061 0 0.067836769 1.0304709 1.0193906
|
||||
39000 0.33775583 0 0.0788316 1.0193906 1.0193906
|
||||
39100 0.34256036 0 0.075874935 1.0083102 1.0193906
|
||||
39200 0.33128527 0 0.071610976 1.0193906 1.0083102
|
||||
@ -493,21 +493,21 @@ Step Temp E_pair Press f_10[3] f_10
|
||||
39800 0.34878036 0 0.0092881327 1.0083102 1.0193906
|
||||
39900 0.35225411 0 -0.011341599 1.0083102 1.0193906
|
||||
40000 0.36309266 0 0.0050869295 1.0304709 1.0083102
|
||||
Loop time of 1.07961 on 4 procs for 40000 steps with 361 atoms
|
||||
Loop time of 1.17534 on 4 procs for 40000 steps with 361 atoms
|
||||
|
||||
Performance: 16005824.195 tau/day, 37050.519 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 14702186.196 tau/day, 34032.838 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.019289 | 0.021061 | 0.024797 | 1.5 | 1.95
|
||||
Bond | 0.21005 | 0.23732 | 0.26838 | 5.0 | 21.98
|
||||
Neigh | 0.15978 | 0.16143 | 0.16328 | 0.4 | 14.95
|
||||
Comm | 0.2817 | 0.32626 | 0.36457 | 5.8 | 30.22
|
||||
Output | 0.0069985 | 0.0075181 | 0.0087821 | 0.8 | 0.70
|
||||
Modify | 0.1463 | 0.15235 | 0.16128 | 1.5 | 14.11
|
||||
Other | | 0.1737 | | | 16.09
|
||||
Pair | 0.019205 | 0.020313 | 0.022204 | 0.8 | 1.73
|
||||
Bond | 0.21255 | 0.23651 | 0.26839 | 4.9 | 20.12
|
||||
Neigh | 0.16301 | 0.16427 | 0.16578 | 0.3 | 13.98
|
||||
Comm | 0.33528 | 0.37951 | 0.4139 | 5.3 | 32.29
|
||||
Output | 0.0084457 | 0.0089972 | 0.010254 | 0.8 | 0.77
|
||||
Modify | 0.15906 | 0.16078 | 0.16308 | 0.4 | 13.68
|
||||
Other | | 0.205 | | | 17.44
|
||||
|
||||
Nlocal: 90.25 ave 91 max 89 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
@ -70,27 +70,27 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137
|
||||
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137
|
||||
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
|
||||
Loop time of 2.31899 on 4 procs for 500 steps with 4000 atoms
|
||||
Loop time of 2.33547 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 93143.824 tau/day, 215.611 timesteps/s
|
||||
Performance: 92486.710 tau/day, 214.090 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1238 | 1.43 | 1.6724 | 19.4 | 61.66
|
||||
Neigh | 0.26414 | 0.3845 | 0.55604 | 20.2 | 16.58
|
||||
Comm | 0.36444 | 0.48475 | 0.61759 | 15.3 | 20.90
|
||||
Output | 0.00027871 | 0.00032145 | 0.00035334 | 0.2 | 0.01
|
||||
Modify | 0.0064867 | 0.0086303 | 0.011487 | 2.3 | 0.37
|
||||
Other | | 0.01078 | | | 0.46
|
||||
Pair | 1.1405 | 1.4342 | 1.6755 | 19.8 | 61.41
|
||||
Neigh | 0.26612 | 0.40331 | 0.57095 | 21.3 | 17.27
|
||||
Comm | 0.3676 | 0.47776 | 0.60114 | 14.4 | 20.46
|
||||
Output | 0.00025606 | 0.00029331 | 0.00032091 | 0.1 | 0.01
|
||||
Modify | 0.0068483 | 0.008993 | 0.012159 | 2.3 | 0.39
|
||||
Other | | 0.01091 | | | 0.47
|
||||
|
||||
Nlocal: 1000 ave 1565 max 584 min
|
||||
Nlocal: 1000 ave 1541 max 597 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 8752 ave 9835 max 8078 min
|
||||
Nghost: 8756.5 ave 9859 max 8068 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 149308 ave 161748 max 133300 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Neighs: 149308 ave 164475 max 126288 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 597231
|
||||
Ave neighs/atom = 149.308
|
||||
@ -110,27 +110,27 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122 4738.2137
|
||||
950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278 4738.2137
|
||||
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
|
||||
Loop time of 2.32391 on 4 procs for 500 steps with 4000 atoms
|
||||
Loop time of 2.16422 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 92946.753 tau/day, 215.155 timesteps/s
|
||||
Performance: 99804.786 tau/day, 231.030 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1054 | 1.4081 | 1.6402 | 19.8 | 60.59
|
||||
Neigh | 0.28061 | 0.4047 | 0.57291 | 19.7 | 17.41
|
||||
Comm | 0.38485 | 0.4918 | 0.62503 | 15.5 | 21.16
|
||||
Output | 0.00028014 | 0.00031483 | 0.00032997 | 0.1 | 0.01
|
||||
Modify | 0.0064781 | 0.0084658 | 0.011106 | 2.2 | 0.36
|
||||
Other | | 0.01051 | | | 0.45
|
||||
Pair | 1.1704 | 1.3643 | 1.5256 | 13.9 | 63.04
|
||||
Neigh | 0.252 | 0.39989 | 0.57798 | 23.0 | 18.48
|
||||
Comm | 0.36005 | 0.38026 | 0.399 | 2.7 | 17.57
|
||||
Output | 0.00026989 | 0.00029516 | 0.00030947 | 0.1 | 0.01
|
||||
Modify | 0.0062692 | 0.0085821 | 0.011907 | 2.6 | 0.40
|
||||
Other | | 0.01089 | | | 0.50
|
||||
|
||||
Nlocal: 1000 ave 1560 max 593 min
|
||||
Nlocal: 1000 ave 1546 max 611 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 8716.25 ave 9788 max 8009 min
|
||||
Nghost: 8720 ave 9802 max 8007 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 150170 ave 164293 max 129469 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Neighs: 150170 ave 167512 max 125941 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 600678
|
||||
Ave neighs/atom = 150.169
|
||||
@ -138,7 +138,7 @@ Neighbor list builds = 53
|
||||
Dangerous builds = 0
|
||||
fix 0 all balance 50 1.0 shift x 5 1.0 weight neigh 0.5 weight time 0.66 weight store WEIGHT
|
||||
run 500
|
||||
Memory usage per processor = 3.06519 Mbytes
|
||||
Memory usage per processor = 3.04802 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
|
||||
1050 0.54629742 -6.2657526 0 -5.4465113 -1.945821 4738.2137
|
||||
@ -151,27 +151,27 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
1400 0.53726924 -6.2518379 0 -5.4461355 -1.8544028 4738.2137
|
||||
1450 0.54525935 -6.2632653 0 -5.4455808 -1.9072158 4738.2137
|
||||
1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866985 4738.2137
|
||||
Loop time of 2.13659 on 4 procs for 500 steps with 4000 atoms
|
||||
Loop time of 2.17454 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 101095.806 tau/day, 234.018 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 99331.198 tau/day, 229.933 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.3372 | 1.3773 | 1.4155 | 2.5 | 64.46
|
||||
Neigh | 0.22376 | 0.37791 | 0.57496 | 25.4 | 17.69
|
||||
Comm | 0.20357 | 0.36123 | 0.52777 | 25.5 | 16.91
|
||||
Output | 0.00029254 | 0.00034094 | 0.00039411 | 0.2 | 0.02
|
||||
Modify | 0.0056622 | 0.0082379 | 0.01147 | 2.9 | 0.39
|
||||
Other | | 0.01156 | | | 0.54
|
||||
Pair | 1.1909 | 1.3814 | 1.5474 | 12.7 | 63.53
|
||||
Neigh | 0.24882 | 0.38781 | 0.5563 | 22.6 | 17.83
|
||||
Comm | 0.35985 | 0.38559 | 0.4055 | 3.0 | 17.73
|
||||
Output | 0.00030994 | 0.00033677 | 0.00035214 | 0.1 | 0.02
|
||||
Modify | 0.0060136 | 0.008362 | 0.011491 | 2.6 | 0.38
|
||||
Other | | 0.01102 | | | 0.51
|
||||
|
||||
Nlocal: 1000 ave 1629 max 525 min
|
||||
Nlocal: 1000 ave 1555 max 581 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 8647.25 ave 9725 max 7935 min
|
||||
Nghost: 8695.5 ave 9791 max 8011 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 150494 ave 161009 max 143434 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
Neighs: 150494 ave 160074 max 132359 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
|
||||
Total # of neighbors = 601974
|
||||
Ave neighs/atom = 150.494
|
||||
@ -181,41 +181,40 @@ run 500
|
||||
Memory usage per processor = 3.06519 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866985 4738.2137
|
||||
1550 0.55327017 -6.2750125 0 -5.4453148 -1.9506584 4738.2137
|
||||
1550 0.55327018 -6.2750125 0 -5.4453148 -1.9506585 4738.2137
|
||||
1600 0.54419003 -6.2612622 0 -5.4451812 -1.8559437 4738.2137
|
||||
1650 0.54710034 -6.2661978 0 -5.4457525 -1.8882831 4738.2137
|
||||
1700 0.53665689 -6.2504958 0 -5.4457117 -1.8068004 4738.2137
|
||||
1750 0.54864706 -6.2681124 0 -5.4453476 -1.8662646 4738.2137
|
||||
1800 0.54476202 -6.2615083 0 -5.4445696 -1.8352824 4738.2137
|
||||
1850 0.54142953 -6.2555505 0 -5.4436093 -1.8005654 4738.2137
|
||||
1900 0.53992431 -6.254135 0 -5.444451 -1.7768688 4738.2137
|
||||
1950 0.54665954 -6.2640971 0 -5.4443128 -1.7947032 4738.2137
|
||||
2000 0.54557798 -6.2625416 0 -5.4443793 -1.8072514 4738.2137
|
||||
Loop time of 2.17499 on 4 procs for 500 steps with 4000 atoms
|
||||
1650 0.54710035 -6.2661979 0 -5.4457525 -1.8882833 4738.2137
|
||||
1700 0.53665692 -6.2504957 0 -5.4457116 -1.8068001 4738.2137
|
||||
1750 0.54864726 -6.2681127 0 -5.4453476 -1.8662658 4738.2137
|
||||
1800 0.54476256 -6.2615132 0 -5.4445736 -1.8352921 4738.2137
|
||||
1850 0.54142913 -6.2555501 0 -5.4436094 -1.8005632 4738.2137
|
||||
1900 0.53992543 -6.2541365 0 -5.4444509 -1.7768749 4738.2137
|
||||
1950 0.54666257 -6.2641014 0 -5.4443125 -1.7947215 4738.2137
|
||||
2000 0.54557432 -6.2625445 0 -5.4443876 -1.8072402 4738.2137
|
||||
Loop time of 2.13804 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 99310.978 tau/day, 229.887 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 101026.937 tau/day, 233.859 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.3333 | 1.3705 | 1.397 | 2.0 | 63.01
|
||||
Neigh | 0.24071 | 0.41014 | 0.62928 | 26.6 | 18.86
|
||||
Comm | 0.19069 | 0.37486 | 0.53972 | 26.6 | 17.23
|
||||
Output | 0.00031614 | 0.00035483 | 0.00040388 | 0.2 | 0.02
|
||||
Modify | 0.0057304 | 0.0083074 | 0.01159 | 2.8 | 0.38
|
||||
Other | | 0.01083 | | | 0.50
|
||||
Pair | 1.2063 | 1.3671 | 1.4849 | 9.7 | 63.94
|
||||
Neigh | 0.25593 | 0.41674 | 0.59932 | 24.5 | 19.49
|
||||
Comm | 0.25287 | 0.33513 | 0.39698 | 9.9 | 15.67
|
||||
Output | 0.00024056 | 0.00026721 | 0.00028205 | 0.1 | 0.01
|
||||
Modify | 0.0058651 | 0.0082419 | 0.011365 | 2.7 | 0.39
|
||||
Other | | 0.01061 | | | 0.50
|
||||
|
||||
Nlocal: 1000 ave 1628 max 523 min
|
||||
Nlocal: 1000 ave 1513 max 612 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 8641.5 ave 9769 max 7941 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
Neighs: 151654 ave 163181 max 145045 min
|
||||
Nghost: 8685.25 ave 9861 max 7992 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
Neighs: 151657 ave 173252 max 122114 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 606616
|
||||
Ave neighs/atom = 151.654
|
||||
Total # of neighbors = 606628
|
||||
Ave neighs/atom = 151.657
|
||||
Neighbor list builds = 56
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:09
|
||||
Total wall time: 0:00:08
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
@ -42,7 +42,7 @@ Neighbor list info ...
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 7 7 7
|
||||
rebalancing time: 0.000447989 seconds
|
||||
rebalancing time: 0.000463963 seconds
|
||||
iteration count = 2
|
||||
time weight factor: 1
|
||||
initial/final max load/proc = 1200 1200
|
||||
@ -71,20 +71,20 @@ Step Temp E_pair E_mol TotEng Press
|
||||
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568
|
||||
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
|
||||
Loop time of 1.42972 on 4 procs for 250 steps with 4000 atoms
|
||||
Loop time of 1.40211 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 75539.346 tau/day, 174.860 timesteps/s
|
||||
Performance: 77026.670 tau/day, 178.302 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.34009 | 0.65732 | 1.1925 | 42.3 | 45.98
|
||||
Neigh | 0.1324 | 0.17067 | 0.19962 | 6.6 | 11.94
|
||||
Comm | 0.03502 | 0.5933 | 0.88766 | 45.1 | 41.50
|
||||
Output | 0.0001173 | 0.00012749 | 0.00013947 | 0.1 | 0.01
|
||||
Modify | 0.0024164 | 0.0032778 | 0.0040991 | 1.0 | 0.23
|
||||
Other | | 0.00502 | | | 0.35
|
||||
Pair | 0.35738 | 0.65181 | 1.1696 | 41.3 | 46.49
|
||||
Neigh | 0.13196 | 0.17021 | 0.20914 | 7.5 | 12.14
|
||||
Comm | 0.034142 | 0.57176 | 0.88483 | 44.5 | 40.78
|
||||
Output | 0.0001142 | 0.0001266 | 0.00014806 | 0.1 | 0.01
|
||||
Modify | 0.0023732 | 0.0032824 | 0.0044029 | 1.3 | 0.23
|
||||
Other | | 0.004928 | | | 0.35
|
||||
|
||||
Nlocal: 1000 ave 1263 max 712 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
@ -98,16 +98,16 @@ Ave neighs/atom = 149.325
|
||||
Neighbor list builds = 23
|
||||
Dangerous builds = 0
|
||||
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
|
||||
rebalancing time: 0.000354052 seconds
|
||||
iteration count = 4
|
||||
rebalancing time: 0.000343084 seconds
|
||||
iteration count = 5
|
||||
time weight factor: 1
|
||||
initial/final max load/proc = 1673.83 1097.18
|
||||
initial/final imbalance factor = 1.67383 1.09718
|
||||
x cuts: 0 0.296875 0.453125 0.605469 1
|
||||
initial/final max load/proc = 1.35965 0.878579
|
||||
initial/final imbalance factor = 1.65405 1.06882
|
||||
x cuts: 0 0.304688 0.460938 0.634766 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
run 250
|
||||
Memory usage per processor = 2.7999 Mbytes
|
||||
Memory usage per processor = 2.78273 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
|
||||
300 0.5477618 -6.2678071 0 -5.4463698 -1.997842
|
||||
@ -115,39 +115,39 @@ Step Temp E_pair E_mol TotEng Press
|
||||
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594
|
||||
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161
|
||||
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015
|
||||
Loop time of 1.10579 on 4 procs for 250 steps with 4000 atoms
|
||||
Loop time of 1.06588 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 97667.971 tau/day, 226.083 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 101324.291 tau/day, 234.547 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.47383 | 0.65917 | 0.86391 | 21.2 | 59.61
|
||||
Neigh | 0.12071 | 0.17144 | 0.23972 | 11.6 | 15.50
|
||||
Comm | 0.10061 | 0.26652 | 0.39924 | 24.8 | 24.10
|
||||
Output | 0.00012779 | 0.00014991 | 0.00018096 | 0.2 | 0.01
|
||||
Modify | 0.0021801 | 0.0032307 | 0.0047314 | 1.8 | 0.29
|
||||
Other | | 0.005272 | | | 0.48
|
||||
Pair | 0.45977 | 0.64931 | 0.82184 | 17.0 | 60.92
|
||||
Neigh | 0.11586 | 0.17099 | 0.23942 | 12.5 | 16.04
|
||||
Comm | 0.10905 | 0.23692 | 0.35707 | 18.4 | 22.23
|
||||
Output | 0.00011897 | 0.00014734 | 0.00017262 | 0.2 | 0.01
|
||||
Modify | 0.0020723 | 0.0032738 | 0.0047829 | 2.0 | 0.31
|
||||
Other | | 0.005239 | | | 0.49
|
||||
|
||||
Nlocal: 1000 ave 1479 max 635 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Nghost: 8759.5 ave 9918 max 7969 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 149356 ave 195930 max 110209 min
|
||||
Nlocal: 1000 ave 1435 max 639 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 8679.75 ave 9430 max 7994 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Neighs: 149356 ave 184268 max 102258 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 597424
|
||||
Ave neighs/atom = 149.356
|
||||
Neighbor list builds = 24
|
||||
Dangerous builds = 0
|
||||
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
|
||||
rebalancing time: 0.000221968 seconds
|
||||
rebalancing time: 0.000194073 seconds
|
||||
iteration count = 4
|
||||
time weight factor: 1
|
||||
initial/final max load/proc = 1200.06 1176.79
|
||||
initial/final imbalance factor = 1.20006 1.17679
|
||||
x cuts: 0 0.306641 0.443359 0.595947 1
|
||||
initial/final max load/proc = 0.948736 0.898491
|
||||
initial/final imbalance factor = 1.15657 1.09532
|
||||
x cuts: 0 0.314453 0.451172 0.602173 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
run 250
|
||||
@ -159,27 +159,27 @@ Step Temp E_pair E_mol TotEng Press
|
||||
650 0.54526651 -6.265098 0 -5.4474027 -2.0303672
|
||||
700 0.54369381 -6.263201 0 -5.4478642 -1.9921967
|
||||
750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675
|
||||
Loop time of 1.10659 on 4 procs for 250 steps with 4000 atoms
|
||||
Loop time of 1.02789 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 97597.325 tau/day, 225.920 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 105069.856 tau/day, 243.217 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.59596 | 0.67205 | 0.81576 | 10.9 | 60.73
|
||||
Neigh | 0.098 | 0.18193 | 0.2707 | 16.7 | 16.44
|
||||
Comm | 0.15524 | 0.24375 | 0.40352 | 19.4 | 22.03
|
||||
Output | 0.00013709 | 0.00017041 | 0.00020695 | 0.2 | 0.02
|
||||
Modify | 0.0016487 | 0.0032793 | 0.0050011 | 2.4 | 0.30
|
||||
Other | | 0.005414 | | | 0.49
|
||||
Pair | 0.51012 | 0.64726 | 0.75553 | 11.2 | 62.97
|
||||
Neigh | 0.10374 | 0.17664 | 0.25597 | 15.7 | 17.19
|
||||
Comm | 0.10147 | 0.19583 | 0.28425 | 16.9 | 19.05
|
||||
Output | 0.00011802 | 0.000139 | 0.00015593 | 0.1 | 0.01
|
||||
Modify | 0.0017936 | 0.0032012 | 0.0047436 | 2.3 | 0.31
|
||||
Other | | 0.004817 | | | 0.47
|
||||
|
||||
Nlocal: 1000 ave 1580 max 493 min
|
||||
Nlocal: 1000 ave 1518 max 524 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Nghost: 8736.5 ave 9808 max 8009 min
|
||||
Nghost: 8714.5 ave 9870 max 7980 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 149124 ave 178715 max 132100 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 149124 ave 173877 max 119242 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 596497
|
||||
Ave neighs/atom = 149.124
|
||||
202
examples/balance/log.5Oct16.balance.g++.4
Normal file
202
examples/balance/log.5Oct16.balance.g++.4
Normal file
@ -0,0 +1,202 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 2d circle of particles inside a box with LJ walls
|
||||
|
||||
variable b index 0
|
||||
|
||||
variable x index 50
|
||||
variable y index 20
|
||||
variable d index 20
|
||||
variable v index 5
|
||||
variable w index 2
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
boundary f f p
|
||||
|
||||
lattice hex 0.85
|
||||
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
|
||||
region box block 0 $x 0 $y -0.5 0.5
|
||||
region box block 0 50 0 $y -0.5 0.5
|
||||
region box block 0 50 0 20 -0.5 0.5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 10
|
||||
create_atoms 1 region circle
|
||||
Created 361 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 0.5 87287 loop geom
|
||||
velocity all set $v $w 0 sum yes
|
||||
velocity all set 5 $w 0 sum yes
|
||||
velocity all set 5 2 0 sum yes
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 10.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
|
||||
|
||||
comm_style tiled
|
||||
fix 10 all balance 50 0.9 rcb
|
||||
|
||||
#compute 1 all property/atom proc
|
||||
#variable p atom c_1%10
|
||||
#dump 2 all custom 50 tmp.dump id v_p x y z
|
||||
|
||||
#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
|
||||
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
||||
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
thermo_style custom step temp epair press f_10[3] f_10
|
||||
thermo 100
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Memory usage per processor = 2.48839 Mbytes
|
||||
Step Temp E_pair Press f_10[3] f_10
|
||||
0 25.701528 -29.143179 -1.2407285 3.2354571 1.0526316
|
||||
100 26.269576 -29.713313 7.9052334 1.2742382 1.0304709
|
||||
200 26.368336 -29.809962 1.6412462 1.2520776 1.0083102
|
||||
300 26.479082 -29.920083 2.3678653 1.2299169 1.0193906
|
||||
400 26.522239 -29.965537 6.6787858 1.1855956 1.0083102
|
||||
500 25.725591 -29.168034 0.67065285 1.2520776 1.0083102
|
||||
600 26.247693 -29.692706 7.9887712 1.3074792 1.0083102
|
||||
700 26.237368 -29.676926 1.5987214 1.2409972 1.0083102
|
||||
800 25.889643 -29.431589 4.6160859 1.2631579 1.0083102
|
||||
900 23.635295 -27.372963 9.029962 1.1634349 1.0083102
|
||||
1000 22.571904 -25.87422 1.8936085 1.1301939 1.0193906
|
||||
1100 17.493795 -21.447274 9.502619 1.0858726 1.0193906
|
||||
1200 17.214458 -20.726965 6.3578918 1.0304709 1.0193906
|
||||
1300 16.42404 -19.757268 3.9028429 1.1191136 1.0083102
|
||||
1400 15.012286 -18.095045 1.7699868 1.0858726 1.0193906
|
||||
1500 13.853156 -16.929243 1.0730365 1.0858726 1.0193906
|
||||
1600 13.655251 -16.659753 2.1723498 1.0747922 1.0083102
|
||||
1700 12.675328 -15.550697 1.8710911 1.0415512 1.0193906
|
||||
1800 12.657349 -15.825827 1.9350712 1.0193906 1.0193906
|
||||
1900 12.857141 -15.773 1.7624119 1.0193906 1.0304709
|
||||
2000 11.856547 -14.727128 1.7186493 1.1080332 1.0083102
|
||||
2100 12.113322 -14.953592 1.4400251 1.0415512 1.0193906
|
||||
2200 11.545208 -14.363826 1.1597272 1.0969529 1.0083102
|
||||
2300 11.433966 -14.302533 1.5537689 1.0969529 1.0083102
|
||||
2400 11.577739 -14.385288 1.3175128 1.0526316 1.0193906
|
||||
2500 11.308903 -14.130976 1.0372 1.0304709 1.0193906
|
||||
2600 11.03881 -13.846505 1.498497 1.0304709 1.0083102
|
||||
2700 10.70089 -13.790867 1.4450907 1.0637119 1.0083102
|
||||
2800 10.805792 -13.563219 1.2192081 1.0415512 1.0083102
|
||||
2900 10.421157 -13.168851 1.402862 1.0304709 1.0083102
|
||||
3000 10.400588 -13.097548 1.0337744 1.0526316 1.0083102
|
||||
3100 10.358923 -13.069844 0.90449608 1.0637119 1.0304709
|
||||
3200 10.006549 -12.712754 1.2690601 1.0415512 1.0083102
|
||||
3300 9.6601046 -12.398878 0.9892202 1.0193906 1.0083102
|
||||
3400 9.8691691 -12.644347 1.0763164 1.0526316 1.0193906
|
||||
3500 9.4257858 -12.095325 1.3422009 1.0747922 1.0193906
|
||||
3600 9.8117461 -12.559789 1.0175443 1.0415512 1.0083102
|
||||
3700 9.1821286 -11.849911 1.4515013 1.0415512 1.0083102
|
||||
3800 9.3099882 -12.081373 0.90072272 1.0193906 1.0193906
|
||||
3900 9.478143 -12.141401 1.0850242 1.0193906 1.0083102
|
||||
4000 9.2104886 -11.866265 0.69822096 1.0304709 1.0083102
|
||||
4100 8.8886161 -11.56296 0.89116764 1.0083102 1.0083102
|
||||
4200 8.7477884 -11.435867 1.155131 1.0415512 1.0083102
|
||||
4300 8.8404671 -11.475073 0.73376033 1.0193906 1.0083102
|
||||
4400 9.0720052 -11.722172 1.1153459 1.0193906 1.0193906
|
||||
4500 8.4943391 -11.10353 0.98158121 1.0304709 1.0193906
|
||||
4600 8.6208392 -11.25783 0.52722218 1.0304709 1.0304709
|
||||
4700 8.355727 -10.974506 0.9215792 1.0526316 1.0083102
|
||||
4800 7.9464294 -10.531082 0.96217105 1.0193906 1.0193906
|
||||
4900 8.1538037 -10.74077 0.93322839 1.0526316 1.0083102
|
||||
5000 8.0560766 -10.668117 0.89914093 1.0083102 1.0083102
|
||||
5100 7.8109289 -10.391977 0.89999269 1.0637119 1.0083102
|
||||
5200 7.5452618 -10.199853 0.85038647 1.0415512 1.0083102
|
||||
5300 7.5551774 -10.134568 0.48669864 1.0193906 1.0193906
|
||||
5400 7.5427574 -10.109261 0.51382249 1.0304709 1.0083102
|
||||
5500 7.3322385 -9.8794018 0.39341727 1.0304709 1.0193906
|
||||
5600 7.1576966 -9.7228317 0.49695339 1.0637119 1.0193906
|
||||
5700 6.9753083 -9.5665538 0.63845281 1.0637119 1.0193906
|
||||
5800 7.2002518 -9.7545436 0.8869362 1.0304709 1.0083102
|
||||
5900 6.7877615 -9.4201982 1.150461 1.0415512 1.0083102
|
||||
6000 7.2316113 -9.7609318 0.56956179 1.0083102 1.0083102
|
||||
6100 6.8517997 -9.3662525 0.69127091 1.0083102 1.0193906
|
||||
6200 6.7332571 -9.2601934 0.64092541 1.0747922 1.0193906
|
||||
6300 7.2653962 -9.812989 1.0089331 1.0415512 1.0193906
|
||||
6400 6.9924469 -9.5198187 0.50623927 1.0193906 1.0083102
|
||||
6500 6.7976268 -9.3171977 0.37708413 1.0304709 1.0193906
|
||||
6600 7.1400261 -9.6453688 0.51672188 1.0415512 1.0193906
|
||||
6700 7.0874791 -9.6159675 0.23431446 1.0193906 1.0083102
|
||||
6800 7.0934248 -9.6288017 0.73112796 1.0083102 1.0193906
|
||||
6900 7.0402806 -9.6881643 0.65441466 1.0193906 1.0193906
|
||||
7000 6.6077988 -9.1981347 0.81515889 1.0193906 1.0083102
|
||||
7100 6.6804693 -9.1892523 0.46231433 1.0193906 1.0083102
|
||||
7200 6.7050761 -9.2536735 0.68422675 1.0083102 1.0083102
|
||||
7300 6.6980524 -9.2116982 0.77722939 1.0083102 1.0193906
|
||||
7400 6.9237141 -9.4504319 0.50584321 1.0083102 1.0193906
|
||||
7500 6.7457236 -9.2517367 0.41774845 1.0193906 1.0083102
|
||||
7600 6.140572 -8.6271314 0.47012282 1.0193906 1.0193906
|
||||
7700 6.3154289 -8.8060017 0.30256453 1.0193906 1.0083102
|
||||
7800 6.4817555 -9.0034539 0.48964815 1.0193906 1.0193906
|
||||
7900 6.5509105 -9.046808 0.26620539 1.0304709 1.0083102
|
||||
8000 6.1907919 -8.7009493 0.36431296 1.0193906 1.0083102
|
||||
8100 6.6773106 -9.1825184 0.63034715 1.0193906 1.0083102
|
||||
8200 6.3651832 -8.865283 0.41221098 1.0193906 1.0193906
|
||||
8300 6.5319342 -9.0474918 0.50861431 1.0193906 1.0193906
|
||||
8400 6.0026097 -8.4829924 0.61261898 1.0304709 1.0193906
|
||||
8500 6.264053 -8.7484184 0.22150916 1.0193906 1.0193906
|
||||
8600 6.4822013 -8.9786803 0.79519176 1.0415512 1.0083102
|
||||
8700 6.1133663 -8.5901382 0.66131133 1.0193906 1.0193906
|
||||
8800 5.7750595 -8.2366077 0.54475083 1.0415512 1.0193906
|
||||
8900 5.7948059 -8.2720683 0.66374336 1.0083102 1.0083102
|
||||
9000 6.0180401 -8.4602116 0.35964058 1.0193906 1.0083102
|
||||
9100 5.6468037 -8.1226322 0.33562506 1.0083102 1.0083102
|
||||
9200 6.0286609 -8.4948458 0.81948932 1.0083102 1.0083102
|
||||
9300 5.3272121 -7.7564142 0.59727196 1.0193906 1.0083102
|
||||
9400 5.3686107 -7.8108198 0.49158335 1.0193906 1.0083102
|
||||
9500 5.5578127 -7.9767984 0.54325782 1.0083102 1.0083102
|
||||
9600 5.3535292 -7.7952435 0.51871219 1.0083102 1.0083102
|
||||
9700 5.2229146 -7.6572219 0.82526944 1.0193906 1.0193906
|
||||
9800 5.5316834 -7.9694409 -0.06268606 1.0193906 1.0083102
|
||||
9900 5.3195142 -7.7834343 0.98223661 1.0083102 1.0083102
|
||||
10000 5.4133458 -7.8543365 0.23338829 1.0304709 1.0083102
|
||||
Loop time of 0.41562 on 4 procs for 10000 steps with 361 atoms
|
||||
|
||||
Performance: 10394107.789 tau/day, 24060.435 timesteps/s
|
||||
98.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.061998 | 0.074455 | 0.095533 | 4.7 | 17.91
|
||||
Neigh | 0.065831 | 0.070617 | 0.081226 | 2.4 | 16.99
|
||||
Comm | 0.11365 | 0.14064 | 0.16052 | 5.3 | 33.84
|
||||
Output | 0.0021498 | 0.0023028 | 0.0026829 | 0.5 | 0.55
|
||||
Modify | 0.040329 | 0.04214 | 0.043329 | 0.5 | 10.14
|
||||
Other | | 0.08546 | | | 20.56
|
||||
|
||||
Nlocal: 90.25 ave 91 max 90 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 22 ave 25 max 18 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Neighs: 252.75 ave 342 max 132 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 1011
|
||||
Ave neighs/atom = 2.80055
|
||||
Neighbor list builds = 3495
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
@ -43,7 +43,7 @@ Neighbor list info ...
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 7 7 7
|
||||
rebalancing time: 0.000452042 seconds
|
||||
rebalancing time: 0.000472069 seconds
|
||||
iteration count = 2
|
||||
group weights: fast=1 slow=1
|
||||
initial/final max load/proc = 1200 1200
|
||||
@ -74,20 +74,20 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137
|
||||
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
|
||||
Loop time of 1.48606 on 4 procs for 250 steps with 4000 atoms
|
||||
Loop time of 1.40299 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 72675.623 tau/day, 168.231 timesteps/s
|
||||
Performance: 76978.657 tau/day, 178.191 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.23243 | 0.67 | 1.2235 | 47.4 | 45.09
|
||||
Neigh | 0.17043 | 0.18781 | 0.21572 | 4.1 | 12.64
|
||||
Comm | 0.036635 | 0.61802 | 1.0727 | 51.6 | 41.59
|
||||
Output | 0.00011992 | 0.00013161 | 0.00015426 | 0.1 | 0.01
|
||||
Modify | 0.005506 | 0.0055596 | 0.0056329 | 0.1 | 0.37
|
||||
Other | | 0.004531 | | | 0.30
|
||||
Pair | 0.22572 | 0.65681 | 1.1571 | 45.2 | 46.82
|
||||
Neigh | 0.16769 | 0.18555 | 0.20139 | 3.0 | 13.23
|
||||
Comm | 0.033973 | 0.55042 | 0.99983 | 51.1 | 39.23
|
||||
Output | 0.00012207 | 0.00013012 | 0.00014353 | 0.1 | 0.01
|
||||
Modify | 0.0053966 | 0.0054266 | 0.0054569 | 0.0 | 0.39
|
||||
Other | | 0.004645 | | | 0.33
|
||||
|
||||
Nlocal: 1000 ave 1001 max 999 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
@ -38,7 +38,7 @@ Neighbor list info ...
