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doc/src/JPG/gran_mixer.png
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@ -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,
|
||||
|
||||
@ -54,30 +54,30 @@ accelerate: run with various acceleration options (OpenMP, GPU, Phi)
|
||||
balance: dynamic load balancing, 2d system
|
||||
body: body particles, 2d system
|
||||
colloid: big colloid particles in a small particle solvent, 2d system
|
||||
comb: models using the COMB potential
|
||||
comb: models using the COMB potential
|
||||
coreshell: core/shell model using CORESHELL package
|
||||
crack: crack propagation in a 2d solid
|
||||
crack: crack propagation in a 2d solid
|
||||
deposit: deposit atoms and molecules on a surface
|
||||
dipole: point dipolar particles, 2d system
|
||||
dreiding: methanol via Dreiding FF
|
||||
eim: NaCl using the EIM potential
|
||||
ellipse: ellipsoidal particles in spherical solvent, 2d system
|
||||
flow: Couette and Poiseuille flow in a 2d channel
|
||||
flow: Couette and Poiseuille flow in a 2d channel
|
||||
friction: frictional contact of spherical asperities between 2d surfaces
|
||||
hugoniostat: Hugoniostat shock dynamics
|
||||
indent: spherical indenter into a 2d solid
|
||||
indent: spherical indenter into a 2d solid
|
||||
kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
|
||||
meam: MEAM test for SiC and shear (same as shear examples)
|
||||
melt: rapid melt of 3d LJ system
|
||||
meam: MEAM test for SiC and shear (same as shear examples)
|
||||
melt: rapid melt of 3d LJ system
|
||||
micelle: self-assembly of small lipid-like molecules into 2d bilayers
|
||||
min: energy minimization of 2d LJ melt
|
||||
msst: MSST shock dynamics
|
||||
min: energy minimization of 2d LJ melt
|
||||
msst: MSST shock dynamics
|
||||
nb3b: use of nonbonded 3-body harmonic pair style
|
||||
neb: nudged elastic band (NEB) calculation for barrier finding
|
||||
nemd: non-equilibrium MD of 2d sheared system
|
||||
neb: nudged elastic band (NEB) calculation for barrier finding
|
||||
nemd: non-equilibrium MD of 2d sheared system
|
||||
obstacle: flow around two voids in a 2d channel
|
||||
peptide: dynamics of a small solvated peptide chain (5-mer)
|
||||
peri: Peridynamic model of cylinder impacted by indenter
|
||||
peri: Peridynamic model of cylinder impacted by indenter
|
||||
pour: pouring of granular particles into a 3d box, then chute flow
|
||||
prd: parallel replica dynamics of vacancy diffusion in bulk Si
|
||||
python: using embedded Python in a LAMMPS input script
|
||||
|
||||
@ -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
|
||||
|
||||
@ -68,7 +68,7 @@ Look at the {in.chain} input script provided in the {bench} directory
|
||||
of the LAMMPS distribution to see the original script that these 2
|
||||
scripts are based on. If that script had the line
|
||||
|
||||
restart 50 tmp.restart :pre
|
||||
restart 50 tmp.restart :pre
|
||||
|
||||
added to it, it would produce 2 binary restart files (tmp.restart.50
|
||||
and tmp.restart.100) as it ran.
|
||||
@ -76,17 +76,17 @@ and tmp.restart.100) as it ran.
|
||||
This script could be used to read the 1st restart file and re-run the
|
||||
last 50 timesteps:
|
||||
|
||||
read_restart tmp.restart.50 :pre
|
||||
read_restart tmp.restart.50 :pre
|
||||
|
||||
neighbor 0.4 bin
|
||||
neigh_modify every 1 delay 1 :pre
|
||||
neighbor 0.4 bin
|
||||
neigh_modify every 1 delay 1 :pre
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all langevin 1.0 1.0 10.0 904297 :pre
|
||||
fix 1 all nve
|
||||
fix 2 all langevin 1.0 1.0 10.0 904297 :pre
|
||||
|
||||
timestep 0.012 :pre
|
||||
timestep 0.012 :pre
|
||||
|
||||
run 50 :pre
|
||||
run 50 :pre
|
||||
|
||||
Note that the following commands do not need to be repeated because
|
||||
their settings are included in the restart file: {units, atom_style,
|
||||
@ -107,25 +107,25 @@ lmp_g++ -r tmp.restart.50 tmp.restart.data :pre
|
||||
|
||||
Then, this script could be used to re-run the last 50 steps:
|
||||
|
||||
units lj
|
||||
atom_style bond
|
||||
pair_style lj/cut 1.12
|
||||
pair_modify shift yes
|
||||
bond_style fene
|
||||
units lj
|
||||
atom_style bond
|
||||
pair_style lj/cut 1.12
|
||||
pair_modify shift yes
|
||||
bond_style fene
|