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 7 7 7
|
||||
rebalancing time: 0.000433922 seconds
|
||||
rebalancing time: 0.00113606 seconds
|
||||
iteration count = 2
|
||||
initial/final max load/proc = 1200 1200
|
||||
initial/final imbalance factor = 1.2 1.2
|
||||
@ -47,7 +47,7 @@ Neighbor list info ...
|
||||
z cuts: 0 1
|
||||
|
||||
balance 1.0 x uniform
|
||||
rebalancing time: 0.000152826 seconds
|
||||
rebalancing time: 0.00050211 seconds
|
||||
iteration count = 0
|
||||
initial/final max load/proc = 1200 1200
|
||||
initial/final imbalance factor = 1.2 1.2
|
||||
@ -57,7 +57,7 @@ balance 1.0 x uniform
|
||||
|
||||
variable weight atom (type==1)*1.0+(type==2)*v_factor
|
||||
balance 1.0 shift x 5 1.1 weight var weight # out weighted_var.txt
|
||||
rebalancing time: 0.000287056 seconds
|
||||
rebalancing time: 0.000926018 seconds
|
||||
iteration count = 2
|
||||
weight variable: weight
|
||||
initial/final max load/proc = 1200 1200
|
||||
@ -67,7 +67,7 @@ balance 1.0 shift x 5 1.1 weight var weight # out weighted_var.txt
|
||||
z cuts: 0 1
|
||||
|
||||
balance 1.0 x uniform
|
||||
rebalancing time: 0.00011611 seconds
|
||||
rebalancing time: 0.000455856 seconds
|
||||
iteration count = 0
|
||||
initial/final max load/proc = 1200 1200
|
||||
initial/final imbalance factor = 1.2 1.2
|
||||
@ -81,7 +81,7 @@ group slow type 2
|
||||
1400 atoms in group slow
|
||||
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor} # out weighted_group.txt
|
||||
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0
|
||||
rebalancing time: 0.000248909 seconds
|
||||
rebalancing time: 0.00071907 seconds
|
||||
iteration count = 2
|
||||
group weights: fast=1 slow=1
|
||||
initial/final max load/proc = 1200 1200
|
||||
@ -110,20 +110,20 @@ Step Temp E_pair E_mol TotEng Press
|
||||
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568
|
||||
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
|
||||
Loop time of 1.41033 on 4 procs for 250 steps with 4000 atoms
|
||||
Loop time of 1.42478 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 76577.913 tau/day, 177.264 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 75800.979 tau/day, 175.465 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.33785 | 0.6592 | 1.1713 | 41.7 | 46.74
|
||||
Neigh | 0.14133 | 0.17129 | 0.19681 | 5.6 | 12.15
|
||||
Comm | 0.039078 | 0.57085 | 0.87566 | 45.3 | 40.48
|
||||
Output | 0.00022721 | 0.00024492 | 0.00026417 | 0.1 | 0.02
|
||||
Modify | 0.0025113 | 0.0033261 | 0.0040808 | 1.0 | 0.24
|
||||
Other | | 0.005427 | | | 0.38
|
||||
Pair | 0.35155 | 0.65282 | 1.1868 | 42.1 | 45.82
|
||||
Neigh | 0.12951 | 0.16927 | 0.20492 | 7.4 | 11.88
|
||||
Comm | 0.03706 | 0.59419 | 0.90483 | 44.8 | 41.70
|
||||
Output | 0.00011921 | 0.00013947 | 0.00015664 | 0.1 | 0.01
|
||||
Modify | 0.0023413 | 0.0032853 | 0.0043154 | 1.2 | 0.23
|
||||
Other | | 0.005085 | | | 0.36
|
||||
|
||||
Nlocal: 1000 ave 1263 max 712 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
@ -75,36 +75,36 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
150 13.992056 47.731988 0 68.714825 140.56926 4738.2137
|
||||
200 11.617635 52.509395 0 69.931491 142.6933 4738.2137
|
||||
250 13.536262 48.330072 0 68.629389 133.91619 4738.2137
|
||||
300 12.619724 50.326376 0 69.25123 132.46494 4738.2137
|
||||
350 14.513005 50.110693 0 71.874758 143.39284 4738.2137
|
||||
400 12.429702 49.690909 0 68.3308 130.0808 4738.2137
|
||||
450 13.928225 50.969523 0 71.856637 144.44675 4738.2137
|
||||
500 13.286368 50.355522 0 70.280091 137.2389 4738.2137
|
||||
Loop time of 4.79482 on 4 procs for 500 steps with 4000 atoms
|
||||
300 12.619739 50.32635 0 69.251226 132.46483 4738.2137
|
||||
350 14.513905 50.104058 0 71.869473 143.37708 4738.2137
|
||||
400 12.410226 49.786147 0 68.396832 130.38693 4738.2137
|
||||
450 13.812498 51.076195 0 71.789763 144.8252 4738.2137
|
||||
500 13.278792 50.270368 0 70.183575 136.8547 4738.2137
|
||||
Loop time of 5.24456 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 45048.596 tau/day, 104.279 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 41185.531 tau/day, 95.337 timesteps/s
|
||||
98.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.85927 | 1.571 | 2.2092 | 51.0 | 32.76
|
||||
Kspace | 0.61247 | 1.982 | 3.2697 | 85.3 | 41.34
|
||||
Neigh | 0.2976 | 0.98099 | 1.8525 | 68.1 | 20.46
|
||||
Comm | 0.090759 | 0.23335 | 0.34356 | 22.4 | 4.87
|
||||
Output | 0.00027442 | 0.00034857 | 0.0004065 | 0.3 | 0.01
|
||||
Modify | 0.013081 | 0.016089 | 0.0201 | 2.3 | 0.34
|
||||
Other | | 0.01104 | | | 0.23
|
||||
Pair | 0.64469 | 1.5898 | 2.5249 | 68.8 | 30.31
|
||||
Kspace | 0.63052 | 2.3872 | 3.9848 | 97.6 | 45.52
|
||||
Neigh | 0.2153 | 0.986 | 1.9625 | 76.8 | 18.80
|
||||
Comm | 0.094079 | 0.25333 | 0.3749 | 23.9 | 4.83
|
||||
Output | 0.0002811 | 0.00035048 | 0.00040078 | 0.3 | 0.01
|
||||
Modify | 0.013268 | 0.016651 | 0.021077 | 2.6 | 0.32
|
||||
Other | | 0.01122 | | | 0.21
|
||||
|
||||
Nlocal: 1000 ave 1853 max 359 min
|
||||
Nlocal: 1000 ave 2010 max 228 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 7773.5 ave 9196 max 6355 min
|
||||
Nghost: 7559.75 ave 9255 max 5915 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 127368 ave 180948 max 71698 min
|
||||
Neighs: 127415 ave 215720 max 45292 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 509471
|
||||
Ave neighs/atom = 127.368
|
||||
Total # of neighbors = 509660
|
||||
Ave neighs/atom = 127.415
|
||||
Neighbor list builds = 124
|
||||
Dangerous builds = 97
|
||||
Total wall time: 0:00:04
|
||||
Total wall time: 0:00:05
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
@ -57,7 +57,7 @@ Neighbor list info ...
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 7 7 7
|
||||
WARNING: No suitable neighbor list found. Neighbor weighted balancing skipped (../imbalance_neigh.cpp:65)
|
||||
WARNING: Balance weight neigh skipped b/c no list found (../imbalance_neigh.cpp:67)
|
||||
Memory usage per processor = 3.0442 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
|
||||
@ -71,26 +71,26 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137
|
||||
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137
|
||||
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
|
||||
Loop time of 2.27598 on 4 procs for 500 steps with 4000 atoms
|
||||
Loop time of 2.30888 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 94904.173 tau/day, 219.686 timesteps/s
|
||||
Performance: 93551.974 tau/day, 216.555 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1158 | 1.4132 | 1.6545 | 19.0 | 62.09
|
||||
Neigh | 0.25541 | 0.38197 | 0.55281 | 20.3 | 16.78
|
||||
Comm | 0.33626 | 0.46086 | 0.58471 | 14.7 | 20.25
|
||||
Output | 0.00030327 | 0.00033396 | 0.0003922 | 0.2 | 0.01
|
||||
Modify | 0.0061643 | 0.0082641 | 0.011169 | 2.4 | 0.36
|
||||
Other | | 0.01137 | | | 0.50
|
||||
Pair | 1.0928 | 1.4128 | 1.6873 | 21.3 | 61.19
|
||||
Neigh | 0.26037 | 0.38342 | 0.55053 | 20.2 | 16.61
|
||||
Comm | 0.33912 | 0.49342 | 0.644 | 18.3 | 21.37
|
||||
Output | 0.00029206 | 0.00033247 | 0.00037789 | 0.2 | 0.01
|
||||
Modify | 0.0062437 | 0.0082552 | 0.010971 | 2.2 | 0.36
|
||||
Other | | 0.01067 | | | 0.46
|
||||
|
||||
Nlocal: 1000 ave 1551 max 604 min
|
||||
Nlocal: 1000 ave 1549 max 605 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 8754.75 ave 9849 max 8074 min
|
||||
Nghost: 8755 ave 9851 max 8071 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 149308 ave 163995 max 129030 min
|
||||
Neighs: 149308 ave 164554 max 128538 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 597231
|
||||
@ -111,26 +111,26 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122 4738.2137
|
||||
950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278 4738.2137
|
||||
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
|
||||
Loop time of 2.14853 on 4 procs for 500 steps with 4000 atoms
|
||||
Loop time of 2.16949 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 100533.652 tau/day, 232.717 timesteps/s
|
||||
Performance: 99562.401 tau/day, 230.469 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1688 | 1.3591 | 1.5126 | 13.1 | 63.26
|
||||
Neigh | 0.24981 | 0.38774 | 0.57835 | 22.5 | 18.05
|
||||
Comm | 0.36101 | 0.38157 | 0.41179 | 3.0 | 17.76
|
||||
Output | 0.00031686 | 0.00034499 | 0.00040627 | 0.2 | 0.02
|
||||
Modify | 0.0059092 | 0.0082516 | 0.011432 | 2.6 | 0.38
|
||||
Other | | 0.01149 | | | 0.53
|
||||
Pair | 1.1466 | 1.3644 | 1.5476 | 15.2 | 62.89
|
||||
Neigh | 0.25492 | 0.38744 | 0.57253 | 22.1 | 17.86
|
||||
Comm | 0.34836 | 0.39805 | 0.45037 | 6.7 | 18.35
|
||||
Output | 0.00028539 | 0.00031531 | 0.00037646 | 0.2 | 0.01
|
||||
Modify | 0.0060055 | 0.008239 | 0.011282 | 2.5 | 0.38
|
||||
Other | | 0.01107 | | | 0.51
|
||||
|
||||
Nlocal: 1000 ave 1559 max 601 min
|
||||
Nlocal: 1000 ave 1569 max 595 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 8717.25 ave 9789 max 8011 min
|
||||
Nghost: 8715.25 ave 9779 max 8018 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 150170 ave 165071 max 129263 min
|
||||
Neighs: 150170 ave 163282 max 132114 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 600678
|
||||
@ -148,29 +148,29 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
1250 0.54848768 -6.2694237 0 -5.4468979 -1.9636797 4738.2137
|
||||
1300 0.54134321 -6.2590728 0 -5.447261 -1.9170271 4738.2137
|
||||
1350 0.53564389 -6.2501521 0 -5.4468871 -1.8642306 4738.2137
|
||||
1400 0.53726925 -6.2518379 0 -5.4461355 -1.8544028 4738.2137
|
||||
1400 0.53726924 -6.2518379 0 -5.4461355 -1.8544028 4738.2137
|
||||
1450 0.54525935 -6.2632653 0 -5.4455808 -1.9072158 4738.2137
|
||||
1500 0.54223342 -6.2591056 0 -5.4459588 -1.886698 4738.2137
|
||||
Loop time of 2.13806 on 4 procs for 500 steps with 4000 atoms
|
||||
1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866985 4738.2137
|
||||
Loop time of 2.17283 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 101026.160 tau/day, 233.857 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 99409.423 tau/day, 230.114 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1911 | 1.3674 | 1.5133 | 12.4 | 63.95
|
||||
Neigh | 0.2394 | 0.37334 | 0.55622 | 22.2 | 17.46
|
||||
Comm | 0.36084 | 0.37761 | 0.409 | 3.0 | 17.66
|
||||
Output | 0.00030899 | 0.00033534 | 0.00039768 | 0.2 | 0.02
|
||||
Modify | 0.0060141 | 0.0083458 | 0.011389 | 2.6 | 0.39
|
||||
Other | | 0.01105 | | | 0.52
|
||||
Pair | 1.1581 | 1.3768 | 1.574 | 15.8 | 63.37
|
||||
Neigh | 0.24753 | 0.3727 | 0.54533 | 21.2 | 17.15
|
||||
Comm | 0.33306 | 0.40373 | 0.47481 | 9.3 | 18.58
|
||||
Output | 0.00036979 | 0.0003832 | 0.00039721 | 0.0 | 0.02
|
||||
Modify | 0.0059896 | 0.0082257 | 0.011168 | 2.5 | 0.38
|
||||
Other | | 0.01095 | | | 0.50
|
||||
|
||||
Nlocal: 1000 ave 1545 max 604 min
|
||||
Nlocal: 1000 ave 1543 max 605 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 8704 ave 9801 max 7983 min
|
||||
Nghost: 8704.5 ave 9803 max 7983 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 150494 ave 165851 max 129789 min
|
||||
Neighs: 150494 ave 166334 max 129306 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 601974
|
||||
@ -180,41 +180,41 @@ Dangerous builds = 0
|
||||
run 500
|
||||
Memory usage per processor = 3.06519 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
1500 0.54223342 -6.2591056 0 -5.4459588 -1.886698 4738.2137
|
||||
1550 0.55327017 -6.2750125 0 -5.4453147 -1.9506581 4738.2137
|
||||
1600 0.54419032 -6.2612626 0 -5.4451812 -1.8559458 4738.2137
|
||||
1650 0.54710059 -6.2661984 0 -5.4457527 -1.8882842 4738.2137
|
||||
1700 0.53665689 -6.2504959 0 -5.4457118 -1.8067985 4738.2137
|
||||
1750 0.54864916 -6.2681196 0 -5.4453516 -1.8662894 4738.2137
|
||||
1800 0.54476391 -6.2615108 0 -5.4445692 -1.8352746 4738.2137
|
||||
1850 0.54142945 -6.2555553 0 -5.4436142 -1.8005732 4738.2137
|
||||
1900 0.53992253 -6.2541407 0 -5.4444594 -1.7768992 4738.2137
|
||||
1950 0.54663678 -6.2640967 0 -5.4443465 -1.7945736 4738.2137
|
||||
2000 0.54563235 -6.2626431 0 -5.4443992 -1.807693 4738.2137
|
||||
Loop time of 2.18212 on 4 procs for 500 steps with 4000 atoms
|
||||
1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866985 4738.2137
|
||||
1550 0.55327018 -6.2750126 0 -5.4453148 -1.9506585 4738.2137
|
||||
1600 0.54419004 -6.2612622 0 -5.4451812 -1.8559437 4738.2137
|
||||
1650 0.54710034 -6.2661938 0 -5.4457484 -1.8882763 4738.2137
|
||||
1700 0.53665691 -6.2504958 0 -5.4457117 -1.8068009 4738.2137
|
||||
1750 0.5486471 -6.2681127 0 -5.4453478 -1.8662656 4738.2137
|
||||
1800 0.54476222 -6.2615086 0 -5.4445695 -1.8352838 4738.2137
|
||||
1850 0.54143048 -6.2555517 0 -5.443609 -1.8005726 4738.2137
|
||||
1900 0.53992511 -6.254136 0 -5.4444508 -1.7768715 4738.2137
|
||||
1950 0.54665895 -6.2640958 0 -5.4443124 -1.7946993 4738.2137
|
||||
2000 0.5455751 -6.2625337 0 -5.4443756 -1.8072242 4738.2137
|
||||
Loop time of 2.20474 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 98986.300 tau/day, 229.135 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 97970.946 tau/day, 226.785 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1776 | 1.3712 | 1.5256 | 13.4 | 62.84
|
||||
Neigh | 0.26314 | 0.4065 | 0.59956 | 22.6 | 18.63
|
||||
Comm | 0.36859 | 0.3845 | 0.41286 | 2.7 | 17.62
|
||||
Output | 0.00031281 | 0.00033575 | 0.00039792 | 0.2 | 0.02
|
||||
Modify | 0.0058827 | 0.0082896 | 0.011639 | 2.7 | 0.38
|
||||
Other | | 0.01133 | | | 0.52
|
||||
Pair | 1.1731 | 1.3783 | 1.5498 | 14.7 | 62.51
|
||||
Neigh | 0.26429 | 0.40654 | 0.59777 | 22.6 | 18.44
|
||||
Comm | 0.36731 | 0.40043 | 0.44935 | 5.2 | 18.16
|
||||
Output | 0.00030565 | 0.00033122 | 0.00039625 | 0.2 | 0.02
|
||||
Modify | 0.0059974 | 0.008266 | 0.01132 | 2.6 | 0.37
|
||||
Other | | 0.01088 | | | 0.49
|
||||
|
||||
Nlocal: 1000 ave 1544 max 605 min
|
||||
Nlocal: 1000 ave 1539 max 607 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 8676.25 ave 9831 max 7985 min
|
||||
Nghost: 8677 ave 9837 max 7981 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
Neighs: 151653 ave 166956 max 130753 min
|
||||
Neighs: 151655 ave 168263 max 129443 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 606611
|
||||
Ave neighs/atom = 151.653
|
||||
Total # of neighbors = 606619
|
||||
Ave neighs/atom = 151.655
|
||||
Neighbor list builds = 56
|
||||
Dangerous builds = 0
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
@ -60,7 +60,7 @@ Neighbor list info ...
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 7 7 7
|
||||
WARNING: No suitable neighbor list found. Neighbor weighted balancing skipped (../imbalance_neigh.cpp:65)
|
||||
WARNING: Balance weight neigh skipped b/c no list found (../imbalance_neigh.cpp:67)
|
||||
Memory usage per processor = 2.90262 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
|
||||
@ -69,34 +69,34 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137
|
||||
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
|
||||
Loop time of 0.943947 on 4 procs for 250 steps with 4000 atoms
|
||||
Loop time of 0.956315 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 114413.252 tau/day, 264.845 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 112933.523 tau/day, 261.420 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.64601 | 0.66027 | 0.67403 | 1.2 | 69.95
|
||||
Neigh | 0.18111 | 0.18828 | 0.1953 | 1.2 | 19.95
|
||||
Comm | 0.072217 | 0.084395 | 0.096822 | 3.4 | 8.94
|
||||
Output | 0.00016904 | 0.00018668 | 0.00020409 | 0.1 | 0.02
|
||||
Modify | 0.005301 | 0.0055165 | 0.0056343 | 0.2 | 0.58
|
||||
Other | | 0.005294 | | | 0.56
|
||||
Pair | 0.5859 | 0.6311 | 0.66986 | 4.1 | 65.99
|
||||
Neigh | 0.16996 | 0.18014 | 0.19678 | 2.4 | 18.84
|
||||
Comm | 0.078254 | 0.13416 | 0.18229 | 10.9 | 14.03
|
||||
Output | 0.00025582 | 0.0002594 | 0.00026608 | 0.0 | 0.03
|
||||
Modify | 0.0051248 | 0.0054137 | 0.0057077 | 0.3 | 0.57
|
||||
Other | | 0.005242 | | | 0.55
|
||||
|
||||
Nlocal: 1000 ave 1004 max 996 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 7674 ave 7678 max 7668 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Neighs: 149349 ave 150214 max 148735 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Nlocal: 1000 ave 1103 max 932 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Nghost: 7617 ave 7871 max 7360 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 149349 ave 169737 max 137211 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 597396
|
||||
Ave neighs/atom = 149.349
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 0
|
||||
run 250
|
||||
Memory usage per processor = 2.9031 Mbytes
|
||||
Memory usage per processor = 2.90266 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
|
||||
300 0.5477618 -6.2678071 0 -5.4463698 -1.997842 4738.2137
|
||||
@ -104,27 +104,27 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137
|
||||
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137
|
||||
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
|
||||
Loop time of 0.886707 on 4 procs for 250 steps with 4000 atoms
|
||||
Loop time of 0.97826 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 121798.994 tau/day, 281.942 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 110400.094 tau/day, 255.556 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.6277 | 0.63292 | 0.64433 | 0.8 | 71.38
|
||||
Neigh | 0.1778 | 0.17937 | 0.18309 | 0.5 | 20.23
|
||||
Comm | 0.05461 | 0.06445 | 0.070518 | 2.3 | 7.27
|
||||
Output | 0.00015926 | 0.00017142 | 0.00018311 | 0.1 | 0.02
|
||||
Modify | 0.0050013 | 0.0050754 | 0.0051844 | 0.1 | 0.57
|
||||
Other | | 0.004719 | | | 0.53
|
||||
Pair | 0.62013 | 0.63258 | 0.63864 | 0.9 | 64.66
|
||||
Neigh | 0.17712 | 0.18068 | 0.18788 | 1.0 | 18.47
|
||||
Comm | 0.14206 | 0.15504 | 0.17108 | 2.7 | 15.85
|
||||
Output | 0.00014997 | 0.00018102 | 0.000247 | 0.3 | 0.02
|
||||
Modify | 0.0047612 | 0.0049355 | 0.0050402 | 0.1 | 0.50
|
||||
Other | | 0.004845 | | | 0.50
|
||||
|
||||
Nlocal: 1000 ave 1008 max 990 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Nghost: 7665.5 ave 7675 max 7650 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 149308 ave 149883 max 148467 min
|
||||
Nlocal: 1000 ave 1003 max 997 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 7662.75 ave 7668 max 7656 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Neighs: 149308 ave 151009 max 146887 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 597231
|
||||
Ave neighs/atom = 149.308
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
@ -38,8 +38,8 @@ Neighbor list info ...
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 7 7 7
|
||||
WARNING: No suitable neighbor list found. Neighbor weighted balancing skipped (../imbalance_neigh.cpp:65)
|
||||
rebalancing time: 0.00040102 seconds
|
||||
WARNING: Balance weight neigh skipped b/c no list found (../imbalance_neigh.cpp:67)
|
||||
rebalancing time: 0.00039506 seconds
|
||||
iteration count = 3
|
||||
neigh weight factor: 0.8
|
||||
initial/final max load/proc = 1200 1000
|
||||
@ -68,20 +68,20 @@ Step Temp E_pair E_mol TotEng Press
|
||||
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568
|
||||
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
|
||||
Loop time of 1.42566 on 4 procs for 250 steps with 4000 atoms
|
||||
Loop time of 1.41104 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
99.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
98.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
balance 1.0 shift x 10 1.0 weight neigh 0.8
|
||||
rebalancing time: 0.000426054 seconds
|
||||
rebalancing time: 0.000409126 seconds
|
||||
iteration count = 10
|
||||
neigh weight factor: 0.8
|
||||
initial/final max load/proc = 1687.06 1002.87
|
||||
initial/final imbalance factor = 1.68662 1.0026
|
||||
x cuts: 0 0.306885 0.452881 0.599335 1
|
||||
initial/final max load/proc = 220132 125739
|
||||
initial/final imbalance factor = 1.75833 1.00436
|
||||
x cuts: 0 0.304443 0.450928 0.626678 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
run 250 post no
|
||||
Memory usage per processor = 2.7999 Mbytes
|
||||
Memory usage per processor = 2.78273 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
|
||||
300 0.5477618 -6.2678071 0 -5.4463698 -1.997842
|
||||
@ -89,16 +89,16 @@ Step Temp E_pair E_mol TotEng Press
|
||||
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594
|
||||
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161
|
||||
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015
|
||||
Loop time of 1.02512 on 4 procs for 250 steps with 4000 atoms
|
||||
Loop time of 1.06236 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
balance 1.0 shift x 10 1.0 weight neigh 0.8
|
||||
rebalancing time: 0.000252008 seconds
|
||||
rebalancing time: 0.000265121 seconds
|
||||
iteration count = 10
|
||||
neigh weight factor: 0.8
|
||||
initial/final max load/proc = 1054.41 1008.56
|
||||
initial/final imbalance factor = 1.05567 1.00976
|
||||
x cuts: 0 0.303588 0.449887 0.597189 1
|
||||
initial/final max load/proc = 147109 128929
|
||||
initial/final imbalance factor = 1.14487 1.00338
|
||||
x cuts: 0 0.304873 0.449926 0.59527 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
run 250 post no
|
||||
@ -110,17 +110,17 @@ Step Temp E_pair E_mol TotEng Press
|
||||
650 0.54526651 -6.265098 0 -5.4474027 -2.0303672
|
||||
700 0.54369381 -6.263201 0 -5.4478642 -1.9921967
|
||||
750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675
|
||||
Loop time of 1.03672 on 4 procs for 250 steps with 4000 atoms
|
||||
Loop time of 1.02794 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
balance 1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6
|
||||
rebalancing time: 0.000267982 seconds
|
||||
rebalancing time: 0.000314951 seconds
|
||||
iteration count = 10
|
||||
neigh weight factor: 0.8
|
||||
time weight factor: 0.6
|
||||
initial/final max load/proc = 1393.27 1116.61
|
||||
initial/final imbalance factor = 1.25201 1.0034
|
||||
x cuts: 0 0.337163 0.448601 0.555904 1
|
||||
initial/final max load/proc = 109.37 93.2369
|
||||
initial/final imbalance factor = 1.17599 1.00252
|
||||
x cuts: 0 0.31323 0.448651 0.560211 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
run 250
|
||||
@ -132,40 +132,40 @@ Step Temp E_pair E_mol TotEng Press
|
||||
900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122
|
||||
950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278
|
||||
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466
|
||||
Loop time of 1.07042 on 4 procs for 250 steps with 4000 atoms
|
||||
Loop time of 1.0482 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 100895.237 tau/day, 233.554 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 103033.455 tau/day, 238.503 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.56894 | 0.64706 | 0.72522 | 8.1 | 60.45
|
||||
Neigh | 0.091286 | 0.17756 | 0.29256 | 20.9 | 16.59
|
||||
Comm | 0.042178 | 0.23721 | 0.40194 | 31.6 | 22.16
|
||||
Output | 0.00012493 | 0.0001505 | 0.00017571 | 0.1 | 0.01
|
||||
Modify | 0.0016253 | 0.0032219 | 0.0054028 | 2.9 | 0.30
|
||||
Other | | 0.005214 | | | 0.49
|
||||
Pair | 0.59706 | 0.65768 | 0.71098 | 5.8 | 62.74
|
||||
Neigh | 0.094988 | 0.17834 | 0.28455 | 19.8 | 17.01
|
||||
Comm | 0.057361 | 0.20341 | 0.34531 | 28.7 | 19.41
|
||||
Output | 0.00013709 | 0.00020045 | 0.0002768 | 0.4 | 0.02
|
||||
Modify | 0.0016088 | 0.0032223 | 0.0052993 | 2.8 | 0.31
|
||||
Other | | 0.005343 | | | 0.51
|
||||
|
||||
Nlocal: 1000 ave 1695 max 489 min
|
||||
Nlocal: 1000 ave 1684 max 506 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 8733.5 ave 10199 max 7650 min
|
||||
Nghost: 8706.25 ave 10207 max 7655 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 150170 ave 163204 max 140236 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 150170 ave 166473 max 132232 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 600681
|
||||
Ave neighs/atom = 150.17
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 0
|
||||
balance 1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6
|
||||
rebalancing time: 0.000238895 seconds
|
||||
rebalancing time: 0.000258207 seconds
|
||||
iteration count = 10
|
||||
neigh weight factor: 0.8
|
||||
time weight factor: 0.6
|
||||
initial/final max load/proc = 1167.62 1095.43
|
||||
initial/final imbalance factor = 1.07395 1.00755
|
||||
x cuts: 0 0.345978 0.449963 0.551398 1
|
||||
initial/final max load/proc = 96.6033 94.7484
|
||||
initial/final imbalance factor = 1.0231 1.00345
|
||||
x cuts: 0 0.315478 0.450068 0.579538 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
run 250
|
||||
@ -177,27 +177,27 @@ Step Temp E_pair E_mol TotEng Press
|
||||
1150 0.54730654 -6.267257 0 -5.4465025 -1.9420678
|
||||
1200 0.5388281 -6.2547963 0 -5.4467562 -1.890178
|
||||
1250 0.54848768 -6.2694237 0 -5.4468979 -1.9636797
|
||||
Loop time of 1.11596 on 4 procs for 250 steps with 4000 atoms
|
||||
Loop time of 1.02694 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 96777.859 tau/day, 224.023 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 105166.691 tau/day, 243.441 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.56315 | 0.66085 | 0.76319 | 10.9 | 59.22
|
||||
Neigh | 0.085606 | 0.18033 | 0.29805 | 21.9 | 16.16
|
||||
Comm | 0.044225 | 0.2661 | 0.4596 | 35.4 | 23.84
|
||||
Output | 0.00015068 | 0.0001756 | 0.00020194 | 0.1 | 0.02
|
||||
Modify | 0.0015557 | 0.0032289 | 0.0054245 | 3.0 | 0.29
|
||||
Other | | 0.005279 | | | 0.47
|
||||
Pair | 0.6025 | 0.64932 | 0.70125 | 5.6 | 63.23
|
||||
Neigh | 0.093299 | 0.17549 | 0.27782 | 19.3 | 17.09
|
||||
Comm | 0.05188 | 0.19352 | 0.31909 | 28.5 | 18.84
|
||||
Output | 0.00022793 | 0.00024354 | 0.00027609 | 0.1 | 0.02
|
||||
Modify | 0.0016394 | 0.0032356 | 0.0052338 | 2.8 | 0.32
|
||||
Other | | 0.005129 | | | 0.50
|
||||
|
||||
Nlocal: 1000 ave 1694 max 462 min
|
||||
Nlocal: 1000 ave 1659 max 494 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 8755.25 ave 10227 max 7675 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 149995 ave 173733 max 125545 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 8646.75 ave 9782 max 7837 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 149995 ave 165511 max 134186 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 599979
|
||||
Ave neighs/atom = 149.995
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
@ -42,7 +42,7 @@ Neighbor list info ...
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 7 7 7
|
||||
rebalancing time: 0.000465155 seconds
|
||||
rebalancing time: 0.001688 seconds
|
||||
iteration count = 10
|
||||
group weights: fast=0.8 slow=2.5
|
||||
storing weight in atom property d_WEIGHT
|
||||
@ -87,26 +87,26 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 4738.2137
|
||||
450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 4738.2137
|
||||
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
|
||||
Loop time of 3.69088 on 2 procs for 500 steps with 4000 atoms
|
||||
Loop time of 4.87829 on 2 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 58522.605 tau/day, 135.469 timesteps/s
|
||||
99.7% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
Performance: 44277.854 tau/day, 102.495 timesteps/s
|
||||
99.2% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.3504 | 2.5517 | 2.7529 | 12.6 | 69.13
|
||||
Neigh | 0.64397 | 0.73493 | 0.82589 | 10.6 | 19.91
|
||||
Comm | 0.084433 | 0.37799 | 0.67156 | 47.7 | 10.24
|
||||
Output | 0.00024199 | 0.00026727 | 0.00029254 | 0.2 | 0.01
|
||||
Modify | 0.013371 | 0.014984 | 0.016598 | 1.3 | 0.41
|
||||
Other | | 0.01102 | | | 0.30
|
||||
Pair | 1.4978 | 2.6788 | 3.8597 | 72.2 | 54.91
|
||||
Neigh | 0.6012 | 0.75888 | 0.91656 | 18.1 | 15.56
|
||||
Comm | 0.073541 | 1.4134 | 2.7532 | 112.7 | 28.97
|
||||
Output | 0.00026584 | 0.00027144 | 0.00027704 | 0.0 | 0.01
|
||||
Modify | 0.013387 | 0.015078 | 0.01677 | 1.4 | 0.31
|
||||
Other | | 0.01191 | | | 0.24
|
||||
|
||||
Nlocal: 2000 ave 2358 max 1642 min
|
||||
Nlocal: 2000 ave 2452 max 1548 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 10463 ave 11178 max 9748 min
|
||||
Nghost: 10456.5 ave 11082 max 9831 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 298070 ave 345748 max 250391 min
|
||||
Neighs: 298070 ave 470560 max 125579 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 596139
|
||||
@ -114,7 +114,7 @@ Ave neighs/atom = 149.035
|
||||
Neighbor list builds = 51
|
||||
Dangerous builds = 0
|
||||
run 500
|
||||
Memory usage per processor = 3.24081 Mbytes
|
||||
Memory usage per processor = 3.24422 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
|
||||
550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236 4738.2137
|
||||
@ -127,26 +127,26 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
900 0.54390586 -6.2615476 0 -5.4458927 -1.9400871 4738.2137
|
||||
950 0.54741732 -6.2665755 0 -5.4456548 -1.9466417 4738.2137
|
||||
1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
|
||||
Loop time of 4.04546 on 2 procs for 500 steps with 4000 atoms
|
||||
Loop time of 5.11308 on 2 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 53393.133 tau/day, 123.595 timesteps/s
|
||||
99.4% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
Performance: 42244.620 tau/day, 97.788 timesteps/s
|
||||
98.9% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.0718 | 2.5709 | 3.0701 | 31.1 | 63.55
|
||||
Neigh | 0.58891 | 0.73311 | 0.87732 | 16.8 | 18.12
|
||||
Comm | 0.068946 | 0.71436 | 1.3598 | 76.4 | 17.66
|
||||
Output | 0.00024986 | 0.00027978 | 0.00030971 | 0.2 | 0.01
|
||||
Modify | 0.012742 | 0.015146 | 0.01755 | 2.0 | 0.37
|
||||
Other | | 0.01163 | | | 0.29
|
||||
Pair | 1.0421 | 2.5613 | 4.0806 | 94.9 | 50.09
|
||||
Neigh | 0.51289 | 0.72321 | 0.93354 | 24.7 | 14.14
|
||||
Comm | 0.069973 | 1.8016 | 3.5332 | 129.0 | 35.24
|
||||
Output | 0.000283 | 0.00028694 | 0.00029087 | 0.0 | 0.01
|
||||
Modify | 0.012173 | 0.015003 | 0.017834 | 2.3 | 0.29
|
||||
Other | | 0.01164 | | | 0.23
|
||||
|
||||
Nlocal: 2000 ave 2384 max 1616 min
|
||||
Nlocal: 2000 ave 2497 max 1503 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 10412.5 ave 11172 max 9653 min
|
||||
Nghost: 10396.5 ave 10916 max 9877 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 300836 ave 358757 max 242914 min
|
||||
Neighs: 300836 ave 484375 max 117296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 601671
|
||||
@ -155,20 +155,20 @@ Neighbor list builds = 51
|
||||
Dangerous builds = 0
|
||||
|
||||
balance 1.0 shift x 10 1.0 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT
|
||||
rebalancing time: 0.000392914 seconds
|
||||
rebalancing time: 0.000527143 seconds
|
||||
iteration count = 10
|
||||
group weights: fast=0.8 slow=2.5
|
||||
storing weight in atom property d_WEIGHT
|
||||
initial/final max load/proc = 3464.4 2800.6
|
||||
initial/final imbalance factor = 1.24172 1.0038
|
||||
x cuts: 0 0.454927 1
|
||||
initial/final max load/proc = 4318.1 2791.9
|
||||
initial/final imbalance factor = 1.54771 1.00068
|
||||
x cuts: 0 0.454292 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
|
||||
fix 0 all balance 50 1.0 shift x 5 1.0 weight var lastweight weight neigh 0.5 weight store WEIGHT
|
||||
|
||||
run 500
|
||||
Memory usage per processor = 3.24081 Mbytes
|
||||
Memory usage per processor = 3.24422 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
|
||||
1050 0.54633412 -6.2656384 0 -5.4463421 -1.9012895 4738.2137
|
||||
@ -179,28 +179,28 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
1300 0.54430333 -6.260995 0 -5.4447442 -1.856351 4738.2137
|
||||
1350 0.55097839 -6.2715909 0 -5.4453299 -1.9014337 4738.2137
|
||||
1400 0.53858139 -6.2526781 0 -5.445008 -1.7965773 4738.2137
|
||||
1450 0.54218439 -6.2574683 0 -5.444395 -1.7901189 4738.2137
|
||||
1500 0.54200616 -6.2571433 0 -5.4443373 -1.8000345 4738.2137
|
||||
Loop time of 3.50707 on 2 procs for 500 steps with 4000 atoms
|
||||
1450 0.54218439 -6.2574683 0 -5.444395 -1.7901188 4738.2137
|
||||
1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000345 4738.2137
|
||||
Loop time of 5.31552 on 2 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 61589.821 tau/day, 142.569 timesteps/s
|
||||
99.8% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
Performance: 40635.746 tau/day, 94.064 timesteps/s
|
||||
98.8% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.4976 | 2.5822 | 2.6669 | 5.3 | 73.63
|
||||
Neigh | 0.69706 | 0.73285 | 0.76865 | 4.2 | 20.90
|
||||
Comm | 0.11878 | 0.16671 | 0.21464 | 11.7 | 4.75
|
||||
Output | 0.00026321 | 0.00028443 | 0.00030565 | 0.1 | 0.01
|
||||
Modify | 0.013662 | 0.014432 | 0.015203 | 0.6 | 0.41
|
||||
Other | | 0.01054 | | | 0.30
|
||||
Pair | 1.157 | 2.6457 | 4.1345 | 91.5 | 49.77
|
||||
Neigh | 0.42836 | 0.74879 | 1.0692 | 37.0 | 14.09
|
||||
Comm | 0.079503 | 1.8922 | 3.7049 | 131.8 | 35.60
|
||||
Output | 0.000386 | 0.00045156 | 0.00051713 | 0.3 | 0.01
|
||||
Modify | 0.010813 | 0.015272 | 0.019732 | 3.6 | 0.29
|
||||
Other | | 0.01305 | | | 0.25
|
||||
|
||||
Nlocal: 2000 ave 2113 max 1887 min
|
||||
Nlocal: 2000 ave 3010 max 990 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 10348.5 ave 10873 max 9824 min
|
||||
Nghost: 10343 ave 12129 max 8557 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 302958 ave 314826 max 291091 min
|
||||
Neighs: 302958 ave 519016 max 86901 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 605917
|
||||
@ -208,43 +208,43 @@ Ave neighs/atom = 151.479
|
||||
Neighbor list builds = 51
|
||||
Dangerous builds = 0
|
||||
run 500
|
||||
Memory usage per processor = 3.24081 Mbytes
|
||||
Memory usage per processor = 3.26138 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
1500 0.54200616 -6.2571433 0 -5.4443373 -1.8000345 4738.2137
|
||||
1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000345 4738.2137
|
||||
1550 0.5371361 -6.250403 0 -5.4449003 -1.7647032 4738.2137
|
||||
1600 0.54679572 -6.2646443 0 -5.4446558 -1.8115723 4738.2137
|
||||
1650 0.53806586 -6.2519009 0 -5.4450039 -1.7409151 4738.2137
|
||||
1700 0.53479442 -6.2469034 0 -5.4449123 -1.7162447 4738.2137
|
||||
1750 0.53714075 -6.2506513 0 -5.4451416 -1.7340207 4738.2137
|
||||
1800 0.52750518 -6.2358818 0 -5.4448219 -1.6875359 4738.2137
|
||||
1850 0.54585315 -6.2629365 0 -5.4443615 -1.7758587 4738.2137
|
||||
1900 0.53011039 -6.238762 0 -5.4437952 -1.6381988 4738.2137
|
||||
1950 0.54287744 -6.2583143 0 -5.4442018 -1.7367676 4738.2137
|
||||
2000 0.52770954 -6.2349628 0 -5.4435964 -1.5593554 4738.2137
|
||||
Loop time of 3.46214 on 2 procs for 500 steps with 4000 atoms
|
||||
1650 0.5380659 -6.2519009 0 -5.4450038 -1.7409149 4738.2137
|
||||
1700 0.53479444 -6.2469033 0 -5.4449122 -1.7162442 4738.2137
|
||||
1750 0.53714076 -6.2506512 0 -5.4451415 -1.7340198 4738.2137
|
||||
1800 0.5275053 -6.2358817 0 -5.4448216 -1.6875364 4738.2137
|
||||
1850 0.54585433 -6.2629377 0 -5.4443609 -1.7758622 4738.2137
|
||||
1900 0.53011157 -6.2387715 0 -5.4438029 -1.6382145 4738.2137
|
||||
1950 0.54287707 -6.2583052 0 -5.4441932 -1.7367502 4738.2137
|
||||
2000 0.52771203 -6.2349621 0 -5.443592 -1.5593714 4738.2137
|
||||
Loop time of 5.52542 on 2 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 62389.230 tau/day, 144.420 timesteps/s
|
||||
99.9% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
Performance: 39092.050 tau/day, 90.491 timesteps/s
|
||||
98.9% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.5495 | 2.5809 | 2.6123 | 2.0 | 74.55
|
||||
Neigh | 0.68762 | 0.72466 | 0.7617 | 4.4 | 20.93
|
||||
Comm | 0.12518 | 0.13173 | 0.13829 | 1.8 | 3.80
|
||||
Output | 0.00024581 | 0.00026357 | 0.00028133 | 0.1 | 0.01
|
||||
Modify | 0.013486 | 0.014313 | 0.015139 | 0.7 | 0.41
|
||||
Other | | 0.01028 | | | 0.30
|
||||
Pair | 0.71557 | 2.5165 | 4.3174 | 113.5 | 45.54
|
||||
Neigh | 0.33034 | 0.71217 | 1.094 | 45.2 | 12.89
|
||||
Comm | 0.079871 | 2.2671 | 4.4544 | 145.3 | 41.03
|
||||
Output | 0.00027609 | 0.00034881 | 0.00042152 | 0.4 | 0.01
|
||||
Modify | 0.0095153 | 0.015319 | 0.021122 | 4.7 | 0.28
|
||||
Other | | 0.01399 | | | 0.25
|
||||
|
||||
Nlocal: 2000 ave 2135 max 1865 min
|
||||
Nlocal: 2000 ave 3030 max 970 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 10311.5 ave 10838 max 9785 min
|
||||
Nghost: 10272.5 ave 12222 max 8323 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 303996 ave 309135 max 298857 min
|
||||
Neighs: 303996 ave 524806 max 83185 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 607992
|
||||
Total # of neighbors = 607991
|
||||
Ave neighs/atom = 151.998
|
||||
Neighbor list builds = 51
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:14
|
||||
Total wall time: 0:00:20
|
||||
@ -1,86 +0,0 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
# 2d polygon nparticle bodies
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style body nparticle 2 6
|
||||
|
||||
read_data data.body
|
||||
orthogonal box = (-15.5322 -15.5322 -0.5) to (15.5322 15.5322 0.5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
100 atoms
|
||||
100 bodies
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style body 5.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
|
||||
fix 1 all nve/body
|
||||
fix 2 all enforce2d
|
||||
|
||||
#compute 1 all body/local type 1 2 3
|
||||
#dump 1 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
|
||||
|
||||
thermo 500
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 12 12 1
|
||||
Memory usage per processor = 3.95249 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -0.63799525 0 0.78760475 -0.15028724
|
||||
500 1.5681124 -1.6060641 0 -0.053632801 0.23819933
|
||||
1000 1.7596217 -1.7290976 0 0.012927885 0.12600944
|
||||
1500 1.5746717 -1.5427933 0 0.016131762 0.21832857
|
||||
2000 1.618761 -1.5563092 0 0.04626422 0.35910744
|
||||
2500 1.7204861 -1.6946681 0 0.0086130985 0.24678557
|
||||
3000 1.7361478 -1.7074239 0 0.011362383 0.28900802
|
||||
3500 1.6065118 -1.5857229 0 0.0047237772 0.43793842
|
||||
4000 1.8157912 -1.7310796 0 0.06655375 0.072835934
|
||||
4500 1.7986098 -1.74424 0 0.036383686 0.25507425
|
||||
5000 1.7182236 -1.7110892 0 -0.010047817 0.19846764
|
||||
5500 1.6246782 -1.5532517 0 0.055179713 0.38134959
|
||||
6000 1.5745671 -1.6393559 0 -0.08053447 0.52399765
|
||||
6500 1.7556697 -1.8091946 0 -0.071081574 0.25253905
|
||||
7000 1.6360783 -1.7317121 0 -0.11199463 0.19797181
|
||||
7500 1.7873556 -1.6976635 0 0.071818533 0.18343875
|
||||
8000 1.4168755 -1.5596513 0 -0.15694455 0.38638741
|
||||
8500 1.659868 -1.6673176 0 -0.024048309 0.17576797
|
||||
9000 1.7040724 -1.6906772 0 -0.0036454592 0.12467855
|
||||
9500 1.6305347 -1.7599864 0 -0.14575703 0.11285404
|
||||
10000 1.7422091 -1.8887509 0 -0.16396383 0.29065244
|
||||
Loop time of 2.35255 on 1 procs for 10000 steps with 100 atoms
|
||||
|
||||
Performance: 1836307.682 tau/day, 4250.712 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.1426 | 2.1426 | 2.1426 | 0.0 | 91.08
|
||||
Neigh | 0.016685 | 0.016685 | 0.016685 | 0.0 | 0.71
|
||||
Comm | 0.026507 | 0.026507 | 0.026507 | 0.0 | 1.13
|
||||
Output | 0.00015068 | 0.00015068 | 0.00015068 | 0.0 | 0.01
|
||||
Modify | 0.16023 | 0.16023 | 0.16023 | 0.0 | 6.81
|
||||
Other | | 0.006348 | | | 0.27
|
||||
|
||||
Nlocal: 100 ave 100 max 100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 82 ave 82 max 82 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 428 ave 428 max 428 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 428
|
||||
Ave neighs/atom = 4.28
|
||||
Neighbor list builds = 776
|
||||
Dangerous builds = 65
|
||||
Total wall time: 0:00:02
|
||||
@ -1,86 +0,0 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
# 2d polygon nparticle bodies
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style body nparticle 2 6
|
||||
|
||||
read_data data.body
|
||||
orthogonal box = (-15.5322 -15.5322 -0.5) to (15.5322 15.5322 0.5)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
100 atoms
|
||||
100 bodies
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style body 5.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
|
||||
fix 1 all nve/body
|
||||
fix 2 all enforce2d
|
||||
|
||||
#compute 1 all body/local type 1 2 3
|
||||
#dump 1 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
|
||||
|
||||
thermo 500
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 12 12 1
|
||||
Memory usage per processor = 3.93947 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -0.63799525 0 0.78760475 -0.15028724
|
||||
500 1.5681124 -1.6060641 0 -0.053632801 0.23819933
|
||||
1000 1.7596217 -1.7290976 0 0.012927885 0.12600944
|
||||
1500 1.5746718 -1.5427933 0 0.016131767 0.21832856
|
||||
2000 1.6187614 -1.5563097 0 0.046264104 0.35910742
|
||||
2500 1.7210993 -1.6955088 0 0.0083794889 0.24522984
|
||||
3000 1.7893309 -1.752166 0 0.019271611 0.1013425
|
||||
3500 1.8922335 -1.7645965 0 0.10871463 0.51383163
|
||||
4000 1.7068531 -1.6754593 0 0.014325271 0.31615632
|
||||
4500 1.6924784 -1.7467381 0 -0.071184511 0.13138777
|
||||
5000 1.7693873 -1.7177224 0 0.033971031 0.15253256
|
||||
5500 1.6829564 -1.6729159 0 -0.0067890531 0.13745591
|
||||
6000 1.9528594 -1.8229135 0 0.11041735 0.21444568
|
||||
6500 1.8827185 -2.0037589 0 -0.13986752 0.044294616
|
||||
7000 1.4723386 -1.6538512 0 -0.19623597 0.23973507
|
||||
7500 1.7787216 -1.729955 0 0.030979334 0.15662931
|
||||
8000 1.8821398 -1.8913154 0 -0.027996988 0.26972798
|
||||
8500 1.7200393 -1.771927 0 -0.069088004 0.48600924
|
||||
9000 1.6731944 -1.702556 0 -0.046093535 0.1259234
|
||||
9500 1.7159449 -1.6430047 0 0.0557808 0.3620955
|
||||
10000 1.4879693 -1.5303732 0 -0.057283589 0.34668456
|
||||
Loop time of 0.853475 on 4 procs for 10000 steps with 100 atoms
|
||||
|
||||
Performance: 5061659.129 tau/day, 11716.804 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.48406 | 0.55202 | 0.69789 | 11.6 | 64.68
|
||||
Neigh | 0.0044043 | 0.0046293 | 0.0049062 | 0.3 | 0.54
|
||||
Comm | 0.091245 | 0.24104 | 0.30869 | 18.0 | 28.24
|
||||
Output | 0.00033712 | 0.00036192 | 0.00039911 | 0.1 | 0.04
|
||||
Modify | 0.040754 | 0.042422 | 0.044837 | 0.7 | 4.97
|
||||
Other | | 0.013 | | | 1.52
|
||||
|
||||
Nlocal: 25 ave 29 max 20 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Nghost: 44 ave 45 max 43 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 104 ave 133 max 64 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 416
|
||||
Ave neighs/atom = 4.16
|
||||
Neighbor list builds = 773
|
||||
Dangerous builds = 31
|
||||
Total wall time: 0:00:00
|
||||
171
examples/body/log.5Oct16.body.g++.1
Normal file
171
examples/body/log.5Oct16.body.g++.1
Normal file
@ -0,0 +1,171 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 2d polygon nparticle bodies
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style body nparticle 2 6
|
||||
|
||||
read_data data.body
|
||||
orthogonal box = (-15.5322 -15.5322 -0.5) to (15.5322 15.5322 0.5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
100 atoms
|
||||
100 bodies
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style body 5.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
fix 1 all nve/body
|
||||
#fix 1 all nvt/body temp 1.44 1.44 1.0
|
||||
fix 2 all enforce2d
|
||||
|
||||
#compute 1 all body/local type 1 2 3
|
||||
#dump 1 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type # zoom 1.6 adiam 1.5 body type 1.0 0
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
thermo 100
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.5
|
||||
ghost atom cutoff = 5.5
|
||||
binsize = 2.75 -> bins = 12 12 1
|
||||
Memory usage per processor = 4.44944 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -0.63799525 0 0.78760475 -0.15028724
|
||||
100 1.642337 -1.0003869 0 0.62552682 0.16140818
|
||||
200 1.470473 -1.2465469 0 0.20922135 0.35146925
|
||||
300 1.4834687 -1.3464946 0 0.12213946 0.40783535
|
||||
400 1.5075814 -1.6170041 0 -0.12449852 0.11302717
|
||||
500 1.5681124 -1.6060641 0 -0.053632801 0.23819933
|
||||
600 1.7129405 -1.6939468 0 0.0018642497 0.46490776
|
||||
700 1.5803869 -1.6182998 0 -0.053716823 0.36807869
|
||||
800 1.6454324 -1.6537709 0 -0.024792836 0.21305673
|
||||
900 1.5454528 -1.6310447 0 -0.10104644 0.22323772
|
||||
1000 1.7596217 -1.7290976 0 0.012927885 0.12600944
|
||||
1100 1.3845533 -1.635035 0 -0.26432721 0.31778997
|
||||
1200 1.6448321 -1.6985254 0 -0.070141617 0.14347958
|
||||
1300 1.6158541 -1.581817 0 0.017878542 0.16186588
|
||||
1400 1.4702758 -1.5210898 0 -0.065516797 0.35241206
|
||||
1500 1.5746718 -1.5427933 0 0.016131764 0.21832857
|
||||
1600 1.5276572 -1.6755951 0 -0.16321447 -0.046196207
|
||||
1700 1.8182153 -1.7471337 0 0.052899504 0.14576284
|
||||
1800 1.8054446 -1.8814075 0 -0.094017352 0.11678153
|
||||
1900 1.6318148 -1.636557 0 -0.021060353 0.29300401
|
||||
2000 1.6187604 -1.5563087 0 0.046264125 0.35910875
|
||||
2100 1.8270056 -1.9189599 0 -0.11022441 -0.031374982
|
||||
2200 1.8203075 -1.8672658 0 -0.065161309 0.38667462
|
||||
2300 2.1336292 -1.8962621 0 0.2160309 0.13286893
|
||||
2400 1.79223 -1.7128682 0 0.061439536 0.30570635
|
||||
2500 1.7208941 -1.6955053 0 0.0081798834 0.24562038
|
||||
2600 1.7755824 -1.7744614 0 -0.016634836 0.11148721
|
||||
2700 1.7308273 -1.744062 0 -0.030542972 0.17938105
|
||||
2800 1.7059134 -1.6131603 0 0.075694024 0.06746694
|
||||
2900 1.7152544 -1.665102 0 0.032999854 0.14918116
|
||||
3000 1.7917767 -1.6654545 0 0.10840436 0.22990289
|
||||
3100 1.7153899 -1.8140872 0 -0.11585128 0.1070804
|
||||
3200 1.5704305 -1.5645642 0 -0.0098380461 0.30331339
|
||||
3300 1.6707504 -1.6224865 0 0.03155641 0.21402203
|
||||
3400 1.7390711 -1.6969145 0 0.024765924 0.25633302
|
||||
3500 1.7601895 -1.7159833 0 0.026604288 0.10350991
|
||||
3600 1.7796243 -1.6848496 0 0.076978483 0.24287746
|
||||
3700 1.8883198 -1.7216992 0 0.14773748 0.071179538
|
||||
3800 1.5757461 -1.6445584 0 -0.084569808 0.23580968
|
||||
3900 1.5509957 -1.6221122 0 -0.086626425 0.2208604
|
||||
4000 1.7403415 -1.6515882 0 0.071349901 0.171317
|
||||
4100 1.6394046 -1.69549 0 -0.072479406 0.18077211
|
||||
4200 1.788413 -1.6410039 0 0.12952501 0.41737981
|
||||
4300 1.7211754 -1.6535323 0 0.050431306 0.1688929
|
||||
4400 1.6034779 -1.7771275 0 -0.18968442 0.091947982
|
||||
4500 1.5692666 -1.6176359 0 -0.064061965 0.31716418
|
||||
4600 1.6454802 -1.5764942 0 0.052531194 0.021026463
|
||||
4700 1.4715049 -1.582096 0 -0.12530612 0.17687943
|
||||
4800 1.5615071 -1.6276031 0 -0.081711137 0.077798682
|
||||
4900 1.6407636 -1.622773 0 0.0015829265 0.28751203
|
||||
5000 1.6390013 -1.7257036 0 -0.10309236 0.35133795
|
||||
5100 1.6540912 -1.7056399 0 -0.068089648 0.52254354
|
||||
5200 1.6438013 -1.7568895 0 -0.12952624 0.16423828
|
||||
5300 1.6791806 -1.756297 0 -0.093908192 0.3151943
|
||||
5400 1.7527095 -1.729977 0 0.0052053655 0.29874227
|
||||
5500 1.7604924 -1.6920395 0 0.050847912 0.2062502
|
||||
5600 1.8225025 -1.6746221 0 0.12965535 0.29423091
|
||||
5700 1.6896356 -1.6591445 0 0.013594822 0.41582329
|
||||
5800 1.575776 -1.6605307 0 -0.10051246 0.17434812
|
||||
5900 1.6893771 -1.6046258 0 0.067857462 0.188486
|
||||
6000 1.6506959 -1.6295482 0 0.0046407782 0.18737656
|
||||
6100 1.8137143 -1.6634096 0 0.13216758 0.22425414
|
||||
6200 1.6337368 -1.6016206 0 0.015778794 0.17026591
|
||||
6300 1.6232904 -1.7102709 0 -0.10321339 0.22621086
|
||||
6400 1.8146767 -1.7354533 0 0.061076657 0.25907309
|
||||
6500 1.5565608 -1.8652953 0 -0.32430015 0.096916202
|
||||
6600 1.6366532 -1.65732 0 -0.037033272 0.30276466
|
||||
6700 1.6612051 -1.6621545 0 -0.017561423 0.16685109
|
||||
6800 1.5574268 -1.6082827 0 -0.066430166 0.37630931
|
||||
6900 1.6556225 -1.6744213 0 -0.035355078 0.11599545
|
||||
7000 1.5078585 -1.6049482 0 -0.11216833 0.37716682
|
||||
7100 1.6147622 -1.7044793 0 -0.10586467 0.48915924
|
||||
7200 1.8022216 -1.7117836 0 0.072415791 0.24007939
|
||||
7300 1.6302834 -1.8522784 0 -0.23829784 0.19326557
|
||||
7400 1.7108472 -1.8993043 0 -0.20556558 0.34554364
|
||||
7500 1.8570536 -1.7135598 0 0.12492326 0.53728185
|
||||
7600 1.7812105 -1.7239897 0 0.039408716 0.44348124
|
||||
7700 1.8724942 -1.7871204 0 0.066648837 0.2529344
|
||||
7800 1.8237412 -1.6467621 0 0.15874169 0.2354529
|
||||
7900 1.7222899 -1.7254585 0 -0.02039155 0.13271481
|
||||
8000 1.6839 -1.5913695 0 0.075691547 0.011932379
|
||||
8100 1.599835 -1.672507 0 -0.088670351 0.11203274
|
||||
8200 1.8369376 -1.7464532 0 0.072115105 0.21380276
|
||||
8300 1.9603301 -1.9121791 0 0.02854768 0.18178367
|
||||
8400 1.7903688 -1.8798475 0 -0.10738231 0.37173469
|
||||
8500 1.687183 -1.760587 0 -0.090275846 0.23751647
|
||||
8600 1.6515772 -1.7918091 0 -0.15674775 0.099895142
|
||||
8700 1.7083909 -1.7297068 0 -0.038399775 0.57093506
|
||||
8800 1.6150569 -1.6976608 0 -0.098754502 0.15348519
|
||||
8900 1.5452011 -1.7517421 0 -0.22199306 0.22143091
|
||||
9000 1.7498686 -1.8569695 0 -0.12459962 0.1989093
|
||||
9100 1.6287336 -1.7505293 0 -0.13808305 0.23881397
|
||||
9200 1.5431194 -1.6845999 0 -0.15691169 0.10646288
|
||||
9300 1.4900229 -1.5671955 0 -0.092072887 0.31588548
|
||||
9400 1.523362 -1.5531592 0 -0.045030785 0.21546483
|
||||
9500 1.5783775 -1.65292 0 -0.090326215 0.25980559
|
||||
9600 1.9192786 -1.9303222 0 -0.030236392 -0.0046632743
|
||||
9700 1.747544 -1.7886479 0 -0.058579385 0.38543046
|
||||
9800 1.6713187 -1.6842507 0 -0.029645137 0.17982115
|
||||
9900 1.7707351 -1.6638268 0 0.089200949 0.2983883
|
||||
10000 1.6466807 -1.592436 0 0.037777866 0.12761693
|
||||
Loop time of 2.33651 on 1 procs for 10000 steps with 100 atoms
|
||||
|
||||
Performance: 1848909.758 tau/day, 4279.884 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.1308 | 2.1308 | 2.1308 | 0.0 | 91.20
|
||||
Neigh | 0.011168 | 0.011168 | 0.011168 | 0.0 | 0.48
|
||||
Comm | 0.02469 | 0.02469 | 0.02469 | 0.0 | 1.06
|
||||
Output | 0.00063729 | 0.00063729 | 0.00063729 | 0.0 | 0.03
|
||||
Modify | 0.15896 | 0.15896 | 0.15896 | 0.0 | 6.80
|
||||
Other | | 0.01025 | | | 0.44
|
||||
|
||||
Nlocal: 100 ave 100 max 100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 82 ave 82 max 82 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 467 ave 467 max 467 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 467
|
||||
Ave neighs/atom = 4.67
|
||||
Neighbor list builds = 468
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
171
examples/body/log.5Oct16.body.g++.4
Normal file
171
examples/body/log.5Oct16.body.g++.4
Normal file
@ -0,0 +1,171 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 2d polygon nparticle bodies
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style body nparticle 2 6
|
||||
|
||||
read_data data.body
|
||||
orthogonal box = (-15.5322 -15.5322 -0.5) to (15.5322 15.5322 0.5)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
100 atoms
|
||||
100 bodies
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style body 5.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
fix 1 all nve/body
|
||||
#fix 1 all nvt/body temp 1.44 1.44 1.0
|
||||
fix 2 all enforce2d
|
||||
|
||||
#compute 1 all body/local type 1 2 3
|
||||
#dump 1 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type # zoom 1.6 adiam 1.5 body type 1.0 0
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
thermo 100
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.5
|
||||
ghost atom cutoff = 5.5
|
||||
binsize = 2.75 -> bins = 12 12 1
|
||||
Memory usage per processor = 4.43864 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -0.63799525 0 0.78760475 -0.15028724
|
||||
100 1.642337 -1.0003869 0 0.62552682 0.16140818
|
||||
200 1.470473 -1.2465469 0 0.20922135 0.35146925
|
||||
300 1.4834687 -1.3464946 0 0.12213946 0.40783535
|
||||
400 1.5075814 -1.6170041 0 -0.12449852 0.11302717
|
||||
500 1.5681124 -1.6060641 0 -0.053632801 0.23819933
|
||||
600 1.7129405 -1.6939468 0 0.0018642497 0.46490776
|
||||
700 1.5803869 -1.6182998 0 -0.053716823 0.36807869
|
||||
800 1.6454324 -1.6537709 0 -0.024792836 0.21305673
|
||||
900 1.5454528 -1.6310447 0 -0.10104644 0.22323772
|
||||
1000 1.7596217 -1.7290976 0 0.012927885 0.12600944
|
||||
1100 1.3845533 -1.635035 0 -0.26432721 0.31778997
|
||||
1200 1.6448321 -1.6985254 0 -0.070141617 0.14347958
|
||||
1300 1.6158541 -1.581817 0 0.017878542 0.16186588
|
||||
1400 1.4702758 -1.5210898 0 -0.065516796 0.35241206
|
||||
1500 1.5746718 -1.5427933 0 0.016131765 0.21832856
|
||||
1600 1.5276572 -1.6755951 0 -0.16321446 -0.046196204
|
||||
1700 1.8182153 -1.7471336 0 0.052899516 0.14576285
|
||||
1800 1.8054446 -1.8814074 0 -0.094017286 0.11678173
|
||||
1900 1.6318146 -1.636557 0 -0.021060549 0.2930043
|
||||
2000 1.6187614 -1.5563095 0 0.046264283 0.3591072
|
||||
2100 1.8270046 -1.9189568 0 -0.11022215 -0.031366859
|
||||
2200 1.8203171 -1.8672823 0 -0.065168391 0.38665482
|
||||
2300 2.1336582 -1.8962717 0 0.21604988 0.13283887
|
||||
2400 1.7923604 -1.7129915 0 0.061445317 0.30554793
|
||||
2500 1.7207328 -1.694912 0 0.008613452 0.24608272
|
||||
2600 1.7761079 -1.7743463 0 -0.015999568 0.11128836
|
||||
2700 1.7327782 -1.7433093 0 -0.027858862 0.17923355
|
||||
2800 1.6869096 -1.6050313 0 0.065009255 0.082020625
|
||||
2900 1.723365 -1.6453122 0 0.06081914 0.11381101
|
||||
3000 1.759037 -1.7499957 0 -0.008549105 0.12711249
|
||||
3100 1.7608876 -1.8502753 0 -0.10699653 0.10597269
|
||||
3200 1.6030658 -1.6772861 0 -0.090250949 0.16058698
|
||||
3300 1.6136204 -1.6247049 0 -0.027220627 0.27194341
|
||||
3400 1.7126562 -1.6002267 0 0.095302885 0.034174254
|
||||
3500 1.5286242 -1.5693205 0 -0.055982557 -0.028526272
|
||||
3600 1.5529814 -1.6309948 0 -0.093543248 0.25627254
|
||||
3700 1.4066962 -1.4583439 0 -0.06571463 0.36890582
|
||||
3800 1.5736098 -1.5849626 0 -0.027088852 0.19376983
|
||||
3900 1.5819362 -1.6452885 0 -0.07917158 0.17494451
|
||||
4000 1.806905 -1.7114262 0 0.077409698 0.059568431
|
||||
4100 1.7116803 -1.7160461 0 -0.02148265 0.12178783
|
||||
4200 1.8262315 -1.6682893 0 0.13967987 0.25082769
|
||||
4300 1.7548351 -1.6835554 0 0.053731392 0.39252317
|
||||
4400 1.7564816 -1.8020325 0 -0.063115749 0.18973764
|
||||
4500 1.727529 -1.771176 0 -0.06092227 0.51752631
|
||||
4600 1.633861 -1.7554104 0 -0.13788808 0.43310585
|
||||
4700 1.6678523 -1.8066719 0 -0.15549814 -0.086702533
|
||||
4800 1.5903598 -1.7410621 0 -0.1666059 0.064914366
|
||||
4900 1.4894085 -1.5982645 0 -0.12375007 0.23124626
|
||||
5000 1.5422574 -1.6830449 0 -0.15621011 0.12943511
|
||||
5100 1.6123243 -1.6577202 0 -0.061519159 0.26031057
|
||||
5200 1.6815554 -1.6889534 0 -0.024213484 0.1747903
|
||||
5300 1.6502994 -1.5929462 0 0.040850243 0.25623758
|
||||
5400 1.5900521 -1.8240806 0 -0.24992903 0.17822148
|
||||
5500 1.6976803 -1.8370034 0 -0.15629992 0.30793026
|
||||
5600 1.737085 -1.6873775 0 0.032336607 0.32235718
|
||||
5700 1.6995769 -1.6328398 0 0.04974131 0.22932613
|
||||
5800 1.6299367 -1.6582188 0 -0.044581533 0.33036589
|
||||
5900 1.6232041 -1.6456588 0 -0.038686805 0.20701623
|
||||