||||
special_bonds 0.0 1.0 1.0 :pre
|
||||
|
||||
read_data tmp.restart.data :pre
|
||||
read_data tmp.restart.data :pre
|
||||
|
||||
neighbor 0.4 bin
|
||||
neigh_modify every 1 delay 1 :pre
|
||||
neighbor 0.4 bin
|
||||
neigh_modify every 1 delay 1 :pre
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all langevin 1.0 1.0 10.0 904297 :pre
|
||||
fix 1 all nve
|
||||
fix 2 all langevin 1.0 1.0 10.0 904297 :pre
|
||||
|
||||
timestep 0.012 :pre
|
||||
timestep 0.012 :pre
|
||||
|
||||
reset_timestep 50
|
||||
run 50 :pre
|
||||
reset_timestep 50
|
||||
run 50 :pre
|
||||
|
||||
Note that nearly all the settings specified in the original {in.chain}
|
||||
script must be repeated, except the {pair_coeff} and {bond_coeff}
|
||||
@ -2092,11 +2092,11 @@ lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 39.948
|
||||
mass 1 39.948
|
||||
pair_style lj/cut 13.0
|
||||
pair_coeff * * 0.2381 3.405
|
||||
timestep $\{dt\}
|
||||
thermo $d :pre
|
||||
thermo $d :pre
|
||||
|
||||
# equilibration and thermalization :pre
|
||||
|
||||
|
||||
@ -552,32 +552,32 @@ lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" :pre
|
||||
|
||||
xlo = lmp.extract_global(name,type) # extract a global quantity
|
||||
# name = "boxxlo", "nlocal", etc
|
||||
# type = 0 = int
|
||||
# 1 = double :pre
|
||||
# type = 0 = int
|
||||
# 1 = double :pre
|
||||
|
||||
coords = lmp.extract_atom(name,type) # extract a per-atom quantity
|
||||
# name = "x", "type", etc
|
||||
# type = 0 = vector of ints
|
||||
# 1 = array of ints
|
||||
# 2 = vector of doubles
|
||||
# 3 = array of doubles :pre
|
||||
# type = 0 = vector of ints
|
||||
# 1 = array of ints
|
||||
# 2 = vector of doubles
|
||||
# 3 = array of doubles :pre
|
||||
|
||||
eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute
|
||||
v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix
|
||||
# id = ID of compute or fix
|
||||
# style = 0 = global data
|
||||
# 1 = per-atom data
|
||||
# 2 = local data
|
||||
# type = 0 = scalar
|
||||
# 1 = vector
|
||||
# 2 = array
|
||||
# i,j = indices of value in global vector or array :pre
|
||||
# style = 0 = global data
|
||||
# 1 = per-atom data
|
||||
# 2 = local data
|
||||
# type = 0 = scalar
|
||||
# 1 = vector
|
||||
# 2 = array
|
||||
# i,j = indices of value in global vector or array :pre
|
||||
|
||||
var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable
|
||||
# name = name of variable
|
||||
# group = group ID (ignored for equal-style variables)
|
||||
# flag = 0 = equal-style variable
|
||||
# 1 = atom-style variable :pre
|
||||
# name = name of variable
|
||||
# group = group ID (ignored for equal-style variables)
|
||||
# flag = 0 = equal-style variable
|
||||
# 1 = atom-style variable :pre
|
||||
|
||||
flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful
|
||||
natoms = lmp.get_natoms() # total # of atoms as int
|
||||
|
||||
@ -14,7 +14,7 @@ atom_style style args :pre
|
||||
|
||||
style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
|
||||
{dpd} or {electron} or {ellipsoid} or {full} or {line} or {meso} or \
|
||||
{molecular} or {peri} or {smd} or {sphere} or {tri} or \
|
||||
{molecular} or {peri} or {smd} or {sphere} or {tri} or \
|
||||
{template} or {hybrid} :ulb,l
|
||||
args = none for any style except the following
|
||||
{body} args = bstyle bstyle-args
|
||||
|
||||
@ -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
|
||||
|
||||
@ -152,11 +152,11 @@ lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 39.948
|
||||
mass 1 39.948
|
||||
pair_style lj/cut 13.0
|
||||
pair_coeff * * 0.2381 3.405
|
||||
timestep $\{dt\}
|
||||
thermo $d :pre
|
||||
thermo $d :pre
|
||||
|
||||
# equilibration and thermalization :pre
|
||||
|
||||
|
||||
@ -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
|
||||
@ -68,9 +68,9 @@ As an example of per-atom potential energy compared to total potential
|
||||
energy, these lines in an input script should yield the same result
|
||||
in the last 2 columns of thermo output:
|
||||
|
||||
compute peratom all pe/atom
|
||||
compute pe all reduce sum c_peratom
|
||||
thermo_style custom step temp etotal press pe c_pe :pre
|
||||
compute peratom all pe/atom
|
||||
compute pe all reduce sum c_peratom
|
||||
thermo_style custom step temp etotal press pe c_pe :pre