6000 1.6912228 -1.6401907 0 0.034119867 0.091519693
|
||||
6100 1.6314651 -1.6045998 0 0.010550658 0.32331621
|
||||
6200 1.7575091 -1.7271281 0 0.012805903 0.14214943
|
||||
6300 1.6830653 -1.7955472 0 -0.12931258 0.38730996
|
||||
6400 1.6323392 -1.7470603 0 -0.13104448 0.16724215
|
||||
6500 1.537874 -1.7277794 0 -0.20528423 0.28976791
|
||||
6600 1.8375539 -1.8388229 0 -0.019644528 0.31704541
|
||||
6700 1.7519102 -1.7739002 0 -0.039509043 0.19065098
|
||||
6800 1.4602447 -1.6902787 0 -0.24463645 0.20244553
|
||||
6900 1.6734836 -1.72224 0 -0.065491224 0.27092829
|
||||
7000 1.8166001 -1.7288037 0 0.069630392 0.43514063
|
||||
7100 1.9080746 -1.7849767 0 0.10401717 0.086258744
|
||||
7200 1.6346559 -1.602179 0 0.016130393 0.37208486
|
||||
7300 1.669382 -1.594527 0 0.058161153 0.12543161
|
||||
7400 1.5858819 -1.447937 0 0.12208615 0.42666321
|
||||
7500 1.6947983 -1.637715 0 0.040135322 -0.020875259
|
||||
7600 1.7085903 -1.6810854 0 0.010419044 0.1341074
|
||||
7700 1.5780919 -1.6213683 0 -0.059057356 0.3826822
|
||||
7800 1.8079476 -1.761193 0 0.028675183 0.034143718
|
||||
7900 1.836977 -1.8401332 0 -0.021525986 0.21458105
|
||||
8000 1.9135057 -1.8302694 0 0.064101272 0.23217665
|
||||
8100 1.8606829 -1.6984146 0 0.14366143 0.18168582
|
||||
8200 1.7474236 -1.7574166 0 -0.027467252 0.26529178
|
||||
8300 1.7637155 -1.7861969 0 -0.040118627 0.12298468
|
||||
8400 1.6564242 -1.477104 0 0.16275596 0.14143164
|
||||
8500 1.5868929 -1.6520125 0 -0.080988476 0.22461508
|
||||
8600 1.7556628 -1.7647169 0 -0.026610688 0.19913257
|
||||
8700 1.804704 -1.7892113 0 -0.0025543811 0.2825016
|
||||
8800 1.6511248 -1.8632147 0 -0.22860119 0.041019097
|
||||
8900 1.8323591 -1.7923506 0 0.021684941 0.21335945
|
||||
9000 1.9100569 -1.955559 0 -0.064602644 0.158775
|
||||
9100 1.7562572 -1.8720716 0 -0.13337695 0.19662119
|
||||
9200 1.6566561 -1.9406507 0 -0.30056122 0.12296597
|
||||
9300 1.8367792 -1.9060138 0 -0.087602325 0.19447518
|
||||
9400 1.8420592 -1.6318148 0 0.19182383 0.50726082
|
||||
9500 1.7773475 -1.6973532 0 0.062220818 0.2487172
|
||||
9600 1.6545313 -1.701977 0 -0.063991036 0.20549434
|
||||
9700 1.7463358 -1.8329845 0 -0.10411212 0.15498427
|
||||
9800 1.7799071 -1.7889616 0 -0.026853542 0.3169291
|
||||
9900 1.5838158 -1.718909 0 -0.15093133 0.46050618
|
||||
10000 1.6100625 -1.7018091 0 -0.10784725 0.10312591
|
||||
Loop time of 0.849795 on 4 procs for 10000 steps with 100 atoms
|
||||
|
||||
Performance: 5083579.790 tau/day, 11767.546 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.47067 | 0.53757 | 0.61119 | 7.9 | 63.26
|
||||
Neigh | 0.0030298 | 0.0032511 | 0.0035295 | 0.3 | 0.38
|
||||
Comm | 0.1592 | 0.23416 | 0.30247 | 12.4 | 27.56
|
||||
Output | 0.0015244 | 0.0016521 | 0.0018895 | 0.4 | 0.19
|
||||
Modify | 0.039954 | 0.0415 | 0.044199 | 0.8 | 4.88
|
||||
Other | | 0.03166 | | | 3.73
|
||||
|
||||
Nlocal: 25 ave 28 max 23 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Nghost: 47.25 ave 49 max 42 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 113.25 ave 132 max 104 min
|
||||
Histogram: 2 0 1 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 453
|
||||
Ave neighs/atom = 4.53
|
||||
Neighbor list builds = 483
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (21 Sep 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
|
||||
|
||||
units real
|
||||
@ -18,6 +18,7 @@ pair_style lj/charmm/coul/charmm 8 12
|
||||
pair_modify mix arithmetic
|
||||
|
||||
fix cmap all cmap charmm22.cmap
|
||||
Reading potential file charmm22.cmap with DATE: 2016-09-26
|
||||
fix_modify cmap energy yes
|
||||
|
||||
read_data gagg.data fix cmap crossterm CMAP
|
||||
@ -169,21 +170,21 @@ Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
|
||||
98000 27.895969 -0.7496449 1.3072185 4.2611888 4.3726077 -2.1320701 0.15376665
|
||||
99000 28.517889 -1.2183957 1.279778 3.957647 4.2638434 -2.2888407 0.042705003
|
||||
100000 28.109211 -1.2538948 0.83671785 4.3734766 4.544545 -2.3076497 0.042189096
|
||||
Loop time of 2.96683 on 1 procs for 100000 steps with 34 atoms
|
||||
Loop time of 2.84552 on 1 procs for 100000 steps with 34 atoms
|
||||
|
||||
Performance: 5824.390 ns/day, 0.004 hours/ns, 33705.963 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 6072.706 ns/day, 0.004 hours/ns, 35142.973 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.98759 | 0.98759 | 0.98759 | 0.0 | 33.29
|
||||
Bond | 1.6463 | 1.6463 | 1.6463 | 0.0 | 55.49
|
||||
Neigh | 0.007688 | 0.007688 | 0.007688 | 0.0 | 0.26
|
||||
Comm | 0.012214 | 0.012214 | 0.012214 | 0.0 | 0.41
|
||||
Output | 0.0010295 | 0.0010295 | 0.0010295 | 0.0 | 0.03
|
||||
Modify | 0.25684 | 0.25684 | 0.25684 | 0.0 | 8.66
|
||||
Other | | 0.05519 | | | 1.86
|
||||
Pair | 0.94207 | 0.94207 | 0.94207 | 0.0 | 33.11
|
||||
Bond | 1.6125 | 1.6125 | 1.6125 | 0.0 | 56.67
|
||||
Neigh | 0.0073986 | 0.0073986 | 0.0073986 | 0.0 | 0.26
|
||||
Comm | 0.012739 | 0.012739 | 0.012739 | 0.0 | 0.45
|
||||
Output | 0.00075531 | 0.00075531 | 0.00075531 | 0.0 | 0.03
|
||||
Modify | 0.21483 | 0.21483 | 0.21483 | 0.0 | 7.55
|
||||
Other | | 0.05524 | | | 1.94
|
||||
|
||||
Nlocal: 34 ave 34 max 34 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (21 Sep 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
|
||||
|
||||
units real
|
||||
@ -18,6 +18,7 @@ pair_style lj/charmm/coul/charmm 8 12
|
||||
pair_modify mix arithmetic
|
||||
|
||||
fix cmap all cmap charmm22.cmap
|
||||
Reading potential file charmm22.cmap with DATE: 2016-09-26
|
||||
fix_modify cmap energy yes
|
||||
|
||||
read_data gagg.data fix cmap crossterm CMAP
|
||||
@ -169,21 +170,21 @@ Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
|
||||
98000 27.981746 -1.2380545 0.84847869 4.311441 4.7340377 -2.4270441 0.023565612
|
||||
99000 27.476625 -0.8569146 0.82550381 4.1656963 4.4064921 -2.4169708 0.160814
|
||||
100000 26.121325 -0.63610855 1.0803389 4.9257118 4.7073263 -2.4010334 0.066303044
|
||||
Loop time of 2.60487 on 4 procs for 100000 steps with 34 atoms
|
||||
Loop time of 2.693 on 4 procs for 100000 steps with 34 atoms
|
||||
|
||||
Performance: 6633.735 ns/day, 0.004 hours/ns, 38389.667 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 6416.646 ns/day, 0.004 hours/ns, 37133.367 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.066848 | 0.26055 | 0.6843 | 48.6 | 10.00
|
||||
Bond | 0.067332 | 0.45486 | 0.93545 | 55.1 | 17.46
|
||||
Neigh | 0.0078266 | 0.007863 | 0.0078835 | 0.0 | 0.30
|
||||
Comm | 0.41829 | 1.3207 | 1.8951 | 50.8 | 50.70
|
||||
Output | 0.0033038 | 0.0036355 | 0.0040481 | 0.4 | 0.14
|
||||
Modify | 0.040861 | 0.15162 | 0.27091 | 27.3 | 5.82
|
||||
Other | | 0.4057 | | | 15.57
|
||||
Pair | 0.065478 | 0.2501 | 0.63682 | 45.6 | 9.29
|
||||
Bond | 0.066944 | 0.44772 | 0.88814 | 53.7 | 16.63
|
||||
Neigh | 0.0076509 | 0.0077319 | 0.0078275 | 0.1 | 0.29
|
||||
Comm | 0.57917 | 1.4166 | 1.9823 | 46.9 | 52.60
|
||||
Output | 0.0033755 | 0.0035856 | 0.0037644 | 0.2 | 0.13
|
||||
Modify | 0.03866 | 0.1366 | 0.23978 | 24.6 | 5.07
|
||||
Other | | 0.4306 | | | 15.99
|
||||
|
||||
Nlocal: 8.5 ave 15 max 2 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Big colloid particles and small LJ particles
|
||||
|
||||
units lj
|
||||
@ -114,20 +114,20 @@ Step Temp E_pair TotEng Press Volume
|
||||
48000 2.0056151 0.087885527 2.0912722 0.94935203 3824.2309
|
||||
49000 2.0079615 0.089440768 2.0951712 0.97596247 3781.8079
|
||||
50000 1.9875181 0.10628651 2.0915963 1.1315334 3749.1501
|
||||
Loop time of 8.47628 on 1 procs for 50000 steps with 900 atoms
|
||||
Loop time of 8.34943 on 1 procs for 50000 steps with 900 atoms
|
||||
|
||||
Performance: 2548287.987 tau/day, 5898.815 timesteps/s
|
||||
Performance: 2587004.175 tau/day, 5988.436 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.0947 | 4.0947 | 4.0947 | 0.0 | 48.31
|
||||
Neigh | 1.3526 | 1.3526 | 1.3526 | 0.0 | 15.96
|
||||
Comm | 0.31602 | 0.31602 | 0.31602 | 0.0 | 3.73
|
||||
Output | 0.0005331 | 0.0005331 | 0.0005331 | 0.0 | 0.01
|
||||
Modify | 2.4242 | 2.4242 | 2.4242 | 0.0 | 28.60
|
||||
Other | | 0.2882 | | | 3.40
|
||||
Pair | 3.9819 | 3.9819 | 3.9819 | 0.0 | 47.69
|
||||
Neigh | 1.3743 | 1.3743 | 1.3743 | 0.0 | 16.46
|
||||
Comm | 0.31324 | 0.31324 | 0.31324 | 0.0 | 3.75
|
||||
Output | 0.00052619 | 0.00052619 | 0.00052619 | 0.0 | 0.01
|
||||
Modify | 2.3748 | 2.3748 | 2.3748 | 0.0 | 28.44
|
||||
Other | | 0.3047 | | | 3.65
|
||||
|
||||
Nlocal: 900 ave 900 max 900 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Big colloid particles and small LJ particles
|
||||
|
||||
units lj
|
||||
@ -114,20 +114,20 @@ Step Temp E_pair TotEng Press Volume
|
||||
48000 2.0168306 0.082111421 2.0967011 0.9214563 3829.1155
|
||||
49000 2.0007804 0.098241181 2.0967985 0.93140657 3755.3901
|
||||
50000 2.0213773 0.071280328 2.0904116 0.9408025 3734.5105
|
||||
Loop time of 3.62754 on 4 procs for 50000 steps with 900 atoms
|
||||
Loop time of 3.66837 on 4 procs for 50000 steps with 900 atoms
|
||||
|
||||
Performance: 5954453.961 tau/day, 13783.458 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 5888181.024 tau/day, 13630.049 timesteps/s
|
||||
98.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.0162 | 1.0554 | 1.0927 | 2.9 | 29.09
|
||||
Neigh | 0.33396 | 0.34264 | 0.35093 | 1.0 | 9.45
|
||||
Comm | 0.73343 | 0.79932 | 0.87689 | 5.7 | 22.03
|
||||
Output | 0.00097108 | 0.0010269 | 0.0011532 | 0.2 | 0.03
|
||||
Modify | 1.1624 | 1.1976 | 1.2436 | 3.2 | 33.01
|
||||
Other | | 0.2316 | | | 6.38
|
||||
Pair | 1.0038 | 1.0256 | 1.0441 | 1.4 | 27.96
|
||||
Neigh | 0.33784 | 0.35406 | 0.36994 | 2.1 | 9.65
|
||||
Comm | 0.82073 | 0.85742 | 0.88285 | 2.5 | 23.37
|
||||
Output | 0.00096369 | 0.0010209 | 0.0011663 | 0.3 | 0.03
|
||||
Modify | 1.178 | 1.1807 | 1.1825 | 0.1 | 32.19
|
||||
Other | | 0.2496 | | | 6.80
|
||||
|
||||
Nlocal: 225 ave 234 max 208 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Pure Cu crystal, structure created by LAMMPS, qeq off
|
||||
|
||||
units metal
|
||||
@ -61,20 +61,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
|
||||
8 10.077179 -3.5063151 -3.5076126 -3.5076126 0 28.578403 3023.4645 14.46 14.46 14.46 0
|
||||
9 10.071123 -3.5063151 -3.5076118 -3.5076118 0 28.865545 3023.4645 14.46 14.46 14.46 0
|
||||
10 10.06436 -3.5063151 -3.5076109 -3.5076109 0 29.186292 3023.4645 14.46 14.46 14.46 0
|
||||
Loop time of 0.244377 on 1 procs for 10 steps with 256 atoms
|
||||
Loop time of 0.244011 on 1 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 0.707 ns/day, 33.941 hours/ns, 40.920 timesteps/s
|
||||
100.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.708 ns/day, 33.890 hours/ns, 40.982 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.24393 | 0.24393 | 0.24393 | 0.0 | 99.82
|
||||
Pair | 0.24357 | 0.24357 | 0.24357 | 0.0 | 99.82
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00022697 | 0.00022697 | 0.00022697 | 0.0 | 0.09
|
||||
Output | 0.00011015 | 0.00011015 | 0.00011015 | 0.0 | 0.05
|
||||
Modify | 4.6968e-05 | 4.6968e-05 | 4.6968e-05 | 0.0 | 0.02
|
||||
Other | | 5.984e-05 | | | 0.02
|
||||
Comm | 0.00023103 | 0.00023103 | 0.00023103 | 0.0 | 0.09
|
||||
Output | 0.00011086 | 0.00011086 | 0.00011086 | 0.0 | 0.05
|
||||
Modify | 4.7445e-05 | 4.7445e-05 | 4.7445e-05 | 0.0 | 0.02
|
||||
Other | | 5.651e-05 | | | 0.02
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Pure Cu crystal, structure created by LAMMPS, qeq off
|
||||
|
||||
units metal
|
||||
@ -61,20 +61,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
|
||||
8 10.076864 -3.5063151 -3.5076125 -3.5076125 0 28.613454 3023.4645 14.46 14.46 14.46 0
|
||||
9 10.070725 -3.5063151 -3.5076118 -3.5076118 0 28.909893 3023.4645 14.46 14.46 14.46 0
|
||||
10 10.063868 -3.5063151 -3.5076109 -3.5076109 0 29.241022 3023.4645 14.46 14.46 14.46 0
|
||||
Loop time of 0.0647703 on 4 procs for 10 steps with 256 atoms
|
||||
Loop time of 0.0643001 on 4 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 2.668 ns/day, 8.996 hours/ns, 154.392 timesteps/s
|
||||
100.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 2.687 ns/day, 8.931 hours/ns, 155.521 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.063009 | 0.063389 | 0.06358 | 0.1 | 97.87
|
||||
Pair | 0.062855 | 0.063074 | 0.063304 | 0.1 | 98.09
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00075269 | 0.00095391 | 0.001322 | 0.7 | 1.47
|
||||
Output | 0.00029755 | 0.00031668 | 0.00032735 | 0.1 | 0.49
|
||||
Modify | 1.5736e-05 | 1.7047e-05 | 1.8835e-05 | 0.0 | 0.03
|
||||
Other | | 9.34e-05 | | | 0.14
|
||||
Comm | 0.00061822 | 0.00085837 | 0.0010862 | 0.6 | 1.33
|
||||
Output | 0.00021434 | 0.00023013 | 0.00025868 | 0.1 | 0.36
|
||||
Modify | 1.4782e-05 | 1.6153e-05 | 1.7405e-05 | 0.0 | 0.03
|
||||
Other | | 0.0001218 | | | 0.19
|
||||
|
||||
Nlocal: 64 ave 64 max 64 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
|
||||
|
||||
units metal
|
||||
@ -51,24 +51,24 @@ Neighbor list info ...
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25 -> bins = 5 5 5
|
||||
Memory usage per processor = 6.39852 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
|
||||
Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Lx Ly Lz Volume
|
||||
0 1 -2.9288959 -2.9290251 -0.23839068 -2.6906344 0.79666672 -1.5933334 25.62 25.62 25.62 16816.568
|
||||
1 1.0007128 -3.0464056 -3.0465348 0.40404394 -3.4505788 0.79666635 -1.5933327 25.62 25.62 25.62 16816.568
|
||||
2 1.0028587 -3.0464056 -3.0465351 0.40404056 -3.4505757 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568
|
||||
Loop time of 0.690546 on 1 procs for 2 steps with 1296 atoms
|
||||
Loop time of 0.661607 on 1 procs for 2 steps with 1296 atoms
|
||||
|
||||
Performance: 0.050 ns/day, 479.546 hours/ns, 2.896 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.052 ns/day, 459.449 hours/ns, 3.023 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.27005 | 0.27005 | 0.27005 | 0.0 | 39.11
|
||||
Pair | 0.26068 | 0.26068 | 0.26068 | 0.0 | 39.40
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00010324 | 0.00010324 | 0.00010324 | 0.0 | 0.01
|
||||
Output | 4.9114e-05 | 4.9114e-05 | 4.9114e-05 | 0.0 | 0.01
|
||||
Modify | 0.4203 | 0.4203 | 0.4203 | 0.0 | 60.86
|
||||
Other | | 4.387e-05 | | | 0.01
|
||||
Comm | 0.00010204 | 0.00010204 | 0.00010204 | 0.0 | 0.02
|
||||
Output | 5.4836e-05 | 5.4836e-05 | 5.4836e-05 | 0.0 | 0.01
|
||||
Modify | 0.40072 | 0.40072 | 0.40072 | 0.0 | 60.57
|
||||
Other | | 4.601e-05 | | | 0.01
|
||||
|
||||
Nlocal: 1296 ave 1296 max 1296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -96,7 +96,7 @@ Neighbor list info ...
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25 -> bins = 5 5 5
|
||||
Memory usage per processor = 8.27781 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
|
||||
Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Lx Ly Lz Volume
|
||||
2 1.0028587 -3.0464056 -3.0465351 0.40403069 -3.4505658 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568
|
||||
3 1.0028587 -3.0917245 -3.091854 0.36260063 -3.4544547 0.79642968 -1.5928594 25.59438 25.59438 25.59438 16766.169
|
||||
4 1.0028587 -3.1396788 -3.1398083 0.3165719 -3.4563802 0.7961845 -1.592369 25.56876 25.56876 25.56876 16715.871
|
||||
@ -122,7 +122,7 @@ Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
|
||||
24 1.0028587 -3.966498 -3.9666275 -0.4616679 -3.5049596 0.79285787 -1.5857157 25.05636 25.05636 25.05636 15730.913
|
||||
25 1.0028587 -3.9686392 -3.9687687 -0.46014255 -3.5086261 0.79286937 -1.5857387 25.034573 25.034573 25.034573 15689.914
|
||||
26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914
|
||||
Loop time of 29.9485 on 1 procs for 24 steps with 1296 atoms
|
||||
Loop time of 29.3376 on 1 procs for 24 steps with 1296 atoms
|
||||
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
@ -138,12 +138,12 @@ Minimization stats:
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.6428 | 7.6428 | 7.6428 | 0.0 | 25.52
|
||||
Neigh | 0.072307 | 0.072307 | 0.072307 | 0.0 | 0.24
|
||||
Comm | 0.0033123 | 0.0033123 | 0.0033123 | 0.0 | 0.01
|
||||
Output | 0.00073075 | 0.00073075 | 0.00073075 | 0.0 | 0.00
|
||||
Modify | 22.217 | 22.217 | 22.217 | 0.0 | 74.18
|
||||
Other | | 0.01276 | | | 0.04
|
||||
Pair | 7.5417 | 7.5417 | 7.5417 | 0.0 | 25.71
|
||||
Neigh | 0.071155 | 0.071155 | 0.071155 | 0.0 | 0.24
|
||||
Comm | 0.0031855 | 0.0031855 | 0.0031855 | 0.0 | 0.01
|
||||
Output | 0.00070429 | 0.00070429 | 0.00070429 | 0.0 | 0.00
|
||||
Modify | 21.709 | 21.709 | 21.709 | 0.0 | 74.00
|
||||
Other | | 0.01167 | | | 0.04
|
||||
|
||||
Nlocal: 1296 ave 1296 max 1296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -171,23 +171,23 @@ Neighbor list info ...
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25 -> bins = 5 5 5
|
||||
Memory usage per processor = 6.65281 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
|
||||
Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Lx Ly Lz Volume
|
||||
26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914
|
||||
27 0.98924824 -3.9686392 -3.9687669 -0.46018036 -3.5085866 0.79286575 -1.5857315 25.034573 25.034573 25.034573 15689.914
|
||||
Loop time of 0.283693 on 1 procs for 1 steps with 1296 atoms
|
||||
Loop time of 0.273439 on 1 procs for 1 steps with 1296 atoms
|
||||
|
||||
Performance: 0.061 ns/day, 394.018 hours/ns, 3.525 timesteps/s
|
||||
100.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.063 ns/day, 379.776 hours/ns, 3.657 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.14656 | 0.14656 | 0.14656 | 0.0 | 51.66
|
||||
Pair | 0.14151 | 0.14151 | 0.14151 | 0.0 | 51.75
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 5.8889e-05 | 5.8889e-05 | 5.8889e-05 | 0.0 | 0.02
|
||||
Output | 2.8849e-05 | 2.8849e-05 | 2.8849e-05 | 0.0 | 0.01
|
||||
Modify | 0.13702 | 0.13702 | 0.13702 | 0.0 | 48.30
|
||||
Other | | 2.337e-05 | | | 0.01
|
||||
Comm | 4.8876e-05 | 4.8876e-05 | 4.8876e-05 | 0.0 | 0.02
|
||||
Output | 2.3127e-05 | 2.3127e-05 | 2.3127e-05 | 0.0 | 0.01
|
||||
Modify | 0.13185 | 0.13185 | 0.13185 | 0.0 | 48.22
|
||||
Other | | 1.192e-05 | | | 0.00
|
||||
|
||||
Nlocal: 1296 ave 1296 max 1296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -216,10 +216,10 @@ fix 2 all deform 1 x scale 1.0001 remap x
|
||||
compute perfx all stress/atom NULL pair
|
||||
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:680)
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690)
|
||||
run 10
|
||||
Memory usage per processor = 7.02781 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
|
||||
Step Lx Ly Lz Xy Xz Yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
|
||||
27 25.034573 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81
|
||||
28 25.034823 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81
|
||||
29 25.035074 25.034573 25.034573 0 0 0 -87059995 -96445744 -96445673 -126501.16 -147663.09 -107878.31
|
||||
@ -231,20 +231,20 @@ Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
|
||||
35 25.036576 25.034573 25.034573 0 0 0 26482035 -39227675 -39227600 -126479.96 -147632.87 -107857.27
|
||||
36 25.036826 25.034573 25.034573 0 0 0 45406330 -29692031 -29691956 -126476.43 -147627.84 -107853.76
|
||||
37 25.037076 25.034573 25.034573 0 0 0 64330788 -20156596 -20156520 -126472.9 -147622.8 -107850.25
|
||||
Loop time of 1.61281 on 1 procs for 10 steps with 1296 atoms
|
||||
Loop time of 1.55219 on 1 procs for 10 steps with 1296 atoms
|
||||
|
||||
Performance: 0.107 ns/day, 224.001 hours/ns, 6.200 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.111 ns/day, 215.582 hours/ns, 6.443 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.6096 | 1.6096 | 1.6096 | 0.0 | 99.80
|
||||
Pair | 1.5493 | 1.5493 | 1.5493 | 0.0 | 99.81
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00054646 | 0.00054646 | 0.00054646 | 0.0 | 0.03
|
||||
Output | 0.0023828 | 0.0023828 | 0.0023828 | 0.0 | 0.15
|
||||
Modify | 0.00019932 | 0.00019932 | 0.00019932 | 0.0 | 0.01
|
||||
Other | | 0.0001204 | | | 0.01
|
||||
Comm | 0.00050259 | 0.00050259 | 0.00050259 | 0.0 | 0.03
|
||||
Output | 0.0021405 | 0.0021405 | 0.0021405 | 0.0 | 0.14
|
||||
Modify | 0.00018573 | 0.00018573 | 0.00018573 | 0.0 | 0.01
|
||||
Other | | 0.0001054 | | | 0.01
|
||||
|
||||
Nlocal: 1296 ave 1296 max 1296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -268,7 +268,7 @@ compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_p
|
||||
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
|
||||
run 10
|
||||
Memory usage per processor = 7.77781 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
|
||||
Step Lx Ly Lz Xy Xz Yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
|
||||
37 25.037076 25.034573 25.034573 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74
|
||||
38 25.037076 25.034573 25.034823 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74
|
||||
39 25.037076 25.034573 25.035074 0 0 0 92791365 -1081679.6 8300643.1 -126464.81 -147612.37 -107844.24
|
||||
@ -280,20 +280,20 @@ Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
|
||||
45 25.037076 25.034573 25.036576 0 0 0 1.5000248e+08 56152550 1.2183572e+08 -126437.47 -147579.98 -107829.23
|
||||
46 25.037076 25.034573 25.036826 0 0 0 1.5953685e+08 65690906 1.4075876e+08 -126432.91 -147574.58 -107826.72
|
||||
47 25.037076 25.034573 25.037076 0 0 0 1.69071e+08 75229058 1.5968192e+08 -126428.35 -147569.18 -107824.22
|
||||
Loop time of 1.56349 on 1 procs for 10 steps with 1296 atoms
|
||||
Loop time of 1.55291 on 1 procs for 10 steps with 1296 atoms
|
||||
|
||||
Performance: 0.111 ns/day, 217.151 hours/ns, 6.396 timesteps/s
|
||||
Performance: 0.111 ns/day, 215.682 hours/ns, 6.440 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5603 | 1.5603 | 1.5603 | 0.0 | 99.79
|
||||
Pair | 1.5499 | 1.5499 | 1.5499 | 0.0 | 99.81
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0005424 | 0.0005424 | 0.0005424 | 0.0 | 0.03
|
||||
Output | 0.0023627 | 0.0023627 | 0.0023627 | 0.0 | 0.15
|
||||
Modify | 0.00018978 | 0.00018978 | 0.00018978 | 0.0 | 0.01
|
||||
Other | | 0.0001137 | | | 0.01
|
||||
Comm | 0.00050187 | 0.00050187 | 0.00050187 | 0.0 | 0.03
|
||||
Output | 0.0021739 | 0.0021739 | 0.0021739 | 0.0 | 0.14
|
||||
Modify | 0.00018835 | 0.00018835 | 0.00018835 | 0.0 | 0.01
|
||||
Other | | 0.0001068 | | | 0.01
|
||||
|
||||
Nlocal: 1296 ave 1296 max 1296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -317,7 +317,7 @@ compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4
|
||||
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
|
||||
run 10
|
||||
Memory usage per processor = 8.54308 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
|
||||
Step Lx Ly Lz Xy Xz Yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
|
||||
47 25.037076 25.034573 25.037076 0 0 0 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72
|
||||
48 25.037076 25.034573 25.037076 0 0 5.0074153e-07 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72
|
||||
49 25.037076 25.034573 25.037076 0 0 1.0014831e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.78 -88830.837
|
||||
@ -329,20 +329,20 @@ Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
|
||||
55 25.037076 25.034573 25.037076 0 0 4.0059322e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.75 25114.443
|
||||
56 25.037076 25.034573 25.037076 0 0 4.5066738e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 44105.323
|
||||
57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 63096.203
|
||||
Loop time of 1.55801 on 1 procs for 10 steps with 1296 atoms
|
||||
Loop time of 1.55278 on 1 procs for 10 steps with 1296 atoms
|
||||
|
||||
Performance: 0.111 ns/day, 216.390 hours/ns, 6.418 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.111 ns/day, 215.664 hours/ns, 6.440 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.555 | 1.555 | 1.555 | 0.0 | 99.80
|
||||
Pair | 1.5499 | 1.5499 | 1.5499 | 0.0 | 99.81
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00052738 | 0.00052738 | 0.00052738 | 0.0 | 0.03
|
||||
Output | 0.0022299 | 0.0022299 | 0.0022299 | 0.0 | 0.14
|
||||
Modify | 0.00018501 | 0.00018501 | 0.00018501 | 0.0 | 0.01
|
||||
Other | | 0.0001023 | | | 0.01
|
||||
Comm | 0.00050759 | 0.00050759 | 0.00050759 | 0.0 | 0.03
|
||||
Output | 0.0021291 | 0.0021291 | 0.0021291 | 0.0 | 0.14
|
||||
Modify | 0.00018358 | 0.00018358 | 0.00018358 | 0.0 | 0.01
|
||||
Other | | 0.0001001 | | | 0.01
|
||||
|
||||
Nlocal: 1296 ave 1296 max 1296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -366,7 +366,7 @@ compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4
|
||||
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
|
||||
run 10
|
||||
Memory usage per processor = 9.29308 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
|
||||
Step Lx Ly Lz Xy Xz Yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
|
||||
57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083
|
||||
58 25.037076 25.034573 25.037076 5.0069146e-07 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083
|
||||
59 25.037076 25.034573 25.037076 1.0013829e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -107434.78 -147563.72 82087.087
|
||||
@ -378,20 +378,20 @@ Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
|
||||
65 25.037076 25.034573 25.037076 4.0055317e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 6499.2334 -147563.69 82087.109
|
||||
66 25.037076 25.034573 25.037076 4.5062231e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 25488.236 -147563.69 82087.113
|
||||
67 25.037076 25.034573 25.037076 5.0069146e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 44477.239 -147563.68 82087.116
|
||||
Loop time of 1.56044 on 1 procs for 10 steps with 1296 atoms
|
||||
Loop time of 1.55248 on 1 procs for 10 steps with 1296 atoms
|
||||
|
||||
Performance: 0.111 ns/day, 216.728 hours/ns, 6.408 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.111 ns/day, 215.622 hours/ns, 6.441 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5574 | 1.5574 | 1.5574 | 0.0 | 99.80
|
||||
Pair | 1.5495 | 1.5495 | 1.5495 | 0.0 | 99.81
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00051975 | 0.00051975 | 0.00051975 | 0.0 | 0.03
|
||||
Output | 0.0022559 | 0.0022559 | 0.0022559 | 0.0 | 0.14
|
||||
Modify | 0.00019503 | 0.00019503 | 0.00019503 | 0.0 | 0.01
|
||||
Other | | 0.0001116 | | | 0.01
|
||||
Comm | 0.00049877 | 0.00049877 | 0.00049877 | 0.0 | 0.03
|
||||
Output | 0.0021408 | 0.0021408 | 0.0021408 | 0.0 | 0.14
|
||||
Modify | 0.00018549 | 0.00018549 | 0.00018549 | 0.0 | 0.01
|
||||
Other | | 0.0001054 | | | 0.01
|
||||
|
||||
Nlocal: 1296 ave 1296 max 1296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -406,4 +406,4 @@ Total # of neighbors = 862272
|
||||
Ave neighs/atom = 665.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:44
|
||||
Total wall time: 0:00:43
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
|
||||
|
||||
units metal
|
||||
@ -51,24 +51,24 @@ Neighbor list info ...
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25 -> bins = 5 5 5
|
||||
Memory usage per processor = 6.28094 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
|
||||
Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Lx Ly Lz Volume
|
||||
0 1 -2.9288959 -2.9290251 -0.23839068 -2.6906344 0.79666672 -1.5933334 25.62 25.62 25.62 16816.568
|
||||
1 1.0007128 -3.0464056 -3.0465348 0.40404394 -3.4505788 0.79666635 -1.5933327 25.62 25.62 25.62 16816.568
|
||||
2 1.0028587 -3.0464056 -3.0465351 0.40404056 -3.4505757 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568
|
||||
Loop time of 0.174112 on 4 procs for 2 steps with 1296 atoms
|
||||
Loop time of 0.168944 on 4 procs for 2 steps with 1296 atoms
|
||||
|
||||
Performance: 0.198 ns/day, 120.911 hours/ns, 11.487 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 0.205 ns/day, 117.322 hours/ns, 11.838 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.067018 | 0.067376 | 0.067552 | 0.1 | 38.70
|
||||
Pair | 0.064867 | 0.065282 | 0.065606 | 0.1 | 38.64
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00030375 | 0.00049108 | 0.00085974 | 1.0 | 0.28
|
||||
Output | 7.8678e-05 | 8.1301e-05 | 8.7023e-05 | 0.0 | 0.05
|
||||
Modify | 0.10611 | 0.10612 | 0.10613 | 0.0 | 60.95
|
||||
Other | | 4.166e-05 | | | 0.02
|
||||
Comm | 0.00026083 | 0.00059474 | 0.001004 | 1.1 | 0.35
|
||||
Output | 7.1049e-05 | 7.3791e-05 | 8.1062e-05 | 0.0 | 0.04
|
||||
Modify | 0.10295 | 0.10296 | 0.10297 | 0.0 | 60.94
|
||||
Other | | 3.177e-05 | | | 0.02
|
||||
|
||||
Nlocal: 324 ave 324 max 324 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
@ -96,7 +96,7 @@ Neighbor list info ...
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25 -> bins = 5 5 5
|
||||
Memory usage per processor = 8.15594 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
|
||||
Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Lx Ly Lz Volume
|
||||
2 1.0028587 -3.0464056 -3.0465351 0.40403069 -3.4505658 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568
|
||||
3 1.0028587 -3.0917245 -3.091854 0.36260063 -3.4544547 0.79642968 -1.5928594 25.59438 25.59438 25.59438 16766.169
|
||||
4 1.0028587 -3.1396788 -3.1398083 0.3165719 -3.4563802 0.7961845 -1.592369 25.56876 25.56876 25.56876 16715.871
|
||||
@ -122,7 +122,7 @@ Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
|
||||
24 1.0028587 -3.966498 -3.9666275 -0.4616679 -3.5049596 0.79285787 -1.5857157 25.05636 25.05636 25.05636 15730.913
|
||||
25 1.0028587 -3.9686392 -3.9687687 -0.46014255 -3.5086261 0.79286937 -1.5857387 25.034573 25.034573 25.034573 15689.914
|
||||
26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914
|
||||
Loop time of 7.73864 on 4 procs for 24 steps with 1296 atoms
|
||||
Loop time of 7.60393 on 4 procs for 24 steps with 1296 atoms
|
||||
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
@ -138,12 +138,12 @@ Minimization stats:
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.8982 | 1.9386 | 1.9643 | 1.8 | 25.05
|
||||
Neigh | 0.017612 | 0.017903 | 0.018068 | 0.1 | 0.23
|
||||
Comm | 0.011921 | 0.037696 | 0.078263 | 13.0 | 0.49
|
||||
Output | 0.00091124 | 0.00094914 | 0.0010424 | 0.2 | 0.01
|
||||
Modify | 5.736 | 5.7361 | 5.7362 | 0.0 | 74.12
|
||||
Other | | 0.007425 | | | 0.10
|
||||
Pair | 1.8378 | 1.8844 | 1.9098 | 2.1 | 24.78
|
||||
Neigh | 0.017217 | 0.01784 | 0.018236 | 0.3 | 0.23
|
||||
Comm | 0.011872 | 0.03777 | 0.08501 | 14.8 | 0.50
|
||||
Output | 0.00087929 | 0.00090992 | 0.00099182 | 0.2 | 0.01
|
||||
Modify | 5.6557 | 5.6558 | 5.6559 | 0.0 | 74.38
|
||||
Other | | 0.007261 | | | 0.10
|
||||
|
||||
Nlocal: 324 ave 328 max 318 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
@ -171,23 +171,23 @@ Neighbor list info ...
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25 -> bins = 5 5 5
|
||||
Memory usage per processor = 6.53094 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
|
||||
Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Lx Ly Lz Volume
|
||||
26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914
|
||||
27 0.98924824 -3.9686392 -3.9687669 -0.46018036 -3.5085866 0.79286575 -1.5857315 25.034573 25.034573 25.034573 15689.914
|
||||
Loop time of 0.0716895 on 4 procs for 1 steps with 1296 atoms
|
||||
Loop time of 0.0698364 on 4 procs for 1 steps with 1296 atoms
|
||||
|
||||
Performance: 0.241 ns/day, 99.569 hours/ns, 13.949 timesteps/s
|
||||
100.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 0.247 ns/day, 96.995 hours/ns, 14.319 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.035934 | 0.036807 | 0.03732 | 0.3 | 51.34
|
||||
Pair | 0.034876 | 0.035652 | 0.036197 | 0.3 | 51.05
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00013494 | 0.00064868 | 0.0015209 | 2.1 | 0.90
|
||||
Output | 3.6955e-05 | 3.8445e-05 | 4.1962e-05 | 0.0 | 0.05
|
||||
Modify | 0.034179 | 0.034181 | 0.034182 | 0.0 | 47.68
|
||||
Other | | 1.472e-05 | | | 0.02
|
||||
Comm | 0.00012708 | 0.00067472 | 0.0014517 | 2.0 | 0.97
|
||||
Output | 3.5048e-05 | 3.6299e-05 | 3.9101e-05 | 0.0 | 0.05
|
||||
Modify | 0.033457 | 0.033461 | 0.033464 | 0.0 | 47.91
|
||||
Other | | 1.24e-05 | | | 0.02
|
||||
|
||||
Nlocal: 324 ave 328 max 318 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
@ -216,10 +216,10 @@ fix 2 all deform 1 x scale 1.0001 remap x
|
||||
compute perfx all stress/atom NULL pair
|
||||
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:680)
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690)
|
||||
run 10
|
||||
Memory usage per processor = 6.90594 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
|
||||
Step Lx Ly Lz Xy Xz Yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
|
||||
27 25.034573 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81
|
||||
28 25.034823 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81
|
||||
29 25.035074 25.034573 25.034573 0 0 0 -87059995 -96445744 -96445673 -126501.16 -147663.09 -107878.31
|
||||
@ -231,20 +231,20 @@ Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
|
||||
35 25.036576 25.034573 25.034573 0 0 0 26482035 -39227675 -39227600 -126479.96 -147632.87 -107857.27
|
||||
36 25.036826 25.034573 25.034573 0 0 0 45406330 -29692031 -29691956 -126476.43 -147627.84 -107853.76
|
||||
37 25.037076 25.034573 25.034573 0 0 0 64330788 -20156596 -20156520 -126472.9 -147622.8 -107850.25
|
||||
Loop time of 0.40881 on 4 procs for 10 steps with 1296 atoms
|
||||
Loop time of 0.395692 on 4 procs for 10 steps with 1296 atoms
|
||||
|
||||
Performance: 0.423 ns/day, 56.779 hours/ns, 24.461 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 0.437 ns/day, 54.957 hours/ns, 25.272 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.38885 | 0.39776 | 0.40386 | 1.0 | 97.30
|
||||
Pair | 0.37577 | 0.38538 | 0.39123 | 1.0 | 97.39
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0020289 | 0.0081917 | 0.017143 | 7.1 | 2.00
|
||||
Output | 0.0026636 | 0.0027153 | 0.0027769 | 0.1 | 0.66
|
||||
Modify | 5.6982e-05 | 5.9664e-05 | 6.628e-05 | 0.0 | 0.01
|
||||
Other | | 8.208e-05 | | | 0.02
|
||||
Comm | 0.0016012 | 0.0074702 | 0.017095 | 7.0 | 1.89
|
||||
Output | 0.0026791 | 0.0027133 | 0.0027606 | 0.1 | 0.69
|
||||
Modify | 5.6028e-05 | 5.8174e-05 | 6.1035e-05 | 0.0 | 0.01
|
||||
Other | | 7.373e-05 | | | 0.02
|
||||
|
||||
Nlocal: 324 ave 328 max 318 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
@ -268,7 +268,7 @@ compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_p
|
||||
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
|
||||
run 10
|
||||
Memory usage per processor = 7.65594 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
|
||||
Step Lx Ly Lz Xy Xz Yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
|
||||
37 25.037076 25.034573 25.034573 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74
|
||||
38 25.037076 25.034573 25.034823 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74
|
||||
39 25.037076 25.034573 25.035074 0 0 0 92791365 -1081679.6 8300643.1 -126464.81 -147612.37 -107844.24
|
||||
@ -280,20 +280,20 @@ Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
|
||||
45 25.037076 25.034573 25.036576 0 0 0 1.5000248e+08 56152550 1.2183572e+08 -126437.47 -147579.98 -107829.23
|
||||
46 25.037076 25.034573 25.036826 0 0 0 1.5953685e+08 65690906 1.4075876e+08 -126432.91 -147574.58 -107826.72
|
||||
47 25.037076 25.034573 25.037076 0 0 0 1.69071e+08 75229058 1.5968192e+08 -126428.35 -147569.18 -107824.22
|
||||
Loop time of 0.407868 on 4 procs for 10 steps with 1296 atoms
|
||||
Loop time of 0.395265 on 4 procs for 10 steps with 1296 atoms
|
||||
|
||||
Performance: 0.424 ns/day, 56.648 hours/ns, 24.518 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 0.437 ns/day, 54.898 hours/ns, 25.300 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.38874 | 0.39706 | 0.40377 | 0.9 | 97.35
|
||||
Pair | 0.37558 | 0.38392 | 0.39002 | 1.0 | 97.13
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.001327 | 0.0080245 | 0.016345 | 6.6 | 1.97
|
||||
Output | 0.0026383 | 0.0026469 | 0.0026655 | 0.0 | 0.65
|
||||
Modify | 5.2929e-05 | 5.6744e-05 | 5.9128e-05 | 0.0 | 0.01
|
||||
Other | | 7.844e-05 | | | 0.02
|
||||
Comm | 0.0023744 | 0.0084905 | 0.016869 | 6.7 | 2.15
|
||||
Output | 0.0026851 | 0.0027224 | 0.0027671 | 0.1 | 0.69
|
||||
Modify | 5.3167e-05 | 5.6148e-05 | 5.8651e-05 | 0.0 | 0.01
|
||||
Other | | 7.594e-05 | | | 0.02
|
||||
|
||||
Nlocal: 324 ave 328 max 318 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
@ -317,7 +317,7 @@ compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4
|
||||
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
|
||||
run 10
|
||||
Memory usage per processor = 8.42123 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
|
||||
Step Lx Ly Lz Xy Xz Yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
|
||||
47 25.037076 25.034573 25.037076 0 0 0 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72
|
||||
48 25.037076 25.034573 25.037076 0 0 5.0074153e-07 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72
|
||||
49 25.037076 25.034573 25.037076 0 0 1.0014831e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.78 -88830.837
|
||||
@ -329,20 +329,20 @@ Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
|
||||
55 25.037076 25.034573 25.037076 0 0 4.0059322e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.75 25114.443
|
||||
56 25.037076 25.034573 25.037076 0 0 4.5066738e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 44105.323
|
||||
57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 63096.203
|
||||
Loop time of 0.408682 on 4 procs for 10 steps with 1296 atoms
|
||||
Loop time of 0.395982 on 4 procs for 10 steps with 1296 atoms
|
||||
|
||||
Performance: 0.423 ns/day, 56.761 hours/ns, 24.469 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 0.436 ns/day, 54.997 hours/ns, 25.254 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.38891 | 0.39738 | 0.40388 | 1.0 | 97.23
|
||||
Pair | 0.37606 | 0.38505 | 0.39068 | 1.0 | 97.24
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0019937 | 0.0084969 | 0.016969 | 6.6 | 2.08
|
||||
Output | 0.0026531 | 0.0026709 | 0.0026915 | 0.0 | 0.65
|
||||
Modify | 5.1975e-05 | 5.6446e-05 | 5.9366e-05 | 0.0 | 0.01
|
||||
Other | | 7.963e-05 | | | 0.02
|
||||
Comm | 0.0021853 | 0.0078424 | 0.016867 | 6.7 | 1.98
|
||||
Output | 0.0029173 | 0.0029593 | 0.0030072 | 0.1 | 0.75
|
||||
Modify | 5.3167e-05 | 5.4538e-05 | 5.722e-05 | 0.0 | 0.01
|
||||
Other | | 7.403e-05 | | | 0.02
|
||||
|
||||
Nlocal: 324 ave 328 max 318 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
@ -366,7 +366,7 @@ compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4
|
||||
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
|
||||
run 10
|
||||
Memory usage per processor = 9.17123 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
|
||||
Step Lx Ly Lz Xy Xz Yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
|
||||
57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083
|
||||
58 25.037076 25.034573 25.037076 5.0069146e-07 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083
|
||||
59 25.037076 25.034573 25.037076 1.0013829e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -107434.78 -147563.72 82087.087
|
||||
@ -378,20 +378,20 @@ Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
|
||||
65 25.037076 25.034573 25.037076 4.0055317e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 6499.2334 -147563.69 82087.109
|
||||
66 25.037076 25.034573 25.037076 4.5062231e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 25488.236 -147563.69 82087.113
|
||||
67 25.037076 25.034573 25.037076 5.0069146e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 44477.239 -147563.68 82087.116
|
||||
Loop time of 0.411159 on 4 procs for 10 steps with 1296 atoms
|
||||
Loop time of 0.393499 on 4 procs for 10 steps with 1296 atoms
|
||||
|
||||
Performance: 0.420 ns/day, 57.105 hours/ns, 24.322 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 0.439 ns/day, 54.653 hours/ns, 25.413 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.3889 | 0.39826 | 0.40584 | 1.1 | 96.86
|
||||
Pair | 0.37563 | 0.38304 | 0.38942 | 1.0 | 97.34
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0024002 | 0.010008 | 0.019374 | 6.8 | 2.43
|
||||
Output | 0.0027368 | 0.0027526 | 0.0027771 | 0.0 | 0.67
|
||||
Modify | 5.6028e-05 | 5.8174e-05 | 6.0081e-05 | 0.0 | 0.01
|
||||
Other | | 8.059e-05 | | | 0.02
|
||||
Comm | 0.0013115 | 0.0077351 | 0.015176 | 6.8 | 1.97
|
||||
Output | 0.002558 | 0.0025953 | 0.0026426 | 0.1 | 0.66
|
||||
Modify | 5.1975e-05 | 5.4598e-05 | 5.8174e-05 | 0.0 | 0.01
|
||||
Other | | 7.737e-05 | | | 0.02
|
||||
|
||||
Nlocal: 324 ave 328 max 318 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
@ -45,24 +45,24 @@ Neighbor list info ...
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25 -> bins = 5 5 5
|
||||
Memory usage per processor = 6.13908 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
Memory usage per processor = 6.5933 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2
|
||||
0 0 -9.3995049 -9.3995049 5.256221 -14.655726 60985.254 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
|
||||
1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
|
||||
Loop time of 0.169538 on 1 procs for 1 steps with 1500 atoms
|
||||
Loop time of 0.165626 on 1 procs for 1 steps with 1500 atoms
|
||||
|
||||
Performance: 0.102 ns/day, 235.469 hours/ns, 5.898 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.104 ns/day, 230.036 hours/ns, 6.038 timesteps/s
|
||||
100.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.16939 | 0.16939 | 0.16939 | 0.0 | 99.91
|
||||
Pair | 0.16548 | 0.16548 | 0.16548 | 0.0 | 99.91
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 6.485e-05 | 6.485e-05 | 6.485e-05 | 0.0 | 0.04
|
||||
Output | 2.9802e-05 | 2.9802e-05 | 2.9802e-05 | 0.0 | 0.02
|
||||
Modify | 3.9101e-05 | 3.9101e-05 | 3.9101e-05 | 0.0 | 0.02
|
||||
Other | | 1.717e-05 | | | 0.01
|
||||
Comm | 6.8188e-05 | 6.8188e-05 | 6.8188e-05 | 0.0 | 0.04
|
||||
Output | 2.8133e-05 | 2.8133e-05 | 2.8133e-05 | 0.0 | 0.02
|
||||
Modify | 3.5763e-05 | 3.5763e-05 | 3.5763e-05 | 0.0 | 0.02
|
||||
Other | | 1.597e-05 | | | 0.01
|
||||
|
||||
Nlocal: 1500 ave 1500 max 1500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -79,28 +79,28 @@ Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
fix 2 all qeq/comb 1 0.003 file fq.out
|
||||
run 5
|
||||
Memory usage per processor = 6.76408 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
Memory usage per processor = 7.2183 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2
|
||||
1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
||||
2 0.13734003 -10.041396 -10.041413 2.7214902 -12.762903 -130794.11 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
||||
3 0.2686308 -10.041388 -10.041423 2.7214912 -12.762914 -130800.39 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
||||
4 0.44445358 -10.041379 -10.041436 2.7214924 -12.762929 -130808.63 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
||||
5 0.66458606 -10.041367 -10.041453 2.7214941 -12.762947 -130818.84 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
||||
6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
||||
Loop time of 1.16742 on 1 procs for 5 steps with 1500 atoms
|
||||
Loop time of 1.12494 on 1 procs for 5 steps with 1500 atoms
|
||||
|
||||
Performance: 0.074 ns/day, 324.284 hours/ns, 4.283 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.077 ns/day, 312.485 hours/ns, 4.445 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.85832 | 0.85832 | 0.85832 | 0.0 | 73.52
|
||||
Pair | 0.82774 | 0.82774 | 0.82774 | 0.0 | 73.58
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00033593 | 0.00033593 | 0.00033593 | 0.0 | 0.03
|
||||
Output | 0.00015116 | 0.00015116 | 0.00015116 | 0.0 | 0.01
|
||||
Modify | 0.30852 | 0.30852 | 0.30852 | 0.0 | 26.43
|
||||
Other | | 9.751e-05 | | | 0.01
|
||||
Comm | 0.00032425 | 0.00032425 | 0.00032425 | 0.0 | 0.03
|
||||
Output | 0.00013924 | 0.00013924 | 0.00013924 | 0.0 | 0.01
|
||||
Modify | 0.29665 | 0.29665 | 0.29665 | 0.0 | 26.37
|
||||
Other | | 8.941e-05 | | | 0.01
|
||||
|
||||
Nlocal: 1500 ave 1500 max 1500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -131,13 +131,13 @@ Neighbor list info ...
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25 -> bins = 5 5 5
|
||||
Memory usage per processor = 7.88908 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
Memory usage per processor = 8.3433 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2
|
||||
6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
||||
7 0.92875014 -10.041833 -10.041953 2.7196698 -12.761623 -130754.01 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
||||
Loop time of 0.64676 on 1 procs for 1 steps with 1500 atoms
|
||||
Loop time of 0.628066 on 1 procs for 1 steps with 1500 atoms
|
||||
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
@ -151,12 +151,12 @@ Minimization stats:
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.34047 | 0.34047 | 0.34047 | 0.0 | 52.64
|
||||
Pair | 0.33072 | 0.33072 | 0.33072 | 0.0 | 52.66
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00012827 | 0.00012827 | 0.00012827 | 0.0 | 0.02
|
||||
Comm | 0.00013089 | 0.00013089 | 0.00013089 | 0.0 | 0.02
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0.30579 | 0.30579 | 0.30579 | 0.0 | 47.28
|
||||
Other | | 0.0003626 | | | 0.06
|
||||
Modify | 0.29688 | 0.29688 | 0.29688 | 0.0 | 47.27
|
||||
Other | | 0.0003412 | | | 0.05
|
||||
|
||||
Nlocal: 1500 ave 1500 max 1500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -191,8 +191,8 @@ Neighbor list info ...
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25 -> bins = 5 5 5
|
||||
Memory usage per processor = 6.76408 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
Memory usage per processor = 7.2183 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2
|
||||
7 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
||||
8 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
||||
9 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
||||
@ -204,20 +204,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
15 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
||||
16 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
||||
17 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
||||
Loop time of 2.31943 on 1 procs for 10 steps with 1500 atoms
|
||||
Loop time of 2.25256 on 1 procs for 10 steps with 1500 atoms
|
||||
|
||||
Performance: 0.075 ns/day, 322.143 hours/ns, 4.311 timesteps/s
|
||||
Performance: 0.077 ns/day, 312.855 hours/ns, 4.439 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.7064 | 1.7064 | 1.7064 | 0.0 | 73.57
|
||||
Pair | 1.6582 | 1.6582 | 1.6582 | 0.0 | 73.62
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00066495 | 0.00066495 | 0.00066495 | 0.0 | 0.03
|
||||
Output | 0.00035143 | 0.00035143 | 0.00035143 | 0.0 | 0.02
|
||||
Modify | 0.61178 | 0.61178 | 0.61178 | 0.0 | 26.38
|
||||
Other | | 0.0002165 | | | 0.01
|
||||
Comm | 0.00064015 | 0.00064015 | 0.00064015 | 0.0 | 0.03
|
||||
Output | 0.00028682 | 0.00028682 | 0.00028682 | 0.0 | 0.01
|
||||
Modify | 0.59326 | 0.59326 | 0.59326 | 0.0 | 26.34
|
||||
Other | | 0.0001378 | | | 0.01
|
||||
|
||||
Nlocal: 1500 ave 1500 max 1500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
@ -45,24 +45,24 @@ Neighbor list info ...
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25 -> bins = 5 5 5
|
||||
Memory usage per processor = 5.96686 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
Memory usage per processor = 6.45428 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2
|
||||
0 0 -9.3995049 -9.3995049 5.256221 -14.655726 60985.254 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
|
||||
1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
|
||||
Loop time of 0.0429993 on 4 procs for 1 steps with 1500 atoms
|
||||
Loop time of 0.0431705 on 4 procs for 1 steps with 1500 atoms
|
||||
|
||||
Performance: 0.402 ns/day, 59.721 hours/ns, 23.256 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 0.400 ns/day, 59.959 hours/ns, 23.164 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.042339 | 0.042613 | 0.042762 | 0.1 | 99.10
|
||||
Pair | 0.041113 | 0.041747 | 0.04291 | 0.3 | 96.70
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0001421 | 0.00029129 | 0.00056505 | 1.0 | 0.68
|
||||
Output | 3.7909e-05 | 4.0174e-05 | 4.6015e-05 | 0.1 | 0.09
|
||||
Modify | 2.4796e-05 | 2.4796e-05 | 2.4796e-05 | 0.0 | 0.06
|
||||
Other | | 3.028e-05 | | | 0.07
|
||||
Comm | 0.00016999 | 0.0013372 | 0.001966 | 1.9 | 3.10
|
||||
Output | 4.2915e-05 | 4.4703e-05 | 4.7922e-05 | 0.0 | 0.10
|
||||
Modify | 1.502e-05 | 2.3365e-05 | 2.9087e-05 | 0.1 | 0.05
|
||||
Other | | 1.83e-05 | | | 0.04
|
||||
|
||||
Nlocal: 375 ave 375 max 375 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
@ -79,28 +79,28 @@ Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
fix 2 all qeq/comb 1 0.003 file fq.out
|
||||
run 5
|
||||
Memory usage per processor = 6.59186 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
Memory usage per processor = 7.07928 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2
|
||||
1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
||||
2 0.13734003 -10.041396 -10.041413 2.7214902 -12.762903 -130794.11 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
||||
3 0.2686308 -10.041388 -10.041423 2.7214912 -12.762914 -130800.39 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
||||
4 0.44445358 -10.041379 -10.041436 2.7214924 -12.762929 -130808.63 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
||||
5 0.66458606 -10.041367 -10.041453 2.7214941 -12.762947 -130818.84 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
||||
6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
||||
Loop time of 0.290755 on 4 procs for 5 steps with 1500 atoms
|
||||
Loop time of 0.282798 on 4 procs for 5 steps with 1500 atoms
|
||||
|
||||
Performance: 0.297 ns/day, 80.765 hours/ns, 17.197 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 0.306 ns/day, 78.555 hours/ns, 17.680 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.21107 | 0.21252 | 0.21354 | 0.2 | 73.09
|
||||
Pair | 0.20467 | 0.20595 | 0.20674 | 0.2 | 72.83
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00075912 | 0.001812 | 0.0032141 | 2.1 | 0.62
|
||||
Output | 0.00020814 | 0.00021452 | 0.00023079 | 0.1 | 0.07
|
||||
Modify | 0.07608 | 0.076133 | 0.076177 | 0.0 | 26.18
|
||||
Other | | 7.701e-05 | | | 0.03
|
||||
Comm | 0.0016997 | 0.0024779 | 0.003768 | 1.7 | 0.88
|
||||
Output | 0.00022483 | 0.00023055 | 0.00024247 | 0.0 | 0.08
|
||||
Modify | 0.074072 | 0.074082 | 0.074091 | 0.0 | 26.20
|
||||
Other | | 5.567e-05 | | | 0.02
|
||||
|
||||
Nlocal: 375 ave 375 max 375 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
@ -131,13 +131,13 @@ Neighbor list info ...
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25 -> bins = 5 5 5
|
||||
Memory usage per processor = 7.71686 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
Memory usage per processor = 8.20428 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2
|
||||
6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
||||
7 0.92875014 -10.041833 -10.041953 2.7196698 -12.761623 -130754.01 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
||||
Loop time of 0.161507 on 4 procs for 1 steps with 1500 atoms
|
||||
Loop time of 0.159283 on 4 procs for 1 steps with 1500 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
@ -151,12 +151,12 @@ Minimization stats:
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.084314 | 0.085016 | 0.085468 | 0.2 | 52.64
|
||||
Pair | 0.082013 | 0.082956 | 0.083975 | 0.3 | 52.08
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00030208 | 0.00076222 | 0.0014489 | 1.7 | 0.47
|
||||
Comm | 0.0003221 | 0.0013521 | 0.0022871 | 2.2 | 0.85
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0.075456 | 0.075471 | 0.07548 | 0.0 | 46.73
|
||||
Other | | 0.0002575 | | | 0.16
|
||||
Modify | 0.074703 | 0.074712 | 0.074719 | 0.0 | 46.91
|
||||
Other | | 0.000263 | | | 0.17
|
||||
|
||||
Nlocal: 375 ave 375 max 375 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
@ -191,8 +191,8 @@ Neighbor list info ...