|
||||
|
||||
NOTE: The per-atom energy does not any Lennard-Jones tail corrections
|
||||
invoked by the "pair_modify tail yes"_pair_modify.html command, since
|
||||
|
||||
@ -16,20 +16,20 @@ ID, group-ID are documented in "compute"_compute.html command :ulb,l
|
||||
property/atom = style name of this compute command :l
|
||||
input = one or more atom attributes :l
|
||||
possible attributes = id, mol, proc, type, mass,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz, mu,
|
||||
radius, diameter, omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz,
|
||||
shapex,shapey, shapez,
|
||||
quatw, quati, quatj, quatk, tqx, tqy, tqz,
|
||||
end1x, end1y, end1z, end2x, end2y, end2z,
|
||||
corner1x, corner1y, corner1z,
|
||||
corner2x, corner2y, corner2z,
|
||||
corner3x, corner3y, corner3z,
|
||||
nbonds,
|
||||
angmomx, angmomy, angmomz,
|
||||
shapex,shapey, shapez,
|
||||
quatw, quati, quatj, quatk, tqx, tqy, tqz,
|
||||
end1x, end1y, end1z, end2x, end2y, end2z,
|
||||
corner1x, corner1y, corner1z,
|
||||
corner2x, corner2y, corner2z,
|
||||
corner3x, corner3y, corner3z,
|
||||
nbonds,
|
||||
vfrac, s0,
|
||||
spin, eradius, ervel, erforce,
|
||||
spin, eradius, ervel, erforce,
|
||||
rho, drho, e, de, cv,
|
||||
i_name, d_name :pre
|
||||
id = atom ID
|
||||
|
||||
@ -15,12 +15,12 @@ compute ID group-ID property/local attribute1 attribute2 ... keyword args ... :p
|
||||
ID, group-ID are documented in "compute"_compute.html command :ulb,l
|
||||
property/local = style name of this compute command :l
|
||||
one or more attributes may be appended :l
|
||||
possible attributes = natom1 natom2 ntype1 ntype2
|
||||
patom1 patom2 ptype1 ptype2
|
||||
batom1 batom2 btype
|
||||
aatom1 aatom2 aatom3 atype
|
||||
datom1 datom2 datom3 dtype
|
||||
iatom1 iatom2 iatom3 itype :pre
|
||||
possible attributes = natom1 natom2 ntype1 ntype2
|
||||
patom1 patom2 ptype1 ptype2
|
||||
batom1 batom2 btype
|
||||
aatom1 aatom2 aatom3 atype
|
||||
datom1 datom2 datom3 dtype
|
||||
iatom1 iatom2 iatom3 itype :pre
|
||||
|
||||
natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff)
|
||||
ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
|
||||
@ -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
|
||||
|
||||
@ -155,8 +155,8 @@ Thus, for example, if you wish to use this compute to find the bond
|
||||
with maximum stretch, you can do it as follows:
|
||||
|
||||
compute 1 all property/local batom1 batom2
|
||||
compute 2 all bond/local dist
|
||||
compute 3 all reduce max c_1\[1\] c_1\[2\] c_2 replace 1 3 replace 2 3
|
||||
compute 2 all bond/local dist
|
||||
compute 3 all reduce max c_1\[1\] c_1\[2\] c_2 replace 1 3 replace 2 3
|
||||
thermo_style custom step temp c_3\[1\] c_3\[2\] c_3\[3\] :pre
|
||||
|
||||
The first two input values in the compute reduce command are vectors
|
||||
|
||||
@ -17,11 +17,11 @@ rigid/local = style name of this compute command :l
|
||||
rigidID = ID of fix rigid/small command or one of its variants :l
|
||||
input = one or more rigid body attributes :l
|
||||
possible attributes = id, mol, mass,
|
||||
x, y, z, xu, yu, zu, ix, iy, iz
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
x, y, z, xu, yu, zu, ix, iy, iz
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz,
|
||||
quatw, quati, quatj, quatk,
|
||||
angmomx, angmomy, angmomz,
|
||||
quatw, quati, quatj, quatk,
|
||||
tqx, tqy, tqz,
|
||||
inertiax, inertiay, inertiaz
|
||||
id = atom ID of atom within body which owns body properties
|
||||
|
||||
@ -128,10 +128,10 @@ d = dimension and V is the volume of the system, the result should be
|
||||
These lines in an input script for a 3d system should yield that
|
||||
result. I.e. the last 2 columns of thermo output will be the same:
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\]
|
||||
variable press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
|
||||
thermo_style custom step temp etotal press v_press :pre
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\]
|
||||
variable press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
|
||||
thermo_style custom step temp etotal press v_press :pre
|
||||
|
||||
[Output info:]
|
||||
|
||||
|
||||
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
@ -218,14 +218,14 @@ larger version.