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25 -> bins = 5 5 5
|
||||
Memory usage per processor = 6.59186 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
Memory usage per processor = 7.07928 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2
|
||||
7 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
||||
8 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
||||
9 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
||||
@ -204,20 +204,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
15 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
||||
16 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
||||
17 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
||||
Loop time of 0.581787 on 4 procs for 10 steps with 1500 atoms
|
||||
Loop time of 0.572819 on 4 procs for 10 steps with 1500 atoms
|
||||
|
||||
Performance: 0.297 ns/day, 80.804 hours/ns, 17.188 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 0.302 ns/day, 79.558 hours/ns, 17.458 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.42265 | 0.42528 | 0.42704 | 0.2 | 73.10
|
||||
Pair | 0.41014 | 0.41529 | 0.42112 | 0.6 | 72.50
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0015607 | 0.0033906 | 0.0059152 | 2.7 | 0.58
|
||||
Output | 0.00046325 | 0.00046599 | 0.00046873 | 0.0 | 0.08
|
||||
Modify | 0.1524 | 0.15252 | 0.1526 | 0.0 | 26.22
|
||||
Other | | 0.0001305 | | | 0.02
|
||||
Comm | 0.0017653 | 0.0076357 | 0.012777 | 4.8 | 1.33
|
||||
Output | 0.00045943 | 0.00046003 | 0.00046039 | 0.0 | 0.08
|
||||
Modify | 0.1493 | 0.14933 | 0.14935 | 0.0 | 26.07
|
||||
Other | | 0.0001076 | | | 0.02
|
||||
|
||||
Nlocal: 375 ave 375 max 375 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
|
||||
|
||||
units metal
|
||||
@ -50,7 +50,7 @@ Step Temp TotEng PotEng E_vdwl E_coul
|
||||
3 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
4 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
5 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
Loop time of 0.206087 on 1 procs for 5 steps with 512 atoms
|
||||
Loop time of 0.201077 on 1 procs for 5 steps with 512 atoms
|
||||
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
@ -66,12 +66,12 @@ Minimization stats:
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.2046 | 0.2046 | 0.2046 | 0.0 | 99.28
|
||||
Pair | 0.1996 | 0.1996 | 0.1996 | 0.0 | 99.27
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00029564 | 0.00029564 | 0.00029564 | 0.0 | 0.14
|
||||
Output | 3.0041e-05 | 3.0041e-05 | 3.0041e-05 | 0.0 | 0.01
|
||||
Comm | 0.00029564 | 0.00029564 | 0.00029564 | 0.0 | 0.15
|
||||
Output | 2.861e-05 | 2.861e-05 | 2.861e-05 | 0.0 | 0.01
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.001161 | | | 0.56
|
||||
Other | | 0.001153 | | | 0.57
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -102,20 +102,20 @@ Memory usage per processor = 5.97955 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul
|
||||
5 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
6 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
Loop time of 0.018579 on 1 procs for 1 steps with 512 atoms
|
||||
Loop time of 0.018162 on 1 procs for 1 steps with 512 atoms
|
||||
|
||||
Performance: 0.930 ns/day, 25.804 hours/ns, 53.824 timesteps/s
|
||||
102.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.951 ns/day, 25.225 hours/ns, 55.060 timesteps/s
|
||||
99.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.018534 | 0.018534 | 0.018534 | 0.0 | 99.76
|
||||
Pair | 0.018118 | 0.018118 | 0.018118 | 0.0 | 99.76
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 2.7895e-05 | 2.7895e-05 | 2.7895e-05 | 0.0 | 0.15
|
||||
Output | 9.0599e-06 | 9.0599e-06 | 9.0599e-06 | 0.0 | 0.05
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 7.868e-06 | | | 0.04
|
||||
Comm | 2.6941e-05 | 2.6941e-05 | 2.6941e-05 | 0.0 | 0.15
|
||||
Output | 8.1062e-06 | 8.1062e-06 | 8.1062e-06 | 0.0 | 0.04
|
||||
Modify | 2.1458e-06 | 2.1458e-06 | 2.1458e-06 | 0.0 | 0.01
|
||||
Other | | 6.914e-06 | | | 0.04
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -140,10 +140,10 @@ fix 2 all deform 1 x scale 1.0001 remap x
|
||||
compute perfx all stress/atom NULL pair
|
||||
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:680)
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690)
|
||||
run 10
|
||||
Memory usage per processor = 6.72955 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
|
||||
Step Lx Ly Lz Xy Xz Yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
|
||||
6 21.727916 21.727916 21.727916 0 0 0 -4.5569391e-06 -9.3041736e-06 -3.863262e-06 5.3686749e-06 -1.5078216e-06 5.1674734e-06
|
||||
7 21.728133 21.727916 21.727916 0 0 0 -2.4800435e-06 -9.5067314e-06 -2.1562734e-06 5.5972954e-06 -2.3715124e-06 3.9555507e-06
|
||||
8 21.72835 21.727916 21.727916 0 0 0 146204.17 77325.788 77325.788 3.5125695e-06 -1.9487795e-06 5.2972201e-06
|
||||
@ -155,20 +155,20 @@ Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
|
||||
14 21.729654 21.727916 21.727916 0 0 0 1023414.2 541206.18 541206.18 5.6537455e-06 -1.9222461e-06 4.3649131e-06
|
||||
15 21.729871 21.727916 21.727916 0 0 0 1169613.3 618507.19 618507.19 5.5850663e-06 -2.204341e-06 6.1719985e-06
|
||||
16 21.730089 21.727916 21.727916 0 0 0 1315811.8 695804.66 695804.66 -1.3406996e-05 2.5348334e-06 6.2581356e-06
|
||||
Loop time of 0.203248 on 1 procs for 10 steps with 512 atoms
|
||||
Loop time of 0.199118 on 1 procs for 10 steps with 512 atoms
|
||||
|
||||
Performance: 0.850 ns/day, 28.229 hours/ns, 49.201 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.868 ns/day, 27.655 hours/ns, 50.221 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.20165 | 0.20165 | 0.20165 | 0.0 | 99.21
|
||||
Pair | 0.19755 | 0.19755 | 0.19755 | 0.0 | 99.21
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00027919 | 0.00027919 | 0.00027919 | 0.0 | 0.14
|
||||
Output | 0.0011773 | 0.0011773 | 0.0011773 | 0.0 | 0.58
|
||||
Modify | 8.1301e-05 | 8.1301e-05 | 8.1301e-05 | 0.0 | 0.04
|
||||
Other | | 5.889e-05 | | | 0.03
|
||||
Comm | 0.00027704 | 0.00027704 | 0.00027704 | 0.0 | 0.14
|
||||
Output | 0.0011551 | 0.0011551 | 0.0011551 | 0.0 | 0.58
|
||||
Modify | 7.8201e-05 | 7.8201e-05 | 7.8201e-05 | 0.0 | 0.04
|
||||
Other | | 5.865e-05 | | | 0.03
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -192,7 +192,7 @@ compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_p
|
||||
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
|
||||
run 10
|
||||
Memory usage per processor = 7.47955 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
|
||||
Step Lx Ly Lz Xy Xz Yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
|
||||
16 21.730089 21.727916 21.727916 0 0 0 1462009.5 773098.59 773098.59 4.2549849e-06 -8.3746497e-07 7.0310015e-06
|
||||
17 21.730089 21.727916 21.728133 0 0 0 1462009.5 773098.59 773098.59 5.1784721e-06 -2.3038152e-06 5.7172699e-06
|
||||
18 21.730089 21.727916 21.72835 0 0 0 1539307.6 850399.75 919275.09 9.5325273e-06 -6.4331187e-07 4.7453557e-06
|
||||
@ -204,20 +204,20 @@ Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
|
||||
24 21.730089 21.727916 21.729654 0 0 0 2003022 1314132.4 1796319.1 2.3497113e-06 -2.3680104e-06 4.7932602e-06
|
||||
25 21.730089 21.727916 21.729871 0 0 0 2080295.4 1391408.8 1942490.6 6.941166e-06 -1.1601937e-06 4.9355658e-06
|
||||
26 21.730089 21.727916 21.730089 0 0 0 2157565.2 1468681.6 2088661.4 5.7633476e-06 -8.4264935e-07 4.0350137e-06
|
||||
Loop time of 0.206357 on 1 procs for 10 steps with 512 atoms
|
||||
Loop time of 0.199616 on 1 procs for 10 steps with 512 atoms
|
||||
|
||||
Performance: 0.837 ns/day, 28.661 hours/ns, 48.460 timesteps/s
|
||||
100.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.866 ns/day, 27.724 hours/ns, 50.096 timesteps/s
|
||||
100.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.20466 | 0.20466 | 0.20466 | 0.0 | 99.18
|
||||
Pair | 0.19798 | 0.19798 | 0.19798 | 0.0 | 99.18
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00027633 | 0.00027633 | 0.00027633 | 0.0 | 0.13
|
||||
Output | 0.0012765 | 0.0012765 | 0.0012765 | 0.0 | 0.62
|
||||
Modify | 7.7963e-05 | 7.7963e-05 | 7.7963e-05 | 0.0 | 0.04
|
||||
Other | | 6.175e-05 | | | 0.03
|
||||
Comm | 0.00028658 | 0.00028658 | 0.00028658 | 0.0 | 0.14
|
||||
Output | 0.0012088 | 0.0012088 | 0.0012088 | 0.0 | 0.61
|
||||
Modify | 7.987e-05 | 7.987e-05 | 7.987e-05 | 0.0 | 0.04
|
||||
Other | | 5.698e-05 | | | 0.03
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -241,7 +241,7 @@ compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4
|
||||
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
|
||||
run 10
|
||||
Memory usage per processor = 8.24482 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
|
||||
Step Lx Ly Lz Xy Xz Yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
|
||||
26 21.730089 21.727916 21.730089 0 0 0 2234831.5 1545950.9 2234831.5 4.8476018e-06 4.2828413e-07 5.75372e-06
|
||||
27 21.730089 21.727916 21.730089 0 0 4.3460177e-07 2234831.5 1545950.9 2234831.5 5.088922e-06 -2.3012471e-06 5.6950612e-06
|
||||
28 21.730089 21.727916 21.730089 0 0 8.6920354e-07 2234831.5 1545950.9 2234831.5 4.7258447e-06 -1.3958256e-06 243.66105
|
||||
@ -253,20 +253,20 @@ Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
|
||||
34 21.730089 21.727916 21.730089 0 0 3.4768142e-06 2234831.5 1545950.9 2234831.5 4.8447261e-06 -1.9614792e-06 1705.6275
|
||||
35 21.730089 21.727916 21.730089 0 0 3.911416e-06 2234831.5 1545950.9 2234831.5 5.1297449e-06 -2.114135e-06 1949.2885
|
||||
36 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 4.5571577e-06 -1.8415232e-06 2192.9496
|
||||
Loop time of 0.203569 on 1 procs for 10 steps with 512 atoms
|
||||
Loop time of 0.199427 on 1 procs for 10 steps with 512 atoms
|
||||
|
||||
Performance: 0.849 ns/day, 28.273 hours/ns, 49.123 timesteps/s
|
||||
100.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.866 ns/day, 27.698 hours/ns, 50.144 timesteps/s
|
||||
100.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.20196 | 0.20196 | 0.20196 | 0.0 | 99.21
|
||||
Pair | 0.19785 | 0.19785 | 0.19785 | 0.0 | 99.21
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00028515 | 0.00028515 | 0.00028515 | 0.0 | 0.14
|
||||
Output | 0.0011783 | 0.0011783 | 0.0011783 | 0.0 | 0.58
|
||||
Modify | 7.7724e-05 | 7.7724e-05 | 7.7724e-05 | 0.0 | 0.04
|
||||
Other | | 6.366e-05 | | | 0.03
|
||||
Comm | 0.00027561 | 0.00027561 | 0.00027561 | 0.0 | 0.14
|
||||
Output | 0.0011613 | 0.0011613 | 0.0011613 | 0.0 | 0.58
|
||||
Modify | 7.6056e-05 | 7.6056e-05 | 7.6056e-05 | 0.0 | 0.04
|
||||
Other | | 6.199e-05 | | | 0.03
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -290,7 +290,7 @@ compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4
|
||||
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
|
||||
run 10
|
||||
Memory usage per processor = 8.99482 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
|
||||
Step Lx Ly Lz Xy Xz Yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
|
||||
36 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 5.1293854e-06 -1.6748595e-06 2436.6106
|
||||
37 21.730089 21.727916 21.730089 4.3455832e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 5.1236563e-06 -3.3624188e-06 2436.6106
|
||||
38 21.730089 21.727916 21.730089 8.6911663e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 243.64727 -0.00013232165 2436.6106
|
||||
@ -302,20 +302,20 @@ Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
|
||||
44 21.730089 21.727916 21.730089 3.4764665e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1705.531 -0.00091806693 2436.6106
|
||||
45 21.730089 21.727916 21.730089 3.9110248e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1949.1783 -0.001049945 2436.6106
|
||||
46 21.730089 21.727916 21.730089 4.3455832e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 2192.8256 -0.0011787861 2436.6106
|
||||
Loop time of 0.204484 on 1 procs for 10 steps with 512 atoms
|
||||
Loop time of 0.200513 on 1 procs for 10 steps with 512 atoms
|
||||
|
||||
Performance: 0.845 ns/day, 28.401 hours/ns, 48.904 timesteps/s
|
||||
Performance: 0.862 ns/day, 27.849 hours/ns, 49.872 timesteps/s
|
||||
100.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.20272 | 0.20272 | 0.20272 | 0.0 | 99.14
|
||||
Pair | 0.19893 | 0.19893 | 0.19893 | 0.0 | 99.21
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00029564 | 0.00029564 | 0.00029564 | 0.0 | 0.14
|
||||
Output | 0.0013256 | 0.0013256 | 0.0013256 | 0.0 | 0.65
|
||||
Modify | 7.844e-05 | 7.844e-05 | 7.844e-05 | 0.0 | 0.04
|
||||
Other | | 6.27e-05 | | | 0.03
|
||||
Comm | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.14
|
||||
Output | 0.0011744 | 0.0011744 | 0.0011744 | 0.0 | 0.59
|
||||
Modify | 7.4387e-05 | 7.4387e-05 | 7.4387e-05 | 0.0 | 0.04
|
||||
Other | | 6.08e-05 | | | 0.03
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
|
||||
|
||||
units metal
|
||||
@ -48,9 +48,9 @@ Step Temp TotEng PotEng E_vdwl E_coul
|
||||
1 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
2 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
3 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
Loop time of 0.0429027 on 4 procs for 3 steps with 512 atoms
|
||||
Loop time of 0.0423422 on 4 procs for 3 steps with 512 atoms
|
||||
|
||||
99.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
97.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
@ -64,12 +64,12 @@ Minimization stats:
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.026284 | 0.032657 | 0.041753 | 3.1 | 76.12
|
||||
Pair | 0.026049 | 0.03263 | 0.041219 | 3.0 | 77.06
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00052333 | 0.0096034 | 0.015953 | 5.7 | 22.38
|
||||
Output | 3.5048e-05 | 3.6538e-05 | 4.1008e-05 | 0.0 | 0.09
|
||||
Comm | 0.00049615 | 0.0090721 | 0.015641 | 5.7 | 21.43
|
||||
Output | 3.314e-05 | 3.5107e-05 | 4.1008e-05 | 0.1 | 0.08
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0006061 | | | 1.41
|
||||
Other | | 0.0006052 | | | 1.43
|
||||
|
||||
Nlocal: 128 ave 164 max 100 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
@ -100,20 +100,20 @@ Memory usage per processor = 5.89733 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul
|
||||
3 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
4 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
Loop time of 0.00605559 on 4 procs for 1 steps with 512 atoms
|
||||
Loop time of 0.00589204 on 4 procs for 1 steps with 512 atoms
|
||||
|
||||
Performance: 2.854 ns/day, 8.411 hours/ns, 165.137 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 2.933 ns/day, 8.183 hours/ns, 169.721 timesteps/s
|
||||
101.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0037332 | 0.0046489 | 0.00595 | 1.2 | 76.77
|
||||
Pair | 0.003751 | 0.0046486 | 0.0057852 | 1.1 | 78.90
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 7.2002e-05 | 0.0013711 | 0.0022838 | 2.2 | 22.64
|
||||
Output | 2.0027e-05 | 2.3484e-05 | 2.5988e-05 | 0.0 | 0.39
|
||||
Modify | 0 | 2.3842e-07 | 9.5367e-07 | 0.1 | 0.00
|
||||
Other | | 1.186e-05 | | | 0.20
|
||||
Comm | 7.391e-05 | 0.001206 | 0.0021 | 2.1 | 20.47
|
||||
Output | 1.9073e-05 | 2.0742e-05 | 2.1935e-05 | 0.0 | 0.35
|
||||
Modify | 0 | 7.1526e-07 | 1.9073e-06 | 0.1 | 0.01
|
||||
Other | | 1.597e-05 | | | 0.27
|
||||
|
||||
Nlocal: 128 ave 164 max 100 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
@ -138,10 +138,10 @@ fix 2 all deform 1 x scale 1.0001 remap x
|
||||
compute perfx all stress/atom NULL pair
|
||||
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:680)
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690)
|
||||
run 10
|
||||
Memory usage per processor = 6.64733 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
|
||||
Step Lx Ly Lz Xy Xz Yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
|
||||
4 21.727916 21.727916 21.727916 0 0 0 0.036618297 0.036625051 0.036618342 -1.7136998e-07 -3.2302114e-06 -1.7543151e-06
|
||||
5 21.728133 21.727916 21.727916 0 0 0 0.036618988 0.036625612 0.036619564 -1.1309366e-06 -2.412817e-06 -2.6316468e-06
|
||||
6 21.72835 21.727916 21.727916 0 0 0 146204.21 77325.824 77325.824 2.3636154e-06 -2.6955085e-06 -5.4243912e-06
|
||||
@ -153,20 +153,20 @@ Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
|
||||
12 21.729654 21.727916 21.727916 0 0 0 1023414.2 541206.21 541206.21 -9.1665744e-07 -1.59238e-06 -7.7617215e-06
|
||||
13 21.729871 21.727916 21.727916 0 0 0 1169613.4 618507.22 618507.22 -1.1565806e-06 -2.0309366e-06 -6.6873647e-06
|
||||
14 21.730089 21.727916 21.727916 0 0 0 1315811.8 695804.69 695804.69 1.8915845e-06 7.7289624e-06 -6.2492306e-06
|
||||
Loop time of 0.0683999 on 4 procs for 10 steps with 512 atoms
|
||||
Loop time of 0.0653707 on 4 procs for 10 steps with 512 atoms
|
||||
|
||||
Performance: 2.526 ns/day, 9.500 hours/ns, 146.199 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 2.643 ns/day, 9.079 hours/ns, 152.974 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.041408 | 0.051284 | 0.065623 | 3.9 | 74.98
|
||||
Pair | 0.041152 | 0.050811 | 0.063103 | 3.5 | 77.73
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0009675 | 0.015306 | 0.025153 | 7.1 | 22.38
|
||||
Output | 0.0016904 | 0.0017211 | 0.001745 | 0.1 | 2.52
|
||||
Modify | 2.4557e-05 | 2.9504e-05 | 3.4809e-05 | 0.1 | 0.04
|
||||
Other | | 5.972e-05 | | | 0.09
|
||||
Comm | 0.00078726 | 0.013075 | 0.02272 | 6.9 | 20.00
|
||||
Output | 0.0013869 | 0.0014045 | 0.0014176 | 0.0 | 2.15
|
||||
Modify | 2.9087e-05 | 3.32e-05 | 3.5048e-05 | 0.0 | 0.05
|
||||
Other | | 4.774e-05 | | | 0.07
|
||||
|
||||
Nlocal: 128 ave 164 max 100 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
@ -190,7 +190,7 @@ compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_p
|
||||
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
|
||||
run 10
|
||||
Memory usage per processor = 7.39733 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
|
||||
Step Lx Ly Lz Xy Xz Yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
|
||||
14 21.730089 21.727916 21.727916 0 0 0 1462009.6 773098.62 773098.62 -6.2271887e-07 -3.134065e-06 -1.4448086e-06
|
||||
15 21.730089 21.727916 21.728133 0 0 0 1462009.6 773098.62 773098.62 -1.4749588e-06 -2.1972704e-06 -2.7974026e-06
|
||||
16 21.730089 21.727916 21.72835 0 0 0 1539307.7 850399.78 919275.13 -1.1741349e-06 8.1321584e-06 -2.1634811e-06
|
||||
@ -202,20 +202,20 @@ Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
|
||||
22 21.730089 21.727916 21.729654 0 0 0 2003022.1 1314132.4 1796319.1 -2.1981227e-06 -2.7285159e-06 -2.0486576e-06
|
||||
23 21.730089 21.727916 21.729871 0 0 0 2080295.4 1391408.8 1942490.6 -3.6986662e-06 -2.430512e-06 -2.6914988e-06
|
||||
24 21.730089 21.727916 21.730089 0 0 0 2157565.2 1468681.6 2088661.4 -7.1345705e-06 -2.6113355e-06 -1.261254e-06
|
||||
Loop time of 0.0679641 on 4 procs for 10 steps with 512 atoms
|
||||
Loop time of 0.065423 on 4 procs for 10 steps with 512 atoms
|
||||
|
||||
Performance: 2.543 ns/day, 9.439 hours/ns, 147.137 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 2.641 ns/day, 9.087 hours/ns, 152.851 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.041426 | 0.05157 | 0.065353 | 3.8 | 75.88
|
||||
Pair | 0.041187 | 0.050801 | 0.063128 | 3.5 | 77.65
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00090528 | 0.014692 | 0.024832 | 7.1 | 21.62
|
||||
Output | 0.0016062 | 0.0016239 | 0.0016341 | 0.0 | 2.39
|
||||
Modify | 1.9789e-05 | 2.6107e-05 | 3.4094e-05 | 0.1 | 0.04
|
||||
Other | | 5.156e-05 | | | 0.08
|
||||
Comm | 0.00077367 | 0.013104 | 0.022709 | 6.9 | 20.03
|
||||
Output | 0.0014305 | 0.0014462 | 0.0014589 | 0.0 | 2.21
|
||||
Modify | 2.0504e-05 | 2.7299e-05 | 3.1233e-05 | 0.1 | 0.04
|
||||
Other | | 4.494e-05 | | | 0.07
|
||||
|
||||
Nlocal: 128 ave 164 max 100 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
@ -239,7 +239,7 @@ compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4
|
||||
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
|
||||
run 10
|
||||
Memory usage per processor = 8.16262 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
|
||||
Step Lx Ly Lz Xy Xz Yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
|
||||
24 21.730089 21.727916 21.730089 0 0 0 2234831.5 1545950.9 2234831.5 -3.9610575e-06 -3.188829e-06 -5.7973926e-07
|
||||
25 21.730089 21.727916 21.730089 0 0 4.3460177e-07 2234831.5 1545950.9 2234831.5 -4.4960939e-06 -2.549801e-06 -1.5603844e-06
|
||||
26 21.730089 21.727916 21.730089 0 0 8.6920354e-07 2234831.5 1545950.9 2234831.5 -5.49227e-06 -4.2895969e-06 243.66104
|
||||
@ -251,20 +251,20 @@ Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
|
||||
32 21.730089 21.727916 21.730089 0 0 3.4768142e-06 2234831.5 1545950.9 2234831.5 -6.62009e-06 -8.621625e-06 1705.6275
|
||||
33 21.730089 21.727916 21.730089 0 0 3.911416e-06 2234831.5 1545950.9 2234831.5 -6.712501e-06 -8.7315457e-06 1949.2885
|
||||
34 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.3958831e-06 -7.1670331e-06 2192.9496
|
||||
Loop time of 0.0681064 on 4 procs for 10 steps with 512 atoms
|
||||
Loop time of 0.0656388 on 4 procs for 10 steps with 512 atoms
|
||||
|
||||
Performance: 2.537 ns/day, 9.459 hours/ns, 146.829 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 2.633 ns/day, 9.116 hours/ns, 152.349 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.041511 | 0.051664 | 0.065403 | 3.8 | 75.86
|
||||
Pair | 0.040685 | 0.050668 | 0.063339 | 3.6 | 77.19
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00090647 | 0.014658 | 0.024812 | 7.1 | 21.52
|
||||
Output | 0.0016921 | 0.0017017 | 0.001713 | 0.0 | 2.50
|
||||
Modify | 2.2173e-05 | 2.7835e-05 | 3.0994e-05 | 0.1 | 0.04
|
||||
Other | | 5.496e-05 | | | 0.08
|
||||
Comm | 0.00077748 | 0.013466 | 0.023423 | 7.0 | 20.52
|
||||
Output | 0.0013893 | 0.0014307 | 0.001461 | 0.1 | 2.18
|
||||
Modify | 2.1935e-05 | 2.6524e-05 | 3.0994e-05 | 0.1 | 0.04
|
||||
Other | | 4.733e-05 | | | 0.07
|
||||
|
||||
Nlocal: 128 ave 164 max 100 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
@ -288,7 +288,7 @@ compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4
|
||||
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
|
||||
run 10
|
||||
Memory usage per processor = 8.91262 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
|
||||
Step Lx Ly Lz Xy Xz Yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
|
||||
34 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.1581426e-06 -1.1350015e-05 2436.6106
|
||||
35 21.730089 21.727916 21.730089 4.3455832e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.7014652e-06 -1.1032048e-05 2436.6106
|
||||
36 21.730089 21.727916 21.730089 8.6911663e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 243.64726 -0.00014128194 2436.6106
|
||||
@ -300,20 +300,20 @@ Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
|
||||
42 21.730089 21.727916 21.730089 3.4764665e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1705.531 -0.00093156087 2436.6106
|
||||
43 21.730089 21.727916 21.730089 3.9110248e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1949.1783 -0.0010618138 2436.6106
|
||||
44 21.730089 21.727916 21.730089 4.3455832e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 2192.8256 -0.0011926577 2436.6106
|
||||
Loop time of 0.0681901 on 4 procs for 10 steps with 512 atoms
|
||||
Loop time of 0.0657181 on 4 procs for 10 steps with 512 atoms
|
||||
|
||||
Performance: 2.534 ns/day, 9.471 hours/ns, 146.649 timesteps/s
|
||||
100.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 2.629 ns/day, 9.128 hours/ns, 152.165 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.041675 | 0.051819 | 0.065549 | 3.8 | 75.99
|
||||
Pair | 0.040015 | 0.050405 | 0.063468 | 3.7 | 76.70
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00088024 | 0.014621 | 0.024764 | 7.2 | 21.44
|
||||
Output | 0.0016496 | 0.0016653 | 0.0016737 | 0.0 | 2.44
|
||||
Modify | 2.0027e-05 | 2.4855e-05 | 3.0756e-05 | 0.1 | 0.04
|
||||
Other | | 6.02e-05 | | | 0.09
|
||||
Comm | 0.00079203 | 0.013852 | 0.024224 | 7.1 | 21.08
|
||||
Output | 0.0013652 | 0.001386 | 0.0014119 | 0.1 | 2.11
|
||||
Modify | 2.0981e-05 | 2.5392e-05 | 3.2902e-05 | 0.1 | 0.04
|
||||
Other | | 4.965e-05 | | | 0.08
|
||||
|
||||
Nlocal: 128 ave 164 max 100 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Pure Si crystal, structure created by LAMMPS, qeq off
|
||||
|
||||
units metal
|
||||
@ -61,20 +61,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
|
||||
8 9.9628496 -4.6284152 -4.6297005 -4.6297005 0 1142.5666 10246.592 21.72 21.72 21.72 0
|
||||
9 9.9267173 -4.6284152 -4.6296958 -4.6296958 0 1143.0353 10246.592 21.72 21.72 21.72 0
|
||||
10 9.8864817 -4.6284152 -4.6296906 -4.6296906 0 1143.5568 10246.592 21.72 21.72 21.72 0
|
||||
Loop time of 0.193527 on 1 procs for 10 steps with 512 atoms
|
||||
Loop time of 0.187379 on 1 procs for 10 steps with 512 atoms
|
||||
|
||||
Performance: 0.893 ns/day, 26.879 hours/ns, 51.672 timesteps/s
|
||||
100.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.922 ns/day, 26.025 hours/ns, 53.368 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.19296 | 0.19296 | 0.19296 | 0.0 | 99.71
|
||||
Pair | 0.18685 | 0.18685 | 0.18685 | 0.0 | 99.72
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00025725 | 0.00025725 | 0.00025725 | 0.0 | 0.13
|
||||
Output | 0.00012445 | 0.00012445 | 0.00012445 | 0.0 | 0.06
|
||||
Modify | 8.3208e-05 | 8.3208e-05 | 8.3208e-05 | 0.0 | 0.04
|
||||
Other | | 0.000104 | | | 0.05
|
||||
Comm | 0.00025797 | 0.00025797 | 0.00025797 | 0.0 | 0.14
|
||||
Output | 0.00011826 | 0.00011826 | 0.00011826 | 0.0 | 0.06
|
||||
Modify | 8.297e-05 | 8.297e-05 | 8.297e-05 | 0.0 | 0.04
|
||||
Other | | 7.2e-05 | | | 0.04
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Pure Si crystal, structure created by LAMMPS, qeq off
|
||||
|
||||
units metal
|
||||
@ -61,20 +61,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
|
||||
8 9.9627224 -4.6284152 -4.6297005 -4.6297005 0 1142.5835 10246.592 21.72 21.72 21.72 0
|
||||
9 9.9265602 -4.6284152 -4.6296958 -4.6296958 0 1143.0565 10246.592 21.72 21.72 21.72 0
|
||||
10 9.8862927 -4.6284152 -4.6296906 -4.6296906 0 1143.5829 10246.592 21.72 21.72 21.72 0
|
||||
Loop time of 0.0531193 on 4 procs for 10 steps with 512 atoms
|
||||
Loop time of 0.0527902 on 4 procs for 10 steps with 512 atoms
|
||||
|
||||
Performance: 3.253 ns/day, 7.378 hours/ns, 188.255 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 3.273 ns/day, 7.332 hours/ns, 189.429 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.046737 | 0.048466 | 0.051893 | 1.0 | 91.24
|
||||
Pair | 0.045993 | 0.047917 | 0.051259 | 0.9 | 90.77
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00082636 | 0.0042595 | 0.0059838 | 3.2 | 8.02
|
||||
Output | 0.00026178 | 0.00027215 | 0.0002954 | 0.1 | 0.51
|
||||
Modify | 2.3842e-05 | 2.563e-05 | 2.8372e-05 | 0.0 | 0.05
|
||||
Other | | 9.644e-05 | | | 0.18
|
||||
Comm | 0.0010545 | 0.0044153 | 0.0063219 | 3.0 | 8.36
|
||||
Output | 0.00030351 | 0.00033081 | 0.00036931 | 0.1 | 0.63
|
||||
Modify | 2.3365e-05 | 2.6286e-05 | 2.8372e-05 | 0.0 | 0.05
|
||||
Other | | 0.0001011 | | | 0.19
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Graphene-OH on Cu2O (110) surface
|
||||
|
||||
units metal
|
||||
@ -46,7 +46,7 @@ Neighbor list info ...
|
||||
master list distance cutoff = 13
|
||||
ghost atom cutoff = 13
|
||||
binsize = 6.5 -> bins = 4 4 6
|
||||
Memory usage per processor = 4.47117 Mbytes
|
||||
Memory usage per processor = 4.95036 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
|
||||
0 300 -4.5167776 -4.5554988 -3.9875717 -0.56792713 -19801.669 17719.012 21.3 24.6 33.8162
|
||||
10 467.10265 -4.5167723 -4.5770615 -4.0093169 -0.56774462 -15438.86 17719.012 21.3 24.6 33.8162
|
||||
@ -59,20 +59,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
|
||||
80 1188.3196 -4.518095 -4.6714721 -4.0978283 -0.57364387 12411.934 17719.012 21.3 24.6 33.8162
|
||||
90 1193.9207 -4.5183329 -4.672433 -4.0976379 -0.57479504 15405.848 17719.012 21.3 24.6 33.8162
|
||||
100 1197.343 -4.5185478 -4.6730896 -4.0971431 -0.57594648 17853.038 17719.012 21.3 24.6 33.8162
|
||||
Loop time of 45.764 on 1 procs for 100 steps with 682 atoms
|
||||
Loop time of 44.821 on 1 procs for 100 steps with 682 atoms
|
||||
|
||||
Performance: 0.038 ns/day, 635.612 hours/ns, 2.185 timesteps/s
|
||||
Performance: 0.039 ns/day, 622.513 hours/ns, 2.231 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 10.987 | 10.987 | 10.987 | 0.0 | 24.01
|
||||
Pair | 10.702 | 10.702 | 10.702 | 0.0 | 23.88
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00317 | 0.00317 | 0.00317 | 0.0 | 0.01
|
||||
Output | 0.0001812 | 0.0001812 | 0.0001812 | 0.0 | 0.00
|
||||
Modify | 34.773 | 34.773 | 34.773 | 0.0 | 75.98
|
||||
Other | | 0.001366 | | | 0.00
|
||||
Comm | 0.0028968 | 0.0028968 | 0.0028968 | 0.0 | 0.01
|
||||
Output | 0.00018311 | 0.00018311 | 0.00018311 | 0.0 | 0.00
|
||||
Modify | 34.115 | 34.115 | 34.115 | 0.0 | 76.11
|
||||
Other | | 0.001503 | | | 0.00
|
||||
|
||||
Nlocal: 682 ave 682 max 682 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -87,4 +87,4 @@ Total # of neighbors = 355216
|
||||
Ave neighs/atom = 520.845
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:48
|
||||
Total wall time: 0:00:47
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Graphene-OH on Cu2O (110) surface
|
||||
|
||||
units metal
|
||||
@ -59,20 +59,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
|
||||
80 1188.3196 -4.518095 -4.6714721 -4.0978283 -0.57364387 12411.934 17719.012 21.3 24.6 33.8162
|
||||
90 1193.9207 -4.5183329 -4.672433 -4.0976379 -0.57479504 15405.848 17719.012 21.3 24.6 33.8162
|
||||
100 1197.343 -4.5185478 -4.6730896 -4.0971431 -0.57594648 17853.038 17719.012 21.3 24.6 33.8162
|
||||
Loop time of 20.7745 on 4 procs for 100 steps with 682 atoms
|
||||
Loop time of 20.2521 on 4 procs for 100 steps with 682 atoms
|
||||
|
||||
Performance: 0.083 ns/day, 288.534 hours/ns, 4.814 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 0.085 ns/day, 281.279 hours/ns, 4.938 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.2393 | 3.5206 | 4.856 | 67.7 | 16.95
|
||||
Pair | 2.1898 | 3.3988 | 4.7081 | 65.6 | 16.78
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.024316 | 1.3586 | 2.6388 | 108.8 | 6.54
|
||||
Output | 0.00034308 | 0.00036204 | 0.00038791 | 0.1 | 0.00
|
||||
Modify | 15.892 | 15.892 | 15.892 | 0.0 | 76.50
|
||||
Other | | 0.002505 | | | 0.01
|
||||
Comm | 0.013637 | 1.3219 | 2.5298 | 105.1 | 6.53
|
||||
Output | 0.00034475 | 0.00035816 | 0.00038099 | 0.1 | 0.00
|
||||
Modify | 15.528 | 15.528 | 15.529 | 0.0 | 76.68
|
||||
Other | | 0.002504 | | | 0.01
|
||||
|
||||
Nlocal: 170.5 ave 245 max 100 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (3 Aug 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 3d Lennard-Jones melt, thermostatted by fix controller
|
||||
|
||||
units lj
|
||||
@ -51,20 +51,20 @@ Step Temp E_pair E_mol TotEng Press
|
||||
400 0.49885979 -6.157314 0 -5.4092114 -2.1544075
|
||||
450 0.50261633 -6.1458076 0 -5.3920716 -2.1080502
|
||||
500 0.51198903 -6.1441158 0 -5.3763242 -2.0677941
|
||||
Loop time of 1.51807 on 1 procs for 500 steps with 4000 atoms
|
||||
Loop time of 1.51804 on 1 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 142286.109 tau/day, 329.366 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 142288.277 tau/day, 329.371 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.2134 | 1.2134 | 1.2134 | 0.0 | 79.93
|
||||
Neigh | 0.16519 | 0.16519 | 0.16519 | 0.0 | 10.88
|
||||
Comm | 0.022159 | 0.022159 | 0.022159 | 0.0 | 1.46
|
||||
Output | 0.00021291 | 0.00021291 | 0.00021291 | 0.0 | 0.01
|
||||
Modify | 0.11073 | 0.11073 | 0.11073 | 0.0 | 7.29
|
||||
Other | | 0.006378 | | | 0.42
|
||||
Pair | 1.2152 | 1.2152 | 1.2152 | 0.0 | 80.05
|
||||
Neigh | 0.16464 | 0.16464 | 0.16464 | 0.0 | 10.85
|
||||
Comm | 0.022342 | 0.022342 | 0.022342 | 0.0 | 1.47
|
||||
Output | 0.00020981 | 0.00020981 | 0.00020981 | 0.0 | 0.01
|
||||
Modify | 0.10936 | 0.10936 | 0.10936 | 0.0 | 7.20
|
||||
Other | | 0.006292 | | | 0.41
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -83,8 +83,9 @@ Dangerous builds not checked
|
||||
fix 10 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol
|
||||
|
||||
# time-average temp for control
|
||||
|
||||
#fix ave all ave/time 5 20 100 c_thermo_temp
|
||||
#fix 10 all controller 100 0.5 0.0 0.0 f_ave 1.5 tcontrol
|
||||
#fix 10 all controller 100 1.0 0.5 0.0 0.0 # f_ave 1.5 tcontrol
|
||||
|
||||
# run with controller
|
||||
|
||||
@ -142,20 +143,20 @@ Step Temp E_pair E_mol TotEng Press
|
||||
2900 1.5287303 -4.8393493 0 -2.546827 5.3276564
|
||||
2950 1.5175567 -4.8779763 0 -2.6022104 5.1592321
|
||||
3000 1.5038518 -4.8714664 0 -2.6162526 5.1494048
|
||||
Loop time of 7.81543 on 1 procs for 2500 steps with 4000 atoms
|
||||
Loop time of 7.82673 on 1 procs for 2500 steps with 4000 atoms
|
||||
|
||||
Performance: 138188.243 tau/day, 319.880 timesteps/s
|
||||
Performance: 137988.733 tau/day, 319.418 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.2599 | 6.2599 | 6.2599 | 0.0 | 80.10
|
||||
Neigh | 0.85839 | 0.85839 | 0.85839 | 0.0 | 10.98
|
||||
Comm | 0.11165 | 0.11165 | 0.11165 | 0.0 | 1.43
|
||||
Output | 0.0010052 | 0.0010052 | 0.0010052 | 0.0 | 0.01
|
||||
Modify | 0.55397 | 0.55397 | 0.55397 | 0.0 | 7.09
|
||||
Other | | 0.03055 | | | 0.39
|
||||
Pair | 6.2774 | 6.2774 | 6.2774 | 0.0 | 80.21
|
||||
Neigh | 0.85491 | 0.85491 | 0.85491 | 0.0 | 10.92
|
||||