|
||||
|
||||
variable x equal 100
|
||||
variable y equal 25
|
||||
lattice hex 0.8442
|
||||
region box block 0 $x 0 $y -0.5 0.5
|
||||
create_box 1 box :pre
|
||||
lattice hex 0.8442
|
||||
region box block 0 $x 0 $y -0.5 0.5
|
||||
create_box 1 box :pre
|
||||
|
||||
variable xx equal 0.0
|
||||
variable yy equal 0.0
|
||||
variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
|
||||
create_atoms 1 box var v set x xx set y yy :pre
|
||||
create_atoms 1 box var v set x xx set y yy :pre
|
||||
|
||||
:c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg)
|
||||
|
||||
|
||||
@ -55,13 +55,13 @@ args = list of arguments for a particular style :l
|
||||
|
||||
{custom} or {custom/gz} or {custom/mpiio} args = list of atom attributes
|
||||
possible attributes = id, mol, proc, procp1, type, element, mass,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu,
|
||||
xsu, ysu, zsu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu,
|
||||
xsu, ysu, zsu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz, mu,
|
||||
radius, diameter, omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz, tqx, tqy, tqz,
|
||||
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
|
||||
angmomx, angmomy, angmomz, tqx, tqy, tqz,
|
||||
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
|
||||
|
||||
id = atom ID
|
||||
mol = molecule ID
|
||||
|
||||
@ -20,14 +20,14 @@ file = name of file to write dump info to :l
|
||||
args = list of arguments for a particular style :l
|
||||
{custom/vtk} args = list of atom attributes
|
||||
possible attributes = id, mol, proc, procp1, type, element, mass,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu,
|
||||
xsu, ysu, zsu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu,
|
||||
xsu, ysu, zsu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz, mu,
|
||||
radius, diameter, omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz, tqx, tqy, tqz,
|
||||
spin, eradius, ervel, erforce,
|
||||
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
|
||||
angmomx, angmomy, angmomz, tqx, tqy, tqz,
|
||||
spin, eradius, ervel, erforce,
|
||||
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
|
||||
|
||||
id = atom ID
|
||||
mol = molecule ID
|
||||
|
||||
@ -215,17 +215,17 @@ to the dump file. The {every} keyword cannot be used with the dump
|
||||
For example, the following commands will
|
||||
write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:
|
||||
|
||||
variable s equal logfreq(10,3,10)
|
||||
dump 1 all atom 100 tmp.dump
|
||||
dump_modify 1 every v_s first yes :pre
|
||||
variable s equal logfreq(10,3,10)
|
||||
dump 1 all atom 100 tmp.dump
|
||||
dump_modify 1 every v_s first yes :pre
|
||||
|
||||
The following commands would write snapshots at the timesteps listed
|
||||
in file tmp.times:
|
||||
|
||||
variable f file tmp.times
|
||||
variable s equal next(f)
|
||||
dump 1 all atom 100 tmp.dump
|
||||
dump_modify 1 every v_s :pre
|
||||
variable s equal next(f)
|
||||
dump 1 all atom 100 tmp.dump
|
||||
dump_modify 1 every v_s :pre
|
||||
|
||||
NOTE: When using a file-style variable with the {every} keyword, the
|
||||
file of timesteps must list a first timestep that is beyond the
|
||||
@ -686,10 +686,10 @@ this is used.
|
||||
variable colors string &
|
||||
"red green blue yellow white &
|
||||
purple pink orange lime gray"
|
||||
variable mol atom mol%10
|
||||
dump 1 all image 250 image.*.jpg v_mol type &
|
||||
zoom 1.6 adiam 1.5
|
||||
dump_modify 1 pad 5 amap 0 10 sa 1 10 $\{colors\} :pre
|
||||
variable mol atom mol%10
|
||||
dump 1 all image 250 image.*.jpg v_mol type &
|
||||
zoom 1.6 adiam 1.5
|
||||
dump_modify 1 pad 5 amap 0 10 sa 1 10 $\{colors\} :pre
|
||||
|
||||
In this case, 10 colors are defined, and molecule IDs are
|
||||
mapped to one of the colors, even if there are 1000s of molecules.
|
||||
|
||||
@ -58,7 +58,7 @@ keyword = {type} or {ave} or {start} or {prefactor} or {file} or {overwrite} or
|
||||
fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
|
||||
fix 1 all ave/correlate 1 50 10000 &
|
||||
c_thermo_press\[1\] c_thermo_press\[2\] c_thermo_press\[3\] &
|
||||
type upper ave running title1 "My correlation data" :pre
|
||||
type upper ave running title1 "My correlation data" :pre
|
||||
fix 1 all ave/correlate 1 50 10000 c_thermo_press\[*\]
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -55,7 +55,7 @@ keyword = {type} or {start} or {file} or {overwrite} or {title1} or {title2} or
|
||||
fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
|
||||
fix 1 all ave/correlate/long 1 10000 &
|
||||
c_thermo_press\[1\] c_thermo_press\[2\] c_thermo_press\[3\] &
|
||||
type upper title1 "My correlation data" nlen 15 ncount 3 :pre
|
||||
type upper title1 "My correlation data" nlen 15 ncount 3 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
||||
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
@ -28,7 +28,7 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
|
||||
factor = multiplicative factor for change in box length at end of run
|
||||
{vel} value = V
|
||||
V = change box length at this velocity (distance/time units),
|
||||
effectively an engineering strain rate
|
||||
effectively an engineering strain rate
|
||||
{erate} value = R
|
||||
R = engineering strain rate (1/time units)
|
||||
{trate} value = R
|
||||
@ -36,10 +36,10 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
|
||||
{volume} value = none = adjust this dim to preserve volume of system
|
||||
{wiggle} values = A Tp
|
||||
A = amplitude of oscillation (distance units)
|
||||
Tp = period of oscillation (time units)
|
||||
Tp = period of oscillation (time units)
|
||||
{variable} values = v_name1 v_name2
|
||||
v_name1 = variable with name1 for box length change as function of time
|
||||
v_name2 = variable with name2 for change rate as function of time
|
||||
v_name2 = variable with name2 for change rate as function of time
|
||||
{xy}, {xz}, {yz} args = style value
|
||||
style = {final} or {delta} or {vel} or {erate} or {trate} or {wiggle}
|
||||
{final} value = tilt
|
||||
@ -48,17 +48,17 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
|
||||
dtilt = change in tilt factor at end of run (distance units)
|
||||
{vel} value = V
|
||||
V = change tilt factor at this velocity (distance/time units),
|
||||
effectively an engineering shear strain rate
|
||||
effectively an engineering shear strain rate
|
||||
{erate} value = R
|
||||
R = engineering shear strain rate (1/time units)
|
||||
{trate} value = R
|
||||
R = true shear strain rate (1/time units)
|
||||
{wiggle} values = A Tp
|
||||
A = amplitude of oscillation (distance units)
|
||||
Tp = period of oscillation (time units)
|
||||
Tp = period of oscillation (time units)
|
||||
{variable} values = v_name1 v_name2
|
||||
v_name1 = variable with name1 for tilt change as function of time
|
||||
v_name2 = variable with name2 for change rate as function of time :pre
|
||||
v_name2 = variable with name2 for change rate as function of time :pre
|
||||
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {remap} or {flip} or {units} :l
|
||||
|
||||
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
@ -120,7 +120,7 @@ The global vector contains four values in this order:
|
||||
To print these quantities to the log file with descriptive column
|
||||
headers, the following LAMMPS commands are suggested:
|
||||
|
||||
fix msst all msst z
|
||||
fix msst all msst z
|
||||
fix_modify msst energy yes
|
||||
variable dhug equal f_msst\[1\]
|
||||
variable dray equal f_msst\[2\]
|
||||
|
||||
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
@ -167,14 +167,14 @@ headers, the following LAMMPS commands are suggested. Here the
|
||||
the thermo keyword {etotal} to print the quantity <i>etot</i>. See
|
||||
also the "thermo_style"_thermo_style.html command.
|
||||
|
||||
fix fix_id all msst z
|
||||
fix_modify fix_id energy yes
|
||||
variable dhug equal f_fix_id\[1\]
|
||||
variable dray equal f_fix_id\[2\]
|
||||
variable lgr_vel equal f_fix_id\[3\]
|
||||
variable lgr_pos equal f_fix_id\[4\]
|
||||
variable T_qm equal f_fix_id\[5\]
|
||||
thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id :pre
|
||||
fix fix_id all msst z
|
||||
fix_modify fix_id energy yes
|
||||
variable dhug equal f_fix_id\[1\]
|
||||
variable dray equal f_fix_id\[2\]
|
||||
variable lgr_vel equal f_fix_id\[3\]
|
||||
variable lgr_pos equal f_fix_id\[4\]
|
||||
variable T_qm equal f_fix_id\[5\]
|
||||
thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id :pre
|
||||
|
||||
The global scalar under the entry f_fix_id is the quantity of thermo
|
||||
energy as an extra part of <i>etot</i>. This global scalar and the
|
||||
|
||||
@ -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.
|
||||
|
||||
@ -17,8 +17,8 @@ store/state = style name of this fix command :l
|
||||
N = store atom attributes every N steps, N = 0 for initial store only :l
|
||||
input = one or more atom attributes :l
|
||||
possible attributes = id, mol, type, mass,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz, mu,
|
||||
radius, diameter, omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz, tqx, tqy, tqz,
|
||||
|
||||
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
|
||||
|
||||
@ -253,7 +253,7 @@ group mobile dynamic all region ss
|
||||
fix 1 mobile nve
|
||||
run $\{nsteps\}
|
||||
group mobile static
|
||||
run $\{nsteps\} :pre
|
||||
run $\{nsteps\} :pre
|
||||
|
||||
NOTE: All fixes and computes take a group ID as an argument, but they
|
||||
do not all allow for use of a dynamic group. If you get an error
|
||||
|
||||
@ -109,19 +109,19 @@ Here is an example of a double loop which uses the if and
|
||||
"jump"_jump.html commands to break out of the inner loop when a
|
||||
condition is met, then continues iterating thru the outer loop.
|
||||
|
||||
label loopa
|
||||
label loopa
|
||||
variable a loop 5
|
||||
label loopb
|
||||
label loopb
|
||||
variable b loop 5
|
||||
print "A,B = $a,$b"
|
||||
print "A,B = $a,$b"
|
||||
run 10000
|
||||
if "$b > 2" then "jump SELF break"
|
||||
next b
|
||||
jump in.script loopb
|
||||
label break
|
||||
if "$b > 2" then "jump SELF break"
|
||||
next b
|
||||
jump in.script loopb
|
||||
label break
|
||||
variable b delete
|
||||
next a
|
||||
jump SELF loopa :pre
|
||||
next a
|
||||
jump SELF loopa :pre
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -103,19 +103,19 @@ Here is an example of a double loop which uses the if and
|
||||
"jump"_jump.html commands to break out of the inner loop when a
|
||||
condition is met, then continues iterating thru the outer loop.