Comm | 0.11304 | 0.11304 | 0.11304 | 0.0 | 1.44
|
||||
Output | 0.00090504 | 0.00090504 | 0.00090504 | 0.0 | 0.01
|
||||
Modify | 0.55013 | 0.55013 | 0.55013 | 0.0 | 7.03
|
||||
Other | | 0.0303 | | | 0.39
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (3 Aug 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 3d Lennard-Jones melt, thermostatted by fix controller
|
||||
|
||||
units lj
|
||||
@ -51,20 +51,20 @@ Step Temp E_pair E_mol TotEng Press
|
||||
400 0.50869337 -6.1435002 0 -5.3806509 -2.0654599
|
||||
450 0.50821435 -6.1436659 0 -5.381535 -2.0660991
|
||||
500 0.51057155 -6.138733 0 -5.3730671 -2.0305015
|
||||
Loop time of 0.453014 on 4 procs for 500 steps with 4000 atoms
|
||||
Loop time of 0.474689 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 476806.251 tau/day, 1103.718 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 455034.992 tau/day, 1053.322 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.32365 | 0.32949 | 0.33618 | 1.0 | 72.73
|
||||
Neigh | 0.043907 | 0.044821 | 0.045741 | 0.3 | 9.89
|
||||
Comm | 0.037718 | 0.04614 | 0.053796 | 3.2 | 10.19
|
||||
Output | 0.00033951 | 0.00036806 | 0.00042248 | 0.2 | 0.08
|
||||
Modify | 0.027845 | 0.028714 | 0.029447 | 0.3 | 6.34
|
||||
Other | | 0.003484 | | | 0.77
|
||||
Pair | 0.31692 | 0.32816 | 0.35039 | 2.3 | 69.13
|
||||
Neigh | 0.042872 | 0.044288 | 0.046693 | 0.7 | 9.33
|
||||
Comm | 0.043676 | 0.070658 | 0.084897 | 6.0 | 14.89
|
||||
Output | 0.00025439 | 0.0002867 | 0.00030446 | 0.1 | 0.06
|
||||
Modify | 0.02728 | 0.028604 | 0.030571 | 0.8 | 6.03
|
||||
Other | | 0.002697 | | | 0.57
|
||||
|
||||
Nlocal: 1000 ave 1027 max 969 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
@ -83,8 +83,9 @@ Dangerous builds not checked
|
||||
fix 10 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol
|
||||
|
||||
# time-average temp for control
|
||||
|
||||
#fix ave all ave/time 5 20 100 c_thermo_temp
|
||||
#fix 10 all controller 100 0.5 0.0 0.0 f_ave 1.5 tcontrol
|
||||
#fix 10 all controller 100 1.0 0.5 0.0 0.0 # f_ave 1.5 tcontrol
|
||||
|
||||
# run with controller
|
||||
|
||||
@ -142,20 +143,20 @@ Step Temp E_pair E_mol TotEng Press
|
||||
2900 1.4994026 -4.8400966 0 -2.591555 5.3231654
|
||||
2950 1.5057915 -4.8842358 0 -2.6261131 5.1645778
|
||||
3000 1.5038806 -4.8661399 0 -2.610883 5.2228747
|
||||
Loop time of 2.26012 on 4 procs for 2500 steps with 4000 atoms
|
||||
Loop time of 2.33203 on 4 procs for 2500 steps with 4000 atoms
|
||||
|
||||
Performance: 477850.096 tau/day, 1106.134 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 463116.726 tau/day, 1072.029 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.625 | 1.654 | 1.6952 | 2.2 | 73.18
|
||||
Neigh | 0.2238 | 0.22532 | 0.22785 | 0.3 | 9.97
|
||||
Comm | 0.18091 | 0.22445 | 0.25435 | 6.1 | 9.93
|
||||
Output | 0.0015404 | 0.0016042 | 0.0017579 | 0.2 | 0.07
|
||||
Modify | 0.14057 | 0.14187 | 0.14303 | 0.2 | 6.28
|
||||
Other | | 0.01285 | | | 0.57
|
||||
Pair | 1.6173 | 1.6621 | 1.7135 | 3.2 | 71.27
|
||||
Neigh | 0.2201 | 0.22394 | 0.23011 | 0.9 | 9.60
|
||||
Comm | 0.22619 | 0.29012 | 0.33801 | 8.8 | 12.44
|
||||
Output | 0.001302 | 0.0013426 | 0.0013707 | 0.1 | 0.06
|
||||
Modify | 0.13805 | 0.14195 | 0.14664 | 0.9 | 6.09
|
||||
Other | | 0.01257 | | | 0.54
|
||||
|
||||
Nlocal: 1000 ave 1014 max 988 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
209
examples/coreshell/log.5Oct16.coreshell.g++.1
Normal file
209
examples/coreshell/log.5Oct16.coreshell.g++.1
Normal file
@ -0,0 +1,209 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Testsystem for core-shell model compared to Mitchel and Finchham
|
||||
# Hendrik Heenen, June 2014
|
||||
|
||||
# ------------------------ INITIALIZATION ----------------------------
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style full
|
||||
|
||||
# ----------------------- ATOM DEFINITION ----------------------------
|
||||
|
||||
fix csinfo all property/atom i_CSID
|
||||
read_data data.coreshell fix csinfo NULL CS-Info
|
||||
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
432 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
216 bonds
|
||||
1 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
|
||||
group cores type 1 2
|
||||
216 atoms in group cores
|
||||
group shells type 3 4
|
||||
216 atoms in group shells
|
||||
|
||||
neighbor 2.0 bin
|
||||
comm_modify vel yes
|
||||
|
||||
# ------------------------ FORCE FIELDS ------------------------------
|
||||
|
||||
kspace_style ewald 1.0e-6
|
||||
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
|
||||
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
|
||||
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
|
||||
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
|
||||
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 63.014 0.0
|
||||
bond_coeff 2 25.724 0.0
|
||||
|
||||
# ------------------------ Equilibration Run -------------------------------
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
|
||||
|
||||
compute CSequ all temp/cs cores shells
|
||||
|
||||
# output via chunk method
|
||||
|
||||
#compute prop all property/atom i_CSID
|
||||
#compute cs_chunk all chunk/atom c_prop
|
||||
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
|
||||
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
|
||||
|
||||
thermo_modify temp CSequ
|
||||
|
||||
# velocity bias option
|
||||
|
||||
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
|
||||
Ewald initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 22
|
||||
ghost atom cutoff = 22
|
||||
binsize = 11 -> bins = 3 3 3
|
||||
velocity all scale 1427 temp CSequ
|
||||
|
||||
fix thermoberendsen all temp/berendsen 1427 1427 0.4
|
||||
fix nve all nve
|
||||
fix_modify thermoberendsen temp CSequ
|
||||
|
||||
# 2 fmsec timestep
|
||||
|
||||
timestep 0.002
|
||||
run 500
|
||||
Ewald initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Memory usage per processor = 15.7472 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
|
||||
0 -635.44099 -675.09865 39.657659 1427 -20613.612 -675.09865 1.6320365 1018.8211 -1695.5518 0 2.7895988e-14 3.594347e-15 13990.5
|
||||
50 -634.17327 -666.17818 32.004909 1151.6314 -4030.3308 -667.95621 37.809071 989.23282 -1694.9981 1.7780231 9.7133792 2.1917971 13990.5
|
||||
100 -631.93508 -661.91226 29.977186 1078.6679 -3172.6296 -664.0672 39.333409 991.36934 -1694.7699 2.1549314 11.091424 2.1704389 13990.5
|
||||
150 -630.1681 -663.12416 32.956057 1185.8565 142.25543 -665.48036 46.253767 982.97455 -1694.7087 2.3561935 11.467914 2.1652594 13990.5
|
||||
200 -628.62323 -663.64923 35.025998 1260.3391 -1623.5465 -665.96879 41.661877 986.81675 -1694.4474 2.3195587 10.597709 2.9538263 13990.5
|
||||
250 -627.31045 -662.01825 34.707801 1248.8894 -1510.5567 -664.50313 42.101716 987.90197 -1694.5068 2.4848735 10.392755 1.6933702 13990.5
|
||||
300 -626.57622 -660.97494 34.398716 1237.7677 -1638.6653 -663.48087 41.653234 989.53228 -1694.6664 2.5059308 11.204363 2.2809764 13990.5
|
||||
350 -625.91962 -665.35838 39.438756 1419.1232 -1352.4038 -667.6167 41.582459 985.53381 -1694.733 2.2583269 10.83105 1.8963306 13990.5
|
||||
400 -625.24851 -660.77642 35.527912 1278.3995 -425.3358 -663.12602 43.890329 987.75201 -1694.7684 2.3495978 11.521967 2.1759207 13990.5
|
||||
450 -624.67742 -662.88674 38.209317 1374.8844 1108.0844 -665.43207 46.964873 982.35206 -1694.749 2.5453361 11.002418 2.0014401 13990.5
|
||||
500 -624.30218 -661.97851 37.676336 1355.7061 -999.37887 -664.60374 42.373166 987.59022 -1694.5671 2.6252269 11.153982 2.8270477 13990.5
|
||||
Loop time of 8.64071 on 1 procs for 500 steps with 432 atoms
|
||||
|
||||
Performance: 9.999 ns/day, 2.400 hours/ns, 57.866 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.824 | 7.824 | 7.824 | 0.0 | 90.55
|
||||
Bond | 0.0024104 | 0.0024104 | 0.0024104 | 0.0 | 0.03
|
||||
Kspace | 0.53534 | 0.53534 | 0.53534 | 0.0 | 6.20
|
||||
Neigh | 0.19522 | 0.19522 | 0.19522 | 0.0 | 2.26
|
||||
Comm | 0.066091 | 0.066091 | 0.066091 | 0.0 | 0.76
|
||||
Output | 0.0003643 | 0.0003643 | 0.0003643 | 0.0 | 0.00
|
||||
Modify | 0.011435 | 0.011435 | 0.011435 | 0.0 | 0.13
|
||||
Other | | 0.005869 | | | 0.07
|
||||
|
||||
Nlocal: 432 ave 432 max 432 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 9338 ave 9338 max 9338 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 297354 ave 297354 max 297354 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 297354
|
||||
Ave neighs/atom = 688.319
|
||||
Ave special neighs/atom = 1
|
||||
Neighbor list builds = 22
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix thermoberendsen
|
||||
|
||||
# ------------------------ Dynamic Run -------------------------------
|
||||
|
||||
run 1000
|
||||
Ewald initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Memory usage per processor = 15.7472 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
|
||||
500 -624.30218 -661.97851 37.676336 1355.7061 -999.37887 -664.60374 42.373166 987.59022 -1694.5671 2.6252269 11.153982 2.8270477 13990.5
|
||||
550 -624.30708 -662.13355 37.826467 1361.1083 326.46254 -664.76811 45.306636 984.72863 -1694.8034 2.6345547 10.879989 1.9751675 13990.5
|
||||
600 -624.30994 -661.8449 37.534969 1350.6193 -984.35215 -664.36139 42.366573 987.8789 -1694.6069 2.516489 10.211098 1.7890339 13990.5
|
||||
650 -624.30501 -659.20596 34.900952 1255.8396 554.8226 -661.96471 46.567453 986.05088 -1694.583 2.7587454 13.15403 2.1657286 13990.5
|
||||
700 -624.30907 -661.85064 37.541572 1350.8569 -135.38668 -664.3843 44.382641 985.80654 -1694.5735 2.5336521 10.991882 2.0402026 13990.5
|
||||
750 -624.30999 -660.52853 36.21854 1303.2503 1196.4145 -663.29701 47.437312 984.08773 -1694.822 2.7684838 11.681986 2.0756933 13990.5
|
||||
800 -624.30488 -659.87594 35.571053 1279.9518 361.87762 -662.81183 45.49882 986.40712 -1694.7178 2.935891 11.519352 3.7801343 13990.5
|
||||
850 -624.30607 -663.64735 39.341278 1415.6157 -42.214824 -666.11278 44.277011 984.33678 -1694.7266 2.4654311 11.03941 1.9211474 13990.5
|
||||
900 -624.30048 -659.04455 34.744072 1250.1946 386.10592 -662.10941 45.864611 986.90301 -1694.877 3.0648637 12.126864 2.467969 13990.5
|
||||
950 -624.30795 -663.3468 39.038856 1404.7337 289.90291 -665.76693 45.27444 983.7762 -1694.8176 2.420128 11.735744 2.053808 13990.5
|
||||
1000 -624.303 -659.5513 35.248296 1268.3381 -896.7132 -662.30776 42.985505 989.11655 -1694.4098 2.7564586 11.38686 1.8136876 13990.5
|
||||
1050 -624.30433 -659.21593 34.911606 1256.223 273.26272 -661.98578 45.834363 986.93885 -1694.759 2.7698415 12.201066 1.9804734 13990.5
|
||||
1100 -624.3035 -660.37975 36.076254 1298.1305 40.2604 -662.88712 45.266447 986.77782 -1694.9314 2.5073688 11.366839 2.2452799 13990.5
|
||||
1150 -624.30832 -658.16356 33.855242 1218.2119 905.45817 -660.85689 47.381273 986.61927 -1694.8574 2.6933378 13.157497 2.3062872 13990.5
|
||||
1200 -624.30971 -665.57285 41.263142 1484.77 -2010.9356 -667.71783 39.858615 987.32002 -1694.8965 2.1449751 9.3563352 1.7115187 13990.5
|
||||
1250 -624.3069 -662.41936 38.112468 1371.3994 223.85833 -665.01906 45.021425 984.67299 -1694.7135 2.5997021 10.137667 1.8129534 13990.5
|
||||
1300 -624.3116 -661.73044 37.418835 1346.4405 524.83698 -664.46475 45.716001 983.98856 -1694.1693 2.734311 11.475107 2.5468008 13990.5
|
||||
1350 -624.30917 -661.34529 37.036121 1332.6693 399.81653 -663.86813 45.373759 985.3362 -1694.5781 2.5228434 10.819603 2.2048214 13990.5
|
||||
1400 -624.31545 -660.75213 36.43668 1311.0996 193.18853 -663.43944 45.172084 985.90744 -1694.519 2.6873128 10.597955 1.9090871 13990.5
|
||||
1450 -624.30419 -660.88131 36.577122 1316.1532 530.40423 -663.62017 46.21726 984.89723 -1694.7347 2.7388564 12.015146 2.6454091 13990.5
|
||||
1500 -624.30236 -660.40336 36.100999 1299.0209 -759.2259 -663.48374 43.382233 987.65506 -1694.521 3.0803837 12.48163 2.2113083 13990.5
|
||||
Loop time of 17.2383 on 1 procs for 1000 steps with 432 atoms
|
||||
|
||||
Performance: 10.024 ns/day, 2.394 hours/ns, 58.011 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 15.619 | 15.619 | 15.619 | 0.0 | 90.61
|
||||
Bond | 0.0048032 | 0.0048032 | 0.0048032 | 0.0 | 0.03
|
||||
Kspace | 1.068 | 1.068 | 1.068 | 0.0 | 6.20
|
||||
Neigh | 0.39623 | 0.39623 | 0.39623 | 0.0 | 2.30
|
||||
Comm | 0.13052 | 0.13052 | 0.13052 | 0.0 | 0.76
|
||||
Output | 0.00067472 | 0.00067472 | 0.00067472 | 0.0 | 0.00
|
||||
Modify | 0.0071197 | 0.0071197 | 0.0071197 | 0.0 | 0.04
|
||||
Other | | 0.01175 | | | 0.07
|
||||
|
||||
Nlocal: 432 ave 432 max 432 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 9327 ave 9327 max 9327 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 297525 ave 297525 max 297525 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 297525
|
||||
Ave neighs/atom = 688.715
|
||||
Ave special neighs/atom = 1
|
||||
Neighbor list builds = 45
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:25
|
||||
209
examples/coreshell/log.5Oct16.coreshell.g++.4
Normal file
209
examples/coreshell/log.5Oct16.coreshell.g++.4
Normal file
@ -0,0 +1,209 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Testsystem for core-shell model compared to Mitchel and Finchham
|
||||
# Hendrik Heenen, June 2014
|
||||
|
||||
# ------------------------ INITIALIZATION ----------------------------
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style full
|
||||
|
||||
# ----------------------- ATOM DEFINITION ----------------------------
|
||||
|
||||
fix csinfo all property/atom i_CSID
|
||||
read_data data.coreshell fix csinfo NULL CS-Info
|
||||
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
432 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
216 bonds
|
||||
1 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
|
||||
group cores type 1 2
|
||||
216 atoms in group cores
|
||||
group shells type 3 4
|
||||
216 atoms in group shells
|
||||
|
||||
neighbor 2.0 bin
|
||||
comm_modify vel yes
|
||||
|
||||
# ------------------------ FORCE FIELDS ------------------------------
|
||||
|
||||
kspace_style ewald 1.0e-6
|
||||
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
|
||||
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
|
||||
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
|
||||
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
|
||||
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 63.014 0.0
|
||||
bond_coeff 2 25.724 0.0
|
||||
|
||||
# ------------------------ Equilibration Run -------------------------------
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
|
||||
|
||||
compute CSequ all temp/cs cores shells
|
||||
|
||||
# output via chunk method
|
||||
|
||||
#compute prop all property/atom i_CSID
|
||||
#compute cs_chunk all chunk/atom c_prop
|
||||
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
|
||||
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
|
||||
|
||||
thermo_modify temp CSequ
|
||||
|
||||
# velocity bias option
|
||||
|
||||
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
|
||||
Ewald initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 22
|
||||
ghost atom cutoff = 22
|
||||
binsize = 11 -> bins = 3 3 3
|
||||
velocity all scale 1427 temp CSequ
|
||||
|
||||
fix thermoberendsen all temp/berendsen 1427 1427 0.4
|
||||
fix nve all nve
|
||||
fix_modify thermoberendsen temp CSequ
|
||||
|
||||
# 2 fmsec timestep
|
||||
|
||||
timestep 0.002
|
||||
run 500
|
||||
Ewald initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Memory usage per processor = 15.2111 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
|
||||
0 -635.44099 -675.09865 39.657659 1427 -20613.612 -675.09865 1.6320365 1018.8211 -1695.5518 0 2.9851021e-14 4.2188475e-15 13990.5
|
||||
50 -634.17349 -666.17817 32.004686 1151.6234 -4030.346 -667.9562 37.809075 989.23283 -1694.9981 1.7780241 9.7133824 2.1917971 13990.5
|
||||
100 -631.93518 -661.91229 29.977104 1078.665 -3172.6554 -664.06722 39.333371 991.36935 -1694.7699 2.1549316 11.09144 2.1704351 13990.5
|
||||
150 -630.16821 -663.12421 32.956001 1185.8545 142.23746 -665.48039 46.253735 982.97455 -1694.7087 2.3561823 11.467862 2.1651502 13990.5
|
||||
200 -628.62229 -663.64928 35.026994 1260.375 -1623.495 -665.96883 41.661825 986.81676 -1694.4474 2.3195535 10.597709 2.9538127 13990.5
|
||||
250 -627.31146 -662.01843 34.706969 1248.8595 -1510.677 -664.50329 42.10159 987.90193 -1694.5068 2.4848607 10.392642 1.6933333 13990.5
|
||||
300 -626.57662 -660.97479 34.398174 1237.7482 -1638.7013 -663.48072 41.653268 989.53239 -1694.6664 2.5059279 11.204558 2.2814875 13990.5
|
||||
350 -625.91972 -665.3583 39.438581 1419.1169 -1352.428 -667.61665 41.5825 985.53386 -1694.733 2.2583465 10.831573 1.8963653 13990.5
|
||||
400 -625.24854 -660.77581 35.527271 1278.3764 -424.57407 -663.12561 43.89225 987.75056 -1694.7684 2.3497967 11.523588 2.1775908 13990.5
|
||||
450 -624.67739 -662.88749 38.210098 1374.9125 1107.8255 -665.43273 46.964166 982.35231 -1694.7492 2.5452345 11.00224 2.0018738 13990.5
|
||||
500 -624.30227 -661.98003 37.677766 1355.7576 -999.27326 -664.60512 42.373091 987.58943 -1694.5676 2.6250858 11.151835 2.8270448 13990.5
|
||||
Loop time of 2.40619 on 4 procs for 500 steps with 432 atoms
|
||||
|
||||
Performance: 35.907 ns/day, 0.668 hours/ns, 207.797 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.7876 | 1.9016 | 2.0542 | 7.0 | 79.03
|
||||
Bond | 0.00064754 | 0.0006901 | 0.00074625 | 0.1 | 0.03
|
||||
Kspace | 0.16854 | 0.31596 | 0.42594 | 16.5 | 13.13
|
||||
Neigh | 0.051607 | 0.051768 | 0.051931 | 0.1 | 2.15
|
||||
Comm | 0.11933 | 0.12412 | 0.12769 | 0.9 | 5.16
|
||||
Output | 0.00039911 | 0.00042087 | 0.00047565 | 0.2 | 0.02
|
||||
Modify | 0.0059447 | 0.0063215 | 0.0067348 | 0.4 | 0.26
|
||||
Other | | 0.005341 | | | 0.22
|
||||
|
||||
Nlocal: 108 ave 119 max 102 min
|
||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||
Nghost: 6516 ave 6545 max 6491 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Neighs: 74337.8 ave 81248 max 69989 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 297351
|
||||
Ave neighs/atom = 688.312
|
||||
Ave special neighs/atom = 1
|
||||
Neighbor list builds = 22
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix thermoberendsen
|
||||
|
||||
# ------------------------ Dynamic Run -------------------------------
|
||||
|
||||
run 1000
|
||||
Ewald initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Memory usage per processor = 15.213 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
|
||||
500 -624.30215 -661.98003 37.677882 1355.7618 -999.26443 -664.60512 42.373091 987.58943 -1694.5676 2.6250858 11.151835 2.8270448 13990.5
|
||||
550 -624.30702 -662.13315 37.826126 1361.096 330.71041 -664.76759 45.316349 984.7201 -1694.804 2.6344423 10.876902 1.9726348 13990.5
|
||||
600 -624.31001 -661.82602 37.516015 1349.9373 -978.11503 -664.34272 42.382797 987.88159 -1694.6071 2.5166949 10.21416 1.787289 13990.5
|
||||
650 -624.30516 -659.19843 34.893268 1255.5631 548.43865 -661.95754 46.556222 986.06829 -1694.582 2.7591048 13.16005 2.1511562 13990.5
|
||||
700 -624.30926 -661.91108 37.601819 1353.0248 -175.1339 -664.4528 44.284398 985.834 -1694.5712 2.5417263 10.972065 1.9847042 13990.5
|
||||
750 -624.30955 -660.4096 36.100048 1298.9866 1222.5932 -663.20741 47.511377 984.09471 -1694.8135 2.7978144 11.761903 2.1481489 13990.5
|
||||
800 -624.30447 -660.30683 36.002357 1295.4714 270.6639 -663.25589 45.210122 986.25515 -1694.7212 2.9490566 11.50988 4.0037749 13990.5
|
||||
850 -624.30774 -663.65149 39.343757 1415.7049 339.356 -666.13397 45.12874 983.38616 -1694.6489 2.4824719 11.01305 2.1691298 13990.5
|
||||
900 -624.30311 -658.78647 34.483353 1240.8132 309.88983 -661.8322 45.836842 987.17541 -1694.8445 3.045732 12.635589 1.9594437 13990.5
|
||||
950 -624.303 -663.59545 39.292454 1413.8588 -649.78872 -665.94289 43.141981 985.63193 -1694.7168 2.347436 11.012602 2.0685819 13990.5
|
||||
1000 -624.3032 -660.59776 36.294555 1305.9856 -753.87453 -663.22012 42.930848 988.41708 -1694.568 2.6223608 10.526403 1.8887197 13990.5
|
||||
1050 -624.3023 -660.7017 36.399405 1309.7584 790.88591 -663.6376 46.453299 984.4785 -1694.5694 2.9359001 11.210429 2.1822375 13990.5
|
||||
1100 -624.30545 -662.76291 38.457457 1383.8132 -853.19698 -665.29416 42.533854 986.84955 -1694.6776 2.5312537 10.517674 2.6445601 13990.5
|
||||
1150 -624.31539 -663.03811 38.722722 1393.3582 -380.13868 -665.58847 43.476852 985.81618 -1694.8815 2.5503626 10.818389 1.9559813 13990.5
|
||||
1200 -624.3093 -659.85835 35.549055 1279.1603 44.140107 -662.93041 44.773497 986.67501 -1694.3789 3.0720506 11.310516 2.2601607 13990.5
|
||||
1250 -624.30277 -663.46462 39.161852 1409.1594 -352.57297 -666.0144 43.477124 984.93408 -1694.4256 2.5497829 10.720231 1.8458373 13990.5
|
||||
1300 -624.30329 -660.15937 35.85608 1290.2079 -348.83001 -662.73568 43.884677 988.07413 -1694.6945 2.5763161 11.369766 2.2580977 13990.5
|
||||
1350 -624.30469 -662.72631 38.421619 1382.5236 1338.9038 -665.20399 47.35379 982.28307 -1694.8408 2.4776776 10.587886 1.7677665 13990.5
|
||||
1400 -624.30499 -662.12513 37.820139 1360.8806 132.00801 -664.73589 44.55252 985.34275 -1694.6312 2.6107622 11.193448 2.1613441 13990.5
|
||||
1450 -624.30207 -661.42856 37.126485 1335.9209 2069.8075 -664.07373 49.544418 981.20445 -1694.8226 2.6451763 13.011189 3.3987593 13990.5
|
||||
1500 -624.29727 -656.99924 32.701969 1176.7137 504.56835 -660.08591 46.605885 987.7602 -1694.452 3.0866635 13.271242 3.025272 13990.5
|
||||
Loop time of 4.96339 on 4 procs for 1000 steps with 432 atoms
|
||||
|
||||
Performance: 34.815 ns/day, 0.689 hours/ns, 201.475 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.6491 | 3.8484 | 4.2642 | 12.4 | 77.54
|
||||
Bond | 0.0013638 | 0.0014506 | 0.0016019 | 0.2 | 0.03
|
||||
Kspace | 0.3347 | 0.73521 | 0.92903 | 27.3 | 14.81
|
||||
Neigh | 0.10979 | 0.11008 | 0.11042 | 0.1 | 2.22
|
||||
Comm | 0.23785 | 0.25289 | 0.2601 | 1.8 | 5.10
|
||||
Output | 0.0008378 | 0.00088245 | 0.00098872 | 0.2 | 0.02
|
||||
Modify | 0.0022187 | 0.0024077 | 0.0026662 | 0.3 | 0.05
|
||||
Other | | 0.01206 | | | 0.24
|
||||
|
||||
Nlocal: 108 ave 112 max 102 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Nghost: 6500.75 ave 6612 max 6392 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 74275 ave 77543 max 69706 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
|
||||
Total # of neighbors = 297100
|
||||
Ave neighs/atom = 687.731
|
||||
Ave special neighs/atom = 1
|
||||
Neighbor list builds = 45
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:07
|
||||
@ -1,188 +0,0 @@
|
||||
LAMMPS (5 Mar 2015)
|
||||
# Testsystem for core-shell model compared to Mitchel and Finchham
|
||||
# Hendrik Heenen, June 2014
|
||||
|
||||
# ------------------------ INITIALIZATION ----------------------------
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style full
|
||||
|
||||
# ----------------------- ATOM DEFINITION ----------------------------
|
||||
|
||||
fix csinfo all property/atom i_CSID
|
||||
read_data data.coreshell fix csinfo NULL CS-Info
|
||||
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
432 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
216 bonds
|
||||
1 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
|
||||
group cores type 1 2
|
||||
216 atoms in group cores
|
||||
group shells type 3 4
|
||||
216 atoms in group shells
|
||||
|
||||
neighbor 2.0 bin
|
||||
comm_modify vel yes
|
||||
|
||||
# ------------------------ FORCE FIELDS ------------------------------
|
||||
|
||||
kspace_style ewald 1.0e-6
|
||||
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
|
||||
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
|
||||
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
|
||||
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
|
||||
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 63.014 0.0
|
||||
bond_coeff 2 25.724 0.0
|
||||
|
||||
# ------------------------ Equilibration Run -------------------------------
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
|
||||
|
||||
compute CSequ all temp/cs cores shells
|
||||
|
||||
# output via chunk method
|
||||
|
||||
#compute prop all property/atom i_CSID
|
||||
#compute cs_chunk all chunk/atom c_prop
|
||||
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
|
||||
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
|
||||
|
||||
thermo_modify temp CSequ
|
||||
|
||||
# velocity bias option
|
||||
|
||||
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
|
||||
Ewald initialization ...
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
master list distance cutoff = 22
|
||||
velocity all scale 1427 temp CSequ
|
||||
|
||||
fix thermoberendsen all temp/berendsen 1427 1427 0.4
|
||||
fix nve all nve
|
||||
fix_modify thermoberendsen temp CSequ
|
||||
|
||||
# 2 fmsec timestep
|
||||
|
||||
timestep 0.002
|
||||
run 500
|
||||
Ewald initialization ...
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Memory usage per processor = 6.86279 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
|
||||
0 -628.35255 -668.0717 39.719144 1427 -20608.918 -668.0717 1.6320365 1025.8481 -1695.5518 0 3.4602128e-14 4.1910919e-15 13990.5
|
||||
50 -632.83924 -664.88103 32.041787 1151.1736 -4098.5062 -668.28414 37.966205 988.74855 -1694.9989 3.4031081 25.060198 9.2894103 13990.5
|
||||
100 -630.51517 -660.52949 30.014321 1078.3323 -3202.2416 -664.01378 39.505874 991.23277 -1694.7524 3.4842892 26.36833 10.674509 13990.5
|
||||
150 -628.58401 -661.59121 33.007195 1185.8581 106.75378 -665.3449 46.400029 982.93422 -1694.6791 3.7536882 27.270427 10.826035 13990.5
|
||||
200 -627.39592 -662.45902 35.063102 1259.7212 -1672.1319 -665.61583 41.658839 987.14579 -1694.4205 3.1568106 23.525213 6.58382 13990.5
|
||||
250 -625.74143 -660.30023 34.558805 1241.6032 -1596.9927 -664.13159 42.148927 988.19127 -1694.4718 3.8313604 27.156726 8.5397995 13990.5
|
||||
300 -625.07332 -659.68738 34.614061 1243.5884 -1525.4995 -663.38119 42.077062 989.22231 -1694.6806 3.6938081 26.233327 9.2896507 13990.5
|
||||
350 -623.86869 -663.20518 39.336492 1413.2524 -1932.3573 -667.15923 40.519069 986.96395 -1694.6422 3.9540529 30.551213 14.69189 13990.5
|
||||
400 -623.55169 -660.39199 36.840301 1323.5711 -1747.3638 -664.07907 41.004982 989.66515 -1694.7492 3.6870716 27.463501 11.288658 13990.5
|
||||
450 -623.03498 -658.41209 35.377106 1271.0025 1243.4895 -662.14754 48.097573 984.42115 -1694.6663 3.735455 24.531264 6.5614635 13990.5
|
||||
500 -622.34231 -660.50992 38.167608 1371.2576 -1301.9479 -664.26607 41.813817 988.57955 -1694.6594 3.7561473 23.595051 5.844275 13990.5
|
||||
Loop time of 8.51483 on 1 procs for 500 steps with 432 atoms
|
||||
|
||||
Pair time (%) = 7.73226 (90.8093)
|
||||
Bond time (%) = 0.00232315 (0.0272836)
|
||||
Kspce time (%) = 0.518208 (6.08594)
|
||||
Neigh time (%) = 0.17925 (2.10514)
|
||||
Comm time (%) = 0.0653358 (0.767317)
|
||||
Outpt time (%) = 0.000309229 (0.00363165)
|
||||
Other time (%) = 0.0171449 (0.201354)
|
||||
|
||||
Nlocal: 432 ave 432 max 432 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 9307 ave 9307 max 9307 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 297357 ave 297357 max 297357 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 297357
|
||||
Ave neighs/atom = 688.326
|
||||
Ave special neighs/atom = 1
|
||||
Neighbor list builds = 21
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix thermoberendsen
|
||||
|
||||
# ------------------------ Dynamic Run -------------------------------
|
||||
|
||||
run 1000
|
||||
Ewald initialization ...
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Memory usage per processor = 6.86279 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
|
||||
500 -622.34231 -660.50992 38.167608 1371.2576 -1301.9479 -664.26607 41.813817 988.57955 -1694.6594 3.7561473 23.595051 5.844275 13990.5
|
||||
550 -622.53283 -661.59223 39.059403 1403.2973 -385.2836 -664.93615 43.738024 985.8195 -1694.4937 3.3439143 21.675844 3.5834691 13990.5
|
||||
600 -622.20391 -659.47921 37.275306 1339.1996 473.13042 -663.45898 46.093667 985.15793 -1694.7106 3.9797724 25.783443 9.4059533 13990.5
|
||||
650 -622.3473 -660.85461 38.507306 1383.462 -1021.6262 -664.41457 42.581674 987.48335 -1694.4796 3.5599548 24.069859 6.9189396 13990.5
|
||||
700 -621.9195 -660.92044 39.000937 1401.1968 71.427836 -664.81486 44.86887 985.26444 -1694.9482 3.894424 28.397753 9.3904596 13990.5
|
||||
750 -622.28852 -658.93918 36.650662 1316.7579 -1249.2306 -662.31101 41.915549 990.48822 -1694.7148 3.3718339 24.259772 4.9454879 13990.5
|
||||
800 -622.31982 -657.72021 35.400389 1271.839 254.0237 -661.60518 45.506498 987.48185 -1694.5935 3.8849638 24.386892 7.4962982 13990.5
|
||||
850 -622.31623 -661.4936 39.177375 1407.5357 37.74414 -665.02673 44.380924 985.14989 -1694.5575 3.5331239 23.316952 5.5622744 13990.5
|
||||
900 -621.83183 -660.10965 38.277816 1375.2171 1738.9676 -664.10328 48.428909 981.86752 -1694.3997 3.9936342 28.519154 11.384782 13990.5
|
||||
950 -622.03652 -659.97862 37.942096 1363.1555 -49.888312 -663.91816 44.582637 986.15057 -1694.6514 3.9395363 27.011672 8.4915326 13990.5
|
||||
1000 -621.71637 -660.69133 38.97496 1400.2635 -46.518055 -665.12412 44.669238 984.85534 -1694.6487 4.432789 29.799247 9.5235093 13990.5
|
||||
1050 -621.90579 -658.42698 36.521187 1312.1062 27.913475 -662.80273 44.953547 986.65365 -1694.4099 4.3757505 28.035827 8.4898226 13990.5
|
||||
1100 -621.92929 -661.57742 39.648126 1424.4485 820.11499 -665.35048 46.491843 982.84734 -1694.6897 3.7730563 27.803982 8.4955015 13990.5
|
||||
1150 -622.36518 -659.3383 36.973112 1328.3426 -799.63876 -662.87451 43.109263 988.96432 -1694.9481 3.5362185 23.473216 4.2340288 13990.5
|
||||
1200 -621.80278 -659.38996 37.587182 1350.4045 173.56518 -663.76385 45.4017 985.49478 -1694.6603 4.3738897 29.25765 11.540749 13990.5
|
||||
1250 -621.89233 -658.13657 36.244239 1302.1562 -194.31216 -662.25387 44.600608 987.50208 -1694.3566 4.1173041 27.781148 11.737589 13990.5
|
||||
1300 -622.01575 -659.4502 37.43445 1344.9172 419.91066 -663.67863 46.041458 984.96293 -1694.683 4.2284307 27.725967 9.666138 13990.5
|
||||
1350 -621.64918 -658.52586 36.876681 1324.8781 -1542.8395 -662.92795 41.627963 989.87571 -1694.4316 4.4020823 30.153096 11.999079 13990.5
|
||||
1400 -621.65713 -657.77765 36.120515 1297.7112 -2133.9795 -662.63382 40.620287 991.32101 -1694.5751 4.8561686 30.546416 11.476013 13990.5
|
||||
1450 -621.92858 -659.45137 37.522795 1348.0912 217.78723 -663.34796 45.334127 985.96702 -1694.6491 3.8965883 27.625033 7.3805255 13990.5
|
||||
1500 -621.9432 -657.57884 35.635634 1280.2907 632.02267 -661.89128 46.527064 986.00347 -1694.4218 4.3124408 28.010625 8.740067 13990.5
|
||||
Loop time of 17.041 on 1 procs for 1000 steps with 432 atoms
|
||||
|
||||
Pair time (%) = 15.4577 (90.7085)
|
||||
Bond time (%) = 0.00465488 (0.0273157)
|
||||
Kspce time (%) = 1.03763 (6.08902)
|
||||
Neigh time (%) = 0.390329 (2.29052)
|
||||
Comm time (%) = 0.131336 (0.770706)
|
||||
Outpt time (%) = 0.000611782 (0.00359005)
|
||||
Other time (%) = 0.0188062 (0.110358)
|
||||
|
||||
Nlocal: 432 ave 432 max 432 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 9406 ave 9406 max 9406 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 297120 ave 297120 max 297120 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 297120
|
||||
Ave neighs/atom = 687.778
|
||||
Ave special neighs/atom = 1
|
||||
Neighbor list builds = 46
|
||||
Dangerous builds = 0
|
||||
@ -1,188 +0,0 @@
|
||||
LAMMPS (5 Mar 2015)
|
||||
# Testsystem for core-shell model compared to Mitchel and Finchham
|
||||
# Hendrik Heenen, June 2014
|
||||
|
||||
# ------------------------ INITIALIZATION ----------------------------
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style full
|
||||
|
||||
# ----------------------- ATOM DEFINITION ----------------------------
|
||||
|
||||
fix csinfo all property/atom i_CSID
|
||||
read_data data.coreshell fix csinfo NULL CS-Info
|
||||
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
432 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
216 bonds
|
||||
1 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
|
||||
group cores type 1 2
|
||||
216 atoms in group cores
|
||||
group shells type 3 4
|
||||
216 atoms in group shells
|
||||
|
||||
neighbor 2.0 bin
|
||||
comm_modify vel yes
|
||||
|
||||
# ------------------------ FORCE FIELDS ------------------------------
|
||||
|
||||
kspace_style ewald 1.0e-6
|
||||
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
|
||||
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
|
||||
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
|
||||
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
|
||||
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 63.014 0.0
|
||||
bond_coeff 2 25.724 0.0
|
||||
|
||||
# ------------------------ Equilibration Run -------------------------------
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
|
||||
|
||||
compute CSequ all temp/cs cores shells
|
||||
|
||||
# output via chunk method
|
||||
|
||||
#compute prop all property/atom i_CSID
|
||||
#compute cs_chunk all chunk/atom c_prop
|
||||
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
|
||||
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
|
||||
|
||||
thermo_modify temp CSequ
|
||||
|
||||
# velocity bias option
|
||||
|
||||
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
|
||||
Ewald initialization ...