|
||||
|
||||
label loopa
|
||||
label loopa
|
||||
variable a loop 5
|
||||
label loopb
|
||||
label loopb
|
||||
variable b loop 5
|
||||
print "A,B = $a,$b"
|
||||
print "A,B = $a,$b"
|
||||
run 10000
|
||||
if "$b > 2" then "jump SELF break"
|
||||
next b
|
||||
jump in.script loopb
|
||||
label break
|
||||
if "$b > 2" then "jump SELF break"
|
||||
next b
|
||||
jump in.script loopb
|
||||
label break
|
||||
variable b delete
|
||||
next a
|
||||
jump SELF loopa :pre
|
||||
next a
|
||||
jump SELF loopa :pre
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
|
||||
0
doc/src/min_style.txt
Executable file → Normal file
0
doc/src/min_style.txt
Executable file → Normal file
@ -116,19 +116,19 @@ Here is an example of a double loop which uses the "if"_if.html and
|
||||
"jump"_jump.html commands to break out of the inner loop when a
|
||||
condition is met, then continues iterating thru the outer loop.
|
||||
|
||||
label loopa
|
||||
label loopa
|
||||
variable a loop 5
|
||||
label loopb
|
||||
label loopb
|
||||
variable b loop 5
|
||||
print "A,B = $a,$b"
|
||||
print "A,B = $a,$b"
|
||||
run 10000
|
||||
if $b > 2 then "jump in.script break"
|
||||
next b
|
||||
jump in.script loopb
|
||||
label break
|
||||
if $b > 2 then "jump in.script break"
|
||||
next b
|
||||
jump in.script loopb
|
||||
label break
|
||||
variable b delete :pre
|
||||
next a
|
||||
jump in.script loopa :pre
|
||||
next a
|
||||
jump in.script loopa :pre
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
|
||||
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
@ -170,7 +170,7 @@ so that there is effectively no interaction (e.g. epsilon = 0.0 in a
|
||||
LJ potential). Or, for {hybrid} and {hybrid/overlay} simulations, you
|
||||
can use this form of the pair_coeff command in your input script:
|
||||
|
||||
pair_coeff 2 3 none :pre
|
||||
pair_coeff 2 3 none :pre
|
||||
|
||||
or this form in the "Pair Coeffs" section of the data file:
|
||||
|
||||
|
||||
@ -188,9 +188,9 @@ lattce(I,J) = lattice structure of I-J reference structure:
|
||||
bcc = body centered cubic
|
||||
dim = dimer
|
||||
b1 = rock salt (NaCl structure)
|
||||
hcp = hexagonal close-packed
|
||||
c11 = MoSi2 structure
|
||||
l12 = Cu3Au structure (lower case L, followed by 12)
|
||||
hcp = hexagonal close-packed
|
||||
c11 = MoSi2 structure
|
||||
l12 = Cu3Au structure (lower case L, followed by 12)
|
||||
b2 = CsCl structure (interpenetrating simple cubic)
|
||||
nn2(I,J) = turn on second-nearest neighbor MEAM formulation for
|
||||
I-J pair (see for example "(Lee)"_#Lee).
|
||||
|
||||
@ -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
|
||||
@ -163,11 +165,11 @@ To print these quantities to the log file (with descriptive column
|
||||
headings) the following commands could be included in an input script:
|
||||
|
||||
compute reax all pair reax/c
|
||||
variable eb equal c_reax\[1\]
|
||||
variable ea equal c_reax\[2\]
|
||||
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
|
||||
variable eqeq equal c_reax\[14\]
|
||||
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
4
doc/src/pair_smtbq.txt
Executable file → Normal file
4
doc/src/pair_smtbq.txt
Executable file → Normal file
@ -158,7 +158,7 @@ Divided line :ul
|
||||
3) Potential parameters:
|
||||
|
||||
Keyword for element1, element2 and interaction potential ('second_moment' or 'buck' or 'buckPlusAttr') between element 1 and 2. If the potential is 'second_moment', specify 'oxide' or 'metal' for metal-oxygen or metal-metal interactions respectively.
|
||||
Potential parameter: <pre><br/> If type of potential is 'second_moment' : {A (eV)}, {p}, {ξ<sup>0</sup>} (eV) and {q} <br/> {r<sub>c1</sub>} (Å), {r<sub>c2</sub>} (Å) and {r<sub>0</sub>} (Å) <br/> If type of potential is 'buck' : {C} (eV) and {ρ} (Å) <br/> If type of potential is 'buckPlusAttr' : {C} (eV) and {ρ} (Å) <br/> {D} (eV), {B} (Å<sup>-1</sup>), {r<sub>1</sub><sup>OO</sup>} (Å) and {r<sub>2</sub><sup>OO</sup>} (Å) </pre>
|
||||
Potential parameter: <pre><br/> If type of potential is 'second_moment' : {A (eV)}, {p}, {ξ<sup>0</sup>} (eV) and {q} <br/> {r<sub>c1</sub>} (Å), {r<sub>c2</sub>} (Å) and {r<sub>0</sub>} (Å) <br/> If type of potential is 'buck' : {C} (eV) and {ρ} (Å) <br/> If type of potential is 'buckPlusAttr' : {C} (eV) and {ρ} (Å) <br/> {D} (eV), {B} (Å<sup>-1</sup>), {r<sub>1</sub><sup>OO</sup>} (Å) and {r<sub>2</sub><sup>OO</sup>} (Å) </pre>
|
||||
Divided line :ul
|
||||
|
||||
4) Tables parameters:
|
||||
@ -185,7 +185,7 @@ Divided line :ul
|
||||
|
||||
8) Mode for the electronegativity equalization (Qeq) :
|
||||
|
||||
Keyword mode: <pre> <br/> QEqAll (one QEq group) | no parameters <br/> QEqAllParallel (several QEq groups) | no parameters <br/> Surface | zlim (QEq only for z>zlim) </pre>
|
||||
Keyword mode: <pre> <br/> QEqAll (one QEq group) | no parameters <br/> QEqAllParallel (several QEq groups) | no parameters <br/> Surface | zlim (QEq only for z>zlim) </pre>
|
||||
Parameter if necessary
|
||||
Divided line :ul
|
||||
|
||||
|
||||
@ -96,15 +96,15 @@ tantalum potential provided in the LAMMPS potentials directory
|
||||
combines the {snap} and {zbl} pair styles. It is invoked
|
||||
by the following commands:
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
pair_style hybrid/overlay &
|
||||
zbl $\{zblcutinner\} $\{zblcutouter\} snap
|
||||
pair_coeff * * zbl 0.0
|
||||
pair_coeff 1 1 zbl $\{zblz\}
|
||||
pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
|
||||
../potentials/Ta06A.snapparam Ta :pre
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
pair_style hybrid/overlay &
|
||||
zbl $\{zblcutinner\} $\{zblcutouter\} snap
|
||||
pair_coeff * * zbl 0.0
|
||||
pair_coeff 1 1 zbl $\{zblz\}
|
||||
pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
|
||||
../potentials/Ta06A.snapparam Ta :pre
|
||||
|
||||
It is convenient to keep these commands in a separate file that can
|
||||
be inserted in any LAMMPS input script using the "include"_include.html
|
||||
|
||||
@ -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
|
||||
|
||||
|
||||
@ -113,8 +113,8 @@ For example, the following commands will write restart files
|
||||
every step from 1100 to 1200, and could be useful for debugging
|
||||
a simulation where something goes wrong at step 1163:
|
||||
|
||||
variable s equal stride(1100,1200,1)
|
||||
restart v_s tmp.restart :pre
|
||||
variable s equal stride(1100,1200,1)
|
||||
restart v_s tmp.restart :pre
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -66,11 +66,11 @@ keywords.
|
||||
|
||||
For example, consider this fix followed by 10 run commands:
|
||||
|
||||
fix 1 all nvt 200.0 300.0 1.0
|
||||
run 1000 start 0 stop 10000
|
||||
run 1000 start 0 stop 10000
|
||||
fix 1 all nvt 200.0 300.0 1.0
|
||||
run 1000 start 0 stop 10000
|
||||
run 1000 start 0 stop 10000
|
||||
...
|
||||
run 1000 start 0 stop 10000 :pre
|
||||
run 1000 start 0 stop 10000 :pre
|
||||
|
||||
The NVT fix ramps the target temperature from 200.0 to 300.0 during a
|
||||
run. If the run commands did not have the start/stop keywords (just
|
||||
|
||||
@ -20,7 +20,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
|
||||
n1, n2, ... = loop factor between rRESPA levels (N-1 values)
|
||||
zero or more keyword/value pairings may be appended to the loop factors
|
||||
keyword = {bond} or {angle} or {dihedral} or {improper} or
|
||||
{pair} or {inner} or {middle} or {outer} or {hybrid} or {kspace}
|
||||
{pair} or {inner} or {middle} or {outer} or {hybrid} or {kspace}
|
||||
{bond} value = M
|
||||
M = which level (1-N) to compute bond forces in
|
||||
{angle} value = M
|
||||
@ -33,14 +33,14 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
|
||||
M = which level (1-N) to compute pair forces in
|
||||
{inner} values = M cut1 cut2
|
||||
M = which level (1-N) to compute pair inner forces in
|
||||
cut1 = inner cutoff between pair inner and
|
||||
pair middle or outer (distance units)
|
||||
cut2 = outer cutoff between pair inner and
|
||||
pair middle or outer (distance units)
|
||||
cut1 = inner cutoff between pair inner and
|
||||
pair middle or outer (distance units)
|
||||
cut2 = outer cutoff between pair inner and
|
||||
pair middle or outer (distance units)
|
||||
{middle} values = M cut1 cut2
|
||||
M = which level (1-N) to compute pair middle forces in
|
||||
cut1 = inner cutoff between pair middle and pair outer (distance units)
|
||||
cut2 = outer cutoff between pair middle and pair outer (distance units)
|
||||
cut1 = inner cutoff between pair middle and pair outer (distance units)
|
||||
cut2 = outer cutoff between pair middle and pair outer (distance units)
|
||||
{outer} value = M
|
||||
M = which level (1-N) to compute pair outer forces in
|
||||
{hybrid} values = M1 M2 ... (as many values as there are hybrid sub-styles
|
||||
@ -230,7 +230,7 @@ rRESPA:
|
||||
|
||||
fix 2 all shake 0.000001 500 0 m 1.0 a 1
|
||||
timestep 4.0
|
||||
run_style respa 2 2 inner 1 4.0 5.0 outer 2 :pre
|
||||
run_style respa 2 2 inner 1 4.0 5.0 outer 2 :pre
|
||||
|
||||
With these settings, users can expect good energy conservation and
|
||||
roughly a 1.5 fold speedup over the {verlet} style with SHAKE and a
|
||||
|
||||
@ -17,13 +17,13 @@ ID = atom ID range or type range or mol ID range or group ID or region ID :l
|
||||
one or more keyword/value pairs may be appended :l
|
||||
keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
|
||||
{charge} or {dipole} or {dipole/random} or {quat} or \
|
||||
{quat/random} or {diameter} or {shape} or \
|
||||
{length} or {tri} or {theta} or {theta/random} or \
|
||||
{quat/random} or {diameter} or {shape} or \
|
||||
{length} or {tri} or {theta} or {theta/random} or \
|
||||
{angmom} or {omega} or \
|
||||
{mass} or {density} or {volume} or {image} or \
|
||||
{bond} or {angle} or {dihedral} or {improper} or \
|
||||
{meso/e} or {meso/cv} or {meso/rho} or \
|
||||
{smd/contact/radius} or {smd/mass/density} or {dpd/theta} or \
|
||||
{mass} or {density} or {volume} or {image} or \
|
||||
{bond} or {angle} or {dihedral} or {improper} or \
|
||||
{meso/e} or {meso/cv} or {meso/rho} or \
|
||||
{smd/contact/radius} or {smd/mass/density} or {dpd/theta} or \
|
||||
{i_name} or {d_name} :l
|
||||
{type} value = atom type
|
||||
value can be an atom-style variable (see below)
|
||||
|
||||
@ -45,8 +45,8 @@ options for "equal-style variables"_variable.html.