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
master list distance cutoff = 22
|
||||
velocity all scale 1427 temp CSequ
|
||||
|
||||
fix thermoberendsen all temp/berendsen 1427 1427 0.4
|
||||
fix nve all nve
|
||||
fix_modify thermoberendsen temp CSequ
|
||||
|
||||
# 2 fmsec timestep
|
||||
|
||||
timestep 0.002
|
||||
run 500
|
||||
Ewald initialization ...
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Memory usage per processor = 6.15182 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
|
||||
0 -628.35255 -668.0717 39.719144 1427 -20608.918 -668.0717 1.6320365 1025.8481 -1695.5518 0 3.6635741e-14 5.3290705e-15 13990.5
|
||||
50 -632.86102 -664.881 32.019982 1150.3902 -4100.2367 -668.28423 37.966091 988.74858 -1694.9989 3.403224 25.060809 9.2893842 13990.5
|
||||
100 -630.51552 -660.52959 30.014075 1078.3235 -3202.4205 -664.01411 39.505563 991.23276 -1694.7524 3.4845198 26.369799 10.674421 13990.5
|
||||
150 -628.58443 -661.59141 33.006978 1185.8503 106.65351 -665.34508 46.399848 982.93423 -1694.6792 3.7536698 27.270648 10.826129 13990.5
|
||||
200 -627.39641 -662.45927 35.062861 1259.7125 -1672.2627 -665.61606 41.658596 987.1458 -1694.4205 3.1567877 23.525464 6.5838195 13990.5
|
||||
250 -625.74093 -660.30053 34.559597 1241.6316 -1597.1305 -664.13208 42.148526 988.19121 -1694.4718 3.831555 27.157597 8.5399516 13990.5
|
||||
300 -625.07349 -659.68703 34.613535 1243.5695 -1525.6663 -663.38085 42.076798 989.22292 -1694.6806 3.6938245 26.233967 9.2898941 13990.5
|
||||
350 -623.86899 -663.20625 39.337263 1413.2801 -1933.067 -667.16008 40.51735 986.96485 -1694.6423 3.9538285 30.550701 14.691984 13990.5
|
||||
400 -623.55154 -660.39034 36.838804 1323.5173 -1746.896 -664.07771 41.006288 989.66515 -1694.7492 3.687369 27.463762 11.289238 13990.5
|
||||
450 -623.03522 -658.41494 35.37972 1271.0964 1245.1415 -662.15059 48.1009 984.41515 -1694.6666 3.7356529 24.533936 6.5615795 13990.5
|
||||
500 -622.34349 -660.51826 38.174772 1371.515 -1306.7035 -664.27406 41.802611 988.58329 -1694.66 3.7557939 23.595131 5.801075 13990.5
|
||||
Loop time of 2.53127 on 4 procs for 500 steps with 432 atoms
|
||||
|
||||
Pair time (%) = 1.94114 (76.6863)
|
||||
Bond time (%) = 0.000725508 (0.0286618)
|
||||
Kspce time (%) = 0.353945 (13.9829)
|
||||
Neigh time (%) = 0.0488738 (1.9308)
|
||||
Comm time (%) = 0.17332 (6.84714)
|
||||
Outpt time (%) = 0.000516713 (0.0204132)
|
||||
Other time (%) = 0.012753 (0.503818)
|
||||
|
||||
Nlocal: 108 ave 132 max 90 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Nghost: 6500 ave 6530 max 6448 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Neighs: 74339.8 ave 91261 max 61188 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 297359
|
||||
Ave neighs/atom = 688.331
|
||||
Ave special neighs/atom = 1
|
||||
Neighbor list builds = 21
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix thermoberendsen
|
||||
|
||||
# ------------------------ Dynamic Run -------------------------------
|
||||
|
||||
run 1000
|
||||
Ewald initialization ...
|
||||
G vector (1/distance) = 0.175257
|
||||
estimated absolute RMS force accuracy = 1.49563e-05
|
||||
estimated relative force accuracy = 1.03866e-06
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
Memory usage per processor = 6.15373 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
|
||||
500 -622.34349 -660.51826 38.174772 1371.515 -1306.7035 -664.27406 41.802611 988.58329 -1694.66 3.7557939 23.595131 5.801075 13990.5
|
||||
550 -622.53431 -661.60445 39.070141 1403.6831 -388.25413 -664.94784 43.727803 985.81836 -1694.494 3.3433892 21.667306 3.5808033 13990.5
|
||||
600 -622.20561 -659.56223 37.356624 1342.1211 428.9464 -663.53655 45.982645 985.19136 -1694.7106 3.974322 25.725869 9.3871295 13990.5
|
||||
650 -622.35823 -660.82051 38.462275 1381.8442 -1009.0888 -664.38771 42.618521 987.47881 -1694.485 3.5671985 24.149905 7.00428 13990.5
|
||||
700 -621.97407 -660.92034 38.946267 1399.2327 142.95891 -664.75916 45.033131 985.16618 -1694.9585 3.8388194 27.934663 8.7392159 13990.5
|
||||
750 -622.29209 -658.81919 36.527095 1312.3185 -952.526 -662.17886 42.618062 989.9262 -1694.7231 3.3596669 24.324239 4.9087128 13990.5
|
||||
800 -622.33521 -658.14785 35.812637 1286.6499 135.34005 -661.96381 45.178323 987.39314 -1694.5353 3.815955 24.107767 7.0978979 13990.5
|
||||
850 -622.37957 -660.474 38.094424 1368.6283 857.3439 -663.9925 46.509627 984.19258 -1694.6947 3.5185004 23.581763 5.0835354 13990.5
|
||||
900 -622.29844 -660.66771 38.369271 1378.5028 2861.462 -664.35013 50.97682 979.13332 -1694.4603 3.6824207 24.493416 6.3661215 13990.5
|
||||
950 -622.35097 -659.43438 37.083412 1332.3054 705.55718 -663.24413 46.294781 984.74433 -1694.2832 3.8097517 24.11493 4.1360943 13990.5
|
||||
1000 -622.08622 -658.28773 36.201516 1300.6213 421.181 -662.27058 45.865645 986.51483 -1694.6511 3.98285 26.774991 7.4172909 13990.5
|
||||
1050 -622.10558 -657.21399 35.108408 1261.3489 -464.31761 -661.46995 44.291275 988.69737 -1694.4586 4.2559609 25.983762 5.4926993 13990.5
|
||||
1100 -622.29369 -658.21246 35.918767 1290.4629 123.81951 -662.20344 45.651482 986.92119 -1694.7761 3.990985 25.85199 5.2327524 13990.5
|
||||
1150 -621.98418 -658.28218 36.297998 1304.0876 546.02432 -662.38868 46.194374 985.7826 -1694.3657 4.1065008 27.128736 6.901853 13990.5
|
||||
1200 -621.76032 -658.36996 36.60964 1315.2841 198.92215 -662.79546 45.536182 986.45023 -1694.7819 4.4255014 30.59935 9.4790152 13990.5
|
||||
1250 -621.77583 -657.79539 36.019569 1294.0844 521.16569 -662.12132 46.16971 986.26128 -1694.5523 4.3259289 29.294668 9.6073346 13990.5
|
||||
1300 -622.0461 -659.54559 37.499494 1347.2541 -854.68333 -663.33538 42.882224 988.27569 -1694.4933 3.7897892 26.707354 8.861147 13990.5
|
||||
1350 -621.7984 -657.10932 35.310914 1268.6244 -1010.1044 -661.35487 42.90716 990.41696 -1694.679 4.2455538 29.623565 10.702495 13990.5
|
||||
1400 -622.2597 -660.89426 38.634556 1388.0337 2292.235 -664.36487 49.907981 980.3269 -1694.5997 3.4706065 25.34727 6.8458703 13990.5
|
||||
1450 -622.36952 -660.43856 38.069033 1367.716 199.44207 -664.44407 45.483438 984.89046 -1694.818 4.0055092 24.149259 3.9431126 13990.5
|
||||
1500 -621.84913 -659.73606 37.886922 1361.1733 -1274.5089 -663.96475 42.049386 988.31676 -1694.3309 4.2286938 28.927291 10.527466 13990.5
|
||||
Loop time of 5.06693 on 4 procs for 1000 steps with 432 atoms
|
||||
|
||||
Pair time (%) = 3.90916 (77.1504)
|
||||
Bond time (%) = 0.00148368 (0.0292816)
|
||||
Kspce time (%) = 0.657798 (12.9822)
|
||||
Neigh time (%) = 0.108943 (2.15008)
|
||||
Comm time (%) = 0.373417 (7.36968)
|
||||
Outpt time (%) = 0.00109911 (0.0216918)
|
||||
Other time (%) = 0.0150309 (0.296647)
|
||||
|
||||
Nlocal: 108 ave 113 max 100 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Nghost: 6461 ave 6519 max 6372 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Neighs: 74316.8 ave 77778 max 69869 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
|
||||
Total # of neighbors = 297267
|
||||
Ave neighs/atom = 688.118
|
||||
Ave special neighs/atom = 1
|
||||
Neighbor list builds = 46
|
||||
Dangerous builds = 0
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 2d LJ crack simulation
|
||||
|
||||
dimension 2
|
||||
@ -76,7 +76,7 @@ fix 2 boundary setforce NULL 0.0 0.0
|
||||
timestep 0.003
|
||||
thermo 200
|
||||
thermo_modify temp new
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
|
||||
|
||||
neigh_modify exclude type 2 3
|
||||
|
||||
@ -124,20 +124,20 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
4600 0.086766447 -3.0437627 0 -2.9634443 -1.0208785 9361.9925
|
||||
4800 0.088195149 -3.0328502 0 -2.9512093 -1.0272063 9395.6122
|
||||
5000 0.089415266 -3.0228825 0 -2.9401122 -1.0215336 9436.1637
|
||||
Loop time of 7.03796 on 1 procs for 5000 steps with 8141 atoms
|
||||
Loop time of 6.89346 on 1 procs for 5000 steps with 8141 atoms
|
||||
|
||||
Performance: 184144.324 tau/day, 710.433 timesteps/s
|
||||
Performance: 188004.255 tau/day, 725.325 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.9472 | 5.9472 | 5.9472 | 0.0 | 84.50
|
||||
Neigh | 0.36178 | 0.36178 | 0.36178 | 0.0 | 5.14
|
||||
Comm | 0.0042093 | 0.0042093 | 0.0042093 | 0.0 | 0.06
|
||||
Output | 0.00080466 | 0.00080466 | 0.00080466 | 0.0 | 0.01
|
||||
Modify | 0.55 | 0.55 | 0.55 | 0.0 | 7.81
|
||||
Other | | 0.1739 | | | 2.47
|
||||
Pair | 5.8036 | 5.8036 | 5.8036 | 0.0 | 84.19
|
||||
Neigh | 0.37434 | 0.37434 | 0.37434 | 0.0 | 5.43
|
||||
Comm | 0.004128 | 0.004128 | 0.004128 | 0.0 | 0.06
|
||||
Output | 0.00077105 | 0.00077105 | 0.00077105 | 0.0 | 0.01
|
||||
Modify | 0.53619 | 0.53619 | 0.53619 | 0.0 | 7.78
|
||||
Other | | 0.1744 | | | 2.53
|
||||
|
||||
Nlocal: 8141 ave 8141 max 8141 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -150,4 +150,4 @@ Total # of neighbors = 71389
|
||||
Ave neighs/atom = 8.76907
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:07
|
||||
Total wall time: 0:00:06
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# 2d LJ crack simulation
|
||||
|
||||
dimension 2
|
||||
@ -76,7 +76,7 @@ fix 2 boundary setforce NULL 0.0 0.0
|
||||
timestep 0.003
|
||||
thermo 200
|
||||
thermo_modify temp new
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
|
||||
|
||||
neigh_modify exclude type 2 3
|
||||
|
||||
@ -124,20 +124,20 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
4600 0.088763719 -3.0446018 0 -2.9624346 -1.027693 9391.6949
|
||||
4800 0.089467982 -3.0337452 0 -2.950926 -1.0232092 9427.4155
|
||||
5000 0.089910902 -3.0237571 0 -2.9405279 -1.0174796 9452.031
|
||||
Loop time of 1.91894 on 4 procs for 5000 steps with 8141 atoms
|
||||
Loop time of 1.97398 on 4 procs for 5000 steps with 8141 atoms
|
||||
|
||||
Performance: 675373.090 tau/day, 2605.606 timesteps/s
|
||||
Performance: 656540.037 tau/day, 2532.948 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.4786 | 1.5057 | 1.5343 | 2.0 | 78.47
|
||||
Neigh | 0.094529 | 0.099406 | 0.1061 | 1.4 | 5.18
|
||||
Comm | 0.071501 | 0.10352 | 0.13214 | 8.6 | 5.39
|
||||
Output | 0.00072479 | 0.00076115 | 0.00084186 | 0.2 | 0.04
|
||||
Modify | 0.13936 | 0.14058 | 0.14196 | 0.2 | 7.33
|
||||
Other | | 0.06895 | | | 3.59
|
||||
Pair | 1.4909 | 1.5203 | 1.5671 | 2.3 | 77.02
|
||||
Neigh | 0.10125 | 0.10271 | 0.10657 | 0.7 | 5.20
|
||||
Comm | 0.076516 | 0.13066 | 0.15771 | 8.8 | 6.62
|
||||
Output | 0.00077796 | 0.00082064 | 0.00091672 | 0.2 | 0.04
|
||||
Modify | 0.13725 | 0.14082 | 0.14325 | 0.6 | 7.13
|
||||
Other | | 0.07865 | | | 3.98
|
||||
|
||||
Nlocal: 2035.25 ave 2064 max 2015 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# sample surface deposition script for atoms
|
||||
|
||||
units lj
|
||||
@ -43,7 +43,7 @@ fix 5 addatoms wall/reflect zhi EDGE
|
||||
thermo_style custom step atoms temp epair etotal press
|
||||
thermo 100
|
||||
thermo_modify temp add
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
|
||||
|
||||
#dump 1 all atom 50 dump.deposit.atom
|
||||
|
||||
@ -164,20 +164,20 @@ Step Atoms Temp E_pair TotEng Press
|
||||
9800 448 0.97167962 -5.185173 -4.8663406 -0.56989109
|
||||
9900 449 1.0038671 -5.1540302 -4.8220162 -0.56356384
|
||||
10000 450 0.95642062 -5.2046982 -4.8858913 -0.70500643
|
||||
Loop time of 5.66464 on 1 procs for 10000 steps with 450 atoms
|
||||
Loop time of 5.63963 on 1 procs for 10000 steps with 450 atoms
|
||||
|
||||
Performance: 762626.084 tau/day, 1765.338 timesteps/s
|
||||
Performance: 766007.688 tau/day, 1773.166 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.2197 | 3.2197 | 3.2197 | 0.0 | 56.84
|
||||
Neigh | 2.1683 | 2.1683 | 2.1683 | 0.0 | 38.28
|
||||
Comm | 0.11987 | 0.11987 | 0.11987 | 0.0 | 2.12
|
||||
Output | 0.00085187 | 0.00085187 | 0.00085187 | 0.0 | 0.02
|
||||
Modify | 0.11944 | 0.11944 | 0.11944 | 0.0 | 2.11
|
||||
Other | | 0.03653 | | | 0.64
|
||||
Pair | 3.1973 | 3.1973 | 3.1973 | 0.0 | 56.69
|
||||
Neigh | 2.1646 | 2.1646 | 2.1646 | 0.0 | 38.38
|
||||
Comm | 0.11922 | 0.11922 | 0.11922 | 0.0 | 2.11
|
||||
Output | 0.00081301 | 0.00081301 | 0.00081301 | 0.0 | 0.01
|
||||
Modify | 0.11702 | 0.11702 | 0.11702 | 0.0 | 2.07
|
||||
Other | | 0.04063 | | | 0.72
|
||||
|
||||
Nlocal: 450 ave 450 max 450 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# sample surface deposition script for atoms
|
||||
|
||||
units lj
|
||||
@ -43,7 +43,7 @@ fix 5 addatoms wall/reflect zhi EDGE
|
||||
thermo_style custom step atoms temp epair etotal press
|
||||
thermo 100
|
||||
thermo_modify temp add
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
|
||||
|
||||
#dump 1 all atom 50 dump.deposit.atom
|
||||
|
||||
@ -164,20 +164,20 @@ Step Atoms Temp E_pair TotEng Press
|
||||
9800 448 1.187781 -5.1672598 -4.7775192 -0.55482592
|
||||
9900 449 0.99538785 -5.1593424 -4.8301329 -0.5886329
|
||||
10000 450 0.95030539 -5.1408028 -4.8240344 -0.4992403
|
||||
Loop time of 4.67299 on 4 procs for 10000 steps with 450 atoms
|
||||
Loop time of 4.38653 on 4 procs for 10000 steps with 450 atoms
|
||||
|
||||
Performance: 924461.293 tau/day, 2139.957 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 984832.436 tau/day, 2279.705 timesteps/s
|
||||
98.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0024376 | 0.84903 | 2.165 | 97.5 | 18.17
|
||||
Neigh | 0.0053134 | 0.57645 | 1.783 | 95.1 | 12.34
|
||||
Comm | 0.54729 | 2.3753 | 4.0958 | 83.6 | 50.83
|
||||
Output | 0.0022168 | 0.00986 | 0.028065 | 10.7 | 0.21
|
||||
Modify | 0.0059755 | 0.037876 | 0.085638 | 16.4 | 0.81
|
||||
Other | | 0.8245 | | | 17.64
|
||||
Pair | 0.0022979 | 0.81396 | 2.0831 | 95.7 | 18.56
|
||||
Neigh | 0.0083807 | 0.57856 | 1.7676 | 93.7 | 13.19
|
||||
Comm | 0.3792 | 2.1868 | 3.8575 | 85.0 | 49.85
|
||||
Output | 0.001919 | 0.008881 | 0.025856 | 10.5 | 0.20
|
||||
Modify | 0.0053477 | 0.035994 | 0.08146 | 16.2 | 0.82
|
||||
Other | | 0.7623 | | | 17.38
|
||||
|
||||
Nlocal: 112.5 ave 250 max 9 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# sample surface deposition script for molecules
|
||||
|
||||
units lj
|
||||
@ -53,7 +53,7 @@ fix 5 addatoms wall/reflect zhi EDGE
|
||||
thermo_style custom step atoms temp epair etotal press
|
||||
thermo 100
|
||||
thermo_modify temp add lost/bond ignore lost warn
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
|
||||
|
||||
#dump 1 all atom 50 dump.deposit.atom
|
||||
|
||||
@ -174,21 +174,21 @@ Step Atoms Temp E_pair TotEng Press
|
||||
9800 546 0.26835398 -7.2214231 -6.8757262 -0.86029096
|
||||
9900 548 0.31676744 -7.264604 -6.884266 -0.74053962
|
||||
10000 550 0.31368419 -7.2759575 -6.8979611 -0.76153366
|
||||
Loop time of 6.58981 on 1 procs for 10000 steps with 550 atoms
|
||||
Loop time of 6.51779 on 1 procs for 10000 steps with 550 atoms
|
||||
|
||||
Performance: 655557.606 tau/day, 1517.494 timesteps/s
|
||||
Performance: 662801.655 tau/day, 1534.263 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.1313 | 4.1313 | 4.1313 | 0.0 | 62.69
|
||||
Bond | 0.01234 | 0.01234 | 0.01234 | 0.0 | 0.19
|
||||
Neigh | 2.1423 | 2.1423 | 2.1423 | 0.0 | 32.51
|
||||
Comm | 0.13504 | 0.13504 | 0.13504 | 0.0 | 2.05
|
||||
Output | 0.0010068 | 0.0010068 | 0.0010068 | 0.0 | 0.02
|
||||
Modify | 0.12665 | 0.12665 | 0.12665 | 0.0 | 1.92
|
||||
Other | | 0.0411 | | | 0.62
|
||||
Pair | 4.0744 | 4.0744 | 4.0744 | 0.0 | 62.51
|
||||
Bond | 0.01209 | 0.01209 | 0.01209 | 0.0 | 0.19
|
||||
Neigh | 2.1316 | 2.1316 | 2.1316 | 0.0 | 32.70
|
||||
Comm | 0.13266 | 0.13266 | 0.13266 | 0.0 | 2.04
|
||||
Output | 0.0008409 | 0.0008409 | 0.0008409 | 0.0 | 0.01
|
||||
Modify | 0.12403 | 0.12403 | 0.12403 | 0.0 | 1.90
|
||||
Other | | 0.04216 | | | 0.65
|
||||
|
||||
Nlocal: 550 ave 550 max 550 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# sample surface deposition script for molecules
|
||||
|
||||
units lj
|
||||
@ -53,7 +53,7 @@ fix 5 addatoms wall/reflect zhi EDGE
|
||||
thermo_style custom step atoms temp epair etotal press
|
||||
thermo 100
|
||||
thermo_modify temp add lost/bond ignore lost warn
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
|
||||
|
||||
#dump 1 all atom 50 dump.deposit.atom
|
||||
|
||||
@ -174,21 +174,21 @@ Step Atoms Temp E_pair TotEng Press
|
||||
9800 546 0.28129876 -7.3140275 -6.9098746 -0.82726219
|
||||
9900 548 0.28891495 -7.3235633 -6.9092268 -0.88128702
|
||||
10000 550 0.29861445 -7.3507915 -6.9161229 -0.73192335
|
||||
Loop time of 5.52188 on 4 procs for 10000 steps with 550 atoms
|
||||
Loop time of 5.59197 on 4 procs for 10000 steps with 550 atoms
|
||||
|
||||
Performance: 782342.427 tau/day, 1810.978 timesteps/s
|
||||
98.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 772536.289 tau/day, 1788.278 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0013716 | 1.0723 | 3.0973 | 122.1 | 19.42
|
||||
Bond | 0.0012324 | 0.0039356 | 0.010944 | 6.5 | 0.07
|
||||
Neigh | 0.0033538 | 0.5728 | 1.8205 | 98.1 | 10.37
|
||||
Comm | 0.44758 | 2.8002 | 5.0381 | 103.8 | 50.71
|
||||
Output | 0.0021229 | 0.01519 | 0.050854 | 16.7 | 0.28
|
||||
Modify | 0.0069635 | 0.039662 | 0.076857 | 15.8 | 0.72
|
||||
Other | | 1.018 | | | 18.43
|
||||
Pair | 0.0012441 | 1.0454 | 2.9987 | 119.8 | 18.70
|
||||
Bond | 0.0012348 | 0.0039268 | 0.010973 | 6.5 | 0.07
|
||||
Neigh | 0.0049584 | 0.57381 | 1.8059 | 96.8 | 10.26
|
||||
Comm | 0.62167 | 2.892 | 5.0562 | 98.9 | 51.72
|
||||
Output | 0.0021472 | 0.014835 | 0.048822 | 16.2 | 0.27
|
||||
Modify | 0.0069871 | 0.038206 | 0.074167 | 15.4 | 0.68
|
||||
Other | | 1.024 | | | 18.31
|
||||
|
||||
Nlocal: 137.5 ave 299 max 2 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# sample surface deposition script for molecules
|
||||
|
||||
units lj
|
||||
@ -58,7 +58,7 @@ fix 6 all shake 0.0001 20 1000 b 1 mol dimer
|
||||
thermo_style custom step atoms temp epair etotal press
|
||||
thermo 100
|
||||
thermo_modify temp add lost/bond ignore lost warn
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
|
||||
|
||||
#dump 1 all atom 50 dump.deposit.atom
|
||||
|
||||
@ -200,21 +200,21 @@ SHAKE stats (type/ave/delta) on step 9000
|
||||
SHAKE stats (type/ave/delta) on step 10000
|
||||
1 1 2.44249e-15
|
||||
10000 550 0.31059632 -6.7463923 -6.6052122 -0.75225652
|
||||
Loop time of 6.33784 on 1 procs for 10000 steps with 550 atoms
|
||||
Loop time of 6.31791 on 1 procs for 10000 steps with 550 atoms
|
||||
|
||||
Performance: 681620.330 tau/day, 1577.825 timesteps/s
|
||||
Performance: 683770.197 tau/day, 1582.801 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.9751 | 3.9751 | 3.9751 | 0.0 | 62.72
|
||||
Bond | 0.012007 | 0.012007 | 0.012007 | 0.0 | 0.19
|
||||
Neigh | 2.0003 | 2.0003 | 2.0003 | 0.0 | 31.56
|
||||
Comm | 0.13159 | 0.13159 | 0.13159 | 0.0 | 2.08
|
||||
Output | 0.00095081 | 0.00095081 | 0.00095081 | 0.0 | 0.02
|
||||
Modify | 0.17719 | 0.17719 | 0.17719 | 0.0 | 2.80
|
||||
Other | | 0.04064 | | | 0.64
|
||||
Pair | 3.9451 | 3.9451 | 3.9451 | 0.0 | 62.44
|
||||
Bond | 0.012146 | 0.012146 | 0.012146 | 0.0 | 0.19
|
||||
Neigh | 2.0103 | 2.0103 | 2.0103 | 0.0 | 31.82
|
||||
Comm | 0.13071 | 0.13071 | 0.13071 | 0.0 | 2.07
|
||||
Output | 0.00093651 | 0.00093651 | 0.00093651 | 0.0 | 0.01
|
||||
Modify | 0.1759 | 0.1759 | 0.1759 | 0.0 | 2.78
|
||||
Other | | 0.04281 | | | 0.68
|
||||
|
||||
Nlocal: 550 ave 550 max 550 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# sample surface deposition script for molecules
|
||||
|
||||
units lj
|
||||
@ -58,7 +58,7 @@ fix 6 all shake 0.0001 20 1000 b 1 mol dimer
|
||||
thermo_style custom step atoms temp epair etotal press
|
||||
thermo 100
|
||||
thermo_modify temp add lost/bond ignore lost warn
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
|
||||
|
||||
#dump 1 all atom 50 dump.deposit.atom
|
||||
|
||||
@ -200,21 +200,21 @@ SHAKE stats (type/ave/delta) on step 9000
|
||||
SHAKE stats (type/ave/delta) on step 10000
|
||||
1 1 2.55351e-15
|
||||
10000 550 0.30296128 -6.7756768 -6.6379672 -0.84420968
|
||||
Loop time of 5.79101 on 4 procs for 10000 steps with 550 atoms
|
||||
Loop time of 5.7633 on 4 procs for 10000 steps with 550 atoms
|
||||
|
||||
Performance: 745983.597 tau/day, 1726.814 timesteps/s
|
||||
Performance: 749570.876 tau/day, 1735.118 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0016487 | 1.0205 | 2.974 | 120.1 | 17.62
|
||||
Bond | 0.0012839 | 0.003953 | 0.010697 | 6.2 | 0.07
|
||||
Neigh | 0.0035315 | 0.52893 | 1.691 | 94.9 | 9.13
|
||||
Comm | 0.57816 | 2.7844 | 4.9123 | 99.7 | 48.08
|
||||
Output | 0.0024757 | 0.0037841 | 0.0065219 | 2.7 | 0.07
|
||||
Modify | 0.41353 | 1.2632 | 3.4168 | 111.3 | 21.81
|
||||
Other | | 0.1862 | | | 3.22
|
||||
Pair | 0.0014243 | 1.0038 | 2.9203 | 118.9 | 17.42
|
||||
Bond | 0.001431 | 0.004068 | 0.010644 | 6.0 | 0.07
|
||||
Neigh | 0.0053701 | 0.53209 | 1.6663 | 92.7 | 9.23
|
||||
Comm | 0.60632 | 2.7675 | 4.853 | 97.7 | 48.02
|
||||
Output | 0.0026648 | 0.003988 | 0.0067949 | 2.6 | 0.07
|
||||
Modify | 0.43492 | 1.2606 | 3.3556 | 108.4 | 21.87
|
||||
Other | | 0.1912 | | | 3.32
|
||||
|
||||
Nlocal: 137.5 ave 300 max 2 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
@ -53,7 +53,7 @@ Neighbor list info ...
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 13 13 2
|
||||
Memory usage per processor = 4.47689 Mbytes
|
||||
Step Temp E_pair erot TotEng Press
|
||||
Step Temp E_pair c_erot TotEng Press
|
||||
0 0 -2.1909822 0 -2.1909822 -2.5750971
|
||||
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
|
||||
1000 0.45259485 -2.8743423 0.22311811 -2.4240104 -0.14864606
|
||||
@ -75,20 +75,20 @@ Step Temp E_pair erot TotEng Press
|
||||
9000 0.42532413 -2.748856 0.21378021 -2.3256584 0.015079949
|
||||
9500 0.42237159 -2.7266142 0.20255034 -2.3063545 -0.15538561
|
||||
10000 0.40758268 -2.778401 0.2746675 -2.3728562 -0.20811978
|
||||
Loop time of 1.04484 on 1 procs for 10000 steps with 200 atoms
|
||||
Loop time of 1.05484 on 1 procs for 10000 steps with 200 atoms
|
||||
|
||||
Performance: 4134616.221 tau/day, 9570.871 timesteps/s
|
||||
Performance: 4095400.088 tau/day, 9480.093 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.87532 | 0.87532 | 0.87532 | 0.0 | 83.78
|
||||
Neigh | 0.037165 | 0.037165 | 0.037165 | 0.0 | 3.56
|
||||
Comm | 0.034433 | 0.034433 | 0.034433 | 0.0 | 3.30
|
||||
Output | 0.00014114 | 0.00014114 | 0.00014114 | 0.0 | 0.01
|
||||
Modify | 0.083179 | 0.083179 | 0.083179 | 0.0 | 7.96
|
||||
Other | | 0.0146 | | | 1.40
|
||||
Pair | 0.88325 | 0.88325 | 0.88325 | 0.0 | 83.73
|
||||
Neigh | 0.038596 | 0.038596 | 0.038596 | 0.0 | 3.66
|
||||
Comm | 0.034257 | 0.034257 | 0.034257 | 0.0 | 3.25
|
||||
Output | 0.00013828 | 0.00013828 | 0.00013828 | 0.0 | 0.01
|
||||
Modify | 0.083041 | 0.083041 | 0.083041 | 0.0 | 7.87
|
||||
Other | | 0.01556 | | | 1.48
|
||||
|
||||
Nlocal: 200 ave 200 max 200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
@ -53,7 +53,7 @@ Neighbor list info ...
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 13 13 2
|
||||
Memory usage per processor = 4.47621 Mbytes
|
||||
Step Temp E_pair erot TotEng Press
|
||||
Step Temp E_pair c_erot TotEng Press
|
||||
0 0 -2.1909822 0 -2.1909822 -2.5750971
|
||||
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
|
||||
1000 0.45259485 -2.8743423 0.22311811 -2.4240104 -0.14864606
|
||||
@ -75,20 +75,20 @@ Step Temp E_pair erot TotEng Press
|
||||
9000 0.42318631 -2.7600929 0.25229644 -2.3390225 0.36820391
|
||||
9500 0.42857449 -2.6958592 0.18686752 -2.2694276 0.15379721
|
||||
10000 0.43323126 -2.71981 0.22185737 -2.2887449 0.038354509
|
||||
Loop time of 0.405458 on 4 procs for 10000 steps with 200 atoms
|
||||
Loop time of 0.406978 on 4 procs for 10000 steps with 200 atoms
|
||||
|
||||
Performance: 10654618.438 tau/day, 24663.469 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 10614834.981 tau/day, 24571.377 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17794 | 0.23423 | 0.25599 | 6.7 | 57.77
|
||||
Neigh | 0.0083153 | 0.010322 | 0.011204 | 1.2 | 2.55
|
||||
Comm | 0.086873 | 0.11001 | 0.17048 | 10.6 | 27.13
|
||||
Output | 0.00028467 | 0.00030136 | 0.00034618 | 0.1 | 0.07
|
||||
Modify | 0.021868 | 0.024962 | 0.026442 | 1.1 | 6.16
|
||||
Other | | 0.02564 | | | 6.32
|
||||
Pair | 0.18518 | 0.23558 | 0.25487 | 6.0 | 57.88
|
||||
Neigh | 0.0090437 | 0.011033 | 0.011971 | 1.1 | 2.71
|
||||
Comm | 0.086857 | 0.10807 | 0.16262 | 9.6 | 26.56
|
||||
Output | 0.00029182 | 0.00031263 | 0.00035739 | 0.1 | 0.08
|
||||
Modify | 0.022396 | 0.025649 | 0.026865 | 1.2 | 6.30
|
||||
Other | | 0.02633 | | | 6.47
|
||||
|
||||
Nlocal: 50 ave 53 max 41 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user