|
||||
For example, the following commands will output thermodynamic info at
|
||||
timesteps 0,10,20,30,100,200,300,1000,2000,etc:
|
||||
|
||||
variable s equal logfreq(10,3,10)
|
||||
thermo v_s :pre
|
||||
variable s equal logfreq(10,3,10)
|
||||
thermo v_s :pre
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
|
||||
@ -23,12 +23,12 @@ args = list of arguments for a particular style :l
|
||||
evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
|
||||
emol, elong, etail,
|
||||
vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
|
||||
xy, xz, yz, xlat, ylat, zlat,
|
||||
xy, xz, yz, xlat, ylat, zlat,
|
||||
bonds, angles, dihedrals, impropers,
|
||||
pxx, pyy, pzz, pxy, pxz, pyz,
|
||||
fmax, fnorm, nbuild, ndanger,
|
||||
cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
|
||||
c_ID, c_ID\[I\], c_ID\[I\]\[J\],
|
||||
pxx, pyy, pzz, pxy, pxz, pyz,
|
||||
fmax, fnorm, nbuild, ndanger,
|
||||
cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
|
||||
c_ID, c_ID\[I\], c_ID\[I\]\[J\],
|
||||
f_ID, f_ID\[I\], f_ID\[I\]\[J\],
|
||||
v_name, v_name\[I\]
|
||||
step = timestep
|
||||
|
||||
@ -52,18 +52,18 @@ style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {st
|
||||
sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
|
||||
random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
|
||||
ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
|
||||
stride(x,y,z), stride2(x,y,z,a,b,c),
|
||||
vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
|
||||
stride(x,y,z), stride2(x,y,z,a,b,c),
|
||||
vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
|
||||
group functions = count(group), mass(group), charge(group),
|
||||
xcm(group,dim), vcm(group,dim), fcm(group,dim),
|
||||
bound(group,dir), gyration(group), ke(group),
|
||||
angmom(group,dim), torque(group,dim),
|
||||
xcm(group,dim), vcm(group,dim), fcm(group,dim),
|
||||
bound(group,dir), gyration(group), ke(group),
|
||||
angmom(group,dim), torque(group,dim),
|
||||
inertia(group,dimdim), omega(group,dim)
|
||||
region functions = count(group,region), mass(group,region), charge(group,region),
|
||||
xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
|
||||
bound(group,dir,region), gyration(group,region), ke(group,reigon),
|
||||
angmom(group,dim,region), torque(group,dim,region),
|
||||
inertia(group,dimdim,region), omega(group,dim,region)
|
||||
xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
|
||||
bound(group,dir,region), gyration(group,region), ke(group,reigon),
|
||||
angmom(group,dim,region), torque(group,dim,region),
|
||||
inertia(group,dimdim,region), omega(group,dim,region)
|
||||
special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)
|
||||
feature functions = is_active(category,feature,exact), is_defined(category,id,exact)
|
||||
atom value = id\[i\], mass\[i\], type\[i\], mol\[i\], x\[i\], y\[i\], z\[i\], vx\[i\], vy\[i\], vz\[i\], fx\[i\], fy\[i\], fz\[i\], q\[i\]
|
||||
@ -219,13 +219,13 @@ script or when the input script is looped over. This can be useful
|
||||
when breaking out of a loop via the "if"_if.html and "jump"_jump.html
|
||||
commands before the variable would become exhausted. For example,
|
||||
|
||||
label loop
|
||||
label loop
|
||||
variable a loop 5
|
||||
print "A = $a"
|
||||
if "$a > 2" then "jump in.script break"
|
||||
next a
|
||||
jump in.script loop
|
||||
label break
|
||||
print "A = $a"
|
||||
if "$a > 2" then "jump in.script break"
|
||||
next a
|
||||
jump in.script loop
|
||||
label break
|
||||
variable a delete :pre
|
||||
|
||||
:line
|
||||
|
||||
@ -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
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user